2023
Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide.
Andrikopoulos, P. and Aron-Wisnewsky, J. and Chakaroun, R. and Myridakis, A. and Forslund, S.K. and Nielsen, T. and Adriouch, S. and Holmes, B. and Chilloux, J. and Vieira-Silva, S. and Falony, G. and Salem, J.E. and Andreelli, F. and Belda, E. and Kieswich, J. and Chechi, K. and Puig-Castellvi, F. and Chevalier, M. and Le Chatelier, E. and Olanipekun, M.T. and Hoyles, L. and Alves, R. and Helft, G. and Isnard, R. and Køber, L. and Coelho, L.P. and Rouault, C. and Gauguier, D. and Gøtze, J.P. and Prifti, E. and Froguel, P. and Zucker, J.D. and Bäckhed, F. and Vestergaard, H. and Hansen, T. and Oppert, J.M. and Blüher, M. and Nielsen, J. and Raes, J. and Bork, P. and Yaqoob, M.M. and Stumvoll, M. and Pedersen, O. and Ehrlich, S.D. and Clément, K. and Dumas, M.E.
Nature Communications 14
(1): 5843.
20 September 2023
Consistency across multi-omics layers in a drug-perturbed gut microbial community.
Wuyts, S. and Alves, R. and Zimmermann-Kogadeeva, M. and Nishijima, S. and Blasche, S. and Driessen, M. and Geyer, P.E and Hercog, R. and Kartal, E. and Maier, L. and Müller, J.B. and Garcia Santamarina, S. and Schmidt, T.S.B. and Sevin, D.C. and Telzerow, A. and Treit, P.V. and Wenzel, T. and Typas, A. and Patil, K.R and Mann, M. and Kuhn, M. and Bork, P.
Molecular Systems Biology 19
(9): e11525.
12 September 2023
Long-read sequencing reveals extensive DNA methylations in human gut phagenome contributed by prevalently phage-encoded methyltransferases.
Sun, C. and Chen, J. and Jin, M. and Zhao, X. and Li, Y. and Dong, Y. and Gao, N. and Liu, Z. and Bork, P. and Zhao, X.M. and Chen, W.H.
Advanced Science 10
(25): 2302159.
5 September 2023
Enterotypes of the human gut mycobiome.
Lai, S. and Yan, Y. and Pu, Y. and Lin, S. and Qiu, J.G. and Jiang, B.H. and Keller, M.I. and Wang, M. and Bork, P. and Chen, W.H. and Zheng, Y. and Zhao, X.M.
Microbiome 11
(1): 179.
11 August 2023
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies.
Kennedy, K.M. and de Goffau, M.C. and Perez-Muñoz, M.E. and Arrieta, M.C. and Bäckhed, F. and Bork, P. and Braun, T. and Bushman, F.D. and Dore, J. and de Vos, W.M. and Earl, A.M. and Eisen, J.A. and Elovitz, M.A. and Ganal-Vonarburg, S.C. and Gänzle, M.G. and Garrett, W.S. and Hall, L.J. and Hornef, M.W. and Huttenhower, C. and Konnikova, L. and Lebeer, S. and Macpherson, A.J. and Massey, R.C. and McHardy, A.C. and Koren, O. and Lawley, T.D. and Ley, R.E. and O'Mahony, L. and O'Toole, P.W. and Pamer, E.G. and Parkhill, J. and Raes, J. and Rattei, T. and Salonen, A. and Segal, E. and Segata, N. and Shanahan, F. and Sloboda, D.M. and Smith, G.C.S. and Sokol, H. and Spector, T.D. and Surette, M.G. and Tannock, G.W. and Walker, A.W. and Yassour, M. and Walter, J.
Nature 613
(7945): 639-649.
26 January 2023
The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest.
Szklarczyk, D. and Kirsch, R. and Koutrouli, M. and Nastou, K. and Mehryary, F. and Hachilif, R. and Gable, A.L. and Fang, T. and Doncheva, N.T. and Pyysalo, S. and Bork, P. and Jensen, L.J. and von Mering, C.
Nucleic Acids Research 51
(D1): D638-D646.
6 January 2023
proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes.
Fullam, A. and Letunic, I. and Schmidt, T.S.B. and Ducarmon, Q.R. and Karcher, N. and Khedkar, S. and Kuhn, M. and Larralde, M. and Maistrenko, O.M. and Malfertheiner, L. and Milanese, A. and Rodrigues, J.F.M. and Sanchis-López, C. and Schudoma, C. and Szklarczyk, D. and Sunagawa, S. and Zeller, G. and Huerta-Cepas, J. and von Mering, C. and Bork, P. and Mende, D.R.
Nucleic Acids Research 51
(D1): D760-D766.
6 January 2023
2022
Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses.
Kunath, B.J. and Hickl, O. and Queirós, P. and Martin-Gallausiaux, C. and Lebrun, L.A. and Halder, R. and Laczny, C.C. and Schmidt, T.S.B. and Hayward, M.R. and Becher, D. and Heintz-Buschart, A. and de Beaufort, C. and Bork, P. and May, P. and Wilmes, P.
Microbiome 10
(1): 243.
28 December 2022
Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments.
Ruscheweyh, H.J. and Milanese, A. and Paoli, L. and Karcher, N. and Clayssen, Q. and Keller, M.I. and Wirbel, J. and Bork, P. and Mende, D.R. and Zeller, G. and Sunagawa, S.
Microbiome 10
(1): 212.
5 December 2022
Dissecting the intracellular pancreatic tumor microbiome at single-cell level.
Schmidt, T.S.B. and Bork, P.
Cancer Cell 40
(10): 1083-1085.
10 October 2022
Drivers and determinants of strain dynamics following fecal microbiota transplantation.
Schmidt, T.S.B. and Li, S.S. and Maistrenko, O.M. and Akanni, W. and Coelho, L.P. and Dolai, S. and Fullam, A. and Glazek, A.M. and Hercog, R. and Herrema, H. and Jung, F. and Kandels, S. and Orakov, A. and Thielemann, R. and von Stetten, M. and Van Rossum, T. and Benes, V. and Borody, T.J. and de Vos, W.M. and Ponsioen, C.Y. and Nieuwdorp, M. and Bork, P.
Nature Medicine 28
(9): 1902-1912.
September 2022
Biosynthetic potential of the global ocean microbiome.
Paoli, L. and Ruscheweyh, H.J. and Forneris, C.C. and Hubrich, F. and Kautsar, S. and Bhushan, A. and Lotti, A. and Clayssen, Q. and Salazar, G. and Milanese, A. and Carlström, C.I. and Papadopoulou, C. and Gehrig, D. and Karasikov, M. and Mustafa, H. and Larralde, M. and Carroll, L.M. and Sánchez, P. and Zayed, A.A. and Cronin, D.R. and Acinas, S.G. and Bork, P. and Bowler, C. and Delmont, T.O. and Gasol, J.M. and Gossert, A.D. and Kahles, A. and Sullivan, M.B. and Wincker, P. and Zeller, G. and Robinson, S.L. and Piel, J. and Sunagawa, S.
Nature 607
(7917): 111-118.
7 July 2022
A faecal microbiota signature with high specificity for pancreatic cancer.
Kartal, E. and Schmidt, T.S.B. and Molina-Montes, E. and Rodríguez-Perales, S. and Wirbel, J. and Maistrenko, O.M. and Akanni, W.A. and Alashkar Alhamwe, B. and Alves, R.J. and Carrato, A. and Erasmus, H.P. and Estudillo, L. and Finkelmeier, F. and Fullam, A. and Glazek, A.M. and Gómez-Rubio, P. and Hercog, R. and Jung, F. and Kandels, S. and Kersting, S. and Langheinrich, M. and Márquez, M. and Molero, X. and Orakov, A. and Van Rossum, T. and Torres-Ruiz, R. and Telzerow, A. and Zych, K. and Benes, V. and Zeller, G. and Trebicka, J. and Real, F.X. and Malats, N. and Bork, P.
Gut 71
(7): 1359-1372.
7 June 2022
Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean.
Delmont, T.O. and Gaia, M. and Hinsinger, D.D. and Frémont, P. and Vanni, C. and Fernandez-Guerra, A. and Eren, A.M. and Kourlaiev, A. and d'Agata, L. and Clayssen, Q. and Villar, E. and Labadie, K. and Cruaud, C. and Poulain, J. and Da Silva, C. and Wessner, M. and Noel, B. and Aury, J.M. and de Vargas, C. and Bowler, C. and Karsenti, E. and Pelletier, E. and Wincker, P. and Jaillon, O.
Cell Genomics 2
(5): 100123.
11 May 2022
Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes.
Khedkar, S. and Smyshlyaev, G. and Letunic, I. and Maistrenko, O.M. and Coelho, L.P. and Orakov, A. and Forslund, S.K. and Hildebrand, F. and Luetge, M. and Schmidt, T.S.B. and Barabas, O. and Bork, P.
Nucleic Acids Research 50
(6): 3155-3168.
8 April 2022
Meconium microbiome of very preterm infants across Germany.
Klopp, J. and Ferretti, P. and Meyer, C.U. and Hilbert, K. and Haiß, A. and Marißen, J. and Henneke, P. and Hudalla, H. and Pirr, S. and Viemann, D. and Zemlin, M. and Forslund, S.K. and Härtel, C. and Bork, P. and Gehring, S. and Van Rossum, T.
mSphere 7
(1): e0080821.
23 February 2022
C. difficile is overdiagnosed in adults and a commensal in infants.
Ferretti, P. and Wirbel, J. and Maistrenko, O.M. and Van Rossum, T. and Alves, R. and Fullam, A. and Akanni, W. and Schudoma, C. and Schwarz, A. and Thielemann, R. and Thomas, L. and Kuhn, M. and Zeller, G. and Schmidt, T.S.B. and Bork, P.
bioRxiv
: 2022.02.16.480740v1.
18 February 2022
Functional and evolutionary significance of unknown genes from uncultivated taxa.
Rodríguez del Río, Á. and Giner-Lamia, J. and Cantalapiedra, C.P. and Botas, J. and Deng, Z. and Hernández-Plaza, A. and Paoli, L. and Schmidt, T.S.B. and Sunagawa, S. and Bork, P. and Coelho, L.P. and Huerta-Cepas, J.
bioRxiv
: 10.1101/2022.01.26.477801.
27 January 2022
Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics.
Pryszlak, A. and Wenzel, T. and Seitz, K.W. and Hildebrand, F. and Kartal, E. and Cosenza, M.R. and Benes, V. and Bork, P. and Merten, C.A.
Cell Reports Methods 2
(1): 100137.
24 January 2022
Towards the biogeography of prokaryotic genes.
Coelho, L.P. and Alves, R. and Del Río, Á.R. and Myers, P.N. and Cantalapiedra, C.P. and Giner-Lamia, J. and Schmidt, T.S. and Mende, D.R. and Orakov, A. and Letunic, I. and Hildebrand, F. and Van Rossum, T. and Forslund, S.K. and Khedkar, S. and Maistrenko, O.M. and Pan, S. and Jia, L. and Ferretti, P. and Sunagawa, S. and Zhao, X.M. and Nielsen, H.B. and Huerta-Cepas, J. and Bork, P.
Nature 601
(7892): 252-256.
13 January 2022
2021
Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean.
Royo-Llonch, M. and Sánchez, P. and Ruiz-González, C. and Salazar, G. and Pedrós-Alió, C. and Sebastián, M. and Labadie, K. and Paoli, L. and M. Ibarbalz, F. and Zinger, L. and Churcheward, B. and Chaffron, S. and Eveillard, D. and Karsenti, E. and Sunagawa, S. and Wincker, P. and Karp-Boss, L. and Bowler, C. and Acinas, S.G.
Nature Microbiology 6
(12): 1561-1574.
December 2021
Unravelling the collateral damage of antibiotics on gut bacteria.
Maier, L. and Goemans, C.V. and Wirbel, J. and Kuhn, M. and Eberl, C. and Pruteanu, M. and Müller, P. and Garcia-Santamarina, S. and Cacace, E. and Zhang, B. and Gekeler, C. and Banerjee, T. and Anderson, E.E. and Milanese, A. and Löber, U. and Forslund, S.K. and Patil, K.R. and Zimmermann, M. and Stecher, B. and Zeller, G. and Bork, P. and Typas, A.
Nature 599
: 120-124.
4 November 2021
A previously undescribed highly prevalent phage identified in a Danish Enteric Virome Catalog.
Van Espen, L. and Bak, E.G. and Beller, L. and Close, L. and Deboutte, W. and Juel, H.B. and Nielsen, T. and Sinar, D. and De Coninck, L. and Frithioff-Bøjsøe, C. and Fonvig, C.E. and Jacobsen, S. and Kjærgaard, M. and Thiele, M. and Fullam, A. and Kuhn, M. and Holm, J.C. and Bork, P. and Krag, A. and Hansen, T. and Arumugam, M. and Matthijnssens, J.
mSystems 6
(5): e00382-21.
26 October 2021
Recurrent frameshift neoantigen vaccine elicits protective immunity with reduced tumor burden and improved overall survival in a Lynch syndrome mouse model.
Gebert, J. and Gelincik, O. and Oezcan-Wahlbrink, M. and Marshall, J.D. and Hernandez-Sanchez, A. and Urban, K. and Long, M. and Cortes, E. and Tosti, E. and Katzenmaier, E.M. and Song, Y. and Elsaadi, A. and Deng, N. and Vilar, E. and Fuchs, V. and Nelius, N. and Yuan, Y.P. and Ahadova, A. and Sei, S. and Shoemaker, R.H. and Umar, A. and Wei, L. and Liu, S. and Bork, P. and Edelmann, W. and von Knebel Doeberitz, M. and Lipkin, S.M. and Kloor, M.
Gastroenterology 161
(4): 288-1302.e13.
October 2021
Drivers and determinants of strain dynamics following faecal microbiota transplantation.
Schmidt, T.S.B. and Li, S.S. and Maistrenko, O.M. and Akanni, W. and Coelho, L.P. and Dolai, S. and Fullam, A. and Glazek, A.M. and Hercog, R. and Herrema, H. and Jung, F. and Kandels, S. and Orakov, A. and Van Rossum, T. and Benes, V. and Borody, T.J. and de Vos, W.M. and Ponsioen, C.Y. and Nieuwdorp, M. and Bork, P.
bioRxiv
: 2021.09.30.462010.
30 September 2021
Bioaccumulation of therapeutic drugs by human gut bacteria.
Klünemann, M. and Andrejev, S. and Blasche, S. and Mateus, A. and Phapale, P. and Devendran, S. and Vappiani, J. and Simon, B. and Scott, T.A. and Kafkia, E. and Konstantinidis, D. and Zirngibl, K. and Mastrorilli, E. and Banzhaf, M. and Mackmull, M.T. and Hövelmann, F. and Nesme, L. and Brochado, A.R. and Maier, L. and Bock, T. and Periwal, V. and Kumar, M. and Kim, Y. and Tramontano, M. and Schultz, C. and Beck, M. and Hennig, J. and Zimmermann, M. and Sévin, D.C. and Cabreiro, F. and Savitski, M.M. and Bork, P. and Typas, A. and Patil, K.R.
Nature 597
: 533-538.
23 September 2021
Coupling proteomics and metabolomics for the unsupervised identification of protein-metabolite interactions in Chaetomium thermophilum.
Li, Y. and Kuhn, M. and Zukowska-Kasprzyk, J. and Hennrich, M.L. and Kastritis, P.L. and O'Reilly, F.J. and Phapale, P. and Beck, M. and Gavin, A.C. and Bork, P.
PLoS ONE 16
(7): e0254429.
9 July 2021
Dispersal strategies shape persistence and evolution of human gut bacteria.
Hildebrand, F. and Gossmann, T.I. and Frioux, C. and Özkurt, E. and Myers, P.N. and Ferretti, P. and Kuhn, M. and Bahram, M. and Nielsen, H.B. and Bork, P.
Cell Host & Microbe 29
(7): 1167-1176.
14 June 2021
GUNC: detection of chimerism and contamination in prokaryotic genomes.
Orakov, A. and Fullam, A. and Coelho, L.P. and Khedkar, S. and Szklarczyk, D. and Mende, D.R. and Schmidt, T.S.B. and Bork, P.
Genome Biology 22
(1): 178.
13 June 2021
Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox.
Wirbel, J. and Zych, K. and Essex, M. and Karcher, N. and Kartal, E. and Salazar, G. and Bork, P. and Sunagawa, S. and Zeller, G.
Genome Biology 22
(1): 93.
30 March 2021
Uncharted biosynthetic potential of the ocean microbiome.
Paoli, L. and Ruscheweyh, H.J. and Forneris, C.C. and Kautsar, S. and Clayssen, Q. and Salazar, G. and Milanese, A. and Gehrig, D. and Larralde, M. and Carroll, L.M. and Sánchez, P. and Zayed, A.A. and Cronin, D.R. and Acinas, S.G. and Bork, P. and Bowler, C. and Delmont, T.O. and Sullivan, M.B. and Wincker, P. and Zeller, G. and Robinson, S.L. and Piel, J. and Sunagawa, S.
bioRxiv
: 2021.03.24.436479.
24 March 2021
OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines.
Gurumayum, S. and Jiang, P. and Hao, X. and Campos, T.L. and Young, N.D. and Korhonen, P.K. and Gasser, R.B. and Bork, P. and Zhao, X.M. and He, L.J. and Chen, W.H.
Nucleic Acids Research 49
(D1): D998-D1003.
8 January 2021
SMART: recent updates, new developments and status in 2020.
Letunic, I. and Khedkar, S. and Bork, P.
Nucleic Acids Research 49
(D1): D458-D460.
8 January 2021
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.
Szklarczyk, D. and Gable, A.L. and Nastou, K.C. and Lyon, D. and Kirsch, R. and Pyysalo, S. and Doncheva, N.T. and Legeay, M. and Fang, T. and Bork, P. and Jensen, L.J. and von Mering, C.
Nucleic Acids Research 49
(D): D605-D612.
8 January 2021
Metagenomic assessment of the global diversity and distribution of bacteria and fungi.
Bahram, M. and Netherway, T. and Frioux, C. and Ferretti, P. and Coelho, L.P. and Geisen, S. and Bork, P. and Hildebrand, F.
Environmental Microbiology 23
(1): 316-326.
January 2021
2020
GUNC: detection of chimerism and contamination in prokaryotic genomes.
Orakov, A. and Fullam, A. and Coelho, L.P. and Khedkar, S. and Szklarczyk, D. and Mende, D.R. and Schmidt, T.S.B. and Bork, P.
bioRxiv
: 2020.12.16.422776.
16 December 2020
Diversity within species: interpreting strains in microbiomes.
Van Rossum, T. and Ferretti, P. and Maistrenko, O.M. and Bork, P.
Nature Reviews Microbiology 18
: 491-506.
September 2020
Tara Oceans: towards global ocean ecosystems biology.
Sunagawa, S. and Acinas, S.G. and Bork, P. and Bowler, C. and Eveillard, D. and Gorsky, G. and Guidi, L. and Iudicone, D. and Karsenti, E. and Lombard, F. and Ogata, H. and Pesant, S. and Sullivan, M.B. and Wincker, P. and de Vargas, C.
Nature Reviews Microbiology 18
(8): 428-445.
August 2020
(Phospho)proteomic profiling of microsatellite unstable CRC cells reveals alterations in nuclear signaling and cholesterol metabolism caused by frameshift mutation of NMD regulator UPF3A.
Michalak, M. and Katzenmaier, E.M. and Roeckel, N. and Woerner, S.M. and Fuchs, V. and Warnken, U. and Yuan, Y.P. and Bork, P. and Neu-Yilik, G. and Kulozik, A. and von Knebel Doeberitz, M. and Kloor, M. and Kopitz, J. and Gebert, J.
International Journal of Molecular Sciences 21
(15): 5234.
23 July 2020
Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity.
Maistrenko, O.M. and Mende, D.R. and Luetge, M. and Hildebrand, F. and Schmidt, T.S.B. and Li, S.S. and Rodrigues, J.F.M. and von Mering, C. and Pedro Coelho, L. and Huerta-Cepas, J. and Sunagawa, S. and Bork, P.
ISME Journal 14
(5): 1247-1259.
May 2020
Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features.
Li, Y. and Kuhn, M. and Gavin, A.C. and Bork, P.
Bioinformatics 36
(4): 1213-1218.
15 February 2020
Dissecting the collateral damage of antibiotics on gut microbes.
Maier, L. and Goemans, C.V. and Pruteanu, M. and Wirbel, J. and Kuhn, M. and Cacace, E. and Banerjee, T. and Anderson, E.E. and Milanese, A. and Löber, U. and Forslund, S.K. and Patil, K.R. and Zeller, G. and Bork, P. and Typas, A.
bioRxiv
: 2020.01.09.893560.
9 January 2020
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes.
Mende, D.R. and Letunic, I. and Maistrenko, O.M. and Schmidt, T.S.B. and Milanese, A. and Paoli, L. and Hernández-Plaza, A. and Orakov, A.N. and Forslund, S.K. and Sunagawa, S. and Zeller, G. and Huerta-Cepas, J. and Coelho, L.P. and Bork, P.
Nucleic Acids Research 48
(D1): D621-D625.
8 January 2020
2019
Gene expression changes and community turnover differentially shape the global ocean metatranscriptome.
Salazar, G. and Paoli, L. and Alberti, A. and Huerta-Cepas, J. and Ruscheweyh, H.J. and Cuenca, M. and Field, C.M. and Coelho, L.P. and Cruaud, C. and Engelen, S. and Gregory, A.C. and Labadie, K. and Marec, C. and Pelletier, E. and Royo-Llonch, M. and Roux, S. and Sánchez, P. and Uehara, H. and Zayed, A.A. and Zeller, G. and Carmichael, M. and Dimier, C. and Ferland, J. and Kandels, S. and Picheral, M. and Pisarev, S. and Poulain, J. and Acinas, S.G. and Babin, M. and Bork, P. and Bowler, C. and de Vargas, C. and Guidi, L. and Hingamp, P. and Iudicone, D. and Karp-Boss, L. and Karsenti, E. and Ogata, H. and Pesant, S. and Speich, S. and Sullivan, M.B. and Wincker, P. and Sunagawa, S.
Cell 179
(5): 1068-1083.
14 November 2019
Quantitative proteome landscape of the NCI-60 cancer cell lines.
Guo, T. and Luna, A. and Rajapakse, V.N. and Koh, C.C. and Wu, Z. and Liu, W. and Sun, Y. and Gao, H. and Menden, M.P. and Xu, C. and Calzone, L. and Martignetti, L. and Auwerx, C. and Buljan, M. and Banaei-Esfahani, A. and Ori, A. and Iskar, M. and Gillet, L. and Bi, R. and Zhang, J. and Zhang, H. and Yu, C. and Zhong, Q. and Varma, S. and Schmitt, U. and Qiu, P. and Zhang, Q. and Zhu, Y. and Wild, P.J. and Garnett, M.J. and Bork, P. and Beck, M. and Liu, K. and Saez-Rodriguez, J. and Elloumi, F. and Reinhold, W.C. and Sander, C. and Pommier, Y. and Aebersold, R.
iScience 21
: 664-680.
31 October 2019
Sample preservation and storage significantly impact taxonomic and functional profiles in metaproteomics studies of the human gut microbiome.
Hickl, O. and Heintz-Buschart, A. and Trautwein-Schult, A. and Hercog, R. and Bork, P. and Wilmes, P. and Becher, D.
Microorganisms 7
(9): 367.
19 September 2019
Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota.
Tito, R.Y. and Chaffron, S. and Caenepeel, C. and Lima-Mendez, G. and Wang, J. and Vieira-Silva, S. and Falony, G. and Hildebrand, F. and Darzi, Y. and Rymenans, L. and Verspecht, C. and Bork, P. and Vermeire, S. and Joossens, M. and Raes, J.
Gut 68
(7): 1180-1189.
7 June 2019
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language.
Coelho, L.P. and Alves, R. and Monteiro, P. and Huerta-Cepas, J. and Freitas, A.T. and Bork, P.
Microbiome 7
(1): 84.
3 June 2019
Ice-age climate adaptations trap the alpine marmot in a state of low genetic diversity.
Gossmann, T.I. and Shanmugasundram, A. and Börno, S. and Duvaux, L. and Lemaire, C. and Kuhl, H. and Klages, S. and Roberts, L.D. and Schade, S. and Gostner, J.M. and Hildebrand, F. and Vowinckel, J. and Bichet, C. and Mülleder, M. and Calvani, E. and Zelezniak, A. and Griffin, J.L. and Bork, P. and Allaine, D. and Cohas, A. and Welch, J.J. and Timmermann, B. and Ralser, M.
Current Biology 29
(10): 1712-1720.
20 May 2019
Disentangling genetic and environmental effects on the proteotypes of individuals.
Romanov, N. and Kuhn, M. and Aebersold, R. and Ori, A. and Beck, M. and Bork, P.
Cell 177
(5): 1308-1318.
16 May 2019
Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.
Wirbel, J. and Pyl, P.T. and Kartal, E. and Zych, K. and Kashani, A. and Milanese, A. and Fleck, J.S. and Voigt, A.Y. and Palleja, A. and Ponnudurai, R. and Sunagawa, S. and Coelho, L.P. and Schrotz-King, P. and Vogtmann, E. and Habermann, N. and Niméus, E. and Thomas, A.M. and Manghi, P. and Gandini, S. and Serrano, D. and Mizutani, S. and Shiroma, H. and Shiba, S. and Shibata, T. and Yachida, S. and Yamada, T. and Waldron, L. and Naccarati, A. and Segata, N. and Sinha, R. and Ulrich, C.M. and Brenner, H. and Arumugam, M. and Bork, P. and Zeller, G.
Nature Medicine 25
(4): 679-689.
April 2019
Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.
Thomas, A.M. and Manghi, P. and Asnicar, F. and Pasolli, E. and Armanini, F. and Zolfo, M. and Beghini, F. and Manara, S. and Karcher, N. and Pozzi, C. and Gandini, S. and Serrano, D. and Tarallo, S. and Francavilla, A. and Gallo, G. and Trompetto, M. and Ferrero, G. and Mizutani, S. and Shiroma, H. and Shiba, S. and Shibata, T. and Yachida, S. and Yamada, T. and Wirbel, J. and Schrotz-King, P. and Ulrich, C.M. and Brenner, H. and Arumugam, M. and Bork, P. and Zeller, G. and Cordero, F. and Dias-Neto, E. and Setubal, J.C. and Tett, A. and Pardini, B. and Rescigno, M. and Waldron, L. and Naccarati, A. and Segata, N.
Nature Medicine 25
(4): 667-678.
April 2019
Microbial abundance, activity and population genomic profiling with mOTUs2.
Milanese, A. and Mende, D.R. and Paoli, L. and Salazar, G. and Ruscheweyh, H.J. and Cuenca, M. and Hingamp, P. and Alves, R. and Costea, P.I. and Coelho, L.P. and Schmidt, T.S.B. and Almeida, A. and Mitchell, A.L. and Finn, R.D. and Huerta-Cepas, J. and Bork, P. and Zeller, G. and Sunagawa, S.
Nature Communications 10
(1): 1014.
4 March 2019
Community-level responses to iron availability in open ocean plankton ecosystems.
Caputi, L. and Carradec, Q. and Eveillard, D. and Kirilovsky, A. and Pelletier, E. and Pierella Karlusich, J.J. and Rocha Jimenez Vieira, F. and Villar, E. and Chaffron, S. and Malviya, S. and Scalco, E. and Acinas, S.G. and Alberti, A. and Aury, J.M. and Benoiston, A.S. and Bertrand, A. and Biard, T. and Bittner, L. and Boccara, M. and Brum, J.R. and Brunet, C. and Busseni, G. and Carratalà, A. and Claustre, H. and Coelho, L.P. and Colin, S. and D'Aniello, S. and Da Silva, C. and Del Core, M. and Doré, H. and Gasparini, S. and Kokoszka, F. and Jamet, J.L. and Lejeusne, C. and Lepoivre, C. and Lescot, M. and Lima‐Mendez, G. and Lombard, F. and Lukeš, J. and Maillet, N. and Madoui, M.A. and Martinez, E. and Mazzocchi, M.G. and Néou, M.B. and Paz‐Yepes, J. and Poulain, J. and Ramondenc, S. and Romagnan, J.B. and Roux, S. and Salvagio Manta, D. and Sanges, R. and Speich, S. and Sprovieri, M. and Sunagawa, S. and Taillandier, V. and Tanaka, A. and Tirichine, L. and Trottier, C. and Uitz, J. and Veluchamy, A. and Veselá, J. and Vincent, F. and Yau, S. and Kandels‐Lewis, S. and Searson, S. and Dimier, C. and Picheral, M. and Bork, P. and Boss, E. and Vargas, C. and Follows, M.J. and Grimsley, N. and Guidi, L. and Hingamp, P. and Karsenti, E. and Sordino, P. and Stemmann, L. and Sullivan, M.B. and Tagliabue, A. and Zingone, A. and Garczarek, L. and d'Ortenzio, F. and Testor, P. and Not, F. and Ribera d'Alcalà, M. and Wincker, P. and Bowler, C. and Iudicone, D.
Global Biogeochemical Cycles 33
(3): 391-419.
March 2019
Extensive transmission of microbes along the gastrointestinal tract.
Schmidt, T.S.B. and Hayward, M.R. and Coelho, L.P. and Li, S.S. and Costea, P.I. and Voigt, A.Y. and Wirbel, J. and Maistrenko, O.M. and Alves, R.J.C. and Bergsten, E. and de Beaufort, C. and Sobhani, I. and Heintz-Buschart, A. and Sunagawa, S. and Zeller, G. and Wilmes, P. and Bork, P.
eLife 8
: e42693.
12 February 2019
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Szklarczyk, D. and Gable, A.L. and Lyon, D. and Junge, A. and Wyder, S. and Huerta-Cepas, J. and Simonovic, M. and Doncheva, N.T. and Morris, J.H. and Bork, P. and Jensen, L.J. and von Mering, C.
Nucleic Acids Research 47
(D1): D607-D613.
8 January 2019
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
Huerta-Cepas, J. and Szklarczyk, D. and Heller, D. and Hernández-Plaza, A. and Forslund, S.K. and Cook, H. and Mende, D.R. and Letunic, I. and Rattei, T. and Jensen, L.J. and von Mering, C. and Bork, P.
Nucleic Acids Research 47
(D1): D309-D314.
8 January 2019
2018
Recovery of gut microbiota of healthy adults following antibiotic exposure.
Palleja, A. and Mikkelsen, K.H. and Forslund, S.K. and Kashani, A. and Allin, K.H. and Nielsen, T. and Hansen, T.H. and Liang, S. and Feng, Q. and Zhang, C. and Pyl, P.T. and Coelho, L.P. and Yang, H. and Wang, J. and Typas, A. and Nielsen, M.F. and Nielsen, H.B. and Bork, P. and Wang, J. and Vilsbøll, T. and Hansen, T. and Knop, F.K. and Arumugam, M. and Pedersen, O.
Nature Microbiology 3
: 1255-1265.
November 2018
Structure and function of the global topsoil microbiome.
Bahram, M. and Hildebrand, F. and Forslund, S.K. and Anderson, J.L. and Soudzilovskaia, N.A. and Bodegom, P.M. and Bengtsson-Palme, J. and Anslan, S. and Coelho, L.P. and Harend, H. and Huerta-Cepas, J. and Medema, M.H. and Maltz, M.R. and Mundra, S. and Olsson, P.A. and Pent, M. and Põlme, S. and Sunagawa, S. and Ryberg, M. and Tedersoo, L. and Bork, P.
Nature 560
(7717): 233-237.
9 August 2018
Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment.
Bahram, M. and Anslan, S. and Hildebrand, F. and Bork, P. and Tedersoo, L.
Environmental Microbiology Reports 11
(4): 487-494.
August 2018
The gut microbiome is associated with behavioural task in honey bees.
Jones, J.C. and Fruciano, C. and Marchant, J. and Hildebrand, F. and Forslund, S. and Bork, P. and Engel, P. and Hughes, W.O.H.
Insectes Sociaux 65
(3): 419-429.
August 2018
Metagenomic analysis of gut microbial communities from a Central Asian population.
Kushugulova, A. and Forslund, S.K. and Costea, P.I. and Kozhakhmetov, S. and Khassenbekova, Z. and Urazova, M. and Nurgozhin, T. and Zhumadilov, Z. and Benberin, V. and Driessen, M. and Hercog, R. and Voigt, A.Y. and Benes, V. and Kandels-Lewis, S. and Sunagawa, S. and Letunic, I. and Bork, P.
BMJ Open 8
(7): e021682.
28 July 2018
Quantifying compartment-associated variations of protein abundance in proteomics data.
Parca, L. and Beck, M. and Bork, P. and Ori, A.
Molecular Systems Biology 14
(7): e8131.
2 July 2018
iPath3.0: interactive pathways explorer v3.
Darzi, Y. and Letunic, I. and Bork, P. and Yamada, T.
Nucleic Acids Research 46
(W1): W510-W513.
2 July 2018
Species-specific activity of antibacterial drug combinations.
Brochado, A.R. and Telzerow, A. and Bobonis, J. and Banzhaf, M. and Mateus, A. and Selkrig, J. and Huth, E. and Bassler, S. and Zamarreño Beas, J. and Zietek, M. and Ng, N. and Foerster, S. and Ezraty, B. and Py, B. and Barras, F. and Savitski, M.M. and Bork, P. and Göttig, S. and Typas, A.
Nature 559
(7713): 259-263.
July 2018
Pervasive protein thermal stability variation during the cell cycle.
Becher, I. and Andrés-Pons, A. and Romanov, N. and Stein, F. and Schramm, M. and Baudin, F. and Helm, D. and Kurzawa, N. and Mateus, A. and Mackmull, M.T. and Typas, A. and Müller, C.W. and Bork, P. and Beck, M. and Savitski, M.M.
Cell 173
(6): 1495-1507.
31 May 2018
Similarity of the dog and human gut microbiomes in gene content and response to diet.
Coelho, L.P. and Kultima, J.R. and Costea, P.I. and Fournier, C. and Pan, Y. and Czarnecki-Maulden, G. and Hayward, M.R. and Forslund, S.K. and Schmidt, T.S.B. and Descombes, P. and Jackson, J.R. and Li, Q. and Bork, P.
Microbiome 6
(1): 72.
19 April 2018
Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies.
Tramontano, M. and Andrejev, S. and Pruteanu, M. and Klünemann, M. and Kuhn, M. and Galardini, M. and Jouhten, P. and Zelezniak, A. and Zeller, G. and Bork, P. and Typas, A. and Patil, K.R.
Nature Microbiology 3
(3): 514-522.
April 2018
Selective maternal seeding and environment shape the human gut microbiome.
Korpela, K. and Costea, P. and Coelho, L.P. and Kandels-Lewis, S. and Willemsen, G. and Boomsma, D.I. and Segata, N. and Bork, P.
Genome Research 28
(4): 561-568.
April 2018
Extensive impact of non-antibiotic drugs on human gut bacteria.
Maier, L. and Pruteanu, M. and Kuhn, M. and Zeller, G. and Telzerow, A. and Anderson, E.E. and Brochado, A.R. and Fernandez, K.C. and Dose, H. and Mori, H. and Patil, K.R. and Bork, P. and Typas, A.
Nature 555
(7698): 623-628.
29 March 2018
Transposase-DNA complex structures reveal mechanisms for conjugative transposition of antibiotic resistance.
Rubio-Cosials, A. and Schulz, E.C. and Lambertsen, L. and Smyshlyaev, G. and Rojas-Cordova, C. and Forslund, K. and Karaca, E. and Bebel, A. and Bork, P. and Barabas, O.
Cell 173
(1): 208-220.
22 March 2018
The human gut microbiome: from association to modulation.
Schmidt, T.S.B. and Raes, J. and Bork, P.
Cell 172
(6): 1198-1215.
8 March 2018
A global ocean atlas of eukaryotic genes.
Carradec, Q. and Pelletier, E. and Da Silva, C. and Alberti, A. and Seeleuthner, Y. and Blanc-Mathieu, R. and Lima-Mendez, G. and Rocha, F. and Tirichine, L. and Labadie, K. and Kirilovsky, A. and Bertrand, A. and Engelen, S. and Madoui, M.A. and Méheust, R. and Poulain, J. and Romac, S. and Richter, D.J. and Yoshikawa, G. and Dimier, C. and Kandels-Lewis, S. and Picheral, M. and Searson, S. and Jaillon, O. and Aury, J.M. and Karsenti, E. and Sullivan, M.B. and Sunagawa, S. and Bork, P. and Not, F. and Hingamp, P. and Raes, J. and Guidi, L. and Ogata, H. and De Vargas, C. and Iudicone, D. and Bowler, C. and Wincker, P.
Nature Communications 9
(1): 373.
25 January 2018
MVP: a microbe-phage interaction database.
Gao, N.L. and Zhang, C. and Zhang, Z. and Hu, S. and Lercher, M.J. and Zhao, X.M. and Bork, P. and Liu, Z. and Chen, W.H.
Nucleic Acids Research 46
(D1): D700-D707.
4 January 2018
Enterotypes in the landscape of gut microbial community composition.
Costea, P.I. and Hildebrand, F. and Manimozhiyan, A. and Baeckhed, F. and Blaser, M.J. and Bushman, F.D. and de Vos, W.M. and Ehrlich, S.D. and Fraser, C.M. and Hattori, M. and Huttenhower, C. and Jeffery, I.B. and Knights, D. and Lewis, J.D. and Ley, R.E. and Ochman, H. and O'Toole, P.W. and Quince, C. and Relman, D.A. and Shanahan, F. and Sunagawa, S. and Wang, J. and Weinstock, G.M. and Wu, G.D. and Zeller, G. and Zhao, L. and Raes, J. and Knight, R. and Bork, P.
Nature Microbiology 3
(1): 8-16.
January 2018
Gut microbiota composition is associated with environmental landscape in honey bees.
Jones, J.C. and Fruciano, C. and Hildebrand, F. and Al Toufalilia, H. and Balfour, N.J. and Bork, P. and Engel, P. and Ratnieks, F.L.W. and Hughes, W.O.H.
Ecology and Evolution 8
(1): 441-451.
January 2018
2017
Subspecies in the global human gut microbiome.
Costea, P.I. and Coelho, L.P. and Sunagawa, S. and Munch, R. and Huerta-Cepas, J. and Forslund, K. and Hildebrand, F. and Kushugulova, A. and Zeller, G. and Bork, P.
Molecular Systems Biology 13
(12): 960.
14 December 2017
Salt-responsive gut commensal modulates T(H)17 axis and disease.
Wilck, N. and Matus, M.G. and Kearney, S.M. and Olesen, S.W. and Forslund, K. and Bartolomaeus, H. and Haase, S. and Mähler, A. and Balogh, A. and Markó, L. and Vvedenskaya, O. and Kleiner, F.H. and Tsvetkov, D. and Klug, L. and Costea, P.I. and Sunagawa, S. and Maier, L. and Rakova, N. and Schatz, V. and Neubert, P. and Frätzer, C. and Krannich, A. and Gollasch, M. and Grohme, D.A. and Côrte-Real, B.F. and Gerlach, R.G. and Basic, M. and Typas, A. and Wu, C. and Titze, J.M. and Jantsch, J. and Boschmann, M. and Dechend, R. and Kleinewietfeld, M. and Kempa, S. and Bork, P. and Linker, R.A. and Alm, E.J. and Müller, D.N.
Nature 551
(7682): 585-589.
30 November 2017
Pole-to-Pole connections: similarities between arctic and antarctic microbiomes and their vulnerability to environmental change.
Kleinteich, J. and Hildebrand, F. and Bahram, M. and Voigt, A.Y. and Wood, S.A. and Jungblut, A.D. and Kuepper, F.C. and Quesada, A. and Camacho, A. and Pearce, D.A. and Convey, P. and Vincent, W.F. and Zarfl, C. and Bork, P. and Dietrich, D.R.
Frontiers in Ecology and Evolution 5
: 137.
10 November 2017
Towards standards for human fecal sample processing in metagenomic studies.
Costea, P.I. and Zeller, G. and Sunagawa, S. and Pelletier, E. and Alberti, A. and Levenez, F. and Tramontano, M. and Driessen, M. and Hercog, R. and Jung, F.E. and Kultima, J.R. and Hayward, M.R. and Coelho, L.P. and Allen-Vercoe, E. and Bertrand, L. and Blaut, M. and Brown, J.R.M. and Carton, T. and Cools-Portier, S. and Daigneault, M. and Derrien, M. and Druesne, A. and de Vos, W.M. and Finlay, B.B. and Flint, H.J. and Guarner, F. and Hattori, M. and Heilig, H. and Luna, R.A. and van Hylckama Vlieg, J. and Junick, J. and Klymiuk, I. and Langella, P. and Le Chatelier, Z. and Mai, V. and Manichanh, C. and Martin, J.C. and Mery, C. and Morita, H. and O'Toole, P.W. and Orvain, C. and Patil, K.R. and Penders, J. and Persson, S. and Pons, N. and Popova, M. and Salonen, A. and Saulnier, D. and Scott, K.P. and Singh, B. and Slezak, K. and Veiga, P. and Versalovic, J. and Zhao, L. and Zoetendal, E.G. and Ehrlich, S.D. and Dore, J. and Bork, P.
Nature Biotechnology 35
(11): 1069-1076.
November 2017
RTK: efficient rarefaction analysis of large datasets.
Saary, P. and Forslund, K. and Bork, P. and Hildebrand, F.
Bioinformatics 33
(16): 2594-2595.
15 August 2017
Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.
Huerta-Cepas, J. and Forslund, K. and Coelho, L.P. and Szklarczyk, D. and Jensen, L.J. and von Mering, C. and Bork, P.
Molecular Biology and Evolution 34
(8): 2115-2122.
1 August 2017
Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.
Alberti, A. and Poulain, J. and Engelen, S. and Labadie, K. and Romac, S. and Ferrera, I. and Albini, G. and Aury, J.M. and Belser, C. and Bertrand, A. and Cruaud, C. and Da Silva, C. and Dossat, C. and Gavory, F. and Gas, S. and Guy, J. and Haquelle, M. and Jacoby, E. and Jaillon, O. and Lemainque, A. and Pelletier, E. and Samson, G. and Wessner, M. and Acinas, S.G. and Royo-Llonch, M. and Cornejo-Castillo, F.M. and Logares, R. and Fernandez-Gomez, B. and Bowler, C. and Cochrane, G. and Amid, C. and Hoopen, P.T. and De Vargas, C. and Grimsley, N. and Desgranges, E. and Kandels-Lewis, S. and Ogata, H. and Poulton, N. and Sieracki, M.E. and Stepanauskas, R. and Sullivan, M.B. and Brum, J.R. and Duhaime, M.B. and Poulos, B.T. and Hurwitz, B.L. and Pesant, S. and Karsenti, E. and Wincker, P.
Scientific Data 4
: 170093.
1 August 2017
MetaSNV: a tool for metagenomic strain level analysis.
Costea, P.I. and Munch, R. and Coelho, L.P. and Paoli, L. and Sunagawa, S. and Bork, P.
PLoS ONE 12
(7): e0182392.
28 July 2017
Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naive Parkinson's disease patients.
Bedarf, J.R. and Hildebrand, F. and Coelho, L.P. and Sunagawa, S. and Bahram, M. and Goeser, F. and Bork, P. and Wuellner, U.
Genome Medicine 9
(1): 39.
28 April 2017
Gut microbiota differs between children with inflammatory bowel disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis.
Knoll, R.L. and Forslund, K. and Kultima, J.R. and Meyer, C.U. and Kullmer, U. and Sunagawa, S. and Bork, P. and Gehring, S.
American Journal of Physiology Gastrointestinal and Liver Physiology 312
(4): G327-G339.
1 April 2017
Metabolic anchor reactions for robust biorefining.
Jouhten, P. and Huerta-Cepas, J. and Bork, P. and Patil, K.R.
Metabolic Engineering 40
: 1-4.
March 2017
Bioinformatics analysis of functional associations of PTMs.
Minguez, P. and Bork, P.
Methods in Molecular Biology 1558
(1558): 303-320.
2 February 2017
OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines.
Chen, W.H. and Lu, G. and Chen, X. and Zhao, X.M. and Bork, P.
Nucleic Acids Research 45
(D1): D940-D944.
4 January 2017
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.
Szklarczyk, D. and Morris, J.H. and Cook, H. and Kuhn, M. and Wyder, S. and Simonovic, M. and Santos, A. and Doncheva, N.T. and Roth, A. and Bork, P. and Jensen, L.J. and von Mering, C.
Nucleic Acids Research 45
(D1): D362-D368.
4 January 2017
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.
Mende, D.R. and Letunic, I. and Huerta-Cepas, J. and Li, S.S. and Forslund, K. and Sunagawa, S. and Bork, P.
Nucleic Acids Research 45
(D1): D529-D534.
4 January 2017
2016
The endosomal transcriptional regulator RNF11 integrates degradation and transport of EGFR.
Scharaw, S. and Iskar, M. and Ori, A. and Boncompain, G. and Laketa, V. and Poser, I. and Lundberg, E. and Perez, F. and Beck, M. and Bork, P. and Pepperkok, R.
Journal of Cell Biology 215
(4): 543-558.
21 November 2016
Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses.
Roux, S. and Brum, J.R. and Dutilh, B.E. and Sunagawa, S. and Duhaime, M.B. and Loy, A. and Poulos, B.T. and Solonenko, N. and Lara, E. and Poulain, J. and Pesant, S. and Kandels-Lewis, S. and Dimier, C. and Picheral, M. and Searson, S. and Cruaud, C. and Alberti, A. and Duarte, C.M. and Gasol, J.M. and Vaque, D. and Bork, P. and Acinas, S.G. and Wincker, P. and Sullivan, M.B.
Nature 537
(7622): 689-693.
29 September 2016
Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.
Huerta-Cepas, J. and Forslund, K. and Szklarczyk, D. and Jensen, L.J. and von Mering, C. and Bork, P.
bioRxiv
: 076331.
22 September 2016
CART - a chemical annotation retrieval toolkit.
Deghou, S. and Zeller, G. and Iskar, M. and Driessen, M. and Castillo, M. and van Noort, V. and Bork, P.
Bioinformatics 32
(18): 2869-2871.
15 September 2016
MOCAT2: a metagenomic assembly, annotation and profiling framework.
Kultima, J.R. and Coelho, L.P. and Forslund, K. and Huerta-Cepas, J. and Li, S.S. and Driessen, M. and Voigt, A.Y. and Zeller, G. and Sunagawa, S. and Bork, P.
Bioinformatics 32
(16): 2520-2523.
15 August 2016
Human gut microbes impact host serum metabolome and insulin sensitivity.
Pedersen, H.K. and Gudmundsdottir, V. and Nielsen, H.B. and Hyotylainen, T. and Nielsen, T. and Jensen, B.A.H. and Forslund, K. and Hildebrand, F. and Prifti, E. and Falony, G. and Le Chatelier, E. and Levenez, F. and Doré, J. and Mattila, I. and Plichta, D.R. and Pöhö, P. and Hellgren, L.I. and Arumugam, M. and Sunagawa, S. and Vieira-Silva, S. and Jørgensen, T. and Holm, J.B. and Trošt, K. and Kristiansen, K. and Brix, S. and Raes, J. and Wang, J. and Hansen, T. and Bork, P. and Brunak, S. and Oresic, M. and Ehrlich, S.D. and Pedersen, O.
Nature 535
(7612): 376-381.
21 July 2016
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees.
Letunic, I. and Bork, P.
Nucleic Acids Research 44
(W1): W242-W245.
8 July 2016
ETE 3: reconstruction, analysis and visualization of phylogenomic data.
Huerta-Cepas, J. and Serra, F. and Bork, P.
Molecular Biology and Evolution 33
(6): 1635-1638.
June 2016
Colorectal cancer and the human gut microbiome: reproducibility with whole-genome shotgun sequencing.
Vogtmann, E. and Hua, X. and Zeller, G. and Sunagawa, S. and Voigt, A.Y. and Hercog, R. and Goedert, J.J. and Shi, J. and Bork, P. and Sinha, R.
PLoS ONE 11
(5): e0155362.
12 May 2016
Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses.
Roux, S. and Brum, J.R. and Dutilh, B.E. and Sunagawa, S. and Duhaime, M.B. and Loy, A. and Poulos, B.T. and Solonenko, N. and Lara, E. and Poulain, J. and Pesant, S. and Kandels-Lewis, S. and Dimier, C. and Picheral, M. and Searson, S. and Cruaud, C. and Alberti, A. and Duarte, C.M. and Gasol, J.M. and Vaque, D. and Bork, P. and Acinas, S.G. and Wincker, P. and Sullivan, M.B.
bioRxiv
: 053090.
12 May 2016
Standardized benchmarking in the quest for orthologs.
Altenhoff, A.M. and Boeckmann, B. and Capella-Gutierrez, S. and Dalquen, D.A. and DeLuca, T. and Forslund, K. and Huerta-Cepas, J. and Linard, B. and Pereira, C. and Pryszcz, L.P. and Schreiber, F. and da Silva, A.S. and Szklarczyk, D. and Train, C.M. and Bork, P. and Lecompte, O. and von Mering, C. and Xenarios, I. and Sjölander, K. and Jensen, L.J. and Martin, M.J. and Muffato, M. and Gabaldón, T. and Lewis, S.E. and Thomas, P.D. and Sonnhammer, E. and Dessimoz, C.
Nature Methods 13
(5): 425-430.
May 2016
Durable coexistence of donor and recipient strains after fecal microbiota transplantation.
Li, S.S. and Zhu, A. and Benes, V. and Costea, P.I. and Hercog, R. and Hildebrand, F. and Huerta-Cepas, J. and Nieuwdorp, M. and Salojaervi, J. and Voigt, A.Y. and Zeller, G. and Sunagawa, S. and de Vos, W.M. and Bork, P.
Science 352
(6285): 586-589.
29 April 2016
Plankton networks driving carbon export in the oligotrophic ocean.
Guidi, L. and Chaffron, S. and Bittner, L. and Eveillard, D. and Larhlimi, A. and Roux, S. and Darzi, Y. and Audic, S. and Berline, L. and Brum, J. and Coelho, L.P. and Espinoza, J.C.I. and Malviya, S. and Sunagawa, S. and Dimier, C. and Kandels-Lewis, S. and Picheral, M. and Poulain, J. and Searson, S. and Stemmann, L. and Not, F. and Hingamp, P. and Speich, S. and Follows, M. and Karp-Boss, L. and Boss, E. and Ogata, H. and Pesant, S. and Weissenbach, J. and Wincker, P. and Acinas, S.G. and Bork, P. and de Vargas, C. and Iudicone, D. and Sullivan, M.B. and Raes, J. and Karsenti, E. and Bowler, C. and Gorsky, G.
Nature 532
(7600): 465-470.
28 April 2016
Energy efficiency trade-offs drive nucleotide usage in transcribed regions.
Chen, W.H. and Lu, G. and Bork, P. and Hu, S. and Lercher, M.J.
Nature Communications 7
: 11334.
21 April 2016
Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton.
Cornejo-Castillo, F.M. and Cabello, A.M. and Salazar, G. and Sanchez-Baracaldo, P. and Lima-Mendez, G. and Hingamp, P. and Alberti, A. and Sunagawa, S. and Bork, P. and de Vargas, C. and Raes, J. and Bowler, C. and Wincker, P. and Zehr, J.P. and Gasol, J.M. and Massana, R. and Acinas, S.G.
Nature Communications 7
: 11071.
22 March 2016
Spatiotemporal variation of mammalian protein complex stoichiometries.
Ori, A. and Iskar, M. and Buczak, K. and Kastritis, P. and Parca, L. and Andres-Pons, A. and Singer, S. and Bork, P. and Beck, M.
Genome Biology 17
(1): 47.
14 March 2016
Bacterial antisense RNAs are mainly the product of transcriptional noise.
Llorens-Rico, V. and Cano, J. and Kamminga, T. and Gil, R. and Latorre, A. and Chen, W.H. and Bork, P. and Glass, J.I. and Serrano, L. and Lluch-Senar, M.
Science Advances 2
(3): e1501363.
4 March 2016
Gut microbiota linked to sexual preference and HIV infection.
Noguera-Julian, M. and Rocafort, M. and Guillen, Y. and Rivera, J. and Casadella, M. and Nowak, P. and Hildebrand, F. and Zeller, G. and Parera, M. and Bellido, R. and Rodriguez, C. and Carrillo, J. and Mothe, B. and Coll, J. and Bravo, I. and Estany, C. and Herrero, C. and Saz, J. and Sirera, G. and Torrela, A. and Navarro, J. and Crespo, M. and Brander, C. and Negredo, E. and Blanco, J. and Guarner, F. and Calle, M.L. and Bork, P. and Soennerborg, A. and Clotet, B. and Paredes, R.
EBioMedicine 5
: 135-146.
March 2016
Integration of multi-omics data of a genome-reduced bacterium: prevalence of post-transcriptional regulation and its correlation with protein abundances.
Chen, W.H. and van Noort, V. and Lluch-Senar, M. and Hennrich, M.L. and Wodke, J.A.H. and Yus, E. and Alibes, A. and Roma, G. and Mende, D.R. and Pesavento, C. and Typas, A. and Gavin, A.C. and Serrano, L. and Bork, P.
Nucleic Acids Research 44
(3): 1192-1202.
18 February 2016
STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.
Szklarczyk, D. and Santos, A. and von Mering, C. and Jensen, L.J. and Bork, P. and Kuhn, M.
Nucleic Acids Research 44
(D1): D380-D384.
4 January 2016
The SIDER database of drugs and side effects.
Kuhn, M. and Letunic, I. and Jensen, L.J. and Bork, P.
Nucleic Acids Research 44
(D1): D1075-D1079.
4 January 2016
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.
Huerta-Cepas, J. and Szklarczyk, D. and Forslund, K. and Cook, H. and Heller, D. and Walter, M.C. and Rattei, T. and Mende, D.R. and Sunagawa, S. and Kuhn, M. and Jensen, L.J. and von Mering, C. and Bork, P.
Nucleic Acids Research 44
(D1): D286-D293.
4 January 2016
2015
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.
Forslund, K. and Hildebrandt, F. and Nielsen, T. and Falony, G. and Le Chatelier, E. and Sunagawa, S. and Prifti, E. and Vieira-Silva, S. and Gudmundsdottir, V. and Pedersen, H.K. and Arumugam, M. and Kristiansen, K. and Voigt, A.Y. and Vestergaard, H. and Hercog, R. and Costea, P.I. and Kultima, J.R. and Li, J. and Jørgensen, T. and Levenez, F. and Dore, J. and Nielsen, H.B. and Brunak, S. and Raes, J. and Hansen, T. and Wang, J. and Ehrlich, S.D. and Bork, P. and Pedersen, O.
Nature 528
(7581): 262-266.
10 December 2015
Operon structure and cotranslational subunit association direct protein assembly in bacteria.
Shieh, Y.W. and Minguez, P. and Bork, P. and Auburger, J.J. and Guilbride, D.L. and Kramer, G. and Bukau, B.
Science 350
(6261): 678-680.
6 November 2015
Integrated transcriptome and proteome analyses reveal organ-specific proteome deterioration in old rats.
Ori, A. and Toyama, B.H. and Harris, M.S. and Bock, T. and Iskar, M. and Bork, P. and Ingolia, N.T. and Hetzer, M.W. and Beck, M.
Cell Systems 1
(3): 224-237.
23 September 2015
Quest for Orthologs entails quest for Tree of Life: in search of the gene stream.
Boeckmann, B. and Marcet-Houben, M. and Rees, J.A. and Forslund, K. and Huerta-Cepas, J. and Muffato, M. and Yilmaz, P. and Xenarios, I. and Bork, P. and Lewis, S.E. and Gabaldon, T.
Genome Biology and Evolution 7
(7): 1988-1999.
1 July 2015
Determinants of community structure in the global plankton interactome.
Lima-Mendez, G. and Faust, K. and Henry, N. and Decelle, J. and Colin, S. and Carcillo, F. and Chaffron, S. and Ignacio-Espinosa, J.C. and Roux, S. and Vincent, F. and Bittner, L. and Darzi, Y. and Wang, J. and Audic, S. and Berline, L. and Bontempi, G. and Cabello, A.M. and Coppola, L. and Cornejo-Castillo, F.M. and d' Ovidio, F. and De Meester, L. and Ferrera, I. and Garet-Delmas, M.J. and Guidi, L. and Lara, E. and Pesant, S. and Royo-Llonch, M. and Salazar, G. and Sanchez, P. and Sebastian, M. and Souffreau, C. and Dimier, C. and Picheral, M. and Searson, S. and Kandels-Lewis, S. and Gorsky, G. and Not, F. and Ogata, H. and Speich, S. and Stemmann, L. and Weissenbach, J. and Wincker, P. and Acinas, S.G. and Sunagawa, S. and Bork, P. and Sullivan, M.B. and Karsenti, E. and Bowler, C. and de Vargas, C. and Raes, J.
Science 348
(6237): 1262073.
22 May 2015
Environmental characteristics of Agulhas rings affect interocean plankton transport.
Villar, E. and Farrant, G.K. and Follows, M. and Garczarek, L. and Speich, S. and Audic, S. and Bittner, L. and Blanke, B. and Brum, J.R. and Brunet, C. and Casotti, R. and Chase, A. and Dolan, J.R. and d'Ortenzio, F. and Gattuso, J.P. and Grima, N. and Guidi, L. and Hill, C.N. and Jahn, O. and Jamet, J.L. and Le Goff, H. and Lepoivre, C. and Malviya, S. and Pelletier, E. and Romagnan, J.B. and Roux, S. and Santini, S. and Scalco, E. and Schwenck, S.M. and Tanaka, A. and Testor, P. and Vannier, T. and Vincent, F. and Zingone, A. and Dimier, C. and Picheral, M. and Searson, S. and Kandels-Lewis, S. and Acinas, S.G. and Bork, P. and Boss, E. and de Vargas, C. and Gorsky, G. and Ogata, H. and Pesant, S. and Sullivan, M.B. and Sunagawa, S. and Wincker, P. and Karsenti, E. and Bowler, C. and Not, F. and Hingamp, P. and Iudicone, D.
Science 348
(6237): 1261447.
22 May 2015
Eukaryotic plankton diversity in the sunlit ocean.
de Vargas, C. and Audic, S. and Henry, N. and Decelle, J. and Mahe, F. and Logares, R. and Lara, E. and Berney, C. and Le Bescot, N. and Probert, I. and Carmichael, M. and Poulain, J. and Romac, S. and Colin, S. and Aury, J.M. and Bittner, L. and Chaffron, S. and Dunthorn, M. and Engelen, S. and Flegontova, O. and Guidi, L. and Horak, A. and Jaillon, O. and Lima-Mendez, G. and Lukes, J. and Malviya, S. and Morard, R. and Mulot, M. and Scalco, E. and Siano, R. and Vincent, F. and Zingone, A. and Dimier, C. and Picheral, M. and Searson, S. and Kandels-Lewis, S. and Acinas, S.G. and Bork, P. and Bowler, C. and Gorsky, G. and Grimsley, N. and Hingamp, P. and Iudicone, D. and Not, F. and Ogata, H. and Pesant, S. and Raes, J. and Sieracki, M.E. and Speich, S. and Stemmann, L. and Sunagawa, S. and Weissenbach, J. and Wincker, P. and Karsenti, E.
Science 348
(6237): 1261605.
22 May 2015
Patterns and ecological drivers of ocean viral communities.
Brum, J.R. and Ignacio-Espinoza, J.C. and Roux, S. and Doulcier, G. and Acinas, S.G. and Alberti, A. and Chaffron, S. and Cruaud, C. and de Vargas, C. and Gasol, J.M. and Gorsky, G. and Gregory, A.C. and Guidi, L. and Hingamp, P. and Iudicone, D. and Not, F. and Ogata, H. and Pesant, S. and Poulos, B.T. and Schwenck, S.M. and Speich, S. and Dimier, C. and Kandels-Lewis, S. and Picheral, M. and Searson, S. and Bork, P. and Bowler, C. and Sunagawa, S. and Wincker, P. and Karsenti, E. and Sullivan, M.B.
Science 348
(6237): 1261498.
22 May 2015
Structure and function of the global ocean microbiome.
Sunagawa, S. and Coelho, L.P. and Chaffron, S. and Kultima, J.R. and Labadie, K. and Salazar, G. and Djahanschiri, B. and Zeller, G. and Mende, D.R. and Alberti, A. and Cornejo-Castillo, F.M. and Costea, P.I. and Cruaud, C. and d'Ovidio, F. and Engelen, S. and Ferrera, I. and Gasol, J.M. and Guidi, L. and Hildebrand, F. and Kokoszka, F. and Lepoivre, C. and Lima-Mendez, G. and Poulain, J. and Poulos, B.T. and Royo-Llonch, M. and Sarmento, H. and Vieira-Silva, S. and Dimier, C. and Picheral, M. and Searson, S. and Kandels-Lewis, S. and Bowler, C. and de Vargas, C. and Gorsky, G. and Grimsley, N. and Hingamp, P. and Iudicone, D. and Jaillon, O. and Not, F. and Ogata, H. and Pesant, S. and Speich, S. and Stemmann, L. and Sullivan, M.B. and Weissenbach, J. and Wincker, P. and Karsenti, E. and Raes, J. and Acinas, S.G. and Bork, P.
Science 348
(6237): 1261359.
22 May 2015
Computational eco-systems biology in Tara Oceans: translating data into knowledge.
Sunagawa, S. and Karsenti, E. and Bowler, C. and Bork, P.
Molecular Systems Biology 11
(5): 809.
21 May 2015
Temporal and technical variability of human gut metagenomes.
Voigt, A.Y. and Costea, P.I. and Kultima, J.R. and Li, S.S. and Zeller, G. and Sunagawa, S. and Bork, P.
Genome Biology 16
(1): 73.
8 April 2015
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.
Minguez, P. and Letunic, I. and Parca, L. and Garcia-Alonso, L. and Dopazo, J. and Huerta-Cepas, J. and Bork, P.
Nucleic Acids Research 43
(Database issue): D494-D502.
28 January 2015
Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium.
Lluch-Senar, M. and Delgado, J. and Chen, W.-H. and Llorens-Rico, V. and O'Reilly, F.J. and Wodke, J.A.H. and Unal, E.B. and Yus, E. and Martinez, S. and Nichols, R.J. and Ferrar, T. and Vivancos, A. and Schmeisky, A. and Stuelke, J. and van Noort, V. and Gavin, A.-C. and Bork, P. and Serrano, L.
Molecular Systems Biology 11
(1): 780.
21 January 2015
2014
Potential of fecal microbiota for early-stage detection of colorectal cancer.
Zeller, G. and Tap, J. and Voigt, A.Y. and Sunagawa, S. and Kultima, J.R. and Costea, P.I. and Amiot, A. and Boehm, J. and Brunetti, F. and Habermann, N. and Hercog, R. and Koch, M. and Luciani, A. and Mende, D.R. and Schneider, M.A. and Schrotz-King, P. and Tournigand, C. and Tran Van Nhieu, J. and Yamada, T. and Zimmermann, J. and Benes, V. and Kloor, M. and Ulrich, C.M. and von Knebel Doeberitz, M. and Sobhani, I. and Bork, P.
Molecular Systems Biology 10
(11): 766.
28 November 2014
A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation.
Trachana, K. and Forslund, K. and Larsson, T. and Powell, S. and Doerks, T. and von Mering, C. and Bork, P.
PLoS ONE 9
(11): e111122.
4 November 2014
Novel drug candidates for the treatment of metastatic colorectal cancer through global inverse gene-expression profiling.
van Noort, V. and Schoelch, S. and Iskar, M. and Zeller, G. and Ostertag, K. and Schweitzer, C. and Werner, K. and Weitz, J. and Koch, M. and Bork, P.
Cancer Research 74
(20): 5690-5699.
15 October 2014
LotuS: an efficient and user-friendly OTU processing pipeline.
Hildebrand, F. and Tito, R.Y. and Voigt, A.Y. and Bork, P. and Raes, J.
Microbiome 2
(1): 30.
30 September 2014
An integrated catalog of reference genes in the human gut microbiome.
Li, J. and Jia, H. and Cai, X. and Zhong, H. and Feng, Q. and Sunagawa, S. and Arumugam, M. and Kultima, J.R. and Prifti, E. and Nielsen, T. and Juncker, A.S. and Manichanh, C. and Chen, B. and Zhang, W. and Levenez, F. and Wang, J. and Xu, X. and Xiao, L. and Liang, S. and Zhang, D. and Zhang, Z. and Chen, W. and Zhao, H. and Al-Aama, J.Y. and Edris, S. and Yang, H. and Wang, J. and Hansen, T. and Nielsen, H.B. and Brunak, S. and Kristiansen, K. and Guarner, F. and Pedersen, O. and Dore, J. and Ehrlich, S.D. and Bork, P. and Wang, J.
Nature Biotechnology 32
(8): 834-841.
August 2014
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.
Nielsen, H.B. and Almeida, M. and Juncker, A.S. and Rasmussen, S. and Li, J. and Sunagawa, S. and Plichta, D.R. and Gautier, L. and Pedersen, A.G. and Le Chatelier, E. and Pelletier, E. and Bonde, I. and Nielsen, T. and Manichanh, C. and Arumugam, M. and Batto, J.M. and Quintanilha Dos Santos, M.B. and Blom, N. and Borruel, N. and Burgdorf, K.S. and Boumezbeur, F. and Casellas, F. and Dore, J. and Dworzynski, P. and Guarner, F. and Hansen, T. and Hildebrand, F. and Kaas, R.S. and Kennedy, S. and Kristiansen, K. and Kultima, J.R. and Leonard, P. and Levenez, F. and Lund, O. and Moumen, B. and Le Paslier, D. and Pons, N. and Pedersen, O. and Prifti, E. and Qin, J. and Raes, J. and Sorensen, S. and Tap, J. and Tims, S. and Ussery, D.W. and Yamada, T. and Renault, P. and Sicheritz-Ponten, T. and Bork, P. and Wang, J. and Brunak, S. and Ehrlich, S.D.
Nature Biotechnology 32
(8): 822-828.
August 2014
Comments on "Human dominant disease genes are enriched in paralogs originating from whole genome duplication".
Chen, W.H. and Zhao, X.M. and van Noort, V. and Bork, P.
PLoS Computational Biology 10
(7): e1003758.
31 July 2014
STITCH 4: integration of protein-chemical interactions with user data.
Kuhn, M. and Szklarczyk, D. and Pletscher-Frankild, S. and Blicher, T.H. and von Mering, C. and Jensen, L.J. and Bork, P.
Nucleic Acids Research 42
(1): D401-D407.
1 January 2014
eggNOG v4.0: nested orthology inference across 3686 organisms.
Powell, S. and Forslund, K. and Szklarczyk, D. and Trachana, K. and Roth, A. and Huerta-Cepas, J. and Gabaldon, T. and Rattei, T. and Creevey, C. and Kuhn, M. and Jensen, L.J. and von Mering, C. and Bork, P.
Nucleic Acids Research 42
(1): D231-D239.
1 January 2014
2013
Evolution and functional cross-talk of protein post-translational modifications.
Beltrao, P. and Bork, P. and Krogan, N.J. and van Noort, V.
Molecular Systems Biology 9
: 714.
22 December 2013
Metagenomic species profiling using universal phylogenetic marker genes.
Sunagawa, S. and Mende, D.R. and Zeller, G. and Izquierdo-Carrasco, F. and Berger, S.A. and Kultima, J.R. and Coelho, L.P. and Arumugam, M. and Tap, J. and Nielsen, H.B. and Rasmussen, S. and Brunak, S. and Pedersen, O. and Guarner, F. and de Vos, W.M. and Wang, J. and Li, J. and Dore, J. and Ehrlich, S.D. and Stamatakis, A. and Bork, P.
Nature Methods 10
(12): 1196-1199.
December 2013
Accurate and universal delineation of prokaryotic species.
Mende, D.R. and Sunagawa, S. and Zeller, G. and Bork, P.
Nature Methods 10
(9): 881-884.
September 2013
Human monogenic disease genes have frequently functionally redundant paralogs.
Chen, W.H. and Zhao, X.M. and van Noort, V. and Bork, P.
PLoS Computational Biology 9
(5): e1003073.
May 2013
Consistent mutational paths predict eukaryotic thermostability.
van Noort, V. and Bradatsch, B. and Arumugam, M. and Amlacher, S. and Bange, G. and Creevey, C. and Falk, S. and Mende, D.R. and Sinning, I. and Hurt, E. and Bork, P.
BMC Evolutionary Biology 13
: 7.
10 January 2013
Genomic variation landscape of the human gut microbiome.
Schloissnig, S. and Arumugam, M. and Sunagawa, S. and Mitreva, M. and Tap, J. and Zhu, A. and Waller, A. and Mende, D.R. and Kultima, J.R. and Martin, J. and Kota, K. and Sunyaev, S.R. and Weinstock, G.M. and Bork, P.
Nature 493
(7430): 45-50.
3 January 2013
PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins.
Minguez, P. and Letunic, I. and Parca, L. and Bork, P.
Nucleic Acids Research 41
(D1): D306-D311.
1 January 2013
STRING v9.1: protein-protein interaction networks, with increased coverage and integration.
Franceschini, A. and Szklarczyk, D. and Frankild, S. and Kuhn, M. and Simonovic, M. and Roth, A. and Lin, J. and Minguez, P. and Bork, P. and von Mering, C. and Jensen, L.J.
Nucleic Acids Research 41
(D1): D808-D815.
1 January 2013
Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding.
Iskar, M. and Zeller, G. and Blattmann, P. and Campillos, M. and Kuhn, M. and Kaminska, K.H. and Runz, H. and Gavin, A.C. and Pepperkok, R. and van Noort, V. and Bork, P.
Molecular Systems Biology 9
: 662.
2013
Systematic identification of proteins that elicit drug side effects.
Kuhn, M. and Al Banchaabouchi, M. and Campillos, M. and Jensen, L.J. and Gross, C. and Gavin, A.C. and Bork, P.
Molecular Systems Biology 9
: 663.
2013
2012
MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit.
Kultima, J.R. and Sunagawa, S. and Li, J. and Chen, W. and Chen, H. and Mende, D.R. and Arumugam, M. and Pan, Q. and Liu, B. and Qin, J. and Wang, J. and Bork, P.
PLoS ONE 7
(10): e47656.
17 October 2012
Drug discovery in the age of systems biology: the rise of computational approaches for data integration.
Iskar, M. and Zeller, G. and Zhao, X.M. and van Noort, V. and Bork, P.
Current Opinion in Biotechnology 23
(4): 609-616.
August 2012
Deciphering a global network of functionally associated post-translational modifications.
Minguez, P. and Parca, L. and Diella, F. and Mende, D.R. and Kumar, R. and Helmer-Citterich, M. and Gavin, A.C. and van Noort, V. and Bork, P.
Molecular Systems Biology 8
: 599.
17 July 2012
Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours.
Yamada, T. and Waller, A.S. and Raes, J. and Zelezniak, A. and Perchat, N. and Perret, A. and Salanoubat, M. and Patil, K.R. and Weissenbach, J. and Bork, P.
Molecular Systems Biology 8
: 581.
8 May 2012
Annotation of the M. tuberculosis hypothetical orfeome: adding functional information to more than half of the uncharacterized proteins.
Doerks, T. and van Noort, V. and Minguez, P. and Bork, P.
PLoS ONE 7
(4): e34302.
2 April 2012
Assessment of metagenomic assembly using simulated next generation sequencing data.
Mende, D.R. and Waller, A.S. and Sunagawa, S. and Jaervelin, A.I. and Chan, M.M. and Arumugam, M. and Raes, J. and Bork, P.
PLoS ONE 7
(2): e31386.
23 February 2012
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.
Powell, S. and Szklarczyk, D. and Trachana, K. and Roth, A. and Kuhn, M. and Muller, J. and Arnold, R. and Rattei, T. and Letunic, I. and Doerks, T. and Jensen, L.J. and von Mering, C. and Bork, P.
Nucleic Acids Research 40
(D1): D284-D289.
1 January 2012
OGEE: an online gene essentiality database.
Chen, W.H. and Minguez, P. and Lercher, M.J. and Bork, P.
Nucleic Acids Research 40
(Database issue): D901-D906.
January 2012
STITCH 3: zooming in on protein-chemical interactions.
Kuhn, M. and Szklarczyk, D. and Franceschini, A. and von Mering, C. and Jensen, L.J. and Bork, P.
Nucleic Acids Research 40
(Database Issue): D876-D880.
January 2012
2011
Prediction of drug combinations by integrating molecular and pharmacological data.
Zhao, X.M. and Iskar, M. and Zeller, G. and Kuhn, M. and van Noort, V. and Bork, P.
PLoS Computational Biology 7
(12): e1002323.
29 December 2011
Identifying single copy orthologs in Metazoa.
Creevey, C.J. and Muller, J. and Doerks, T. and Thompson, J.D. and Arendt, D. and Bork, P.
PLoS Computational Biology 7
(12): e1002269.
1 December 2011
Orthology prediction methods: a quality assessment using curated protein families.
Trachana, K. and Larsson, T.A. and Powell, S. and Chen, W.H. and Doerks, T. and Muller, J. and Bork, P.
BioEssays 33
(10): 769-780.
October 2011
Network neighbors of drug targets contribute to drug side-effect similarity.
Brouwers, L. and Iskar, M. and Zeller, G. and van Noort, V. and Bork, P.
PLoS ONE 6
(7): e22187.
13 July 2011
Enterotypes of the human gut microbiome.
Arumugam, M. and Raes, J. and Pelletier, E. and Le Paslier, D. and Yamada, T. and Mende, D.R. and Fernandes, G.R. and Tap, J. and Bruls, T. and Batto, J.M. and Bertalan, M. and Borruel, N. and Casellas, F. and Fernandez, L. and Gautier, L. and Hansen, T. and Hattori, M. and Hayashi, T. and Kleerebezem, M. and Kurokawa, K. and Leclerc, M. and Levenez, F. and Manichanh, C. and Nielsen, H.B. and Nielsen, T. and Pons, N. and Poulain, J. and Qin, J. and Sicheritz-Ponten, T. and Tims, S. and Torrents, D. and Ugarte, E. and Zoetendal, E.G. and Wang, J. and Guarner, F. and Pedersen, O. and de Vos, W.M. and Brunak, S. and Dore, J. and Weissenbach, J. and Ehrlich, S.D. and Bork, P.
Nature 473
(7346): 174-180.
12 May 2011
Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data.
Raes, J. and Letunic, I. and Yamada, T. and Jensen, L.J. and Bork, P.
Molecular Systems Biology 7
: 473.
15 March 2011
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored.
Szklarczyk, D. and Franceschini, A. and Kuhn, M. and Simonovic, M. and Roth, A. and Minguez, P. and Doerks, T. and Stark, M. and Muller, J. and Bork, P. and Jensen, L.J. and von Mering, C.
Nucleic Acids Research 39
(Database issue): D561-D568.
January 2011
2010
A network of conserved co-occurring motifs for the regulation of alternative splicing.
Suyama, M. and Harrington, E.D. and Vinokourova, S. and von Knebel Doeberitz, M. and Ohara, O. and Bork, P.
Nucleic Acids Research 38
(22): 7916-7926.
1 December 2010
SmashCell: a software framework for the analysis of single-cell amplified genome sequences.
Harrington, E.D. and Arumugam, M. and Raes, J. and Bork, P. and Relman, D.A.
Bioinformatics 26
(23): 2979-2980.
1 December 2010
SmashCommunity: A metagenomic annotation and analysis tool.
Arumugam, M. and Harrington, E.D. and Foerstner, K.U. and Raes, J. and Bork, P.
Bioinformatics 26
(23): 2977-2978.
1 December 2010
Drug-induced regulation of target expression.
Iskar, M. and Campillos, M. and Kuhn, M. and Jensen, L.J. and van Noort, V. and Bork, P.
PLoS Computational Biology 6
(9): e1000925.
9 September 2010
Systems analysis of iron metabolism: the network of iron pools and fluxes.
Lopes, T.J. and Luganskaja, T. and Vujic-Spasic, M. and Hentze, M.W. and Muckenthaler, M.U. and Schumann, K. and Reich, J.G.
BMC Systems Biology 4
(1): 112.
13 August 2010
Ontologies in quantitative biology: a basis for comparison, integration, and discovery.
Jensen, L.J. and Bork, P.
PLoS Biology 8
(5): e1000374.
25 May 2010
High-resolution transcription atlas of the mitotic cell cycle in budding yeast.
Granovskaia, M.V. and Jensen, L.J. and Ritchie, M.E. and Toedling, J. and Ning, Y. and Bork, P. and Huber, W. and Steinmetz, L.M.
Genome Biology 11
(3): R24.
1 March 2010
Evolution and regulation of cellular periodic processes: a role for paralogues.
Trachana, K. and Jensen, L.J. and Bork, P.
EMBO Reports 11
(3): 233-238.
March 2010
Ancient animal microRNAs and the evolution of tissue identity.
Christodoulou, F. and Raible, F. and Tomer, R. and Simakov, O. and Trachana, K. and Klaus, S. and Snyman, H. and Hannon, G.J. and Bork, P. and Arendt, D.
Nature 463
(7284): 1084-1088.
25 February 2010
AQUA: Automated quality improvement for multiple sequence alignments.
Muller, J. and Creevey, C.J. and Thompson, J.D. and Arendt, D. and Bork, P.
Bioinformatics 26
(2): 263-265.
15 January 2010
Iron absorption and distribution in TNF(DeltaARE/+) mice, a model of chronic inflammation.
Schuemann, K. and Herbach, N. and Kerling, C. and Seifert, M. and Fillebeen, C. and Prysch, I. and Reich, J. and Weiss, G. and Pantopoulos, K.
Journal of Trace Elements in Medicine and Biology 24
(1): 58-66.
January 2010
STITCH 2: an interaction network database for small molecules and proteins.
Kuhn, M. and Szklarczyk, D. and Franceschini, A. and Campillos, M. and von Mering, C. and Jensen, L.J. and Beyer, A. and Bork, P.
Nucleic Acids Research 38
(Database issue): D552-D556.
January 2010
SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology.
Woerner, S.M. and Yuan, Y.P. and Benner, A. and Korff, S. and von Knebel Doeberitz, M. and Bork, P.
Nucleic Acids Research 38
(Database issue): D682-D689.
January 2010
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.
Muller, J. and Szklarczyk, D. and Julien, P. and Letunic, I. and Roth, A. and Kuhn, M. and Powell, S. and von Mering, C. and Doerks, T. and Jensen, L.J. and Bork, P.
Nucleic Acids Research 38
(Database issue): D190-D195.
January 2010
A side effect resource to capture phenotypic effects of drugs.
Kuhn, M. and Campillos, M. and Letunic, I. and Jensen, L.J. and Bork, P.
Molecular Systems Biology 6
: 343.
2010
Neue Wege der Stammzellforschung: Reprogrammierung von differenzierten Koerperzellen [New methods in stem cell research: reprogramming of differentiated body cells].
Beier, H.M. and Fehse, B. and Friedrich, B. and Goetz, M. and Hansmann, I. and Hucho, F. and Koechy, K. and Mueller-Roeber, B. and Rheinberger, H.J. and Reich, J. and Ropers, H.H. and Schoeler, H.R. and Schoene-Seifert, B. and Sperling, K. and Tanner, K. and Taupitz, J. and Wobus, A.M.
Journal fuer Reproduktionsmedizin und Endokrinologie 7
(2): 68-77.
2010
2009
Impact of genome reduction on bacterial metabolism and its regulation.
Yus, E. and Maier, T. and Michalodimitrakis, K. and van Noort, V. and Yamada, T. and Chen, W.H. and Wodke, J.A. and Gueell, M. and Martinez, S. and Bourgeois, R. and Kuehner, S. and Raineri, E. and Letunic, I. and Kalinina, O.V. and Rode, M. and Herrmann, R. and Gutierrez-Gallego, R. and Russell, R.B. and Gavin, A.C. and Bork, P. and Serrano, L.
Science 326
(5957): 1263-1268.
27 November 2009
Proteome organization in a genome-reduced bacterium.
Kuehner, S. and van Noort, V. and Betts, M.J. and Leo-Macias, A. and Batisse, C. and Rode, M. and Yamada, T. and Maier, T. and Bader, S. and Beltran-Alvarez, P. and Castano-Diez, D. and Chen, W.H. and Devos, D. and Gueell, M. and Norambuena, T. and Racke, I. and Rybin, V. and Schmidt, A. and Yus, E. and Aebersold, R. and Herrmann, R. and Boettcher, B. and Frangakis, A.S. and Russell, R.B. and Serrano, L. and Bork, P. and Gavin, A.C.
Science 326
(5957): 1235-1240.
27 November 2009
Transcriptome complexity in a genome-reduced bacterium.
Gueell, M. and van Noort, V. and Yus, E. and Chen, W.H. and Leigh-Bell, J. and Michalodimitrakis, K. and Yamada, T. and Arumugam, M. and Doerks, T. and Kuehner, S. and Rode, M. and Suyama, M. and Schmidt, S. and Gavin, A.C. and Bork, P. and Serrano, L.
Science 326
(5957): 1268-1271.
27 November 2009
Evolution of biomolecular networks - lessons from metabolic and protein interactions.
Yamada, T. and Bork, P.
Nature Reviews Molecular Cell Biology 10
(11): 791-803.
November 2009
Ageing-related chromatin defects through loss of the NURD complex.
Pegoraro, G. and Kubben, N. and Wickert, U. and Goehler, H. and Hoffmann, K. and Misteli, T.
Nature Cell Biology 11
(10): 1261-1267.
October 2009
Dopamine-glutamate abnormalities in the frontal cortex associated with the catechol-O-methyltransferase (COMT) in schizophrenia.
Brisch, R. and Bernstein, H.G. and Krell, D. and Dobrowolny, H. and Bielau, H. and Steiner, J. and Gos, T. and Funke, S. and Stauch, R. and Knueppel, S. and Bogerts, B.
Brain Research 1269
: 166-175.
7 May 2009
FragIdent - automatic identification and characterisation of cDNA-fragments.
Seelow, D. and Goehler, H. and Hoffmann, K.
BMC Genomics 10
: 95.
2 March 2009
ASTD: The Alternative Splicing and Transcript Diversity database.
Koscielny, G. and Texier, V.L. and Gopalakrishnan, C. and Kumanduri, V. and Riethoven, J.J. and Nardone, F. and Stanley, E. and Fallsehr, C. and Hofmann, O. and Kull, M. and Harrington, E. and Boue, S. and Eyras, E. and Plass, M. and Lopez, F. and Ritchie, W. and Moucadel, V. and Ara, T. and Pospisil, H. and Herrmann, A. and Reich, J.G. and Guigo, R. and Bork, P. and Doeberitz, M.V. and Vilo, J. and Hide, W. and Apweiler, R. and Thanaraj, T.A. and Gautheret, D.
Genomics 93
(3): 213-220.
March 2009
Quantifying environmental adaptation of metabolic pathways in metagenomics.
Gianoulis, T.A. and Raes, J. and Patel, P.V. and Bjornson, R. and Korbel, J.O. and Letunic, I. and Yamada, T. and Paccanaro, A. and Jensen, L.J. and Snyder, M. and Bork, P. and Gerstein, M.B.
Proceedings of the National Academy of Sciences of the United States of America 106
(5): 1374-1379.
3 February 2009
Sequence-based feature prediction and annotation of proteins.
Juncker, A.S. and Jensen, L.J. and Pierleoni, A. and Bernsel, A. and Tress, M.L. and Bork, P. and von Heijne, G. and Valencia, A. and Ouzounis, C.A. and Casadio, R. and Brunak, S.
Genome Biology 10
(2): 206.
2 February 2009
Discovering functional novelty in metagenomes: examples from light-mediated processes.
Singh, A.H. and Doerks, T. and Letunic, I. and Raes, J. and Bork, P.
Journal of Bacteriology 191
(1): 32-41.
January 2009
InterPro: the integrative protein signature database.
Hunter, S. and Apweiler, R. and Attwood, T.K. and Bairoch, A. and Bateman, A. and Binns, D. and Bork, P. and Das, U. and Daugherty, L. and Duquenne, L. and Finn, R.D. and Gough, J. and Haft, D. and Hulo, N. and Kahn, D. and Kelly, E. and Laugraud, A. and Letunic, I. and Lonsdale, D. and Lopez, R. and Madera, M. and Maslen, J. and McAnulla, C. and McDowall, J. and Mistry, J. and Mitchell, A. and Mulder, N. and Natale, D. and Orengo, C. and Quinn, A.F. and Selengut, J.D. and Sigrist, C.J. and Thimma, M. and Thomas, P.D. and Valentin, F. and Wilson, D. and Wu, C.H. and Yeats, C.
Nucleic Acids Research 37
(Database Issue): D211-D215.
January 2009
SMART 6: recent updates and new developments.
Letunic, I. and Doerks, T. and Bork, P.
Nucleic Acids Research 37
(Database Issue): D229-D232.
January 2009
STRING 8--a global view on proteins and their functional interactions in 630 organisms.
Jensen, L.J. and Kuhn, M. and Stark, M. and Chaffron, S. and Creevey, C. and Muller, J. and Doerks, T. and Julien, P. and Roth, A. and Simonovic, M. and Bork, P. and von Mering, C.
Nucleic Acids Research 37
(Database Issue): D412-D416.
January 2009
2008
A nitrile hydratase in the eukaryote monosiga brevicollis.
Foerstner, K.U. and Doerks, T. and Muller, J. and Raes, J. and Bork, P.
PLoS ONE 3
(12): e3976.
19 December 2008
Selective maintenance of Drosophila tandemly-arranged duplicated genes during evolution.
Quijano, C. and Tomancak, P. and Lopez-Marti, J. and Suyama, M. and Bork, P. and Milan, M. and Torrents, D. and Manzanares, M.
Genome Biology 9
(12): R176.
16 December 2008
Modelling phagosomal lipid networks that regulate actin assembly.
Kuehnel, M. and Mayorga, L.S. and Dandekar, T. and Thakar, J. and Schwarz, R. and Anes, E. and Griffiths, G. and Reich, J.
BMC Systems Biology 2
(1): 107.
5 December 2008
Heat shock protein-90-alpha, a prolactin-STAT5 target gene identified in breast cancer cells, is involved in apoptosis regulation.
Perotti, C. and Liu, R. and Parusel, C. and Boecher, N. and Schultz, J. and Bork, P. and Pfitzner, E. and Groner, B. and Shemanko, C.
Breast Cancer Research 10
(6): R94.
13 November 2008
Frameshift mutations in coding repeats of protein tyrosine phosphatase genes in colorectal tumors with microsatellite instability.
Korff, S. and Woerner, S.M. and Yuan, Y.P. and Bork, P. and von Knebel Doeberitz, M. and Gebert, J.
BMC Cancer 8
(1): 329.
10 November 2008
A computational screen for type I polyketide synthases in metagenomics shotgun data.
Foerstner, K.U. and Doerks, T. and Creevey, C.J. and Doerks, A. and Bork, P.
PLoS ONE 3
(10): e3515.
27 October 2008
Biochemistry. Not comparable, but complementary.
Jensen, L.J. and Bork, P.
Science 322
(5898): 56-57.
3 October 2008
Linear motif atlas for phosphorylation-dependent signaling.
Miller, M.L. and Jensen, L.J. and Diella, F. and Jorgensen, C. and Tinti, M. and Li, L. and Hsiung, M. and Parker, S.A. and Bordeaux, J. and Sicheritz-Ponten, T. and Olhovsky, M. and Pasculescu, A. and Alexander, J. and Knapp, S. and Blom, N. and Bork, P. and Li, S. and Cesareni, G. and Pawson, T. and Turk, B.E. and Yaffe, M.B. and Brunak, S. and Linding, R.
Science Signaling 1
(35): ra2.
2 September 2008
Sircah: a tool for the detection and visualization of alternative transcripts.
Harrington, E.D. and Bork, P.
Bioinformatics 24
(17): 1959-1960.
1 September 2008
Molecular eco-systems biology: towards an understanding of community function.
Raes, J. and Bork, P.
Nature Reviews Microbiology 6
(9): 693-699.
September 2008
Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages.
Pincus, D. and Letunic, I. and Bork, P. and Lim, W.A.
Proceedings of the National Academy of Sciences of the United States of America 105
(28): 9680-9684.
15 July 2008
Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?
Palleja, A. and Harrington, E.D. and Bork, P.
BMC Genomics 9
(1): 335.
15 July 2008
Drug target identification using side-effect similarity.
Campillos, M. and Kuhn, M. and Gavin, A.C. and Jensen, L.J. and Bork, P.
Science 321
(5886): 263-266.
11 July 2008
A molecular study of microbe transfer between distant environments.
Hooper, S.D. and Raes, J. and Foerstner, K.U. and Harrington, E.D. and Dalevi, D. and Bork, P.
PLoS ONE 3
(7): e2607.
9 July 2008
KEGG Atlas mapping for global analysis of metabolic pathways.
Okuda, S. and Yamada, T. and Hamajima, M. and Itoh, M. and Katayama, T. and Bork, P. and Goto, S. and Kanehisa, M.
Nucleic Acids Research 36
(Web Server Issue): W423-W426.
1 July 2008
Circular reasoning rather than cyclic expression.
Jensen, L.J. and de Lichtenberg, U. and Jensen, T.S. and Brunak, S. and Bork, P.
Genome Biology 9
(6): 403.
23 June 2008
Computational lipidology: predicting lipoprotein density profiles in human blood plasma.
Huebner, K. and Schwager, T. and Winkler, K. and Reich, J.G. and Holzhuetter, H.G.
PLoS Computational Biology 4
(5): e1000079.
23 May 2008
Genetiker in Berlin-Buch [Geneticists in Berlin-Buch].
Max-Delbrueck-Centrum fuer Molekulare Medizin, MDC, ed.
Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin.
May 2008
Max Delbrueck - der Physiker. Und die Grundlegung der Biologie [Max Delbrueck - the Physicist. Laying the Foundation of Biology].
Reich, J.
In:
Genetiker in Berlin-Buch [Geneticists in Berlin-Buch].
Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, 12-22.
May 2008
The genome of the model beetle and pest tribolium castaneum.
Nature 452
(7190): 949-955.
24 April 2008
Non-random retention of protein-coding overlapping genes in Metazoa.
Solda', G. and Suyama, M. and Pelucchi, P. and Boi, S. and Guffanti, A. and Rizzi, E. and Bork, P. and Tenchini, M.L. and Ciccarelli, F.D.
BMC Genomics 9
(1): 174.
16 April 2008
Large-scale prediction of drug-target relationships.
Kuhn, M. and Campillos, M. and Gonzalez, P. and Jensen, L.J. and Bork, P.
FEBS Letters 582
(8): 1283-1290.
9 April 2008
Predicting biological networks from genomic data.
Harrington, E.D. and Jensen, L.J. and Bork, P.
FEBS Letters 582
(8): 1251-1258.
9 April 2008
iPath: interactive exploration of biochemical pathways and networks.
Letunic, I. and Yamada, T. and Kanehisa, M. and Bork, P.
Trends in Biochemical Sciences 33
(3): 101-103.
March 2008
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans.
King, N. and Westbrook, M.J. and Young, S.L. and Kuo, A. and Abedin, M. and Chapman, J. and Fairclough, S. and Hellsten, U. and Isogai, Y. and Letunic, I. and Marr, M. and Pincus, D. and Putnam, N. and Rokas, A. and Wright, K.J. and Zuzow, R. and Dirks, W. and Good, M. and Goodstein, D. and Lemons, D. and Li, W. and Lyons, J.B. and Morris, A. and Nichols, S. and Richter, D.J. and Salamov, A. and Sequencing, J.G.I. and Bork, P. and Lim, W.A. and Manning, G. and Miller, W.T. and McGinnis, W. and Shapiro, H. and Tjian, R. and Grigoriev, I.V. and Rokhsar, D.
Nature 451
(7180): 783-788.
14 February 2008
Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families.
Shah, P.K. and Tripathi, L.P. and Jensen, L.J. and Gahnim, M. and Mason, C. and Furlong, E.E. and Rodrigues, V. and White, K.P. and Bork, P. and Sowdhamini, R.
Gene 407
(1-2): 199-215.
15 January 2008
4DXpress: a database for cross-species expression pattern comparisons.
Haudry, Y. and Berube, H. and Letunic, I. and Weeber, P.D. and Gagneur, J. and Girardot, C. and Kapushesky, M. and Arendt, D. and Bork, P. and Brazma, A. and Furlong, E.E. and Wittbrodt, J. and Henrich, T.
Nucleic Acids Research 36
(Database issue): D847-D853.
January 2008
NetworKIN: a resource for exploring cellular phosphorylation networks.
Linding, R. and Jensen, L.J. and Pasculescu, A. and Olhovsky, M. and Colwill, K. and Bork, P. and Yaffe, M.B. and Pawson, T.
Nucleic Acids Research 36
(Database issue): D695-D699.
January 2008
STITCH: interaction networks of chemicals and proteins.
Kuhn, M. and von Mering, C. and Campillos, M. and Jensen, L.J. and Bork, P.
Nucleic Acids Research 36
(Database issue): D684-D688.
January 2008
SuperTarget and Matador: resources for exploring drug-target relationships.
Guenther, S. and Kuhn, M. and Dunkel, M. and Campillos, M. and Senger, C. and Petsalaki, E. and Ahmed, J. and Urdiales, E.G. and Gewiess, A. and Jensen, L.J. and Schneider, R. and Skoblo, R. and Russell, R.B. and Bourne, P.E. and Bork, P. and Preissner, R.
Nucleic Acids Research 36
(Database issue): D919-D922.
January 2008
eggNOG: automated construction and annotation of orthologous groups of genes.
Jensen, L.J. and Julien, P. and Kuhn, M. and von Mering, C. and Muller, J. and Doerks, T. and Bork, P.
Nucleic Acids Research 36
(Database issue): D250-D254.
January 2008
In gratitude: Charlie.
Reich, J.
Beginnings 28
(4): 39.
2008
Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat.
Kunin, V. and Raes, J. and Harris, J.K. and Spear, J.R. and Walker, J.J. and Ivanova, N. and von Mering, C. and Bebout, B.M. and Pace, N.R. and Bork, P. and Hugenholtz, P.
Molecular Systems Biology 4
: 198.
2008
Modern genome annotation: The BioSapiens network.
Yeats, C. and Orengo, C. and Veuthey, A.L. and Boeckmann, B. and Jensen, L.J. and Valencia, A. and Rausell, A. and Bork, P.
In:
Modern Genome Annotation.
Springer, 213-238.
ISBN 978-3-211-75122-0
2008
Protein-protein interactions: Analysis and prediction.
Frishman, D. and Albrecht, M. and Blankenburg, H. and Bork, P. and Harrington, E.D. and Hermjakob, H. and Jensen, L.J. and Juan, D.A. and Lengauer, T. and Pagel, P. and Schachter, V. and Valencia, A.
In:
Modern Genome Annotation.
Springer, 353-410.
ISBN 978-3-211-75122-0
2008
2007
Genome-wide experimental determination of barriers to horizontal gene transfer.
Sorek, R. and Zhu, Y. and Creevey, C.J. and Francino, M.P. and Bork, P. and Rubin, E.M.
Science 318
(5855): 1449-1452.
30 November 2007
Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing.
Eulalio, A. and Rehwinkel, J. and Stricker, M. and Huntzinger, E. and Yang, S.F. and Doerks, T. and Dorner, S. and Bork, P. and Boutros, M. and Izaurralde, E.
Genes & Development 21
(20): 2558-2570.
15 October 2007
Get the most out of your metagenome: computational analysis of environmental sequence data.
Raes, J. and Foerstner, K.U. and Bork, P.
Current Opinion in Microbiology 10
(5): 490-498.
October 2007
Mutations in the gene encoding the 3'-5' DNA exonuclease TREX1 are associated with systemic lupus erythematosus.
Lee-Kirsch, M.A. and Gong, M. and Chowdhury, D. and Senenko, L. and Engel, K. and Lee, Y.A. and de Silva, U. and Bailey, S.L. and Witte, T. and Vyse, T.J. and Kere, J. and Pfeiffer, C. and Harvey, S. and Wong, A. and Koskenmies, S. and Hummel, O. and Rohde, K. and Schmidt, R.E. and Dominiczak, A.F. and Gahr, M. and Hollis, T. and Perrino, F.W. and Lieberman, J. and Huebner, N.
Nature Genetics 39
(9): 1065-1067.
September 2007
Variants in a novel epidermal collagen gene (COL29A1) are associated with atopic dermatitis.
Soederhaell, C. and Marenholz, I. and Kerscher, T. and Rueschendorf, F. and Esparza-Gordillo, J. and Worm, M. and Gruber, C. and Mayr, G. and Albrecht, M. and Rohde, K. and Schulz, H. and Wahn, U. and Huebner, N. and Lee, Y.A.
PLoS Biology 5
(9): e242.
September 2007
Quantitative assessment of protein function prediction from metagenomics shotgun sequences.
Harrington, E.D. and Singh, A.H. and Doerks, T. and Letunic, I. and von Mering, C. and Jensen, L.J. and Raes, J. and Bork, P.
Proceedings of the National Academy of Sciences of the United States of America 104
(35): 13913-13918.
28 August 2007
Evolution of cell cycle control: same molecular machines, different regulation.
de Lichtenberg, U. and Jensen, T.S. and Brunak, S. and Bork, P. and Jensen, L.J.
Cell Cycle 6
(15): 1819-1825.
1 August 2007
Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism.
Pachkov, M. and Dandekar, T. and Korbel, J. and Bork, P. and Schuster, S.
Gene 396
(2): 215-225.
15 July 2007
A German genome-wide linkage scan for type 2 diabetes supports the existence of a metabolic syndrome locus on chromosome 1p36.13 and a type 2 diabetes locus on chromosome 16p12.2.
Hoffmann, K. and Mattheisen, M. and Dahm, S. and Nuernberg, P. and Roe, C. and Johnson, J. and Cox, N.J. and Wichmann, H.E. and Wienker, T.F. and Schulze, J. and Schwarz, P.E. and Lindner, T.H.
Diabetologia 50
(7): 1418-1422.
July 2007
Update of the G2D tool for prioritization of gene candidates to inherited diseases.
Perez-Iratxeta, C. and Bork, P. and Andrade-Navarro, M.A.
Nucleic Acids Research 35
(Web Server Issue): W212-W216.
July 2007
Systematic discovery of in vivo phosphorylation networks.
Linding, R. and Jensen, L.J. and Ostheimer, G.J. and van Vugt, M.A. and Jorgensen, C. and Miron, I.M. and Diella, F. and Colwill, K. and Taylor, L. and Elder, K. and Metalnikov, P. and Nguyen, V. and Pasculescu, A. and Jin, J. and Park, J.G. and Samson, L.D. and Woodgett, J.R. and Russell, R.B. and Bork, P. and Yaffe, M.B. and Pawson, T.
Cell 129
(7): 1415-1426.
29 June 2007
Splicing factors stimulate polyadenylation via USEs at non-canonical 3' end formation signals.
Danckwardt, S. and Kaufmann, I. and Gentzel, M. and Foerstner, K.U. and Gantzert, A.S. and Gehring, N.H. and Neu-Yilik, G. and Bork, P. and Keller, W. and Wilm, M. and Hentze, M.W. and Kulozik, A.E.
EMBO Journal 26
(11): 2658-2669.
6 June 2007
Protein function space: viewing the limits or limited by our view?
Raes, J. and Harrington, E.D. and Singh, A.H. and Bork, P.
Current Opinion in Structural Biology 17
(3): 362-369.
June 2007
Sequence-based factors influencing the expression of heterologous genes in the yeast Pichia pastoris: A comparative view on 79 human genes.
Boettner, M. and Steffens, C. and von Mering, C. and Bork, P. and Stahl, U. and Lang, C.
Journal of Biotechnology 130
(1): 1-10.
31 May 2007
Ein kurzer Essay zur politischen Lage beim Stammzellgesetz [A short essay on the political situation concerning the stem cell law].
Reich, J.
Biospektrum 13
(3): 227.
May 2007
Quantitative phylogenetic assessment of microbial communities in diverse environments.
von Mering, C. and Hugenholtz, P. and Raes, J. and Tringe, S.G. and Doerks, T. and Jensen, L.J. and Ward, N. and Bork, P.
Science 315
(5815): 1126-1130.
23 February 2007
Prediction of effective genome size in metagenomic samples.
Raes, J. and Korbel, J.O. and Lercher, M.J. and von Mering, C. and Bork, P.
Genome Biology 8
(1): R10.
15 January 2007
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.
Letunic, I. and Bork, P.
Bioinformatics 23
(1): 127-128.
1 January 2007
Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis.
Hooper, S.D. and Boue, S. and Krause, R. and Jensen, L.J. and Mason, C.E. and Ghanim, M. and White, K.P. and Furlong, E.E. and Bork, P.
Molecular Systems Biology 3
: 72.
January 2007
New developments in the InterPro database.
Mulder, N.J. and Apweiler, R. and Attwood, T.K. and Bairoch, A. and Bateman, A. and Binns, D. and Bork, P. and Buillard, V. and Cerutti, L. and Copley, R. and Courcelle, E. and Das, U. and Daugherty, L. and Dibley, M. and Finn, R. and Fleischmann, W. and Gough, J. and Haft, D. and Hulo, N. and Hunter, S. and Kahn, D. and Kanapin, A. and Kejariwal, A. and Labarga, A. and Langendijk-Genevaux, P.S. and Lonsdale, D. and Lopez, R. and Letunic, I. and Madera, M. and Maslen, J. and McAnulla, C. and McDowall, J. and Mistry, J. and Mitchell, A. and Nikolskaya, A.N. and Orchard, S. and Orengo, C. and Petryszak, R. and Selengut, J.D. and Sigrist, C.J. and Thomas, P.D. and Valentin, F. and Wilson, D. and Wu, C.H. and Yeats, C.
Nucleic Acids Research 35
(Database Issue): D224-D228.
January 2007
Quantification of insect genome divergence.
Zdobnov, E.M. and Bork, P.
Trends in Genetics 23
(1): 16-20.
January 2007
STRING 7 - recent developments in the integration and prediction of protein interactions.
von Mering, C. and Jensen, L.J. and Kuhn, M. and Chaffron, S. and Doerks, T. and Krueger, B. and Snel, B. and Bork, P.
Nucleic Acids Research 35
(Database Issue): D358-D362.
January 2007
2006
Opsins and clusters of sensory G-protein-coupled receptors in the sea urchin genome.
Raible, F. and Tessmar-Raible, K. and Arboleda, E. and Kaller, T. and Bork, P. and Arendt, D. and Arnone, M.I.
Developmental Biology 300
(1): 461-475.
1 December 2006
The tumour-Clostridium phenomenon: 50 years of developmental research.
Schmidt, W. and Fabricius, E.M. and Schneeweiss, U.
International Journal of Oncology 29
(6): 1479-1492.
1 December 2006
Computational characterization of multiple Gag-like human proteins.
Campillos, M. and Doerks, T. and Shah, P.K. and Bork, P.
Trends in Genetics 22
(11): 585-589.
November 2006
Insights into social insects from the genome of the honeybee Apis mellifera.
Nature 443
(7114): 931-949.
26 October 2006
Assessing systems properties of yeast mitochondria through an interaction map of the organelle.
Perocchi, F. and Jensen, L.J. and Gagneur, J. and Ahting, U. and von Mering, C. and Bork, P. and Prokisch, H. and Steinmetz, L.M.
PLoS Genetics 2
(10): 1612-1624.
20 October 2006
Co-evolution of transcriptional and post-translational cell-cycle regulation.
Jensen, L.J. and Jensen, T.S. and de Lichtenberg, U. and Brunak, S. and Bork, P.
Nature 443
(7111): 594-597.
4 October 2006
Concordant association of lipid gene variation with a combined HDL/LDL-cholesterol phenotype in two European populations.
Bauerfeind, A. and Knoblauch, H. and Costanza, M.C. and Luganskaja, T. and Toliat, M.R. and Nuernberg, P. and Luft, F.C. and Reich, J.G. and Morabia, A.
Human Heredity 61
(3): 123-131.
August 2006
mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes.
Behm-Ansmant, I. and Rehwinkel, J. and Doerks, T. and Stark, A. and Bork, P. and Izaurralde, E.
Genes & Development 20
: 1885-1898.
15 July 2006
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.
Suyama, M. and Torrents, D. and Bork, P.
Nucleic Acids Research 34
(Web Server Issue): W609-W612.
1 July 2006
Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes.
Suyama, M. and Harrington, E. and Bork, P. and Torrents, D.
PLoS Computational Biology 2
(6): e76 (627-636).
30 June 2006
Stammzellforschung und Zelltherapie. Stand des Wissens und der Rahmenbedingungen in Deutschland / Supplement zum Gentechnologiebericht.
Wobus, A.M. and Hucho, F. and van den Daele, W. and Koechy, K. and Reich, J. and Rheinberger, H.J. and Mueller-Roeber, B. and Sperling, K. and Boysen, M. and Koelsch, M. and Hauskeller, C. and Taupitz, J.
Forschungsberichte der Interdisziplinaeren Arbeitsgruppen der Berlin-Brandenburgischen Akademie der Wissenschaften, Bd. 15
.
Elsevier, Muenchen.
ISBN 3-8274-1790-2
27 June 2006
Verification of predicted alternatively spliced Wnt genes reveals two new splice variants (CTNNB1 and LRP5) and altered Axin-1 expression during tumour progression.
Pospisil, H. and Herrmann, A. and Butherus, K. and Pirson, S. and Reich, J.G. and Kemmner, W.
BMC Genomics 7
: 148.
13 June 2006
A degradation-sensitive anionic trypsinogen (PRSS2) variant protects against chronic pancreatitis.
Witt, H. and Sahin-Toth, M. and Landt, O. and Chen, J.M. and Kaehne, T. and Drenth, J.P. and Kukor, Z. and Szepessy, E. and Halangk, W. and Dahm, S. and Rohde, K. and Schulz, H.U. and Le Marechal, C. and Akar, N. and Ammann, R.W. and Truninger, K. and Bargetzi, M. and Bhatia, E. and Castellani, C. and Cavestro, G.M. and Cerny, M. and Destro-Bisol, G. and Spedini, G. and Eiberg, H. and Jansen, J.B. and Koudova, M. and Rausova, E. and Macek, M. and Malats, N. and Real, F.X. and Menzel, H.J. and Moral, P. and Galavotti, R. and Pignatti, P.F. and Rickards, O. and Spicak, J. and Zarnescu, N.O. and Boeck, W. and Gress, T.M. and Friess, H. and Ockenga, J. and Schmidt, H. and Pfuetzer, R. and Loehr, M. and Simon, P. and Weiss, F.U. and Lerch, M.M. and Teich, N. and Keim, V. and Berg, T. and Wiedenmann, B. and Luck, W. and Groneberg, D.A. and Becker, M. and Keil, T. and Kage, A. and Bernardova, J. and Braun, M. and Gueldner, C. and Halangk, J. and Rosendahl, J. and Witt, U. and Treiber, M. and Nickel, R. and Ferec, C.
Nature Genetics 38
(6): 668-673.
June 2006
A temporal map of transcription factor activity: Mef2 directly regulates target genes at all stages of muscle development.
Sandmann, T. and Jensen, L.J. and Jakobsen, J.S. and Karzynski, M.M. and Eichenlaub, M.P. and Bork, P. and Furlong, E.E.
Developmental Cell 10
: 797-807.
June 2006
LSAT: learning about alternative transcripts in MEDLINE.
Shah, P.K. and Bork, P.
Bioinformatics 22
(7): 857-865.
1 April 2006
Proteome survey reveals modularity of the yeast cell machinery.
Gavin, A.C. and Aloy, P. and Grandi, P. and Krause, R. and Boesche, M. and Marzioch, M. and Rau, C. and Jensen, L.J. and Bastuck, S. and Duempelfeld, B. and Edelmann, A. and Heurtier, M.A. and Hoffman, V. and Hoefert, C. and Klein, K. and Hudak, M. and Michon, A.M. and Schelder, M. and Schirle, M. and Remor, M. and Rudi, T. and Hooper, S. and Bauer, A. and Bouwmeester, T. and Casari, G. and Drewes, G. and Neubauer, G. and Rick, J.M. and Kuster, B. and Bork, P. and Russell, R.B. and Superti-Furga, G.
Nature 440
(7084): 631-636.
30 March 2006
Comparative analysis of environmental sequences: potential and challenges.
Foerstner, K.U. and von Mering, C. and Bork, P.
Philosophical Transactions of the Royal Society of London Series B Biological Sciences 361
(1467): 519-523.
29 March 2006
Extraction of regulatory gene/protein networks from Medline.
Saric, J. and Jensen, L.J. and Ouzounova, R. and Rojas, I. and Bork, P.
Bioinformatics 22
: 645-650.
15 March 2006
Toward automatic reconstruction of a highly resolved tree of life.
Ciccarelli, F.D. and Doerks, T. and von Mehring, C. and Creevey, C.J. and Snel, B. and Bork, P.
Science 311
(5765): 1283-1287.
3 March 2006
Similar gene expression profiles do not imply similar tissue functions.
Yanai, I. and Korbel, J.O. and Boue, S. and McWeeney, S.K. and Bork, P. and Lercher, M.J.
Trends in Genetics 22
(3): 132-138.
March 2006
Literature mining for the biologist: from information retrieval to biological discovery.
Jensen, L.J. and Saric, J. and Bork, P.
Nature Reviews Genetics 7
(2): 119-129.
February 2006
Identification and analysis of evolutionarily cohesive functional modules in protein networks.
Campillos, M. and von Mering, C. and Jensen, L.J. and Bork, P.
Genome Research 16
: 374-382.
31 January 2006
Was uns der Wurm sagt. Die Prinzipien des Lebens sind universell. Mediziner muessen die Grenzen ihrer Fachgebiete ueberwinden, um vom Tier zu lernen, was kranke Menschen retten kann.
Reich, J.
Zeit 61
: 31-32.
5 January 2006
SMART 5: domains in the context of genomes and networks.
Letunic, I. and Copley, R.R. and Pils, B. and Pinkert, S. and Schultz, J. and Bork, P.
Nucleic Acids Research 34
(Database Issue): D257-D260.
1 January 2006
2005
Linkage analysis of alcohol dependence using MOD scores.
Strauch, K. and Fuerst, R. and Rueschendorf, F. and Windemuth, C. and Dietter, J. and Flaquer, A. and Baur, M.P. and Wienker, T.F.
BMC Genetics 6
(Suppl 1): S162.
30 December 2005
The effect of single-nucleotide polymorphism marker selection on patterns of haplotype blocks and haplotype frequency estimates.
Nothnagel, M. and Rohde, K.
American Journal of Human Genetics 77
(6): 988-998.
1 December 2005
Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii.
Raible, F. and Tessmar-Raible, K. and Osoegawa, K. and Wincker, P. and Jubin, C. and Balavoine, G. and Ferrier, D. and Benes, V. and de Jong, P. and Weissenbach, J. and Bork, P. and Arendt, D.
Science 310
: 1325-1326.
25 November 2005
Spore number control and breeding in Saccharomyces cerevisiae: a key role for a self-organizing system.
Taxis, C. and Keller, P. and Kavagiou, Z. and Jensen, L.J. and Colombelli, J. and Bork, P. and Stelzer, E.H. and Knop, M.
Journal of Cell Biology 171
(4): 627-640.
21 November 2005
Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets.
Rehwinkel, J. and Letunic, I. and Raes, J. and Bork, P. and Izaurralde, E.
RNA 11
(10): 1530-1544.
October 2005
Environments shape the nucleotide composition of genomes.
Foerstner, K.U. and von Mering, C. and Hooper, S.D. and Bork, P.
EMBO Reports 6
(12): 1208-1213.
30 September 2005
Medusa: a simple tool for interaction graph analysis.
Hooper, S.D. and Bork, P.
Bioinformatics 21
(24): 4432-4433.
27 September 2005
Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii.
Suyama, M. and Lathe, W.C. and Bork, P.
FEBS Letters 579
(24): 5281-5286.
21 September 2005
Initial sequence of the chimpanzee genome and comparison with the human genome.
Mikkelsen, T.S. and Hillier, L.W. and Eichler, E.E. and Zody, M.C. and Jaffe, D.B. and Yang, S.P. and Enard, W. and Hellmann, I. and Lindblad-Toh, K. and Altheide, T.K. and Archidiacono, N. and Bork, P. and Butler, J. and Chang, J.L. and Cheng, Z. and Chinwalla, A.T. and de Jong, P. and Delehaunty, K.D. and Fronick, C.C. and Fulton, L.L. and Gilad, Y. and Glusman, G. and Gnerre, S. and Graves, T.A. and Hayakawa, T. and Hayden, K.E. and Huang, X.Q. and Ji, H.K. and Kent, W.J. and King, M.C. and Kulbokas, E.J. and Lee, M.K. and Liu, G. and Lopez-Otin, C. and Makova, K.D. and Man, O. and Mardis, E.R. and Mauceli, E. and Miner, T.L. and Nash, W.E. and Nelson, J.O. and Paeaebo, S. and Patterson, N.J. and Pohl, C.S. and Pollard, K.S. and Pruefer, K. and Puente, X.S. and Reich, D. and Rocchi, M. and Rosenbloom, K. and Ruvolo, M. and Richter, D.J. and Schaffner, S.F. and Smit, A.F.A. and Smith, S.M. and Suyama, M. and Taylor, J. and Torrents, D. and Tuzun, E. and Varki, A. and Velasco, G. and Ventura, M. and Wallis, J.W. and Wendl, M.C. and Wilson, R.K. and Lander, E.S. and Waterston, R.H.
Nature 437
(7055): 69-87.
1 September 2005
Use of haplotypes and SNPs in lipid-relevant genes for the analysis and diagnosis of cardiovascular diseases [Verwendung von Haplotypen und SNPs in Genen des Fettstoffwechsels fuer die Analyse und Diagnose von kardiovaskulaeren Krankheiten].
Nuernberg, P. and Reich, J.G. and Luft, F.C. and Knoblauch, H. and Bauerfeind, A. and Luganskaja, T. and Rohde, K.
EP1566449.
24 August 2005
G2D: A tool for mining genes associated with disease.
Perez-Iratxeta, C. and Wjst, M. and Bork, P. and Andrade, M.A.
BMC Genetics 6
: 45.
22 August 2005
Very-KIND is a novel nervous system specific guanine nucleotide exchange factor for Ras GTPases.
Mees, A. and Rock, R. and Ciccarelli, F.D. and Leberfinger, C.B. and Borawski, J.M. and Bork, P. and Wiese, S. and Gessler, M. and Kerkhoff, E.
Gene Expression Patterns 6
: 79-85.
11 August 2005
DCD - a novel plant specific domain in proteins involved in development and programmed cell death.
Tenhaken, R. and Doerks, T. and Bork, P.
BMC Bioinformatics 6
: 169.
11 July 2005
Structural genomics of human proteins - target selection and generation of a public catalog of expression clones.
Buessow, K. and Scheich, C. and Sievert, V. and Harttig, U. and Schultz, J. and Simon, B. and Bork, P. and Lehrach, H. and Heinemann, U.
Microbial Cell Factories 4
: 21.
5 July 2005
Extraction of transcript diversity from scientific literature.
Shah, P.K. and Jensen, L.J. and Boue, S. and Bork, P.
PLoS Computational Biology 1
(1): e10.
24 June 2005
Systematic association of genes to phenotypes by genome and literature mining.
Korbel, J.O. and Doerks, T. and Jensen, L.J. and Perez-Iratxeta, C. and Kaczanowski, S. and Hooper, S.D. and Andrade, M.A. and Bork, P.
PLoS Biology 3
(5): e134.
5 April 2005
Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.
Zdobnov, E.M. and Campillos, M. and Harrington, E.D. and Torrents, D. and Bork, P.
Nucleic Acids Research 33
(3): 946-954.
16 February 2005
Dynamic complex formation during the yeast cell cycle.
de Lichtenberg, U. and Jensen, L.J. and Brunak, S. and Bork, P.
Science 307
(5710): 724-727.
4 February 2005
Genomewide linkage analysis identifies novel genetic loci for lung function in mice.
Reinhard, C. and Meyer, B. and Fuchs, H. and Stoeger, T. and Eder, G. and Rueschendorf, F. and Heyder, J. and Nuernberg, P. and Hrabe de Angelis, M. and Schulz, H.
American Journal of Respiratory and Critical Care Medicine 171
: 880-888.
7 January 2005
The definition of multilocus haplotype blocks and common diseases.
Nothnagel, M.
UNSPECIFIED thesis, UNSPECIFIED.
6 January 2005
A theoretical framework for detecting signal transfer routes in signalling networks.
Zevedei-Oancea, I. and Schuster, S.
Computers & Chemical Engineering 29
(3): 597-617.
1 January 2005
Association of ANKH gene polymorphisms with radiographic hand bone size and geometry in a Chuvasha population.
Malkin, I. and Dahm, S. and Suk, A. and Kobyliansky, E. and Toliat, M.R. and Ruf, N. and Livshits, G. and Nuernberg, P.
Bone 36
(2): 365-373.
1 January 2005
Association of the HLA region with multiple sclerosis as confirmed by a genome screen using >10,000 SNPs on DNA chips.
Goedde, R. and Rohde, K. and Becker, C. and Toliat, M. and Entz, P. and Suk, A. and Mueller, N. and Sindern, E. and Haupts, M. and Schimrigk, S. and Nuernberg, P. and Epplen, J.
Journal of Molecular Medicine 83
(6): 486-494.
1 January 2005
Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages.
Bourque, G. and Zdobnov, E.M. and Bork, P. and Pevzner, P.A. and Tesler, G.
Genome Research 15
: 98-110.
1 January 2005
Comparative metagenomics of microbial communities.
Tringe, S.G. and von Mering, C. and Kobayashi, A. and Salamov, A.A. and Chen, K. and Chang, H.W. and Podar, M. and Short, J.M. and Mathur, E.J. and Detter, J.C. and Bork, P. and Hugenholtz, P. and Rubin, E.M.
Science 308
: 554-557.
1 January 2005
Comparison of computational methods for the identification of cell cycle regulated genes.
de Lichtenberg, U. and Jensen, L.J. and Fausboll, A. and Jensen, T.S. and Bork, P. and Brunak, S.
Bioinformatics 21
: 1164-1171.
1 January 2005
Complex genomic rearrangements lead to novel primate gene function.
Ciccarelli, F.D. and von Mering, C. and Suyama, M. and Harrington, E.D. and Izaurralde, E. and Bork, P.
Genome Research 15
(3): 343-351.
1 January 2005
Consistency of genome-based methods in measuring Metazoan evolution.
Zdobnov, E.M. and von Mering, C. and Letunic, I. and Bork, P.
FEBS Letters 579
: 3355-3361.
1 January 2005
Ein Repr㲥ntationsformat zur standardisierten Beschreibung und wissensbasierten Modellierung genomischer Expressionsdaten (Dissertation, Humboldt Universit㲬 Berlin, 2005).
Schober, D.
UNSPECIFIED thesis, UNSPECIFIED.
1 January 2005
GandrKB - ontological microarray annotation and visualization.
Schober, D. and Leser, U. and Zenke, M. and Reich, J.
Bioinformatics 21
(11): 2785-2786.
1 January 2005
Generation and annotation of the DNA sequences of human chromosomes 2 and 4.
Hillier, L.W. and Graves, T.A. and Fulton, R.S. and Fulton, L.A. and Pepin, K.H. and Minx, P. and Wagner-McPherson, C. and Layman, D. and Wylie, K. and Sekhon, M. and Becker, M.C. and Fewell, G.A. and Delehaunty, K.D. and Miner, T.L. and Nash, W.E. and Kremitzki, C. and Oddy, L. and Du, H. and Sun, H. and Bradshaw-Cordum, H. and Ali, J. and Carter, J. and Cordes, M. and Harris, A. and Isak, A. and van Brunt, A. and Nguyen, C. and Du, F. and Courtney, L. and Kalicki, J. and Ozersky, P. and Abbott, S. and Armstrong, J. and Belter, E.A. and Caruso, L. and Cedroni, M. and Cotton, M. and Davidson, T. and Desai, A. and Elliott, G. and Erb, T. and Fronick, C. and Gaige, T. and Haakenson, W. and Haglund, K. and Holmes, A. and Harkins, R. and Kim, K. and Kruchowski, S.S. and Strong, C.M. and Grewal, N. and Goyea, E. and Hou, S. and Levy, A. and Martinka, S. and Mead, K. and McLellan, M.D. and Meyer, R. and Randall-Maher, J. and Tomlinson, C. and uphin-Kohlberg, S. and Kozlowicz-Reilly, A. and Shah, N. and Swearengen-Shahid, S. and Snider, J. and Strong, J.T. and Thompson, J. and Yoakum, M. and Leonard, S. and Pearman, C. and Trani, L. and Radionenko, M. and Waligorski, J.E. and Wang, C. and Rock, S.M. and Tin-Wollam, A.M. and Maupin, R. and Latreille, P. and Wendl, M.C. and Yang, S.P. and Pohl, C. and Wallis, J.W. and Spieth, J. and Bieri, T.A. and Berkowicz, N. and Nelson, J.O. and Osborne, J. and Ding, L. and Meyer, R. and Sabo, A. and Shotland, Y. and Sinha, P. and Wohldmann, P.E. and Cook, L.L. and Hickenbotham, M.T. and Eldred, J. and Williams, D. and Jones, T.A. and She, X. and Ciccarelli, F.D. and Izaurralde, E. and Taylor, J. and Schmutz, J. and Myers, R.M. and Cox, D.R. and Huang, X. and McPherson, J.D. and Mardis, E.R. and Clifton, S.W. and Warren, W.C. and Chinwalla, A.T. and Eddy, S.R. and Marra, M.A. and Ovcharenko, I. and Furey, T.S. and Miller, W. and Eichler, E.E. and Bork, P. and Suyama, M. and Torrents, D. and Waterston, R.H. and Wilson, R.K.
Nature 434
: 724-731.
1 January 2005
Humanisierte Maeuse und chimaerische Menschen.
Reich, J.
Forschung & Lehre 12
: 304.
1 January 2005
InterPro, progress and status in 2005.
Mulder, N.J. and Apweiler, R. and Attwood, T.K. and Bairoch, A. and Bateman, A. and Binns, D. and Bradley, P. and Bork, P. and Bucher, P. and Cerutti, L. and Copley, R. and Courcelle, E. and Das, U. and Durbin, R. and Fleischmann, W. and Gough, J. and Haft, D. and Harte, N. and Hulo, N. and Kahn, D. and Kanapin, A. and Krestyaninova, M. and Lonsdale, D. and Lopez, R. and Letunic, I. and Madera, M. and Maslen, J. and McDowall, J. and Mitchell, A. and Nikolskaya, A.N. and Orchard, S. and Pagni, M. and Ponting, C.P. and Quevillon, E. and Selengut, J. and Sigrist, C.J. and Silventoinen, V. and Studholme, D.J. and Vaughan, R. and Wu, C.H.
Nucleic Acids Research 33
(Database Issue): D201-D205.
1 January 2005
Is there biological research beyond Systems Biology? A comparative analysis of terms.
Bork, P.
Molecular Systems Biology 1
: 2005.0012 (Article Number).
1 January 2005
Lack of association of the G protein-coupled receptor for asthma susceptibility gene with atopic dermatitis.
Soederhaell, C. and Marenholz, I. and Nickel, R. and Grueber, C. and Kehrt, R. and Rohde, K. and Griffioen, R.W. and Meglio, P. and Tarani, L. and Gustafsson, D. and Hoffmann, U. and Gerstner, B. and Mueller, S. and Wahn, U. and Lee, Y.A.
Journal of Allergy and Clinical Immunology 116
(1): 220-221.
1 January 2005
Quantitative trait locus analysis reveals two intragenic sites that influence O6-alkylguanine-DNA alkyltransferase activity in peripheral blood mononuclear cells.
Margison, G.P. and Heighway, J. and Pearson, S. and McGown, G. and Thorncroft, M.R. and Watson, A.J. and Harrison, K.L. and Lewis, S.J. and Rohde, K. and Barber, P.V. and Povey, A.C. and O'Donnell, P. and Santibanez-Koref, M.F.
Carcinogenesis 26
(8): 1473-1480.
1 January 2005
STRING: known and predicted protein-protein associations, integrated and transferred across organisms.
von Mering, C. and Jensen, L.J. and Snel, B. and Hooper, S.D. and Krupp, M. and Foglierini, M. and Jouffre, N. and Huynen, M.A. and Bork, P.
Nucleic Acids Research 33
(Database Issue): D433-D437.
1 January 2005
Structural similarity to bridge sequence space: Finding new families on the bridges.
Shah, P.K. and Aloy, P. and Bork, P. and Russell, R.B.
Protein Science 14
(5): 1305-1314.
1 January 2005
The WHy domain mediates the response to desiccation in plants and bacteria.
Ciccarelli, F.D. and Bork, P.
Bioinformatics 21
: 1304-1307.
1 January 2005
Towards cellular systems in 4D.
Bork, P. and Serrano, L.
Cell 121
: 507-509.
1 January 2005
2004
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
Hillier, L.W. and Miller, W. and Birney, E. and Warren, W. and Hardison, R.C. and Ponting, C.P. and Bork, P. and Burt, D.W. and Groenen, M.A.M. and Delany, M.E. and Dodgson, J.B. and Chinwalla, A.T. and Cliften, P.F. and Clifton, S.W. and Delehaunty, K.D. and Fronick, C. and Fulton, R.S. and Graves, T.A. and Kremitzki, C. and Layman, D. and Magrini, V. and McPherson, J.D. and Miner, T.L. and Minx, P. and Nash, W.E. and Nhan, M.N. and Nelson, J.O. and Oddy, L.G. and Pohl, C.S. and Randall-Maher, J. and Smith, S.M. and Wallis, J.W. and Yang, S.P. and Romanov, M.N. and Rondelli, C.M. and Paton, B. and Smith, J. and Morrice, D. and Daniels, L. and Tempest, H.G. and Robertson, L. and Masabanda, J.S. and Griffin, D.K. and Vignal, A. and Fillon, V. and Jacobbson, L. and Kerje, S. and Andersson, L. and Crooijmans, R.P.M. and Aerts, J. and van der Poel, J.J. and Ellegren, H. and Caldwell, R.B. and Hubbard, S.J. and Grafham, D.V. and Kierzek, A.M. and McLaren, S.R. and Overton, I.M. and Arakawa, H. and Beattie, K.J. and Bezzubov, Y. and Boardman, P.E. and Bonfield, J.K. and Croning, M.D.R. and Davies, R.M. and Francis, M.D. and Humphray, S.J. and Scott, C.E. and Taylor, R.G. and Tickle, C. and Brown, W.R.A. and Rogers, J. and Buerstedde, J.M. and Wilson, S.A. and Stubbs, L. and Ovcharenko, I. and Gordon, L. and Lucas, S. and Miller, M.M. and Inoko, H. and Shiina, T. and Kaufman, J. and Salomonsen, J. and Skjoedt, K. and Wong, G.K.S. and Wang, J. and Liu, B. and Wang, J. and Yu, J. and Yang, H.M. and Nefedov, M. and Koriabine, M. and de Jong, P.J. and Goodstadt, L. and Webber, C. and Dickens, N.J. and Letunic, I. and Suyama, M. and Torrents, D. and von Mering, C. and Zdobnov, E.M. and Makova, K. and Nekrutenko, A. and Elnitski, L. and Eswara, P. and King, D.C. and Yang, S. and Tyekucheva, S. and Radakrishnan, A. and Harris, R.S. and Chiaromonte, F. and Taylor, J. and He, J.B. and Rijnkels, M. and Griffiths-Jones, S. and Ureta-Vidal, A. and Hoffman, M.M. and Severin, J. and Searle, S.M.J. and Law, A.S. and Speed, D. and Waddington, D. and Cheng, Z. and Tuzun, E. and Eichler, E. and Bao, Z.R. and Flicek, P. and Shteynberg, D.D. and Brent, M.R. and Bye, J.M. and Huckle, E.J. and Chatterji, S. and Dewey, C. and Pachter, L. and Kouranov, A. and Mourelatos, Z. and Hatzigeorgiou, A.G. and Paterson, A.H. and Ivarie, R. and Brandstrom, M. and Axelsson, E. and Backstrom, N. and Berlin, S. and Webster, M.T. and Pourquie, O. and Reymond, A. and Ucla, C. and Antonarakis, S.E. and Long, M.Y. and Emerson, J.J. and Betran, E. and Dupanloup, I. and Kaessmann, H. and Hinrichs, A.S. and Bejerano, G. and Furey, T.S. and Harte, R.A. and Raney, B. and Siepel, A. and Kent, W.J. and Haussler, D. and Eyras, E. and Castelo, R. and Abril, J.F. and Castellano, S. and Camara, F. and Parra, G. and Guigo, R. and Bourque, G. and Tesler, G. and Pevzner, P.A. and Smit, A. and Fulton, L.A. and Mardis, E.R. and Wilson, R.K.
Nature 432
(7018): 695-716.
9 December 2004
Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes.
Doerks, T. and von Mering, C. and Bork, P.
Nucleic Acids Research 32
(21): 6321-6326.
1 December 2004
Gene expression profiling of the rat superior olivary complex using serial analysis of gene expression.
Koehl, A. and Schmidt, N. and Rieger, A. and Pilgram, S.M. and Letunic, I. and Bork, P. and Soto, F. and Friauf, E. and Nothwang, H.G.
European Journal of Neuroscience 20
: 3244-3258.
1 December 2004
Shared components of protein complexes - versatile building blocks or biochemical artefacts?
Krause, R. and von Mering, C. and Bork, P. and Dandekar, T.
BioEssays 26
: 1333-1343.
1 December 2004
PASBio: predicate-argument structures for event extraction in molecular biology.
Wattarujeekrit, T. and Shah, P.K. and Collier, N.
BMC Bioinformatics 5
: 155.
19 October 2004
Homology-based functional proteomics by mass spectrometry: application to the Xenopus microtubule-associated proteome.
Liska, A.J. and Popov, A.V. and Sunyaev, S. and Coughlin, P. and Habermann, B. and Shevchenko, A. and Bork, P. and Karsenti, E. and Shevchenko, A.
Proteomics 4
: 2707-2721.
1 September 2004
BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments.
Suyama, M. and Torrents, D. and Bork, P.
Bioinformatics 20
: 1968-1970.
12 August 2004
Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs.
Korbel, J.O. and Jensen, L.J. and von Mering, C. and Bork, P.
Nature Biotechnology 22
(7): 911-917.
1 July 2004
ArrayProspector: a web resource of functional associations inferred from microarray expression data.
Jensen, L.J. and Lagarde, J. and von Mering, C. and Bork, P.
Nucleic Acids Research 32
(Web Server Issue): W445-W448.
1 July 2004
Riboswitch finder - a tool for identification of riboswitch RNAs.
Bengert, P. and Dandekar, T.
Nucleic Acids Research 32
(Web Server Issue): W154-W159.
1 July 2004
Haplotypes and SNPs in 13 lipid-relevant genes explain most of the genetic variance in high-density lipoprotein and low-density lipoprotein cholesterol.
Knoblauch, H. and Bauerfeind, A. and Toliat, M.R. and Becker, C. and Luganskaja, T. and Guenther, U.P. and Rohde, K. and Schuster, H. and Junghans, C. and Luft, F.C. and Nuernberg, P. and Reich, J.G.
Human Molecular Genetics 13
(10): 993-1004.
15 May 2004
Structure-based assembly of protein complexes in yeast.
Aloy, P. and Boettcher, B. and Ceulemans, H. and Leutwein, C. and Mellwig, C. and Fischer, S. and Gavin, A.C. and Bork, P. and Superti-Furga, G. and Serrano, L. and Russell, R.B.
Science 303
(5666): 2026-2029.
26 March 2004
Acropectorovertebral dysgenesis (F syndrome) maps to chromosome 2q36.
Thiele, H. and McCann, C. and vant Padje, S. and Schwabe, G.C. and Hennies, H.C. and Camera, G. and Opitz, J. and Laxova, R. and Mundlos, S. and Nuernberg, P.
Journal of Medical Genetics 41
(3): 213-218.
March 2004
RanBP2/Nup358 provides a major binding site for NXF1-p15 dimers at the nuclear pore complex and functions in nuclear mRNA export.
Forler, D. and Rabut, G. and Ciccarelli, F.D. and Herold, A. and Koecher, T. and Niggeweg, R. and Bork, P. and Ellenberg, J. and Izaurralde, E.
Molecular and Cellular Biology 24
: 1155-1167.
1 February 2004
Phaenotypische Charakterisierung einer DFNA6-Familie mit Tieftonschwerhoerigkeit [Phenotypic characterization of a DFNA6 family with low-frequency hearing loss].
Toth, T. and Kupka, S. and Nuernberg, P. and Thiele, H. and Zenner, H.R. and Sziklai, I. and Pfister, M.
HNO 52
(2): 132-136.
February 2004
A genotype-phenotype correlation with gender-effect for hearing impairment caused by TECTA mutations.
Pfister, M. and Thiele, H. and Van Camp, G. and Fransen, E. and Apaydin, F. and Aydin, O. and Leistenschneider, P. and Devoto, M. and Zenner, H.P. and Blin, N. and Nuernberg, P. and Ozkarakas, H. and Kupka, S.
Cellular Physiology and Biochemistry 14
(4-6): 369-376.
1 January 2004
A molecular genetic and statistical approach for the diagnosis of dual-site cancers.
Brinkmann, D. and Ryan, A. and Ayhan, A. and McCluggage, W.G. and Feakins, R. and Santibanez-Koref, M.F. and Mein, C.A. and Gayther, S.A. and Jacobs, I.J.
Journal of the National Cancer Institute 96
(19): 1441-1446.
1 January 2004
Compositional asymmetries and predicted origins of replication of the Saccharomyces cerevisiae genome.
Korbel, J.O. and Assmus, H. and Kielbasa, S. and Herzel, H.
In:
Bioinformatics of Genome Regulation and Structure.
Kluwer, Boston, Mass. [u.a.], 33-38.
ISBN 978-1-4757-4613-6
1 January 2004
EASED: Extended alternatively spliced EST database.
Pospisil, H. and Herrmann, A. and Bortfeldt, R.H. and Reich, J.
Nucleic Acids Research 32
(Database Issue): D70-D74.
1 January 2004
Empirische Totipotenz und metaphysische Gattungszugehoerigkeit bei der moralischen Beurteilung des vorgeburtlichen menschlichen Lebens.
Reich, J.
Zeitschrift fuer medizinische Ethik 50
(2): 115-130.
1 January 2004
Estimating rates of alternative splicing in mammals and invertebrates.
Harrington, E.D. and Boue, S. and Valcarcel, J. and Reich, J.G. and Bork, P.
Nature Genetics 36
(9): 916-917.
1 January 2004
Extracting regulatory gene expression networks from PubMed.
Saric, J. and Jensen, L.J. and Ouzounova, R. and Rojas, I. and Bork, P.
In:
42nd Annual Meeting of the Association for Computational Linguistics : ACL 04 ; proceedings of the conference and workshops ; Forum Convention Centre, Barcelona, July 21 - 26, 2004.
ACL, New Brunswick, NJ, 191-198.
ISBN 1-932432-34-5
1 January 2004
Gene annotation from scientific literature using mappings between keyword systems.
Perez, A.J. and Perez-Iratxeta, C. and Bork, P. and Thode, G. and Andrade-Navarro, M.A.
Bioinformatics 20
(13): 2084-2091.
1 January 2004
Global analysis of bacterial transcription factors to predict cellular target processes.
Doerks, T. and Andrade, M.A. and Lathe, W. and von Mering, C. and Bork, P.
Trends in Genetics 20
(3): 126-131.
1 January 2004
In NF1, CFTR, PER3, CARS and SYT7, alternatively included exons show higher conservation of surrounding intron sequences than constitutive exons.
Kaufmann, D. and Kenner, O. and Nuernberg, P. and Vogel, W. and Bartelt, B.
European Journal of Human Genetics 12
(2): 139-149.
1 January 2004
Metabolic pathway analysis in biotechnology.
Schuster, S.
In:
Metabolic Engineering in the Post Genomic Era.
Horizon Bioscience, Wymondham, 181-208.
ISBN 0-9545232-2-9
1 January 2004
Quality analysis and integration of large-scale molecular data sets.
Jensen, L.J. and Bork, P.
Drug Discovery Today: TARGETS 3
: 51-56.
1 January 2004
SMART 4.0: towards genomic data integration.
Letunic, I. and Copley, R.R. and Schmidt, S. and Ciccarelli, F.D. and Doerks, T. and Schultz, J. and Ponting, C.P. and Bork, P.
Nucleic Acids Research 32
(Database Issue): D142-D144.
1 January 2004
Sequences and topology. Genes and structures in context.
Bork, P. and Orengo, C.A.
Current Opinion in Structural Biology 14
: 261-263.
1 January 2004
Splice variants of gene expression - A source for diversity of the human proteome.
Reich, J.G. and Pospisil, H.
In:
XII International Congress on Genes, Gene Families, and Isozymes : Berlin, Germany, July 19 - 24, 2003.
Monduzzi, Bologna, 3-9.
ISBN 88-758-7006-3
1 January 2004
The HUPO PSI's Molecular Interaction format - a community standard for the representation of protein interaction data.
Hermjakob, H. and Montecchi-Palazzi, L. and Bader, G. and Wojcik, R. and Salwinski, L. and Ceol, A. and Moore, S. and Orchard, S. and Sarkans, U. and von Mering, C. and Roechert, B. and Poux, S. and Jung, E. and Mersch, H. and Kersey, P. and Lappe, M. and Li, Y.X. and Zeng, R. and Rana, D. and Nikolski, M. and Husi, H. and Brun, C. and Shanker, K. and Grant, S.G.N. and Sander, C. and Bork, P. and Zhu, W.M. and Pandey, A. and Brazma, A. and Jacq, B. and Vidal, M. and Sherman, D. and Legrain, P. and Cesareni, G. and Xenarios, L. and Eisenberg, D. and Steipe, B. and Hogue, C. and Apweiler, R.
Nature Biotechnology 22
(2): 177-183.
1 January 2004
The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources.
Crass, T. and Antes, I. and Basekow, R. and Bork, P. and Buning, C. and Christensen, M. and Claussen, H. and Ebeling, C. and Ernst, P. and Gailus-Durner, V. and Glatting, K.H. and Gohla, R. and Goessling, F. and Grote, K. and Heidtke, K. and Herrmann, A. and O'Keeffe, S. and Kiesslich, O. and Kolibal, S. and Korbel, J.O. and Lengauer, T. and Liebich, I. and van der Linden, M. and Luz, H. and Meissner, K. and von Mering, C. and Mevissen, H.T. and Mewes, H.W. and Michael, H. and Mokrejs, M. and Mueller, T. and Pospisil, H. and Rarey, M. and Reich, J.G. and Schneider, R. and Schomburg, D. and Schulze-Kremer, S. and Schwarzer, K. and Sommer, I. and Springstubbe, S. and Suhai, S. and Thoppae, G. and Vingron, M. and Warfsmann, J. and Werner, T. and Wetzler, D. and Wingender, E. and Zimmer, R.
Bioinformatics 20
(2): 268-270.
1 January 2004
Trends in biochemical systems : Computational analysis of biochemical systems.
Dandekar, T.
Trends in Biochemical Sciences 26
: 637.
1 January 2004
2003
Similarity by state/descent and genetic vector spaces: analysis of a longitudinal family study.
Stassen, H.H. and Hoffman, K. and Scharfetter, C.
BMC Genetics 4
(Suppl 1): S59.
31 December 2003
The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold.
Ciccarelli, F.D. and Izaurralde, E. and Bork, P.
BMC Bioinformatics 4
: 64.
19 December 2003
A database on alternative splice forms on the integrated genetic map service (IGMS).
Pospisil, H. and Herrmann, A. and Pankow, H. and Reich, J.
In Silico Biology 3
(1-2): 229-234.
16 December 2003
Biosensor (neuer Bauart).
Dandekar, T.
DE4338732A1 ; DE4338732C2.
11 December 2003
A genome-wide survey of human pseudogenes.
Torrents, D. and Suyama, M. and Zdobnov, E. and Bork, P.
Genome Research 13
: 2559-2567.
1 December 2003
Alternative splicing and evolution.
Boue, S. and Letunic, I. and Bork, P.
BioEssays 25
: 1031-1034.
1 November 2003
Protein disorder prediction: Implications for structural proteomics.
Linding, R. and Jensen, L.J. and Diella, F. and Bork, P. and Gibson, T.J. and Russell, R.B.
Structure with Folding & Design 11
(11): 1453-1459.
1 November 2003
Functionality of system components: conservation of protein function in protein feature space.
Jensen, L.J. and Ussery, D.W. and Brunak, S.
Genome Research 13
: 2444-2449.
November 2003
Under what conditions signal transduction pathways are highly flexible in response to external forcing? A case study on calcium oscillations.
Marhl, M. and Schuster, S.
Journal of Theoretical Biology 224
(4): 491-500.
21 October 2003
A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens.
Krause, R. and von Mering, C. and Bork, P.
Bioinformatics 19
: 1901-1908.
12 October 2003
Distinct methylation profiles of glioma subtypes.
Uhlmann, K. and Rohde, K. and Zeller, C. and Szymas, J. and Vogel, S. and Marczinek, K. and Thiel, G. and Nuernberg, P. and Laird, P.W.
International Journal of Cancer 106
(1): 52-59.
10 August 2003
A method for classifying metabolites in topological pathway analyses based on minimization of pathway number.
Dandekar, T. and Moldenhauer, F. and Bulik, S. and Bertram, H. and Schuster, S.
Biosystems 70
(3): 255-270.
August 2003
Association scan of the novel psoriasis susceptibility region on chromosome 19: evidence for both susceptible and protective loci.
Hensen, P. and Windemuth, C. and Hueffmeier, U. and Rueschendorf, F. and Stadelmann, A. and Hoppe, V. and Fenneker, D. and Staender, M. and Schmitt-Egenolf, M. and Wienker, T.F. and Traupe, H. and Reis, A.
Experimental Dermatology 12
(4): 490-496.
August 2003
Interleukin-10 promoter polymorphism IL10.G and familial early onset psoriasis.
Hensen, P. and Asadullah, K. and Windemuth, C. and Rueschendorf, F. and Hueffmeier, U. and Staender, M. and Schmitt-Egenolf, M. and Wienker, T.F. and Reis, A. and Traupe, H.
British Journal of Dermatology 149
(2): 381-385.
August 2003
The KIND module: a putative signalling domain evolved from the C lobe of the protein kinase fold.
Ciccarelli, F.D. and Bork, P. and Kerkhoff, E.
Trends in Biochemical Sciences 28
(7): 349-352.
7 July 2003
A software tool-box for analysis of regulatory RNA elements.
Bengert, P. and Dandekar, T.
Nucleic Acids Research 31
(13): 3441-3445.
1 July 2003
An example of the prisoner's dilemma in biochemistry.
Frick, T. and Schuster, S.
Naturwissenschaften 90
: 327-331.
1 July 2003
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins.
Puntervoll, P. and Linding, R. and Gemund, C. and Chabanis-Davidson, S. and Mattingsdal, M. and Cameron, S. and Martin, D.M.A. and Ausiello, G. and Brannetti, B. and Costantini, A. and Ferre, F. and Maselli, V. and Via, A. and Cesareni, G. and Diella, F. and Superti-Furga, G. and Wyrwicz, L. and Ramu, C. and McGuigan, C. and Gudavalli, R. and Letunic, I. and Bork, P. and Rychlewski, L. and Kuester, B. and Helmer-Citterich, M. and Hunter, W.N. and Aasland, R. and Gibson, T.J.
Nucleic Acids Research 31
(13): 3625-3630.
1 July 2003
Update on XplorMed: a web server for exploring scientific literature.
Perez-Iratxeta, C. and Perez, A.J. and Bork, P. and Andrade-Navarro, M.A.
Nucleic Acids Research 31
(13): 3866-3868.
1 July 2003
Murine susceptibility to Chagas' disease maps to chromosomes 5 and 17.
Graefe, S.E. and Meyer, B.S. and Mueller-Myhsok, B. and Rueschendorf, F. and Drosten, C. and Laue, T. and Steeg, C. and Nuernberg, P. and Fleischer, B.
Genes and Immunity 4
(5): 321-325.
July 2003
Systematic discovery of analogous enzymes in thiamin biosynthesis.
Morett, E. and Korbel, J. and Rajan, E. and Saab-Rincon, G. and Olvera, L. and Olvera, M. and Steffen, S. and Snel, B. and Bork, P.
Nature Biotechnology 21
(7): 790-795.
July 2003
Protein feature based identification of cell cycle regulated proteins in yeast.
de Lichtenberg, U. and Jensen, T.S. and Jensen, L.J. and Brunak, S.
Journal of Molecular Biology 329
: 663-674.
13 June 2003
Topological analysis of metabolic networks based on Petri net theory.
Zevedei-Oancea, I. and Schuster, S.
In Silico Biology 3
(3): 323-345.
7 June 2003
Genome-wide linkage reveals a locus for human essential (primary) hypertension on chromosome 12p.
Gong, M. and Zhang, H.Y. and Schulz, H. and Lee, Y.A. and Sun, K. and Bähring, S. and Luft, F.C. and Nuernberg, P. and Reis, A. and Rohde, K. and Ganten, D. and Hui, R.T. and Huebner, N.
Human Molecular Genetics 12
(11): 1273-1277.
1 June 2003
Metabolites: a helping hand for pathway evolution?
Schmidt, S. and Sunyaev, S. and Bork, P. and Dandekar, T.
Trends in Biochemical Sciences 28
(6): 336-341.
June 2003
Information extraction from full text scientific articles: Where are the keywords?
Shah, P. and Perez-Iratxeta, C. and Bork, P. and Andrade, M.A.
BMC Bioinformatics 4
(1): 20.
29 May 2003
Entropy as a Measure for Linkage Disequilibrium over Multilocus Haplotype Blocks.
Nothnagel, M. and Fuerst, R. and Rohde, K.
Human Heredity 54
(4): 186-198.
May 2003
Single nucleotide polymorphism haplotypes in the cholesteryl-ester transfer protein (CETP) gene and lipid phenotypes.
Bauerfeind, A. and Knoblauch, H. and Schuster, H. and Luft, F.C. and Reich, J.G.
Human Heredity 54
(4): 166-173.
May 2003
Pathogenesis of DNA repair-deficient cancers: a statistical meta-analysis of putative Real Common Target genes.
Woerner, S.M. and Benner, A. and Sutter, C. and Schiller, M. and Yuan, Y.P. and Keller, G. and Bork, P. and Doeberitz, M.V. and Gebert, J.F.
Oncogene 22
(15): 2226-2235.
17 April 2003
Evaluation of annotation strategies using an entire genome sequence.
Iliopoulos, I. and Tsoka, S. and Andrade, M.A. and Enright, A.J. and Carroll, M. and Poullet, P. and Promponas, V. and Liakopoulos, T. and Palaios, G. and Pasquier, C. and Hamodrakas, S. and Tamames, J. and Yagnik, A.T. and Tramontano, A. and Devos, D. and Blaschke, C. and Valencia, A. and Brett, D. and Martin, D. and Leroy, C. and Rigoutsos, I. and Sander, C. and Ouzounis, C.A.
Bioinformatics 19
(6): 717-726.
12 April 2003
Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome.
Jensen, L.J. and Skovgaard, M. and Sicheritz-Ponten, T. and Jorgensen, M.K. and Lundegaard, C. and Pedersen, C.C. and Petersen, N. and Ussery, D.
BMC Genomics 4
(1): 12.
2 April 2003
The identification of a conserved domain in both spartin and spastin, mutated in hereditary spastic paraplegia.
Ciccarelli, F.D. and Proukakis, C. and Patel, H. and Cross, H. and Azam, S. and Patton, M.A. and Bork, P. and Crosby, A.H.
Genomics 81
(4): 437-441.
April 2003
Prediction of human protein function according to Gene Ontology categories.
Jensen, L.J. and Gupta, R. and Staerfeldt, H.H. and Brunak, S.
Bioinformatics 19
: 635-642.
22 March 2003
A second large family with catatonic schizophrenia supports the region distally of CHRNA7 on chromosome 15q14-15.
Meyer, J. and Rueschendorf, F. and Lesch, K.P.
Molecular Psychiatry 8
: 259-260.
1 March 2003
Increase of functional diversity by alternative splicing.
Kriventseva, E.V. and Koch, I. and Apweiler, R. and Vingron, M. and Bork, P. and Gelfand, M.S. and Sunyaev, S.
Trends in Genetics 19
(3): 124-128.
March 2003
Association of genetic traits to estimated haplotypes from SNP genotypes using EM algorithm and Markov chain Monte Carlo techniques.
Rohde, K. and Fuerst, R.
Human Heredity 56
(1-3): 41-47.
1 January 2003
Bioinformatics in the post-sequence era.
Kanehisa, M. and Bork, P.
Nature Genetics 33
: 305-310.
1 January 2003
Computational analysis of biochemical systems (book review).
Dandekar, T.
Trends in Biochemical Sciences 26
: 637-637.
1 January 2003
Detection and characterization of pseudogenes.
Torrents, D. and Suyama, M. and Bork, P.
In:
Bioinformatics and Genomes : Current Perspectives.
Horizon Scientific Press, Wymondham, 197-209.
ISBN 1-898486-47-6
1 January 2003
Function prediction and protein networks.
Huynen, M.A. and Snel, B. and von Mering, C. and Bork, P.
Current Opinion in Cell Biology 15
: 191-198.
1 January 2003
Genome evolution reveals biochemical networks and functional modules.
von Mering, C. and Zdobnov, E.M. and Tsoka, S. and Ciccarelli, F.D. and Pereira-Leal, J.B. and Ouzounis, C.A. and Bork, P.
Proceedings of the National Academy of Sciences of the United States of America 100
(26): 15428-15433.
1 January 2003
High rate of gene displacement in vitamine biosynthetic pathways.
Morett, E. and Saab-Rincon, G. and Merino, E. and Bork, P. and Rajan, E. and Olvera, L. and Olvera, M.
In:
Bioinformatics and Genomes : Current Perspectives.
Horizon Scientific Press, Wymondham, 69-79.
ISBN 1-898486-47-6
1 January 2003
Impact of selection, mutation rate and genetic drift on human genetic variation.
Sunyaev, S. and Kondrashov, F.A. and Bork, P. and Ramensky, V.
Human Molecular Genetics 12
(24): 3325-3330.
1 January 2003
Making predictions about robustness and flexibility from metabolic network structure.
Schuster, S. and Klamt, S. and Stelling, J.
In:
Proceedings of German Conference on Bioinformatics 2003 : Garching 12.-14. Oct. 2003.
Belleville Verl., Muenchen, 129-134.
ISBN 3-936298-80-7
1 January 2003
Nanoelectrospray tandem mass spectrometry and sequence similarity searching for identification of proteins from organisms with unknown genomes.
Shevchenko, A. and Sunyaev, S. and Liska, A. and Bork, P. and Shevchenko, A.
Methods in Molecular Biology 211
: 221-234.
1 January 2003
Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways.
Gatfield, D. and Unterholzner, L. and Ciccarelli, F.D. and Bork, P. and Izaurralde, E.
EMBO Journal 22
: 3960-3970.
1 January 2003
STRING: a database of predicted functional associations between proteins.
von Mering, C. and Huynen, M. and Jaeggi, D. and Schmidt, S. and Bork, P. and Snel, B.
Nucleic Acids Research 31
(1): 258-261.
1 January 2003
The DNA sequence of human chromosome 7.
Hillier, L.W. and Fulton, R.S. and Fulton, L.A. and Graves, T.A. and Pepin, K.H. and Wagner-McPherson, C. and Layman, D. and Maas, J. and Jaeger, S. and Walker, R. and Wylie, K. and Sekhon, M. and Becker, M.C. and O'Laughlin, M.D. and Schaller, M.E. and Fewell, G.A. and Delehaunty, K.D. and Miner, T.L. and Nash, W.E. and Cordes, M. and Du, H. and Sun, H. and Edwards, J. and Bradshaw-Cordum, H. and Ali, J. and Andrews, S. and Isak, A. and VanBrunt, A. and Nguyen, C. and Du, F.Y. and Lamar, B. and Courtney, L. and Kalicki, J. and Ozersky, P. and Bielicki, L. and Scott, K. and Holmes, A. and Harkins, R. and Harris, A. and Strong, C.M. and Hou, S.F. and Tomlinson, C. and Dauphin-Kohlberg, S. and Kozlowicz-Reilly, A. and Leonard, S. and Rohlfing, T. and Rock, S.M. and Tin-Wollam, A.M. and Abbott, A. and Minx, P. and Maupin, R. and Strowmatt, C. and Latreille, P. and Miller, N. and Johnson, D. and Murray, J. and Woessner, J.P. and Wendl, M.C. and Yang, S.P. and Schultz, B.R. and Wallis, J.W. and Spieth, J. and Bieri, T.A. and Nelson, J.O. and Berkowicz, N. and Wohldmann, P.E. and Cook, L.L. and Hickenbotham, M.T. and Eldred, J. and Williams, D. and Bedell, J.A. and Mardis, E.R. and Clifton, S.W. and Chissoe, S.L. and Marra, M.A. and Raymond, C. and Haugen, E. and Gillett, W. and Zhou, Y. and James, R. and Phelps, K. and Iadanoto, S. and Bubb, K. and Simms, E. and Levy, R. and Clendenning, J. and Kaul, R. and Kent, W.J. and Furey, T.S. and Baertsch, R.A. and Brent, M.R. and Keibler, E. and Flicek, P. and Bork, P. and Suyama, M. and Bailey, J.A. and Portnoy, M.E. and Torrents, D. and Chinwalla, A.T. and Gish, W.R. and Eddy, S.R. and McPherson, J.D. and Olson, M.V. and Eichler, E.E. and Green, E.D. and Waterston, R.H. and Wilson, R.K.
Nature 424
: 157-164.
1 January 2003
The InterPro Database, 2003 brings increased coverage and new features.
Mulder, N.J. and Apweiler, R. and Attwood, T.K. and Bairoch, A. and Barrell, D. and Bateman, A. and Binns, D. and Biswas, M. and Bradley, P. and Bork, P. and Bucher, P. and Copley, R.R. and Courcelle, E. and Das, U. and Durbin, R. and Falquet, L. and Fleischmann, W. and Griffiths-Jones, S. and Haft, D. and Harte, N. and Hulo, N. and Kahn, D. and Kanapin, A. and Krestyaninova, M. and Lopez, R. and Letunic, I. and Lonsdale, D. and Silventoinen, V. and Orchard, S.E. and Pagni, M. and Peyruc, D. and Ponting, C.P. and Selengut, J.D. and Servant, F. and Sigrist, C.J.A. and Vaughan, R. and Zdobnov, E.M.
Nucleic Acids Research 31
(1): 315-318.
1 January 2003
The way we write - Country-specific variations of the English language in the biomedical literature.
Netzel, R. and Perez-Iratxeta, C. and Bork, P. and Andrade, M.A.
EMBO Reports 4
: 446-451.
1 January 2003
Using in vitro prediction models instead of the rabbit eye irritation test to classify and label new chemicals: a post hoc data analysis of the international EC/HO validation study.
Moldenhauer, F.
Alternatives to Laboratory Animals 31
(1): 31-46.
January 2003
Es wird ein Mensch gemacht. Moeglichkeit und Grenzen der Gentechnik.
Reich, J.
Rowohlt, Berlin.
ISBN 3871344710
2003
Praediktive Diagnostik und genetisches Design: Ein Blick in die Zukunft.
Reich, J.
Zeitschrift fuer Biopolitik 2
(2): 89-98.
2003
2002
Initial sequencing and comparative analysis of the mouse genome.
Waterston, R.H. and Lindblad-Toh, K. and Birney, E. and Rogers, J. and Abril, J.F. and Agarwal, P. and Agarwala, R. and Ainscough, R. and Alexandersson, M. and An, P. and Antonarakis, S.E. and Attwood, J. and Baertsch, R. and Bailey, J. and Barlow, K. and Beck, S. and Berry, E. and Birren, B. and Bloom, T. and Bork, P. and Botcherby, M. and Bray, N. and Brent, M.R. and Brown, D.G. and Brown, S.D. and Bult, C. and Burton, J. and Butler, J. and Campbell, R.D. and Carninci, P. and Cawley, S. and Chiaromonte, F. and Chinwalla, A.T. and Church, D.M. and Clamp, M. and Clee, C. and Collins, F.S. and Cook, L.L. and Copley, R.R. and Coulson, A. and Couronne, O. and Cuff, J. and Curwen, V. and Cutts, T. and Daly, M. and David, R. and Davies, J. and Delehaunty, K.D. and Deri, J. and Dermitzakis, E.T. and Dewey, C. and Dickens, N.J. and Diekhans, M. and Dodge, S. and Dubchak, I. and Dunn, D.M. and Eddy, S.R. and Elnitski, L. and Emes, R.D. and Eswara, P. and Eyras, E. and Felsenfeld, A. and Fewell, G.A. and Flicek, P. and Foley, K. and Frankel, W.N. and Fulton, L.A. and Fulton, R.S. and Furey, T.S. and Gage, D. and Gibbs, R.A. and Glusman, G. and Gnerre, S. and Goldman, N. and Goodstadt, L. and Grafham, D. and Graves, T.A. and Green, E.D. and Gregory, S. and Guigo, R. and Guyer, M. and Hardison, R.C. and Haussler, D. and Hayashizaki, Y. and Hillier, L.W. and Hinrichs, A. and Hlavina, W. and Holzer, T. and Hsu, F. and Hua, A. and Hubbard, T. and Hunt, A. and Jackson, I. and Jaffe, D.B. and Johnson, L.S. and Jones, M. and Jones, T.A. and Joy, A. and Kamal, M. and Karlsson, E.K. and Karolchik, D. and Kasprzyk, A. and Kawai, J. and Keibler, E. and Kells, C. and Kent, W.J. and Kirby, A. and Kolbe, D.L. and Korf, I. and Kucherlapati, R.S. and Kulbokas, E.J. and Kulp, D. and Landers, T. and Leger, J.P. and Leonard, S. and Letunic, I. and LeVine, R. and Li, J. and Li, M. and Lloyd, C. and Lucas, S. and Ma, B. and Maglott, D.R. and Mardis, E.R. and Matthews, L. and Mauceli, E. and Mayer, J.H. and McCarthy, M. and McCombie, W.R. and McLaren, S. and McLay, K. and McPherson, J.D. and Meldrim, J. and Meredith, B. and Mesirov, J.P. and Miller, W. and Miner, T.L. and Mongin, E. and Montgomery, K.T. and Morgan, M. and Mott, R. and Mullikin, J.C. and Muzny, D.M. and Nash, W.E. and Nelson, J.O. and Nhan, M.N. and Nicol, R. and Ning, Z. and Nusbaum, C. and O'Connor, M.J. and Okazaki, Y. and Oliver, K. and Overton-Larty, E. and Pachter, L. and Parra, G. and Pepin, K.H. and Peterson, J. and Pevzner, P. and Plumb, R. and Pohl, C.S. and Poliakov, A. and Ponce, T.C. and Ponting, C.P. and Potter, S. and Quail, M. and Reymond, A. and Roe, B.A. and Roskin, K.M. and Rubin, E.M. and Rust, A.G. and Santos, R. and Sapojnikov, V. and Schultz, B. and Schultz, J. and Schwartz, M.S. and Schwartz, S. and Scott, C. and Seaman, S. and Searle, S. and Sharpe, T. and Sheridan, A. and Shownkeen, R. and Sims, S. and Singer, J.B. and Slater, G. and Smit, A. and Smith, D.R. and Spencer, B. and Stabenau, A. and Stange-Thomann, N. and Sugnet, C. and Suyama, M. and Tesler, G. and Thompson, J. and Torrents, D. and Trevaskis, E. and Tromp, J. and Ucla, C. and Ureta-Vidal, A. and Vinson, J.P. and von Niederhausern, A.C. and Wade, C.M. and Wall, M. and Weber, R.J. and Weiss, R.B. and Wendl, M.C. and West, A.P. and Wetterstrand, K. and Wheeler, R. and Whelan, S. and Wierzbowski, J. and Willey, D. and Williams, S. and Wilson, R.K. and Winter, E. and Worley, K.C. and Wyman, D. and Yang, S. and Yang, S.P. and Zdobnov, E.M. and Zody, M.C. and Lander, E.S.
Nature 420
(6915): 520-562.
5 December 2002
DNA testing for familial hypercholesterolemia: improving disease recognition and patient care.
Vergopoulos, A. and Knoblauch, H. and Schuster, H.
American Journal of Pharmacogenomics 2
(4): 253-262.
December 2002
Metabolic network structure determines key aspects of functionality and regulation.
Stelling, J. and Klamt, S. and Bettenbrock, K. and Schuster, S. and Gilles, E.D.
Nature 420
(6912): 190-193.
14 November 2002
Mechanisms of carcinogenicity/chemotherapy by O(6)-methylguanine.
Margison, G.P. and Santibanez-Koref, M.F. and Povey, A.C.
Mutagenesis 17
(6): 483-487.
November 2002
Power and sample size calculations for case-control genetic association tests when errors are present: Application to single nucleotide polymorphisms.
Gordon, D. and Finch, S.J. and Nothnagel, M. and Ott, J.
Human Heredity 54
(1): 22-33.
November 2002
The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract.
Schell, M.A. and Karmirantzou, M. and Snel, B. and Vilanova, D. and Berger, B. and Pessi, G. and Zwahlen, M.C. and Desiere, F. and Bork, P. and Delley, M. and Pridmore, R.D. and Arigoni, F.
Proceedings of the National Academy of Sciences of the United States of America 99
(22): 14422-14427.
29 October 2002
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster.
Zdobnov, E.M. and von Mering, C. and Letunic, I. and Torrents, D. and Suyama, M. and Copley, R.R. and Christophides, G.K. and Thomasova, D. and Holt, R.A. and Subramanian, G.M. and Mueller, H.M. and Dimopoulos, G. and Law, J.H. and Wells, M.A. and Birney, E. and Charlab, R. and Halpern, A.L. and Kokoza, E. and Kraft, C.L. and Lai, Z. and Lewis, S. and Louis, C. and Barillas-Mury, C. and Nusskern, D. and Rubin, G.M. and Salzberg, S.L. and Sutton, G.G. and Topalis, P. and Wides, R. and Wincker, P. and Yandell, M. and Collins, F.H. and Ribeiro, J. and Gelbart, W.M. and Kafatos, F.C. and Bork, P.
Science 298
(5591): 149-159.
4 October 2002
The genome sequence of the malaria mosquito Anopheles gambiae.
Holt, R.A. and Subramanian, G.M. and Halpern, A. and Sutton, G.G. and Charlab, R. and Nusskern, D.R. and Wincker, P. and Clark, A.G. and Ribeiro, J.M.C. and Wides, R. and Salzberg, S.L. and Loftus, B. and Yandell, M. and Majoros, W.H. and Rusch, D.B. and Lai, Z.W. and Kraft, C.L. and Abril, J.F. and Anthouard, V. and Arensburger, P. and Atkinson, P.W. and Baden, H. and de Berardinis, V. and Baldwin, D. and Benes, V. and Biedler, J. and Blass, C. and Bolanos, R. and Boscus, D. and Barnstead, M. and Cai, S. and Center, A. and Chatuverdi, K. and Christophides, G.K. and Chrystal, M.A. and Clamp, M. and Cravchik, A. and Curwen, V. and Dana, A. and Delcher, A. and Dew, I. and Evans, C.A. and Flanigan, M. and Grundschober-Freimoser, A. and Friedli, L. and Gu, Z.P. and Guan, P. and Guigo, R. and Hillenmeyer, M.E. and Hladun, S.L. and Hogan, J.R. and Hong, Y.S. and Hoover, J. and Jaillon, O. and Ke, Z.X. and Kodira, C. and Kokoza, E. and Koutsos, A. and Letunic, I. and Levitsky, A. and Liang, Y. and Lin, J.J. and Lobo, N.F. and Lopez, J.R. and Malek, J.A. and McIntosh, T.C. and Meister, S. and Miller, J. and Mobarry, C. and Mongin, E. and Murphy, S.D. and O'Brochta, D.A. and Pfannkoch, C. and Qi, R. and Regier, M.A. and Remington, K. and Shao, H.G. and Sharakhova, M.V. and Sitter, C.D. and Shetty, J. and Smith, T.J. and Strong, R. and Sun, J.T. and Thomasova, D. and Ton, L.Q. and Topalis, P. and Tu, Z.J. and Unger, M.F. and Walenz, B. and Wang, A.H. and Wang, J. and Wang, M. and Wang, X.L. and Woodford, K.J. and Wortman, J.R. and Wu, M. and Yao, A. and Zdobnov, E.M. and Zhang, H.Y. and Zhao, Q. and Zhao, S.Y. and Zhu, S.P.C. and Zhimulev, I. and Coluzzi, M. and della Torre, A. and Roth, C.W. and Louis, C. and Kalush, F. and Mural, R.J. and Myers, E.W. and Adams, M.D. and Smith, H.O. and Broder, S. and Gardner, M.J. and Fraser, C.M. and Birney, E. and Bork, P. and Brey, P.T. and Venter, J.C. and Weissenbach, J. and Kafatos, F.C. and Collins, F.H. and Hoffman, S.L.
Science 298
(5591): 129-149.
4 October 2002
Association of the 867Asp variant of the human anion exchanger 3 gene with common subtypes of idiopathic generalized epilepsy.
Sander, T. and Toliat, M.R. and Heils, A. and Leschik, G. and Becker, C. and Rueschendorf, F. and Rohde, K. and Mundlos, S. and Nuernberg, P.
Epilepsy Research 51
(3): 249-255.
1 October 2002
Comparative analysis of protein interaction networks.
Bork, P.
Bioinformatics 18 Suppl 2
: S64.
1 October 2002
Discussion: Conservation of gene co-regulation in prokaryotes and eukaryotes.
Snel, B. and Bork, P. and Huynen, M.
Trends in Biotechnology 20
(10): 410.
1 October 2002
Periodic catatonia: confirmation of linkage to chromosome 15 and further evidence for genetic heterogeneity.
Stoeber, G. and Seelow, D. and Rueschendorf, F. and Ekici, A. and Beckmann, H. and Reis, A.
Human Genetics 111
(4-5): 323-330.
October 2002
Treatment of multifunctional enzymes in metabolic pathway analysis.
Schuster, S. and Zevedei-Oancea, I.
Biophysical Chemistry 99
(1): 63-75.
3 September 2002
Human non-synonymous SNPs: server and survey.
Ramensky, V. and Bork, P. and Sunyaev, S.
Nucleic Acids Research 30
(17): 3894-3900.
1 September 2002
InterPro: an integrated documentation resource for protein families, domains and functional sites.
Mulder, N.J. and Apweiler, R. and Attwood, T.K. and Bairoch, A. and Bateman, A. and Binns, D. and Biswas, M. and Bradley, P. and Bork, P. and Bucher, P. and Copley, R. and Courcelle, E. and Durbin, R. and Falquet, L. and Fleischmann, W. and Gouzy, J. and Griffith-Jones, S. and Haft, D. and Hermjakob, H. and Hulo, N. and Kahn, D. and Kanapin, A. and Krestyaninova, M. and Lopez, R. and Letunic, I. and Orchard, S. and Pagni, M. and Peyruc, D. and Ponting, C.P. and Servant, F. and Sigrist, C.J.
Briefings in Bioinformatics 3
: 225-235.
1 September 2002
Structure of transfection-active histone H1/DNA complexes.
Lucius, H. and Haberland, A. and Zaitsev, S. and Dalluege, R. and Schneider, M. and Boettger, M.
Molecular Biology Reports 28
(3): 157-165.
September 2002
NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria.
Andrade, M.A. and Ciccarelli, F.D. and Perez-Iratxeta, C. and Bork, P.
Genome Biology 3
(9): research0047.
15 August 2002
Applying metabolic pathway analysis to make good use of methanol.
Schuster, S. and Klamt, S.
Trends in Biotechnology 20
(8): 322-322.
1 August 2002
SPG20 is mutated in Troyer syndrome, an hereditary spastic paraplegia.
Patel, H. and Cross, H. and Proukakis, C. and Hershberger, R. and Bork, P. and Ciccarelli, F.D. and Patton, M.A. and McKusick, V.A. and Crosby, A.H.
Nature Genetics 31
: 347-348.
1 August 2002
The rhodanese/Cdc25 phosphatase superfamily. Sequence-structure-function relations.
Bordo, D. and Bork, P.
EMBO Reports 3
: 741-746.
1 August 2002
Predicting protein cellular localization using a domain projection method.
Mott, R. and Schultz, J. and Bork, P. and Ponting, C.P.
Genome Research 12
(8): 1168-1174.
August 2002
Reaction routes in biochemical reaction systems: Algebraic properties, validated calculation procedure and example from nucleotide metabolism.
Schuster, S. and Hilgetag, C. and Woods, J.H. and Fell, D.A.
Journal of Mathematical Biology 45
(2): 153-181.
August 2002
Worldwide scientific publishing activity.
Perez-Iratxeta, C. and Andrade, M.A.
Science 297
(5581): 519-519.
26 July 2002
Association of genes to genetically inherited diseases using data mining.
Perez-Iratxeta, C. and Bork, P. and Andrade, M.A.
Nature Genetics 31
(3): 316-319.
July 2002
Genome organization: Teamed up for transcription.
von Mering, C. and Bork, P.
Nature 417
(6891): 797-798.
20 June 2002
Common exon duplication in animals and its role in alternative splicing.
Letunic, I. and Copley, R.R. and Bork, P.
Human Molecular Genetics 11
: 1561-1567.
15 June 2002
Comparative genomic analysis in the region of a major Plasmodium-refractoriness locus of Anopheles gambiae.
Thomasova, D. and Ton, L.Q. and Copley, R.R. and Zdobnov, E.M. and Wang, X. and Hong, Y.S. and Sim, C. and Bork, P. and Kafatos, F.C. and Collins, F.H.
Proceedings of the National Academy of Sciences of the United States of America 99
: 8179-8184.
11 June 2002
Common haplotypes in five genes influence genetic variance of LDL and HDL cholesterol in the general population.
Knoblauch, H. and Bauerfeind, A. and Kraehenbuehl, C. and Daury, A. and Rohde, K. and Bejanin, S. and Essioux, L. and Schuster, H. and Luft, F.C. and Reich, J.
Human Molecular Genetics 11
(12): 1477-1485.
1 June 2002
Exploring Medline abstracts with XplorMed.
Perez-Iratxeta, C. and Bork, P. and Andrade, M.A.
Drugs of Today 38
: 381-389.
1 June 2002
Computing fuzzy associations for the analysis of biological literature.
Perez-Iratxeta, C. and Keer, H.S. and Bork, P. and Andrade, M.A.
Biotechniques 32
(6): 1380-1385.
June 2002
Proteinkomplexe und Netzwerke: Neue Herausforderungen fuer die Proteomik.
von Mering, C. and Bork, P.
GenomXpress 2002
(2): 2-4.
June 2002
Comparative assessment of large-scale data sets of protein-protein interactions.
von Mering, C. and Krause, R. and Snel, B. and Cornell, M. and Oliver, S.G. and Fields, S. and Bork, P.
Nature 417
(6887): 399-403.
23 May 2002
Mapping of gene loci for nephronophthisis type 4 and Senior-Loken syndrome, to chromosome 1p36.
Schuermann, M.J. and Otto, E. and Becker, A. and Saar, K. and Rueschendorf, F. and Polak, B.C. and Ala-Mello, S. and Hoefele, J. and Wiedensohler, A. and Haller, M. and Omran, H. and Nuernberg, P. and Hildebrandt, F.
American Journal of Human Genetics 70
(5): 1240-1246.
May 2002
Identification of attenuation and antitermination regulation in prokaryotes.
Lathe, W.C. and Suyama, M. and Bork, P.
Genome Biology 3
: preprint0003.1.
30 April 2002
The identification of functional modules from the genomic association of genes.
Snel, B. and Bork, P. and Huynen, M.A.
Proceedings of the National Academy of Sciences of the United States of America 99
: 5890-5895.
30 April 2002
Embryonic stem cells - The debate in Germany.
Reich, J.G.
Science 296
(5566): 265-265.
12 April 2002
BSD: a novel domain in transcription factors and synapse-associated proteins.
Doerks, T. and Huber, S. and Buchner, E. and Bork, P.
Trends in Biochemical Sciences 27
(4): 168-170.
1 April 2002
SHOT: a web server for the construction of genome phylogenies.
Korbel, J.O. and Snel, B. and Huynen, M.A. and Bork, P.
Trends in Genetics 18
: 158-162.
1 March 2002
A versatile structural domain analysis server using profile weight matrices.
Schmidt, S. and Bork, P. and Dandekar, T.
Journal of Chemical Information and Computer Sciences 42
(2): 405-407.
March 2002
Integration of genome data and protein structures: prediction of protein folds, protein interactions and 'molecular phenotypes' of single nucleotide polymorphisms (Reprinted from Current Opinion in Structural Biology, vol 11, pg 125-130, 2001).
Sunyaev, S.R. and Lathe, W. and Bork, P.
Trends in Genetics
(Suppl. March): S19-S24.
March 2002
Functional organization of the yeast proteome by systematic analysis of protein complexes.
Gavin, A.C. and Boesche, M. and Krause, R. and Grandi, P. and Marzioch, M. and Bauer, A. and Schultz, J. and Rick, J.M. and Michon, A.M. and Cruciat, C.M. and Remor, M. and Hoefert, C. and Schelder, M. and Brajenovic, M. and Ruffner, H. and Merino, A. and Klein, K. and Hudak, M. and Dickson, D. and Rudi, T. and Gnau, V. and Bauch, A. and Bastuck, S. and Huhse, B. and Leutwein, C. and Heurtier, M.A. and Copley, R.R. and Edelmann, A. and Querfurth, E. and Rybin, V. and Drewes, G. and Raida, M. and Bouwmeester, T. and Bork, P. and Seraphin, B. and Kuester, B. and Neubauer, G. and Superti-Furga, G.
Nature 415
(6868): 141-147.
10 January 2002
A complex prediction: three-dimensional model of the yeast exosome.
Aloy, P. and Ciccarelli, F.D. and Leutwein, C. and Gavin, A.C. and Superti-Furga, G. and Bork, P. and Boettcher, B. and Russell, R.B.
EMBO Reports 3
: 628-635.
1 January 2002
A self-organizing model for the development of orientation selectivity and ocular dominance patterns in the visual nervous system.
Muro, E.M. and Andrade, M.A. and Moran, F.
Neural Network World 12
(4): 319-332.
1 January 2002
AMOP, a protein module aternativelly spliced in cancer cells.
Ciccarelli, F.D. and Doerks, T. and Bork, P.
Trends in Biochemical Sciences 27
: 113-115.
1 January 2002
Alternative splicing and genome complexity.
Brett, D. and Pospisil, H. and Valcarel, J. and Reich, J. and Bork, P.
Nature Genetics 30
(1): 29-30.
1 January 2002
CASH - a beta-helix domain widespread among carbohydrate-binding proteins.
Ciccarelli, F.D. and Copley, R.R. and Doerks, T. and Russell, R.B. and Bork, P.
Trends in Biochemical Sciences 27
(2): 59-62.
1 January 2002
Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria.
Klamt, S. and Schuster, S. and Gilles, E.D.
Biotechnology and Bioengineering 77
(7): 734-751.
1 January 2002
Calculating as many fluxes as possible in underdetermined metabolic networks.
Klamt, S. and Schuster, S.
Molecular Biology Reports 29
(1-2): 243-248.
1 January 2002
Exclusion of the neuronal nicotinic acetylcholine receptor alpha 7 subunit gene as a candidate for catatonic schizophrenia in a large family supporting the chromosome 15q13-22 locus.
Meyer, J. and Ortega, G. and Schraut, K. and Nuernberg, G. and Rueschendorf, F. and Saar, K. and Moessner, R. and Wienker, T.F. and Reis, A. and Stoeber, G. and Lesch, K.P.
Molecular Psychiatry 7
: 220-223.
1 January 2002
Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae.
Schuster, S. and Pfeiffer, T. and Moldenhauer, F. and Koch, I. and Dandekar, T.
Bioinformatics 18
(2): 351-361.
1 January 2002
Genome and protein evolution in eukaryotes.
Copley, R.R. and Letunic, I. and Bork, P.
Current Opinion in Chemical Biology 6
: 39-45.
1 January 2002
Genomes in flux: The evolution of archaeal and proteobacterial gene content.
Snel, B. and Bork, P. and Huynen, M.A.
Genome Research 12
(1): 17-25.
1 January 2002
HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources.
Fredman, D. and Siegfried, M. and Yuan, Y.P. and Bork, P. and Lehvaslaiho, H. and Brookes, A.J.
Nucleic Acids Research 30
(1): 387-391.
1 January 2002
Identification and characterization of UEV3, a human cDNA with similarities to inactive E2 ubiquitin-conjugating enzymes.
Kloor, M. and Bork, P. and Duwe, A. and Klaes, R. and Doeberitz, M.V. and Ridder, R.
Biochimica et Biophysica Acta - Gene Structure and Expression 1579
: 219-224.
1 January 2002
Immunity-related genes and gene families in Anopheles gambiae.
Christophides, G.K. and Zdobnov, E. and Barillas-Mury, C. and Birney, E. and Blandin, S. and Blass, C. and Brey, P.T. and Collins, F.H. and Danielli, A. and Dimopoulos, G. and Hetru, C. and Hoa, N. and Hoffmann, J.A. and Kanzok, S.M. and Letunic, I. and Levashina, E.A. and Loukeris, T.G. and Lycett, G. and Meister, S. and Michel, K. and Mueller, H.M. and Osta, M.A. and Paskewitz, S.M. and Reichhart, J.M. and Rzhetsky, A. and Troxler, L. and Vernick, K.D. and Vlachou, D. and Volz, J. and von Mering, C. and Xu, J.N. and Zheng, L.B. and Bork, P. and Kafatos, F.C.
Science 298
: 159-165.
1 January 2002
Mapping the combinatorial regulation by transcription factors.
Schuster, S.
Trends in Biotechnology 20
(1): 5-6.
1 January 2002
Modelling of simple and complex calcium oscillations - From single-cell responses to intercellular signalling.
Schuster, S. and Marhl, M. and Hoefer, T.
European Journal of Biochemistry 269
(5): 1333-1355.
1 January 2002
O6-alkylguanine-DNA alkyltransferase: role in carcinogenesis and chemotherapy.
Margison, G.P. and Santibanez-Koref, M.F.
BioEssays 24
(3): 255-266.
1 January 2002
Protein domain analysis in the era of complete genomes.
Copley, R.R. and Doerks, T. and Letunic, I. and Bork, P.
FEBS Letters 513
(1): 129-134.
1 January 2002
Recent improvements to the SMART domain-based sequence annotation resource.
Letunic, I. and Goodstadt, L. and Dickens, N.J. and Doerks, T. and Schultz, J. and Mott, R. and Ciccarelli, F. and Copley, R.R. and Ponting, C.P. and Bork, P.
Nucleic Acids Research 30
(1): 242-244.
1 January 2002
STAT6 as an asthma candidate gene: polymorphism-screening, association and haplotype analysis in a Caucasian sib-pair study.
Duetsch, G. and Illig, T. and Loesgen, S. and Rohde, K. and Klopp, N. and Herbon, N. and Gohlke, H. and Altmueller, J. and Wjst, M.
Human Molecular Genetics 11
(6): 613-621.
1 January 2002
Statistical gene mapping of traits in humans--hypertension as a complex trait: is it amenable to genetic analysis?
Nothnagel, M. and Ott, J.
Seminars in Nephrology 22, 2
: 105-114.
1 January 2002
Systematic identification of novel protein domain families associated with nuclear functions.
Doerks, T. and Copley, R.R. and Schultz, J. and Ponting, C.P. and Bork, P.
Genome Research 12
(1): 47-56.
1 January 2002
Use of network analysis of metabolic systems in bioengineering.
Schuster, S. and Klamt, S. and Weckwerth, W. and Moldenhauer, F. and Pfeiffer, T.
Bioprocess and Biosystems Engineering 24
(6): 363-372.
1 January 2002
An essay on individual sequence variation in Expressed Sequence Tags(ESTs).
Reich, J. and Brett, D. and Hanke, J.
In:
Genomics and Proteomics: Functional and Computational Aspects.
Springer, 83-94.
ISBN 978-0-306-46312-9
2002
Microarrays, Genexpressionsanalyse und Bioinformatik.
Schober, D.
Biospektrum 8
(3): 307-310.
2002
Sequence analysis of multidomain proteins: Past perspectives and future directions.
Copley, R.R. and Ponting, C.P. and Schultz, J. and Bork, P.
Advances in Protein Chemistry 61
: 75-98.
2002
2001
The Spir actin organizers are involved in vesicle transport processes.
Kerkhoff, E. and Simpson, J.C. and Leberfinger, C.B. and Otto, I.M. and Doerks, T. and Bork, P. and Rapp, U.R. and Raabe, T. and Pepperkok, R.
Current Biology 11
: 1963-1968.
11 December 2001
Novel protein domains and repeats in Drosophila melanogaster: insights into structure, function, and evolution.
Ponting, C.P. and Mott, R. and Bork, P. and Copley, R.R.
Genome Research 11
: 1996-2008.
1 December 2001
Medical target prediction from genome sequence: combining different sequence analysis algorithms with expert knowledge and input from artificial intelligence approaches.
Dandekar, T. and Du, F. and Schirmer, R.H. and Schmidt, S.
Computers and Chemistry 26
(1): 15-21.
December 2001
The phosphoglucose isomerase from the hyperthermophilic archaeon Pyrococcus furiosus is a unique glycolytic enzyme that belongs to the cupin superfamily.
Verhees, C.H. and Huynen, M.A. and Ward, D.E. and Schiltz, E. and de Vos, W.M. and van der Oost, J.
Journal of Biological Chemistry 276
(44): 40926-40932.
2 November 2001
When genetic distance matters: measuring genetic differentiation at microsatellite loci in whole-genome scans of recent and incipient mosquito species.
Wang, R. and Zheng, L. and Toure, Y.T. and Dandekar, T. and Kafatos, F.C.
Proceedings of the National Academy of Sciences of the United States of America 98
(19): 10769-10774.
11 September 2001
Protons and sodium ions acting as intracellular carrier pigeons?
Schuster, S.
Trends in Biotechnology 19
(9): 330-330.
1 September 2001
Modularity in the gain and loss of genes: applications for function prediction.
Ettema, T. and van der Oost, J. and Huynen, M.
Trends in Genetics 17
(9): 485-487.
September 2001
Structure--function characterization of cellulose synthase: relationship to other glycosyltransferases.
Saxena, I.M. and Brown, R.M. and Dandekar, T.
Phytochemistry 57
: 1135-1148.
1 August 2001
A rapid bioinformatic method identifies novel genes with direct clinical relevance to colon cancer.
Brett, D. and Kemmner, W. and Koch, G. and Roefzaad, C. and Gross, S. and Schlag, P.M.
Oncogene 20
(33): 4581-4585.
27 July 2001
What can silent mutations tell us?
Schuster, S.
Trends in Biotechnology 19
(7): 242-242.
1 July 2001
A combination of the F-box motif and kelch repeats defines a large Arabidopsis family of F-box proteins.
Andrade, M.A. and Gonzalez-Guzman, M. and Serrano, R. and Rodriguez, P.L.
Plant Molecular Biology 46
(5): 603-614.
July 2001
Inversions and the dynamics of eukaryotic gene order.
Huynen, M.A. and Snel, B. and Bork, P.
Trends in Genetics 17
(6): 304-306.
1 June 2001
A compartment model to calculate time-dependent concentration profiles of topically applied chemical compounds in the anterior compartments of the rabbit eye.
Pospisil, H. and Holzhuetter, H.G.
Alternatives to Laboratory Animals 29
: 347-365.
3 May 2001
Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching.
Shevchenko, A. and Sunyaev, S. and Loboda, A. and Shevchenko, A. and Bork, P. and Ens, W. and Standing, K.G.
Analytical Chemistry 73
(9): 1917-1926.
1 May 2001
Solvent entropy-driven searching for protein modeling examined and tested in simplified models.
Koenig, R. and Dandekar, T.
Protein Engineering 14
: 329-335.
1 May 2001
Simulation of plasticity in the adult visual cortex.
Andrade-Navarro, M.A. and Muro, E.M. and Moran, F.
Biological Cybernetics 84
(6): 445-451.
May 2001
Towards the genetic basis of periodic catatonia: pedigree sample for genome scan I and II.
Stoeber, G. and Pfuhlmann, B. and Nuernberg, G. and Schmidtke, A. and Reis, A. and Franzek, E. and Wienker, T.F.
European Archives of Psychiatry and Clinical Neuroscience 251
(Suppl 1): I25-I30.
May 2001
Flux determination by isotopomer balancing - a successful application of theory to experiment.
Schuster, S.
Trends in Biotechnology 19
(3): 85.
1 March 2001
Initial sequencing and analysis of the human genome.
Lander, E.S. and Linton, L.M. and Birren, B. and Nusbaum, C. and Zody, M.C. and Baldwin, J. and Devon, K. and Dewar, K. and Doyle, M. and FitzHugh, W. and Funke, R. and Gage, D. and Harris, K. and Heaford, A. and Howland, J. and Kann, L. and Lehoczky, J. and LeVine, R. and McEwan, P. and McKernan, K. and Meldrim, J. and Mesirov, J.P. and Miranda, C. and Morris, W. and Naylor, J. and Raymond, C. and Rosetti, M. and Santos, R. and Sheridan, A. and Sougnez, C. and Stange-Thomann, N. and Stojanovic, N. and Subramanian, A. and Wyman, D. and Rogers, J. and Sulston, J. and Ainscough, R. and Beck, S. and Bentley, D. and Burton, J. and Clee, C. and Carter, N. and Coulson, A. and Deadman, R. and Deloukas, P. and Dunham, A. and Dunham, I. and Durbin, R. and French, L. and Grafham, D. and Gregory, S. and Hubbard, T. and Humphray, S. and Hunt, A. and Jones, M. and Lloyd, C. and McMurray, A. and Matthews, L. and Mercer, S. and Milne, S. and Mullikin, J.C. and Mungall, A. and Plumb, R. and Ross, M. and Shownkeen, R. and Sims, S. and Waterston, R.H. and Wilson, R.K. and Hillier, L.W. and McPherson, J.D. and Marra, M.A. and Mardis, E.R. and Fulton, L.A. and Chinwalla, A.T. and Pepin, K.H. and Gish, W.R. and Chissoe, S.L. and Wendl, M.C. and Delehaunty, K.D. and Miner, T.L. and Delehaunty, A. and Kramer, J.B. and Cook, L.L. and Fulton, R.S. and Johnson, D.L. and Minx, P.J. and Clifton, S.W. and Hawkins, T. and Branscomb, E. and Predki, P. and Richardson, P. and Wenning, S. and Slezak, T. and Doggett, N. and Cheng, J.F. and Olsen, A. and Lucas, S. and Elkin, C. and Uberbacher, E. and Frazier, M. and Gibbs, R.A. and Muzny, D.M. and Scherer, S.E. and Bouck, J.B. and Sodergren, E.J. and Worley, K.C. and Rives, C.M. and Gorrell, J.H. and Metzker, M.L. and Naylor, S.L. and Kucherlapati, R.S. and Nelson, D.L. and Weinstock, G.M. and Sakaki, Y. and Fujiyama, A. and Hattori, M. and Yada, T. and Toyoda, A. and Itoh, T. and Kawagoe, C. and Watanabe, H. and Totoki, Y. and Taylor, T. and Weissenbach, J. and Heilig, R. and Saurin, W. and Artiguenave, F. and Brottier, P. and Bruls, T. and Pelletier, E. and Robert, C. and Wincker, P. and Rosenthal, A. and Platzer, M. and Nyakatura, G. and Taudien, S. and Rump, A. and Yang, H.M. and Yu, J. and Wang, J. and Huang, G.Y. and Gu, J. and Hood, L. and Rowen, L. and Madan, A. and Qin, S.Z. and Davis, R.W. and Federspiel, N.A. and Abola, A.P. and Proctor, M.J. and Myers, R.M. and Schmutz, J. and Dickson, M. and Grimwood, J. and Cox, D.R. and Olson, M.V.
Nature 409
(6822): 860-921.
15 February 2001
The draft sequences. Filling in the gaps.
Bork, P. and Copley, R.
Nature 409
(6822): 818-820.
15 February 2001
Molecular characterization of a cDNA encoding functional human CLK4 kinase and localization to chromosome 5q35 [correction of 4q35].
Schultz, J. and Jones, T. and Bork, P. and Sheer, D. and Blencke, S. and Steyrer, S. and Wellbrock, U. and Bevec, D. and Ullrich, A. and Wallasch, C.
Genomics 71
: 368-370.
1 February 2001
A novel form of "central pouchlike" cataract, with sutural opacities, maps to chromosome 15q21-22.
Vanita, A. and Singh, J.R. and Sarhadi, V.K. and Singh, D. and Reis, A. and Rueschendorf, F. and Becker-Follmann, J. and Jung, M. and Sperling, K.
American Journal of Human Genetics 68
(2): 509-514.
February 2001
The black-pearl gene of Drosophila defines a novel conserved protein family and is required for larval growth and survival.
Becker, S. and Gehrsitz, A. and Bork, P. and Buchner, S. and Buchner, E.
Gene 262
: 15-22.
10 January 2001
Fundamental Study - Enumerating all connected maximal common subgraphs in two graphs.
Koch, I.
Theoretical Computer Science 250
(1-2): 1-30.
6 January 2001
Assignment of PGL3 to chromosome 1 (q21-q23) in a family with autosomal dominant non-chromaffin paraganglioma.
Niemann, S. and Becker-Follmann, J. and Nuernberg, G. and Rueschendorf, F. and Sieweke, N. and Huegens-Penzel, M. and Traupe, H. and Wienker, T.F. and Reis, A. and Mueller, U.
American Journal of Medical Genetics 98
(1): 32-36.
1 January 2001
Bifurcation analysis of calcium oscillations: time-scale separation, canards, and frequency lowering.
Schuster, S. and Marhl, M.
Journal of Biological Systems 9
(4): 291-314.
1 January 2001
Characterization of a mutation in the lens-specific MP70 encoding gene of the mouse leading to a dominant cataract.
Graw, J. and Loster, J. and Soewarto, D. and Fuchs, H. and Meyer, B. and Reis, A. and Wolf, E. and Balling, R. and de Angelis, M.H.
Experimental Eye Research 73
(6): 867-876.
1 January 2001
Comparison of ARM and HEAT protein repeats.
Andrade, M.A. and Petosa, C. and O'Donoghue, S.I. and Mueller, C.W. and Bork, P.
Journal of Molecular Biology 309
(1): 1-18.
1 January 2001
Cooperation and competition in the evolution of ATP-producing pathways.
Pfeiffer, T. and Schuster, S. and Bonhoeffer, S.
Science 292
: 504-507.
1 January 2001
DDT - a novel domain in different transcription and chromosome remodeling factors.
Doerks, T. and Copley, R. and Bork, P.
Trends in Biochemical Sciences 26
: 145-146.
1 January 2001
Evolution of prokaryotic gene order: genome rearrangements in closely related species.
Suyama, M. and Bork, P.
Trends in Genetics 17
(1): 10-13.
1 January 2001
Evolution of tuf genes: ancient duplication, differential loss and gene conversion.
Lathe, W.C. and Bork, P.
FEBS Letters 502
(3): 113-116.
1 January 2001
Fine mapping and single nucleotide polymorphism association results of candidate genes for asthma and related phenotypes.
Immervoll, T. and Loesgen, S. and Duetsch, G. and Gohlke, H. and Herbon, N. and Klugbauer, S. and Dempfle, A. and Bickeboeller, H. and Becker-Follmann, J. and Rueschendorf, F. and Saar, K. and Reis, A. and Wichmann, H.E. and Wjst, M.
Human Mutation 18
: 327-336.
1 January 2001
Frameshift peptide-derived T-cell epitopes: a source of novel tumor-specific antigens.
Linnebacher, M. and Gebert, J. and Rudy, W. and Woerner, S. and Yuan, Y.P. and von Knebel-Doeberitz, M.
International Journal of Cancer 93
(1): 6-11.
1 January 2001
Genome sequences and great expectations.
Iliopoulos, I. and Tsoka, S. and Andrade, M.A. and Janssen, P. and Audit, B. and Tramontano, A. and Valencia, A. and Leroy, C. and Sander, C. and Ouzounis, C.A.
Genome Biology 2
(1): Interactions0001.1-Interactions0001.3.
1 January 2001
Genome speak.
Bork, P. and Copley, R.
Nature 409
: 815.
1 January 2001
Haplotyping and estimation of haplotype frequencies for closely linked biallelic multilocus genetic phenotypes including nuclear family information.
Rohde, K. and Fuerst, R.
Human Mutation 17
(4): 289-295.
1 January 2001
Hydrogenosomes: convergent adaptations of mitochondria to anaerobic environments.
Hackstein, J.H.P. and Akhmanova, A.S. and Voncken, F. and van Hoek, A. and Alen, T. and Boxma, B. and Moon-van der Staay, S.Y. and Staay, G. and Leunissen, J. and Huynen, M.A. and Rosenberg, J. and Veenhuis, M.
Zoology 104
: 290-302.
1 January 2001
Identification of cellular interactions in RNA and protein molecules.
Dandekar, T. and Du, F. and Bertram, H.
Nonlinear Analysis Theory Methods & Applications 47
: 225-234.
1 January 2001
Integration of genome data and protein structures: prediction of protein folds, protein interactions and 'molecular phenotypes' of single nucleotide polymorphisms.
Sunyaev, S.R. and Lathe, W. and Bork, P.
Current Opinion in Structural Biology 11
(1): 125-130.
1 January 2001
Localisation of a gene for an autosomal recessive syndrome of macrocephaly, multiple epiphyseal dysplasia, and distinctive facies to chromosome 15q26.
Bayoumi, R. and Saar, K. and Lee, Y.A. and Nuernberg, G. and Reis, A. and Nur-E-Kamal, M. and Al Gazali, L.I.
Journal of Medical Genetics 38
(6): 369-373.
1 January 2001
Post-translational GPI lipid anchor modification of proteins in kingdoms of life: analysis of protein sequence data from complete genomes.
Eisenhaber, B. and Bork, P. and Eisenhaber, F.
Protein Engineering 14
(1): 17-25.
1 January 2001
Prediction of deleterious human alleles.
Sunyaev, S.R. and Ramensky, V. and Koch, I. and Lathe, W. and Kondrashov, A.S. and Bork, P.
Human Molecular Genetics 10
(6): 591-597.
1 January 2001
Protein repeats: Structures, functions, and evolution.
Andrade, M.A. and Perez-Iratxeta, C. and Ponting, C.P.
Journal of Structural Biology 134
(2-3): 117-131.
1 January 2001
Refinement of the gene locus for autosomal dominant medullary cystic kidney disease type 1 (MCKD1) and construction of a physical and partial transcriptional map of the region.
Fuchshuber, A. and Kroiss, S. and Karle, S. and Berthold, S. and Huck, K. and Burton, C. and Rahman, N. and Koptides, M. and Deltas, C. and Otto, E. and Rueschendorf, F. and Feest, T. and Hildebrandt, F.
Genomics 72
(3): 278-284.
1 January 2001
Systematic identification of genes with coding microsatellites mutated in DNA mismatch repair-deficient cancer cells.
Woerner, S.M. and Gebert, J. and Yuan, Y.P. and Sutter, C. and Ridder, R. and Bork, P. and von Knebel-Doeberitz, M.
International Journal of Cancer 93
(1): 12-19.
1 January 2001
The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly.
Huynen, M.A. and Snel, B. and Bork, P. and Gibson, T.J.
Human Molecular Genetics 10
(21): 2463-2468.
1 January 2001
XplorMed: a tool for exploring MEDLINE abstracts.
Perez-Iratxeta, C. and Bork, P. and Andrade, M.A.
Trends in Biochemical Sciences 26
(9): 573-575.
1 January 2001
Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences.
Iyer, L.M. and Aravind, L. and Bork, P. and Hofmann, K. and Mushegian, A.R. and Zhulin, I.B. and Koonin, E.V.
Genome Biology 2
(12): RESEARCH0051.
2001
The large-scale organization of metabolic networks.
Dandekar, T. and Schuster, S.
Chemtracts 14
: 137-141.
2001
2000
TAP (NXF1) belongs to a multigene family of putative RNA export factors with a conserved modular architecture.
Herold, A. and Suyama, M. and Rodrigues, J.P. and Braun, I.C. and Kutay, U. and Carmo-Fonseca, M. and Bork, P. and Izaurralde, E.
Molecular and Cellular Biology 20
: 8996-9008.
1 December 2000
Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III.
Gonczy, P. and Echeverri, G. and Oegema, K. and Coulson, A. and Jones, S.J. and Copley, R.R. and Duperon, J. and Oegema, J. and Brehm, M. and Cassin, E. and Hannak, E. and Kirkham, M. and Pichler, S. and Flohrs, K. and Goessen, A. and Leidel, S. and Alleaume, A.M. and Martin, C. and Ozlu, N. and Bork, P. and Hyman, A.A.
Nature 408
(6810): 331-336.
16 November 2000
Homology among (betaalpha)8barrels: implications for the evolution of metabolic pathways.
Copley, R.R. and Bork, P.
Journal of Molecular Biology 303
: 627-641.
3 November 2000
A complete enumeration and classification of two-locus disease models.
Li, W.T. and Reich, J.
Human Heredity 50
(6): 334-349.
1 November 2000
Breeding of Escherichia coli based in colour - commentary.
Schuster, S.
Trends in Biotechnology 18
(11): 442.
1 November 2000
Splitting schizophrenia: Periodic catatonia-susceptibility locus on chromosome 15q15.
Stoeber, G. and Saar, K. and Rueschendorf, F. and Meyer, J. and Nuernberg, G. and Jatzke, S. and Franzek, E. and Reis, A. and Lesch, K.P. and Wienker, T.F. and Beckmann, H.
American Journal of Human Genetics 67
: 1201-1207.
1 November 2000
GRAM, a novel domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins.
Doerks, T. and Strauss, M. and Brendel, M. and Bork, P.
Trends in Biochemical Sciences 25
(10): 483-485.
1 October 2000
Gene context conservation of a higher order than operons.
Lathe, W.C. and Snel, B. and Bork, P.
Trends in Biochemical Sciences 25
(10): 474-479.
1 October 2000
Genomewide scan in German families reveals evidence for a novel psoriasis-susceptibility locus on chromosome 19p13.
Lee, Y.A. and Rueschendorf, F. and Windemuth, C. and Schmitt-Egenolf, M. and Stadelmann, A. and Nuernberg, G. and Staender, M. and Wienker, T.F. and Reis, A. and Traupe, H.
American Journal of Human Genetics 67
(4): 1020-1024.
1 October 2000
Multiple sclerosis associated amino acids of polymorphic regions relevant for the HLA antigen binding are confined to HLA-DR2.
Zipp, F. and Windemuth, C. and Pankow, H. and Dichgans, J. and Wienker, T.F. and Martin, R. and Mueller, C.
Human Immunology 61
(10): 1021-1030.
1 October 2000
STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene.
Snel, B. and Lehmann, G. and Bork, P. and Huynen, M.A.
Nucleic Acids Research 28
(18): 3442-3444.
15 September 2000
EST analysis online: WWW tools for detection of SNPs and alternative splice forms.
Brett, D. and Lehmann, G. and Hanke, J. and Gross, S. and Reich, J. and Bork, P.
Trends in Genetics 16
(9): 416-418.
1 September 2000
Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.
Dandekar, T. and Huynen, M.A. and Regula, J. and Ueberle, B. and Zimmermann, C.U. and Andrade, M.A. and Doerks, T. and Sanches-Pulido, L. and Snel, B. and Suyama, M. and Yuan, Y.P. and Herrmann, R. and Bork, P.
Nucleic Acids Research 28
(17): 3278-3288.
1 September 2000
Biotechnology in silicio. Metabolic proteomics of Haemophilus influenzae : commentary.
Schuster, S.
Trends in Biotechnology 18
(8): 328-328.
1 August 2000
Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences.
Huynen, M. and Snel, B. and Lathe, W. and Bork, P.
Genome Research 10
(8): 1204-1210.
1 August 2000
SNP frequencies in human genes - an excess of rare alleles and differing modes of selection.
Sunyaev, S.R. and Lathe, W.C. and Ramensky, V.E. and Bork, P.
Trends in Genetics 16
(8): 335-337.
1 August 2000
The 3'-untranslated region of the human estrogen receptor alpha gene mediates rapid messenger ribonucleic acid turnover.
Kenealy, M.R. and Flouriot, G. and Sonntag-Buck, V. and Dandekar, T. and Brand, H. and Gannon, F.
Endocrinology 141
(8): 2805-2813.
August 2000
DNA recognition, strand selectivity, and cleavage mode during integrase family site-specific recombination.
Tribble, G. and Ahn, Y.T. and Lee, J. and Dandekar, T. and Jayaram, M.
Journal of Biological Chemistry 275
(29): 22255-22267.
21 July 2000
A tumor suppressor locus in familial and sporadic chordoma maps to 1p36.
Miozzo, M. and Dalpra, L. and Riva, P. and Volonte, M. and Macciardi, F. and Pericotti, S. and Tibiletti, M.G. and Cerati, M. and Rohde, K. and Larizza, L. and Conti, A.M.F.
International Journal of Cancer 87
(1): 68-72.
1 July 2000
Automated annotation of GPI anchor sites: case study C-elegans.
Eisenhaber, B. and Bork, P. and Yuan, Y.P. and Loeffler, G. and Eisenhaber, F.
Trends in Biochemical Sciences 25
(7): 340-341.
1 July 2000
L27, a novel heterodimerization domain in receptor targeting proteins Lin-2 and Lin-7.
Doerks, T. and Bork, P. and Kamberov, E. and Makarova, O. and Muecke, S. and Margolis, B.
Trends in Biochemical Sciences 25
: 317-318.
1 July 2000
NAIL - Network Analysis Interface for Linking HMMER results.
Sanchez-Pulido, L. and Yuan, Y.P. and Andrade, M.A. and Bork, P.
Bioinformatics 16
(7): 656-657.
1 July 2000
Prediction of structural domains of TAP reveals details of its interaction with p15 and nucleoporins.
Suyama, M. and Doerks, T. and Braun, I.C. and Sattler, M. and Izaurralde, E. and Bork, P.
EMBO Reports 1
(1): 53-58.
1 July 2000
Automated extraction of information in molecular biology.
Andrade, M.A. and Bork, P.
FEBS Letters 476
(1-2): 12-17.
30 June 2000
Anopheles gambiae pilot gene discovery project: Identification of mosquito innate immunity genes from expressed sequence tags generated from immune-competent cell lines.
Dimopoulos, G. and Casavant, T.L. and Chang, S.R. and Scheetz, T. and Roberts, C. and Donohue, M. and Schultz, J. and Benes, V. and Bork, P. and Ansorge, W. and Soares, M.B. and Kafatos, F.C.
Proceedings of the National Academy of Sciences of the United States of America 97
(12): 6619-6624.
6 June 2000
Exploitation of gene context.
Huynen, M.A. and Snel, B. and Lathe, W. and Bork, P.
Current Opinion in Structural Biology 10
(3): 366-370.
1 June 2000
More than 1,000 putative new human signalling proteins revealed by EST data mining.
Schultz, J. and Doerks, T. and Ponting, C.P. and Copley, R.R. and Bork, P.
Nature Genetics 25
(2): 201-204.
1 June 2000
Sequences and topology. Genome and proteome informatics - Editorial overview.
Bork, P. and Eisenberg, D.
Current Opinion in Structural Biology 10
(3): 341-342.
1 June 2000
Crystal structures of the membrane-binding C2 domain of human coagulation factor V structure of the C2 domain of human factor VIII at 1.5 A resolution.
Dandekar, T.
Chemtracts 13
(6): 398-401.
June 2000
Homology-based method for identification of protein repeats using statistical significance estimates.
Andrade, M.A. and Ponting, C.P. and Gibson, T.J. and Bork, P.
Journal of Molecular Biology 298
(3): 521-537.
5 May 2000
Towards a structural basis of human non-synonymous single nucleotide polymorphisms.
Sunyaev, S.R. and Ramensky, V. and Bork, P.
Trends in Genetics 16
(5): 198-200.
1 May 2000
Minimal T-Invariants in biochemical petri nets.
Schuster, S. and Moldenhauer, F.
In:
Modellierung und Simulation Metabolischer Netzwerke.
Universitaet Magdeburg, Fakultaet fuer Informatik, Magdeburg, 3-10.
May 2000
Powers and pitfalls in sequence analysis: The 70% hurdle.
Bork, P.
Genome Research 10
(4): 398-400.
1 April 2000
The p150-Spir protein provides a link between c-Jun N-terminal kinase function and actin reorganization.
Otto, I.M. and Raabe, T. and Rennefahrt, U.E. and Bork, P. and Rapp, U.R. and Kerkhoff, E.
Current Biology 10
: 345-348.
23 March 2000
A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks.
Schuster, S. and Fell, D.A. and Dandekar, T.
Nature Biotechnology 18
(3): 326-332.
1 March 2000
Stochastic sensing of organic analytes by a pore-forming protein containing a molecular adapter.
Schultzberg, M. and Boulin, C. and Dandekar, T.
Chemtracts 13
(3): 198-202.
March 2000
Neuartige selektive Beschichtungsmethode fuer die Oberflaechenbehandlung (z.B. von Sensoren und Leiterplatinen).
Koenig, R. and Dandekar, T.
DE19833683A1.
3 February 2000
Cellular information transfer regarded from a stoichiometry and control analysis perspective.
Schuster, S. and Kholodenko, B.N. and Westerhoff, H.V.
Biosystems 55
(1-3): 73-81.
1 February 2000
Discovery, scoring and utilization of human single nucleotide polymorphisms: a multidisciplinary problem.
Isaksson, A. and Landegren, U. and Syvanen, A.C. and Bork, P. and Stein, C. and Ortigao, F. and Brookes, A.J.
European Journal of Human Genetics 8
: 154-156.
1 February 2000
Isolated familial somatotropinomas: Establishment of linkage to chromosome 11q13.1-11q13.3 and evidence for a potential second locus at chromosome 2p16-12.
Gadelha, M.R. and Une, K.N. and Rohde, K. and Vaisman, M. and Kineman, R.D. and Frohman, L.A.
Journal of Clinical Endocrinology and Metabolism 85
(2): 707-714.
1 February 2000
The GeneQuiz web server: protein functional analysis through the Web.
Hoersch, S. and Leroy, C. and Brown, N.P. and Andrade, M.A. and Sander, C.
Trends in Biochemical Sciences 25
(1): 33-35.
28 January 2000
A cholesterol-lowering gene maps to chromosome 13q.
Knoblauch, H. and Mueller-Myhsok, B. and Busjahn, A. and Avi, L.B. and Bähring, S. and Baron, H. and Heath, S.C. and Uhlmann, R. and Faulhaber, H.D. and Shpitzen, S. and Aydin, A. and Reshef, A. and Rosenthal, M. and Eliav, O. and Muhl, A. and Lowe, A. and Schurr, D. and Harats, D. and Jeschke, E. and Friedlander, Y. and Schuster, H. and Luft, F.C. and Leitersdorf, E.
American Journal of Human Genetics 66
(1): 157-166.
1 January 2000
A mitochondrial ancestry of the hydrogenosomes of Nyctotherus ovalis.
van Hoek, A.H.A.M. and Akhmanova, A.S. and Huynen, M.A. and Hackstein, J.H.P.
Molecular Biology and Evolution 17
(1): 202-206.
1 January 2000
A pathway model of lipid metabolism to predict the effect of genetic variability on lipid levels.
Knoblauch, H. and Schuster, H. and Luft, J.C. and Reich, J.
Journal of Molecular Medicine 78
: 507-515.
1 January 2000
EST comparison indicates 38% of human mRNAs contain possible alternative splice forms.
Brett, D. and Hanke, J. and Lehmann, G. and Haase, S. and Delbrueck, S. and Krueger, S. and Reich, J. and Bork, P.
FEBS Letters 474
(1): 83-86.
1 January 2000
Evolution of domain families.
Ponting, C.P. and Schultz, J. and Copley, R. and Andrade, M.A. and Bork, P.
Advances in Protein Chemistry 54
: 185-244.
1 January 2000
Gene and context: Integrative approaches to genome analysis.
Huynen, M.A. and Snel, B.
Advances in Protein Chemistry 54
: 345-379.
1 January 2000
Genome evolution - gene fusion versus gene fission.
Snel, B. and Bork, P. and Huynen, M.
Trends in Genetics 16
: 9-11.
1 January 2000
HGBASE: a database of SNPs and other variations in and around human genes.
Brookes, A.J. and Lehvaslaiho, H. and Siegfried, M. and Boehm, J.G. and Yuan, Y.P. and Sarkar, C.M. and Bork, P. and Ortigao, F.
Nucleic Acids Research 28
(1): 356-360.
1 January 2000
METATOOL: eine Software zur Analyse und Vorhersage metabolischer Stoffwechselwege.
Moldenhauer, F. and Lange, M. and Hofestaedt, R. and Schuster, S.
In:
Modellierung und Simulation metabolischer Netzwerke : DFG-Workshop im Rahmen des DFG-Schwerpunktes Informatikmethoden zur Analyse und Interpretation großer genomischer Datenmengen ; 19. - 20. Mai 2000 in Magdeburg, Otto-von-Guericke-Universitaet.
Preprint / Otto-von-Guericke-Universitaet Magdeburg, Fakultaet fuer Informatik ; 2000,10
.
Otto-von-Guericke-Univ., Fakultaet fuer Informatik, Magdeburg, 34-38.
1 January 2000
Preface: Protein sequence analysis.
Bork, P.
Advances in Protein Chemistry 54
: xi-xv.
1 January 2000
REF, an evolutionary conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export.
Stutz, F. and Bachi, A. and Doerks, T. and Braun, I.C. and Seraphin, B. and Wilm, P. and Bork, P. and Izaurralde, E.
RNA 6
: 638-638.
1 January 2000
Recent developments in metabolic pathway analysis and their potential implications for biotechnology and medicine.
Schuster, S. and Dandekar, T. and Mauch, K. and Reuss, M. and Fell, D.
In:
Technological and Medical Implications of Metabolic Control Analysis.
Kluwer Acad. Publ., Dordrecht, 57-66.
1 January 2000
SMART: a web-based tool for the study of genetically mobile domains.
Schultz, J. and Copley, R.R. and Doerks, T. and Ponting, C.P. and Bork, P.
Nucleic Acids Research 28
(1): 231-234.
1 January 2000
Structural analysis of metabolic networks: elementary flux modes, analgy to Petri Nets, and application to Mycoplasma pneumoniae.
Schuster, S. and Pfeiffer, T. and Moldenhauer, F. and Koch, I. and Dandekar, T.
In:
German Conference on Bioinformatics 2000 : Proceedings of the German Conference on Bioinformatics, October 5 - 7, 2000, Heidelberg.
Logos-Verl., Berlin, 115-120.
ISBN 3-89722-498-4
1 January 2000
Topological analysis of metabolic networks. Application to the metabolism of Mycoplasma pneumoniae.
Pfeiffer, T. and Dandekar, T. and Moldenhauer, F. and Schuster, S.
In:
Bio Thermo Kinetics. Animating the Cellular Map.
Univ.Press, Stellenbosch, 229-234.
1 January 2000
Comparative genome analysis: exploiting the context of genes to infer evolution and predict function.
Bork, P. and Snel, B. and Lehmann, G. and Suyama, M. and Dandekar, T. and Lathe, W. and Huynen, M.
Computational Biology 1
: 281-294.
2000
Exploitation of gene context to infer evolution and to predict function.
Bork, P. and Snel, B. and Lehmann, G. and Suyama, M. and Dandekar, T. and Lathe, W. and Huynen, M.
In:
Comparative Genomics : Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families.
Computational Biology ; 1
.
Kluwer, Dordrecht, 281-294.
ISBN 0-7923-6583-6 ; 0-7923-6584-4
2000
Individual variation in protein-coding sequences of human genome.
Sunyaev, S. and Hanke, J. and Brett, D. and Aydin, A. and Zastrow, I. and Lathe, W. and Bork, P. and Reich, J.
Advances in Protein Chemistry 54
: 409-437.
2000
Structural analysis of metabolic networks: elementary flux modes, analogy to petri nets, and application to Mycoplasma pneumoniae.
Schuster, S. and Pfeiffer, T. and Moldenhauer, F. and Koch, I. and Dandekar, T.
In:
GCB 2000 : Proceedings of the German Conference on Bioinformatics, October 5 - 7, 2000, Heidelberg.
Logos, Berlin, 115-120.
ISBN 3-89722-498-4
2000
Using time-dependent petri nets for the analysis of metabolic networks.
Heiner, M. and Koch, I. and Schuster, S.
In:
Modellierung und Simulation Metabolischer Netzwerke.
Universitaet Magdeburg, Fakultaet fuer Informatik, Magdeburg, 15-21.
2000
1999
The three-dimensional structure of the HRDC domain and implications for the Werner and Bloom syndrome proteins.
Liu, Z. and Macias, M.J. and Bottomley, M.J. and Stier, G. and Linge, J.P. and Nilges, M. and Bork, P. and Sattler, M.
Structure with Folding & Design 7
: 1557-1566.
15 December 1999
A genetic framework for floral patterning.
Koch, G. and Dandekar, T.
Chemtracts 12
(13): 956-959.
December 1999
RNA-catalysed nucleotide synthesis.
Koch, G. and Dandekar, T.
Chemtracts 12
(13): 938-943.
December 1999
Refined genetic algorithm simulations to model proteins.
Koenig, R. and Dandekar, T.
Journal of Molecular Modeling 5
(12): 317-324.
December 1999
Lateral gene transfer, genome surveys, and the phylogeny of prokaryotes.
Huynen, M.A. and Snel, B. and Bork, P.
Science 286
(5444): 1443a.
19 November 1999
View from the east.
Reich, J.G.
Science 286
(5442): 1087-1087.
5 November 1999
Pore-forming peptides of Entamoeba dispar : similarity and divergence to amoebapores in structure, expression and activity.
Nickel, R. and Ott, C. and Dandekar, T. and Leippe, M.
European Journal of Biochemistry 265
(3): 1002-1007.
1 November 1999
Functional classes in the three domains of life.
Andrade, M.A. and Ouzounis, C. and Sander, C. and Tamames, J. and Valencia, A.
Journal of Molecular Evolution 49
(5): 551-557.
November 1999
Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes.
Sunyaev, S.R. and Hanke, J. and Aydin, A. and Wirkner, U. and Zastrow, I. and Reich, J. and Bork, P.
Journal of Molecular Medicine 77
(11): 754-760.
November 1999
Die genomische Struktur des ATM-Gens und Hinweise auf die Moeglichkeit umfangreicher Deletionen.
Platzer, M. and Wiehe, T. and Rohde, K. and Sandoval, N. and Rosenthal, A.
In:
Ataxia teleangiectatica.
Medizinische Genetik, Muenchen, 17-19.
10 October 1999
Phospholipases A2 and Wnts are unlikely to share a common ancestor.
Copley, R.R. and Ponting, C.P. and Bork, P.
Current Biology 9
: R718-R719.
7 October 1999
Alternative splicing of human genes - more the rule than the exception?
Hanke, J. and Brett, D. and Zastrow, I. and Aydin, A. and Delbrueck, S. and Lehmann, G. and Luft, F.C. and Reich, J. and Bork, P.
Trends in Genetics 15
: 389-390.
1 October 1999
Solution structure of the receptor tyrosine kinase EphB2 SAM domain and identification of two distinct homotypic interaction sites.
Smalla, M. and Schmieder, P. and Kelly, M. and Ter Laak, A. and Krause, G. and Ball, L. and Wahl, M. and Bork, P. and Oschkinat, H.
Protein Science 8
: 1954-1961.
1 October 1999
Prediction of potential GPI-modification sites in proprotein sequences.
Eisenhaber, B. and Bork, P. and Eisenhaber, F.
Journal of Molecular Biology 292
: 741-758.
24 September 1999
Quality-of-life assessment in the old using the WHOQOL 100: differences between patients with senile dementia and patients with cancer.
Struttmann, T. and Fabro, M. and Romieu, G. and de Roquefeuil, G. and Touchon, J. and Dandekar, T. and Ritchie, K.
International Psychogeriatrics 11
: 273-279.
1 September 1999
Mutation of the mouse klotho gene leads to a syndrome resembling ageing. Condensation and commentary.
Sharma, K. and Kelly, L. and Dandekar, T.
Chemtracts 12
(10): 703-707.
September 1999
Domain organization of Mac-2 binding protein and its oligomerization to linear and ring-like structures.
Mueller, S.A. and Sasaki, T. and Bork, P. and Wolpensinger, B. and Schulthess, T. and Timpl, R. and Engel, A. and Engel, J.
Journal of Molecular Biology 291
: 801-813.
27 August 1999
A latrophilin/CL-1-like GPS domain in polycystin-1.
Ponting, C.P. and Hofmann, K. and Bork, P.
Current Biology 9
(16): R585-R588.
26 August 1999
Neutral evolution of mutational robustness.
van Nimwegen, E. and Crutchfield, J.P. and Huynen, M.
Proceedings of the National Academy of Sciences of the United States of America 96
: 9716-9720.
17 August 1999
Variation and evolution of the citric-acid cycle: a genomic perspective.
Huynen, M.A. and Dandekar, T. and Bork, P.
Trends in Microbiology 7
(7): 281-291.
9 July 1999
Characterization of polymorphisms in the promoter of the human angiotensin II subtype 1 (AT1) receptor gene.
Erdmann, J. and Riedel, K. and Rohde, K. and Folgmann, I. and Wienker, T.F. and Fleck, E. and Regitz-Zagrosek, V.
Annals of Human Genetics 63 Part 4
: 369-374.
1 July 1999
Domains in plexins: links to integrins and transcription factors.
Bork, P. and Doerks, T. and Springer, T.A. and Snel, B.
Trends in Biochemical Sciences 24
: 261-263.
1 July 1999
Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries.
Eisenhaber, F. and Bork, P.
Bioinformatics 15
: 528-535.
1 July 1999
Genome comparisons to monitor molecular evolution.
Bork, P. and Dandekar, T. and Snel, B. and Huynen, M.A.
In:
Microbial Evolution and Infection : 50th Congress of the Deutsche Gesellschaft fuer Hygiene und Mikrobiologie (DGHM) and the 25th Annual Meeting of the Deutsche Gesellschaft fuer Infektiologie (DGI).
Einhorn-Presse Verlag, Reinbek, 80-92.
ISBN 3-88756-811-7
1 July 1999
[An approach to the inverse folding problem based on the multiple alignment].
Sunyaev, S.R. and Eisenhaber, F. and Tumanyan, V.G.
Biofizika 44
(4): 620-623.
July 1999
Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer.
Ponting, C.P. and Aravind, L. and Schultz, J. and Bork, P. and Koonin, E.V.
Journal of Molecular Biology 289
: 729-745.
18 June 1999
A novel transactivation domain in parkin.
Morett, E. and Bork, P.
Trends in Biochemical Sciences 24
: 229-231.
1 June 1999
Metabolic pathway analysis: Basic concepts and scientific applications in the post-genomic era.
Schilling, C.H. and Schuster, S. and Palsson, B.O. and Heinrich, R.
Biotechnology Progress 15
(3): 296-303.
1 May 1999
No Sec7-homology domain in guanine-nucleotide-exchange factors that act on Ras and Rho.
Ponting, C.P. and Bork, P. and Schultz, J. and Aravind, L.
Trends in Biochemical Sciences 24
: 177-178.
1 May 1999
PSIC: profile extraction from sequence alignments with position-specific counts of independent observations.
Sunyaev, S.R. and Eisenhaber, F. and Rodchenkov, I.V. and Eisenhaber, B. and Tumanyan, V.G. and Kuznetsov, E.N.
Protein Engineering 12
: 387-394.
1 May 1999
Automated genome sequence analysis and annotation.
Andrade, M.A. and Brown, N.P. and Leroy, C. and Hoersch, S. and de Daruvar, A. and Reich, C. and Franchini, A. and Tamames, J. and Valencia, A. and Ouzounis, C. and Sander, C.
Bioinformatics 15
(5): 391-412.
May 1999
Analyzing the interplay between secondary and tertiary structure predictions in folding simulations with a genetic algorithm.
Dandekar, T. and Du, F.
Journal of Molecular Modeling 5
(4): 78-89.
1 April 1999
Improving genetic algorithms for protein folding simulations by systematic crossover.
Koenig, R. and Dandekar, T.
Biosystems 50
(1): 17-25.
April 1999
Microinjected glutathione reductase crystals as indicators of the redox status in living cells.
Keese, M.A. and Saffrich, R. and Dandekar, T. and Becker, K. and Schirmer, R.H.
FEBS Letters 447
(2-3): 135-138.
26 March 1999
Fine mapping of the antigen-antibody interaction of scFv215, a recombinant antibody inhibiting RNA polymerase II from Drosophila melanogaster.
Liu, Z. and Song, D. and Kramer, A. and Martin, A.C. and Dandekar, T. and Schneider-Mergener, J. and Bautz, E.K. and Duebel, S.
Journal of Molecular Recognition 12
(2): 103-111.
24 March 1999
The mahogany protein is a receptor involved in suppression of obesity.
Nagle, D.L. and McGrail, S.H. and Vitale, J. and Wolf, E.A. and Dussault, B.J. and DiRocco, L. and Holmgren, L. and Montagno, J. and Bork, P. and Huszar, D. and Fairchild-Huntress, V. and Ge, P. and Keilty, J. and Ebeling, C. and Baldini, L. and Gilchrist, J. and Burn, P. and Carlson, G.A. and Moore, K.J.
Nature 398
: 148-152.
11 March 1999
Exploring the metabolic and genetic control of gene expression on a genomic scale.
Koenig, R. and Dandekar, T.
Chemtracts 12
(3): 148-152.
March 1999
Mice lacking bombesin receptor subtype-3 develop metabolic defects and obesity (Condensation and commentary).
Kelly, L. and Sharma, K. and Dandekar, T.
Chemtracts 12
: 223-228.
March 1999
Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering.
Schuster, S. and Dandekar, T. and Fell, D.A.
Trends in Biotechnology 17
(2): 53-60.
1 February 1999
A point of entry into genomics.
Bork, P. and Huynen, M.
Nature Genetics 23
: 273-273.
1 January 1999
Applying logic programming to derive novel functional information of genomes.
Bansal, A. and Bork, P.
In:
Practical Aspects of Declarative Languages : First International Workshop, PADL'99 ; San Antonio, Texas, USA, January 18 - 19, 1999 ; Proceedings.
Lecture Notes in Computer Sciences ; 1551
.
Springer, Berlin [u.a.], 275-289.
ISBN 3-540-65527-1
1 January 1999
Associative database of protein sequences.
Hanke, J. and Lehmann, G. and Bork, P. and Reich, J.
Bioinformatics 15
: 741-748.
1 January 1999
Automatic extraction of biological information from scientific text: protein-protein interactions.
Blaschke, C. and Andrade, M.A. and Ouzounis, C. and Valencia, A.
In:
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB'99) : Heidelberg, Germany, August 6 - 10, 1999.
ISMB Conference Series ; 7
.
AAAI Press, Menlo Park, Calif., 60-67.
ISBN 1-57735-083-9
1 January 1999
Genome phylogeny based on gene content.
Snel, B. and Bork, P. and Huynen, M.A.
Nature Genetics 21
: 108-110.
1 January 1999
METATOOL: for studying metabolic networks.
Pfeiffer, T. and Sanchez-Valdenebro, I. and Nuno, J.C. and Montero, F. and Schuster, S.
Bioinformatics 15
: 251-257.
1 January 1999
Modular control analysis of slipping enzymes.
Schuster, S. and Westerhoff, H.V.
Biosystems 49
: 1-15.
1 January 1999
Pathway alignment: application to the comparative analysis of glycolytic enzymes.
Dandekar, T. and Schuster, S. and Snel, B. and Huynen, M. and Bork, P.
Biochemical Journal 343
: 115-124.
1 January 1999
Position-specific annotation of protein function based on multiple homologs.
Andrade, M.A.
In:
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB'99) : Heidelberg, Germany, August 6 - 10, 1999.
ISMB Conference Series ; 7
.
AAAI Press, Menlo Park, Calif., 28-33.
ISBN 1-57735-083-9
1 January 1999
Protein families in multicellular organisms.
Copley, R.R. and Schultz, J. and Ponting, C.P. and Bork, P.
Current Opinion in Structural Biology 9
: 408-415.
1 January 1999
SMART: identification and annotation of domains from signalling and extracellular protein sequences.
Ponting, C.P. and Schultz, J. and Milpetz, F. and Bork, P.
Nucleic Acids Research 27
(1): 229-232.
1 January 1999
Sequence analysis.
Gibson, T. and Bork, P.
In:
Encyclopedia of Molecular Biology.
Wiley Biotechnology Encyclopedias
.
Wiley, New York [u.a.], 2320-2324.
ISBN 0-471-15302-8
1 January 1999
Studies on the stoichiometric structure of enzymatic reaction systems.
Schuster, S.
Theory in Biosciences 118
: 125-139.
1 January 1999
Use and limitations of modular metabolic control analysis in medicine and biotechnology.
Schuster, S.
Metabolic Engineering 1
: 232-242.
1 January 1999
Altern und Sterben - evolutionsbiologische und soziobiologische Begruendungen.
Dandekar, T.
Praxis der Naturwissenschaften - Biologie 48
: 1-16.
1999
Bioinformatik.
Bork, P.
Biospektrum 5
(3/1999): 172.
1999
1998
Homology-based gene prediction using neural nets.
Cai, Y.D. and Bork, P.
Analytical Biochemistry 265
: 269-274.
15 December 1998
Genomic organization of a 225-kb region in Xq28 containing the gene for X-linked myotubular myopathy (MTM1) and a related gene (MTMR1).
Kioschis, P. and Wiemann, S. and Heiss, N.S. and Francis, F. and Goetz, C. and Poustka, A. and Taudien, S. and Platzer, M. and Wiehe, T. and Beckmann, G. and Weber, J. and Nordsiek, G. and Rosenthal, A.
Genomics 54
: 256-266.
1 December 1998
Identical variant TSG101 transcripts in soft tissue sarcomas and various non-neoplastic tissues.
Willeke, F. and Ridder, R. and Bork, P. and Klaes, R. and Mechtersheimer, G. and Schwarzbach, M. and Zimmer, D. and Kloor, M. and Lehnert, T. and Herfarth, C. and Knebel-Doeberitz, M.
Molecular Carcinogenesis 23
: 195-200.
1 December 1998
Phylogenetic analysis of nucleotide sequences: an algebraic approach.
Schmidt, W.
Mathematical Biosciences 154
: 39-55.
1 December 1998
Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase.
Eisenhaber, B. and Bork, P. and Eisenhaber, F.
Protein Engineering 11
: 1155-1161.
1 December 1998
Verbesserter einschichtiger Biosensor.
Dandekar, T. and Boulin, C.
DE19721698A1.
26 November 1998
A pyrimidine-rich exonic splicing suppressor binds multiple RNA splicing factors and inhibits spliceosome assembly.
Zheng, Z.M. and Huynen, M. and Baker, C.C.
Proceedings of the National Academy of Sciences of the United States of America 95
(24): 14088-14093.
24 November 1998
Predicting function: From genes to genomes and back.
Bork, P. and Dandekar, T. and Diaz-Lazcoz, Y. and Eisenhaber, F. and Huynen, M. and Yuan, Y.P.
Journal of Molecular Biology 283
: 707-725.
6 November 1998
Conservation of gene order: a fingerprint of proteins that physically interact.
Dandekar, T. and Snel, B. and Huynen, M. and Bork, P.
Trends in Biochemical Sciences 23
(9): 324-328.
1 September 1998
Multi-locus nonparametric linkage analysis of complex trait loci with neural networks.
Lucek, P. and Hanke, J. and Reich, J. and Solla, S.A. and Ott, J.
Human Heredity 48
: 275-284.
1 September 1998
Stops genejockeys being taken for a ride.
Eisenhaber, F.
Elsevier.
1 September 1998
Automatic detection of conserved RNA structure elements in complete RNA virus genomes.
Hofacker, I.L. and Fekete, M. and Flamm, C. and Huynen, M.A. and Rauscher, S. and Stolorz, P.E. and Stadler, P.F.
Nucleic Acids Research 26
(16): 3825-3836.
15 August 1998
Evolution of new protein function: recombinational enhancer Fis originated by horizontal gene transfer from the transcriptional regulator NtrC.
Morett, E. and Bork, P.
FEBS Letters 433
: 108-112.
14 August 1998
Measuring genome evolution.
Huynen, M.A. and Bork, P.
Proceedings of the National Academy of Sciences of the United States of America 95
(11): 5849-5856.
26 May 1998
SMART, a simple modular architecture research tool: Identification of signaling domains.
Schultz, J. and Milpetz, F. and Bork, P. and Ponting, C.P.
Proceedings of the National Academy of Sciences of the United States of America 95
(11): 5857-5864.
26 May 1998
Differential gene expression in mammary carcinoma cell lines: identification of DRIM, a new gene down-regulated in metastasis.
Schwirzke, M. and Gnirke, A. and Bork, P. and Tarin, D. and Weidle, U.H.
Anticancer Research 18
: 1409-1421.
1 May 1998
Nibrin, a novel DNA double-strand break repair protein, is mutated in Nijmegen breakage syndrome.
Varon, R. and Vissinga, C. and Platzer, M. and Cerosaletti, K.M. and Chrzanowska, K.H. and Saar, K. and Beckmann, G. and Seemanova, E. and Cooper, P.R. and Nowak, N.J. and Stumm, M. and Weemaes, C.M.R. and Gatti, R.A. and Wilson, R.K. and Digweed, M. and Rosenthal, A. and Sperling, K. and Concannon, P. and Reis, A.
Cell 93
(3): 467-476.
1 May 1998
The frequency distribution of gene family sizes in complete genomes.
Huynen, M.A. and van Nimwegen, E.
Molecular Biology and Evolution 15
(5): 583-589.
1 May 1998
Processing of the precursors to small nucleolar RNAs and rRNAs requires common components.
Petfalski, E. and Dandekar, T. and Henry, Y. and Tollervey, D.
Molecular and Cellular Biology 18
(3): 1181-1189.
March 1998
Characterization of targeting domains by sequence analysis: glycogen-binding domains in protein phosphatases.
Bork, P. and Dandekar, T. and Eisenhaber, F. and Huynen, M.
Journal of Molecular Medicine 76
: 77-79.
1 February 1998
Are knowledge-based potentials derived from protein structure sets discriminative with respect to amino acid types?
Sunyaev, S.R. and Eisenhaber, F. and Argos, P. and Kuznetsov, E.N. and Tumanyan, V.G.
Proteins: Structure, Function, and Bioinformatics 31
: 225-246.
1 January 1998
Characterization of naturally occurring myosin heavy chain antisense mRNA in rat heart.
Luther, H.P. and Haase, H. and Hohaus, A. and Beckmann, G. and Reich, J. and Morano, I.
Journal of Cellular Biochemistry 70
: 110-120.
1 January 1998
Conformational stability studies of the pleckstrin DEP domain: definition of the domain boundaries.
Kharrat, A. and Millevoi, S. and Baraldi, E. and Ponting, C.P. and Bork, P. and Pastore, A.
Biochimica et Biophysica Acta 1385
: 157-164.
1 January 1998
Control analysis of metabolic systems involving quasi- equilibrium reactions.
Kholodenko, B.N. and Schuster, S. and Garcia, J. and Westerhoff, H.V. and Cascante, M.
Biochimica et Biophysica Acta 1379
: 337-352.
1 January 1998
Determination of the fold of the core protein of Hepatitis B virus by electron cryomicroscopy.
Dandekar, T. and Argos, P.
Chemtracts 11
: 161-165.
1 January 1998
Differential genome analysis applied to the species-specific features of Helicobacter pylori.
Huynen, M. and Dandekar, T. and Bork, P.
FEBS Letters 426
: 1-5.
1 January 1998
Ein graphentheoretischer Ansatz zum paarweisen und multiplen Vergleich von Proteinstrukturen.
Koch, I.
Wissenschaft und Technik, Berlin.
ISBN 3-89685-446-1
1 January 1998
Elementary modes analysis ilustrated with human red cell metabolism.
Schuster, S. and Fell, D.A. and Pfeiffer, T. and Dandekar, T. and Bork, P.
In:
Bio Thermokinetics in the Post Genomic Era.
Chalmers, Goeteborg, 332-339.
1 January 1998
Frame: detection of genomic sequencing errors.
Brown, N.P. and Sander, C. and Bork, P.
Bioinformatics 14
: 367-371.
1 January 1998
Homology-based fold predictions for Mycoplasma genitalium proteins.
Huynen, M. and Doerks, T. and Eisenhaber, F. and Orengo, C. and Sunyaev, S.R. and Yuan, Y.P. and Bork, P.
Journal of Molecular Biology 280
: 323-326.
1 January 1998
Influence of calcium binding to proteins on calcium oscillation. A mathematical model.
Schuster, S. and Marhl, M. and Brumen, M. and Heinrich, R.
In:
Information Processing in Cells and Tissues.
Plenum Press, New York, 137-150.
1 January 1998
Mammalian protein homologous to VAT-1 of torpedo californica: isolation from Ehrlich Ascites Tumor cells, biochemical characterization and organization of its gene.
Hayess, K. and Kraft, R. and Sachsinger, J. and Janke, J. and Jandrig, B. and Beckmann, G. and Rohde, K. and Benndorf, R.
Journal of Cellular Biochemistry 69
: 304-315.
1 January 1998
Merging extracellular domains: Fold prediction for laminin G- like and amino-terminal thrombospondin-like modules based on homology to pentraxins.
Beckmann, G. and Hanke, J. and Bork, P. and Reich, J.
Journal of Molecular Biology 275
: 725-730.
1 January 1998
Mitochondria as an important factor in the maintenance of constant amplitudes of cytosolic calcium oscillations.
Marhl, M. and Schuster, S. and Brumen, M.
Biophysical Chemistry 71
: 125-132.
1 January 1998
Modelling oscillations of calcium and endoplasmic reticulum transmembrane potential role of the signalling and buffering proteins and of the size of the Ca2+ sequestering ER subcompartments.
Marhl, M. and Schuster, S. and Brumen, M. and Heinrich, R.
Bioelectrochemistry and Bioenergetics 46
: 79-90.
1 January 1998
Modelling the interrelation between the transmembrane potential and pH difference across membranes with electrogenic proton transport upon build-up of the proton-motive force.
Schuster, S. and Ouhabi, R. and Rigoulet, M. and Mazat, J.P.
Bioelectrochemistry and Bioenergetics 45
: 181-192.
1 January 1998
Predicting functions from protein sequences - where are the bottlenecks?
Bork, P. and Koonin, E.V.
Nature Genetics 18
: 313-318.
1 January 1998
Protein annotation: detective work for function prediction.
Doerks, T. and Bairoch, A. and Bork, P.
Trends in Genetics 14
: 248-250.
1 January 1998
Questions about RNA secondary structures in HIV and HPV.
Huynen, M.A. and Konings, D.A.M.
In:
Viral Regulatory Structures and their Degeneracy.
Addison Wesley Longman, Massachusetts, 143-162.
1 January 1998
Regulatory RNA.
Dandekar, T. and Sharma, K.
Springer, Heidelberg.
ISBN 3-540-64343-5
1 January 1998
Sequences and topology deriving biological knowledge from genomic sequences.
Bork, P. and Eisenberg, D.
Current Opinion in Structural Biology 8
: 331-332.
1 January 1998
Structural basis for the binding of a globular antifreeze to ice.
Dandekar, T. and Argos, P.
Chemtracts 11
: 229-232.
1 January 1998
Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches.
Dandekar, T. and Beyer, K. and Bork, P. and Kenealy, M.R. and Pantopoulos, K. and Hentze, M. and Sonntag-Buck, V. and Flouriot, G. and Gannon, F. and Keller, W. and Schreiber, S.
Bioinformatics 14
: 271-278.
1 January 1998
The modelling of metabolic systems. Structure, control and optimality.
Heinrich, R. and Schuster, S.
Biosystems 47
: 61-77.
1 January 1998
Towards detection of orthologues in sequence databases.
Yuan, Y.P. and Eulenstein, O. and Vingron, M. and Bork, P.
Bioinformatics 14
: 285-289.
1 January 1998
Wanted: subcellular localization of proteins based on sequence.
Eisenhaber, F. and Bork, P.
Trends in Cell Biology 8
: 169-170.
1 January 1998
Isolation and molecular characterization of a surface-bound proteinase of Entamoeba histolytica.
Jacobs, T. and Bruchhaus, I. and Dandekar, T. and Tannich, E. and Leippe, M.
Molecular Microbiology 27
(2): 269-276.
January 1998
Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families.
Andrade, M.A. and Valencia, A.
Bioinformatics 14
(7): 600-607.
1998
Sequence and structure of proteins.
Eisenhaber, F. and Bork, P.
In:
On Recombinant Proteins, Monoclonal Antibodies and Therapeutic Genes.
Biotechnology ; 5
.
Wiley-VCH, Weinheim, 43-86.
1998
1997
Computational methods for the prediction of protein folds.
Dandekar, T. and Koenig, R.
Biochimica et Biophysica Acta 1343
: 1-15.
14 November 1997
Gene families: the taxonomy of protein paralogs and chimeras.
Henikoff, S. and Greene, E.A. and Pietrokovski, S. and Bork, P. and Attwood, T.K. and Hood, L.
Science 278
(5338): 609-614.
24 October 1997
Probabilistic evaluation of similarity between pairs of three-dimensional protein structures utilizing temperature factors.
Carugo, O. and Eisenhaber, F.
Journal of Applied Crystallography 30
(5/1): 547-549.
1 October 1997
Refined mapping of the epilepsy susceptibility locus EJM1 on chromosome 6.
Sander, T. and Bockenkamp, B. and Hildmann, T. and Blasczyk, R. and Kretz, R. and Wienker, T.F. and Volz, A. and Schmitz, B. and Beckmannagetta, G. and Riess, O. and Epplen, J.T. and Janz, D. and Ziegler, A.
Neurology 49
(3): 842-847.
1 September 1997
Localization of the gene causing keratolytic winter erythema to chromosome 8p22-p23, and evidence for a founder effect in south african afrikaans-speakers.
Starfield, M. and Hennies, H.C. and Jung, M. and Jenkins, T. and Wienker, T.F. and Hull, P. and Spurdle, A. and Kuester, W. and Ramsay, M. and Reis, A.
American Journal of Human Genetics 61
(2): 370-378.
August 1997
A novel class of RanGTP binding proteins.
Goerlich, D. and Dabrowski, M. and Bischoff, F.R. and Kutay, U. and Bork, P. and Hartmann, E. and Prehn, S. and Izaurralde, E.
Journal of Cell Biology 138
(1): 65-80.
14 July 1997
A genome wide search for susceptibility loci in three european malignant hyperthermia pedigrees.
Robinson, R.I. and Monnier, N. and Wolz, W. and Jung, M. and Reis, A. and Nuernberg, G. and Curran, J.L. and Monsieurs, K. and Stieglitz, P. and Heytens, L. and Fricker, R. and Vanbroeckhoven, C. and Deufel, T. and Hopkins, P.M. and Lunardi, J. and Mueller, C.R.
Human Molecular Genetics 6
(6): 953-961.
June 1997
The gene for the ataxia telangiectasia variant, nijmegen breakage syndrome, maps to a 1 cm interval on chromosome 8q21.
Saar, K. and Chrzanowska, K.H. and Stumm, M. and Jung, M. and Nuernberg, G. and Wienker, T.F. and Seemanova, E. and Wegner, R.D. and Reis, A. and Sperling, K.
American Journal of Human Genetics 60
(3): 605-610.
March 1997
Strong indication for a breast cancer susceptibility gene on chromosome 8p12-p22: linkage analysis in german breast cancer families.
Seitz, S. and Rohde, K. and Bender, E. and Nothnagel, A. and Koelble, K. and Schlag, P.M. and Scherneck, S.
Oncogene 14
(6): 741-743.
13 February 1997
A putative nucleic acid-binding domain in Werner's and Bloom's syndrome helicases.
Morozov, V. and Mushegian, A.R. and Koonin, E.V. and Bork, P.
Trends in Biochemical Sciences 22
: 417-418.
1 January 1997
A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins.
Bork, P. and Hofmann, K. and Bucher, P. and Neuwald, A. and Altschul, S.F. and Koonin, E.V.
FASEB Journal 11
(1): 68-76.
1 January 1997
Allelic association of juvenile absence epilepsy with a glur5 kainate receptor gene (grik1) polymorphism.
Sander, T. and Hildmann, T. and Kretz, R. and Fuerst, R. and Sailer, U. and Bauer, G. and Schmitz, B. and Beck-Mannagetta, G. and Wienker, T.F. and Janz, D.
American Journal of Medical Genetics 74
: 416-421.
1 January 1997
Analysis of genetic linkage and somatic loss of heterozygosity in affected pairs of first-degree relatives.
Rohde, K. and Teare, M.D. and Koref, M.S.
American Journal of Human Genetics 61
: 418-422.
1 January 1997
Applying experimental data to protein fold prediction with the genetic algorithm.
Dandekar, T. and Argos, P.
Protein Engineering 10
: 877-893.
1 January 1997
Artificial neural network method for predicting the specificity of GalNAc-transferase.
Cai, Y.D. and Yu, H. and Chou, K.C.
Journal of Protein Chemistry 16
: 689-700.
1 January 1997
Assessing the reliability of RNA folding using statistical mechanics.
Huynen, M.A. and Guttel, R. and Konings, D.A.M.
Journal of Molecular Biology 267
: 1104-1112.
1 January 1997
BRCA1 mutations and phenotype.
Grade, K. and Hoeffken, K. and Kath, R. and Nothnagel, A. and Bender, E. and Scherneck, S.
Journal of Cancer Research and Clinical Oncology 123
: 69-70.
1 January 1997
Bioinformatics and molecular medicine: introduction and call for papers.
Bork, P.
Journal of Molecular Medicine 75
: 3-4.
1 January 1997
Comparative genome analysis: From sequences to functions.
Bork, P.
Developments in Industrial Microbiology 34
: 21-23.
1 January 1997
Cytoplasmic signalling domains: the next generation.
Bork, P. and Schultz, J. and Ponting, C.P.
Trends in Biochemical Sciences 22
: 296-298.
1 January 1997
Deletion at 12p in a japanese child with brachydactyly overlaps the assigned locus of brachydactyly with hypertension in a turkish family.
Bähring, S. and Nagai, T. and Toka, H.R. and Nitz, I. and Toka, O. and Aydin, A. and Muhl, A. and Wienker, T.F. and Schuster, H. and Luft, F.C.
American Journal of Human Genetics 60
: 732-735.
1 January 1997
Deletion mapping and linkage analysis provide strong indication for the involvement of the human chromosome region 8p12-p22 in breast carcinogenesis.
Seitz, S. and Rohde, K. and Bender, E. and Nothnagel, A. and Pidde, H. and Ullrich, O.M. and El-Zehairy, A. and Haensch, W. and Jandrig, B. and Koelble, K. and Schlag, P.M. and Scherneck, S.
British Journal of Cancer 76
: 983-991.
1 January 1997
Differential genome display.
Huynen, M.A. and Diaz-Lazcoz, Y. and Bork, P.
Trends in Genetics 13
: 389-390.
1 January 1997
Ein graphentheoretischer Ansatz zum paarweisen und multiplen Vergleich von Proteinstrukturen.
Koch, I.
UNSPECIFIED thesis, UNSPECIFIED.
1 January 1997
Evidence of two components of repair of radiation damage in pig skin: Analysis of quantal response data based on a compartmental dose-response model.
Schmidt, W.
In:
Modelling in Clinical Radiobiology.
Albert-Ludwigs-University Freiburg, Freiburg, 92-102.
1 January 1997
Free radicals and memory loss.
Dandekar, T.
Redox Report 3
: 71-73.
1 January 1997
Genome maps 8. Building gene families. Wall chart.
Greene, E.A. and Pietrokovski, S. and Henikoff, S. and Bork, P. and Attwood, T.K. and Hood, L. and Bairoch, A.
Science 278
: 615-626.
1 January 1997
Improving protein structure prediction by new strategies: experimental insights and the genetic algorithm.
Dandekar, T.
Journal of Molecular Modeling 3
: 312-314.
1 January 1997
Localisation of a gene for Papillon-Lefevre syndrome to chromosome 11q14-q21 by homozygosity mapping.
Laass, M.W. and Hennies, H.C. and Preis, S. and Stevens, H.P. and Jung, M. and Leigh, I.M. and Wienker, T.F. and Reis, A.
Human Genetics 101
: 376-382.
1 January 1997
Localization of the gene for Wieacker Wolff syndrome in the pericentromeric region of the X chromosome.
Kloos, D.U. and Jakubiczka, S. and Wienker, T.F. and Wolff, G. and Wieacker, P.
Human Genetics 100
: 426-430.
1 January 1997
Molecular modeling of amoebapore and nk lysin: a four-alpha-helix bundle motif of cytolytic peptides from distantly related organisms.
Dandekar, T. and Leippe, M.
Folding & Design 2
: 47-52.
1 January 1997
Neurovascular compression at the ventrolateral medulla in autosomal dominant hypertension and brachydactyly.
Naraghi, R. and Schuster, H. and Toka, H.R. and Bähring, S. and Toka, O. and Oeztekin, O. and Bilginturan, N. and Knoblauch, H. and Wienker, T.F. and Busjahn, A. and Haller, H. and Fahlbusch, R. and Luft, F.C.
Stroke 28
: 1749-1754.
1 January 1997
On the classification and evolution of protein modules.
Hegyi, H. and Bork, P.
Journal of Protein Chemistry 16
: 545-551.
1 January 1997
Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs.
Mushegian, A.R. and Bassett, D.E. and Boguski, M.S. and Bork, P. and Koonin, E.V.
Proceedings of the National Academy of Sciences of the United States of America 94
: 5831-5836.
1 January 1997
Probing Flp: a new approach to analyze the structure of a DNA recognizing protein by combining the genetic algorithm, mutagenesis and non-canonical DNA target sites.
Saxena, P. and Whang, I. and Voziyanov, Y. and Harkey, C. and Argos, P. and Jayaram, M. and Dandekar, T.
Biochimica et Biophysica Acta 1340
: 187-204.
1 January 1997
RNA ligands selected by cleavage stimulation factor (CstF) contain distinct sequence motifs that function as downstream elements in 3' end processing of pre-mRNA.
Beyer, K. and Dandekar, T. and Keller, W.
Journal of Biological Chemistry 272
: 26769-26779.
1 January 1997
Relationship of polymorphisms in the renin angiotensin system and in e selectin of patients with early severe coronary heart disease.
Wenzel, K. and Blackburn, A. and Ernst, M. and Affeldt, M. and Hanke, R. and Baumann, G. and Felix, S.B. and Kleber, F.X. and Rohde, K. and Glaser, C. and Speer, A.
Journal of Molecular Medicine 75
: 57-61.
1 January 1997
SAM as a protein interaction domain involved in developmental regulation.
Schultz, J. and Ponting, C. and Hofmann, K. and Bork, P.
Protein Science 6
: 249-253.
1 January 1997
SPRY domains in ryanodine receptors (Ca2+ release channels).
Ponting, C. and Schultz, J. and Bork, P.
Trends in Biochemical Sciences 22
: 193-194.
1 January 1997
Secreted fringe like signaling molecules may be glycosyltransferases.
Yuan, Y.P. and Schultz, J. and Mlodzik, M. and Bork, P.
Cell 88
: 9-11.
1 January 1997
The breast cancer gene product TSG101: a regulator of ubiquitination?
Ponting, C.P. and Cai, Y.D. and Bork, P.
Journal of Molecular Medicine 75
: 467-469.
1 January 1997
The sequence alerting server-a new WEB server.
Hegyi, H. and Lai, J. and Bork, P.
Computer Applications in the Biosciences 13
: 619-620.
1 January 1997
Use of a modified binding model for the investigation of affinity dependence on antibody concentration in immunoassay systems.
Strohner, P. and Sarrach, D. and Reich, J.
Journal of Immunological Methods 203
: 113-122.
1 January 1997
1996
Linkage of the gene for the triple a syndrome to chromosome 12q13 near the type II keratin gene cluster.
Weber, A. and Wienker, T.F. and Jung, M. and Easton, D. and Dean, H.J. and Heinrichs, C. and Reis, A. and Clark, A.J.L.
Human Molecular Genetics 5
(12): 2061-2066.
1 December 1996
BRCA1 protein products ... Functional motifs...
Koonin, E.V. and Altschul, S.F. and Bork, P.
Nature Genetics 13
(3): 266-268.
1 July 1996
Structure and distribution of modules in extracellular proteins.
Bork, P. and Downing, A.K. and Kieffer, B. and Campbell, I.D.
Quaterly Reviews of Biophysics 29
(2): 119-167.
1 May 1996
A distance measure based on binary character data and its application to phylogeny reconstruction.
Schmidt, W. and Mueller, E.C.
Bulletin of Mathematical Biology 58
: 449-469.
1 January 1996
Ancient duplication of dna polymerase inferred from analysis of complete bacterial genomes.
Koonin, E.V. and Bork, P.
Trends in Biochemical Sciences 21
(4): 128-129.
1 January 1996
Angiotensin converting enzyme and heart chymase gene polymorphisms in hypertrophic cardiomyopathy.
Pfeufer, A. and Osterziel, K.J. and Urata, H. and Borck, G. and Schuster, H. and Wienker, T.F. and Dietz, R. and Luft, F.C.
American Journal of Cardiology 78
: 362-364.
1 January 1996
Applying motif and profile searches.
Bork, P. and Gibson, T.
Methods in Enzymology 266
: 162-184.
1 January 1996
Autosomal dominant hypertension and brachydactyly in a turkish kindred resembles essential hypertension.
Schuster, H. and Wienker, T.F. and Toka, H.R. and Bähring, S. and Jeschke, E. and Toka, O. and Busjahn, A. and Hempel, A. and Tahlhammer, C. and Oelkers, W. and Kunze, J. and Bilginturan, N. and Haller, H. and Luft, F.C.
Hypertension 28
: 1085-1092.
1 January 1996
BRCA1 mutations in German breast-cancer families.
Jandrig, B. and Grade, K. and Seitz, S. and Waindzoch, B. and Mueller, M. and Bender, E. and Nothnagel, A. and Rohde, K. and Schlag, P.M. and Kath, R. and Hoeffken, K. and Scherneck, S.
International Journal of Cancer 68
: 188-192.
1 January 1996
Bioinformatik: Proteinsequenzen und Sekundaerstruktur-Vorhersagen.
Rohde, K.
In:
Methoden in der Proteinanalytik.
Springer, Berlin, 311-333.
1 January 1996
Common subtypes of idiopathic generalized epilepsies: lack of linkage to d20s19 close to candidate loci (ebn1, eegv1) on chromosome 20.
Sander, T. and Hildmann, T. and Wienker, T.F. and Ramel, C. and Beckmannagetta, G. and Bianchi, A. and Sailer, U. and Berek, K. and Bauer, G. and Neitzel, H. and Schmitz, B. and Durner, M. and Johnson, K.J. and Janz, D.
American Journal of Medical Genetics 67
(1): 31-39.
1 January 1996
Comparison of CD45 extracellular domain sequences from divergent vertebate species suggests the conservation of three fibronectin type III domains.
Okumura, M. and Matthew, R.J. and Robb, B. and Litmann, G.W. and Bork, P. and Thomas, M.L.
Journal of Immunology 157
: 1569-1575.
1 January 1996
DNA polymorphisms in adhesion molecule genes: a new risk factor for early atherosclerosis.
Wenzel, K. and Ernst, M. and Rohde, K. and Baumann, G. and Speer, A.
Human Genetics 97
(1): 15-20.
1 January 1996
Exclusion of linkage between idiopathic generalized epilepsies and the GABAA receptor alpha1 and gamma2 subunit gene cluster on chromosome 5.
Sander, T. and Hildmann, T. and Janz, D. and Wienker, T.F. and Bianchi, A. and Bauer, G. and Sailer, U. and Scaramelli, A. and Neitzel, H. and Schmitz, B. and Bailey, M.E.S. and Beckmannagetta, G. and Johnson, K.J. and Darlison, M.G.
Epilepsy Research 23
(3): 235-244.
1 January 1996
Exon shuffling and other ways of module exchange: comment.
Bork, P.
Matrix Biology 15
: 311-312.
1 January 1996
Friedreich's ataxia protein: phylogenetic evidence for mitochondrial dysfunction.
Gibson, T. and Koonin, E.V. and Musco, G. and Pastore, A. and Bork, P.
Trends in Neurosciences 19
: 465-468.
1 January 1996
Glycoprotein mediated cell binding of lectin coated liposomes.
Schaefer, H. and Stahn, R. and Schreiber, J. and Schmidt, W.
Journal of Liposome Research 6
: 479-496.
1 January 1996
Go hunting in sequence databases but watch out for the traps.
Bork, P. and Bairoch, A.
Trends in Genetics 12
: 425-427.
1 January 1996
Identification and mutation analysis of the complete gene for the Chediak-Higashi syndrome.
Nagle, D.L. and Karim, M. and Woolf, E.A. and Holmgren, L. and Bork, P. and Misumi, D. and McGrail, D. and Dussault, J.R. and Duyk, G. and Spritz, R.A. and Moore, K.J.
Nature Genetics 14
: 307-312.
1 January 1996
Identification of residues within the shc phosphotyrosine binding phosphotyrosine interaction domain crucial for phosphopeptide interaction.
Yajnik, V. and Blaikie, P. and Bork, P. and Margolis, B.
Journal of Biological Chemistry 271
(4): 1813-1816.
1 January 1996
Internal repeats in the BRCA2 protein sequence.
Bork, P. and Blomberg, N. and Nilges, M.
Nature Genetics 13
: 22-23.
1 January 1996
Kohonen map as visualization tool for the analysis of protein sequences: multiple alignments, domains and segments of secondary structures.
Hanke, J. and Reich, J.
Computer Applications in the Biosciences 12
: 447-454.
1 January 1996
Metabolism and evolution of Haemophilus influenzae deduced from a whole genome comparison with Escherichia coli.
Tatusov, R.L. and Mushegian, A.R. and Bork, P. and Brown, N.P. and Hayes, W.S. and Borodovsky, M. and Rudd, K.E. and Koonin, E.V.
Current Biology 6
(3): 279-291.
1 January 1996
Non-orthologous gene displacement.
Koonin, E.V. and Mushegian, A.R. and Bork, P.
Trends in Genetics 12
: 334-336.
1 January 1996
On the classification of modular proteins.
Henrissat, B. and Bork, P.
Protein Engineering 9
: 725-726.
1 January 1996
Pleckstrin's repeat performance: a novel domain in g protein signaling.
Ponting, C.P. and Bork, P.
Trends in Biochemical Sciences 21
: 245-246.
1 January 1996
Protein sequence motifs.
Bork, P. and Koonin, E.V.
Current Opinion in Structural Biology 6
: 366-376.
1 January 1996
Role of T cell receptor delta gene in susceptibility to celiac disease.
Roschmann, E. and Wienker, T.F. and Volk, B.A.
Journal of Molecular Medicine 74
(2): 93-98.
1 January 1996
Self-organizing hierarchic networks for pattern recognition in protein sequence.
Hanke, J. and Beckmann, G. and Bork, P. and Reich, J.
Protein Science 5
: 72-82.
1 January 1996
Severe autosomal dominant hypertension and brachydactyly in a unique turkish kindred maps to human chromosome 12.
Schuster, H. and Wienker, T.F. and Bähring, S. and Bilginturan, N. and Toka, H.R. and Neitzel, H. and Jeschke, E. and Toka, O. and Gilbert, D. and Lowe, A. and Ott, J. and Haller, H. and Luft, F.C.
Nature Genetics 13
(1): 98-100.
1 January 1996
Sperm-egg binding protein or proto-oncogene?
Bork, P.
Science 271
(5254): 1431-1432.
1 January 1996
Structural motifs of the pkd1 protein.
Lohning, C. and Pohlschmidt, M. and Glucksmannkuis, M.A. and Duyk, G. and Bork, P. and Schneider, M.O. and Reeders, S.T. and Frischauf, A.M.
Nephrology Dialysis Transplantation 11 Suppl.
: 2-4.
1 January 1996
The protein phosphatase 2C (PP2C) superfamily: detection of bacterial homologues.
Bork, P. and Brown, N.P. and Hegyi, H. and Schultz, J.
Protein Science 5
: 1421-1425.
1 January 1996
Von Genomsequenzen zu Proteinfunktionen.
Bork, P.
Informationstechnik und technische Informatik 5
: 20-26.
1 January 1996
1995
Heat repeats in Huntington's disease protein.
Andrade, M.A. and Bork, P.
Nature Genetics 11
(2): 115-116.
1 October 1995
Polycystic kidney disease: the complete structure of the PKD1 gene and its protein.
Gluecksmann-Kuis, M.A. and Tayber, O. and Woolf, E.A. and Bougueleret, L. and Deng, N.H. and Alperin, G.D. and Iris, F. and Hawkins, F. and Munro, C. and Lakey, N. and Duyk, G. and Schneider, M.C. and Geng, L. and Zhang, F. and Zhao, Z.H. and Torosian, S. and Zhou, J. and Reeders, S.T. and Bork, P. and Pohlschmidt, M. and Lohning, C. and Kraus, B. and Nowicka, U. and Leung, A.L.S. and Frischauf, A.M.
Cell 81
(2): 289-298.
21 April 1995
A comment on "Can measurement of potential doubling time (TPOT) be compared between laboratories ? A quality control study".
Schmidt, W.
Cytometry 21
: 218-219.
1 January 1995
A phosphotyrosine interaction domain.
Bork, P. and Margolis, B.
Cell 80
(5): 693-694.
1 January 1995
A program using loss-of-constitutional- heterozygosity data to ascertain the location of predisposing genes in cancer families.
Rohde, K. and Teare, M.D. and Scherneck, S. and Santibanez-Koref, M.F.
Human Heredity 45
: 337-345.
1 January 1995
An angiotensin-converting enzyme gene variant is associated with acute myocardial infarction in women but not in men.
Schuster, H. and Wienker, T.F. and Stremmler, U. and Noll, B. and Steinmetz, A. and Luft, F.C.
American Journal of Cardiology 76
(8): 601-603.
1 January 1995
Analysis of marker genes contributing to coeliac disease susceptibility.
Roschmann, E. and Wienker, T.F. and Gerok, W. and Volk, A.
Advances in Experimental Medicine and Biology 371 B
: 1339-1343.
1 January 1995
Challenging times for bioinformatics.
Casari, G. and Andrade, M.A. and Bork, P. and Daruvar, A. and Ouzounis, C. and Schneider, R. and Tamames, J. and Valencia, A. and Sander, C.
Nature 376
: 647-648.
1 January 1995
Characterization of a novel protein-binding module - the WW domain.
Sudol, M. and Chen, H.I. and Bourgeret, C. and Einbond, A. and Bork, P.
FEBS Letters 369
(1): 67-71.
1 January 1995
Characterization of the mammalian YAP (Yes-associated protein) gene and its role in defining a novel module - the WW domain.
Sudol, M. and Bork, P. and Einbond, A. and Kastury, K. and Druck, T. and Negrini, M. and Huebner, K. and Lehman, D.
Journal of Biological Chemistry 270
: 14733-14741.
1 January 1995
Divergent evolution of a beta/alpha-barrel subclass: detection of numerous phosphate-binding sites by motif search.
Bork, P. and Gellerich, J. and Groth, H. and Hooft, R. and Martin, F.
Protein Science 4
: 268-274.
1 January 1995
Exploring the Mycoplasma capricolum genome: a small bacterium reveals its physiology.
Bork, P. and Ouzounis, C. and Casari, G. and Schneider, R. and Sander, C. and Dolan, M. and Gilbert, W. and Gillevet, P.M.
Molecular Microbiology 16
: 955-967.
1 January 1995
Klonierung des Brustkrebsgens BRCA1. Stellungnahme erarbeitet durch eine adhoc-Gruppe im Rahmen des "Gesamtprogramms zur Krebsbekaempfung".
Chang-Claude, J. and Hundsdoerfer, G. and Jonat, W. and Scherneck, S. and Wienker, T.F.
Frauenarzt 36
(5): 572-574.
1 January 1995
More WW domains.
Bork, P. and Sudol, M.
Trends in Biochemical Sciences 20
: 54-54.
1 January 1995
New protein functions in yeast chromosome VIII.
Ouzounis, C. and Bork, P. and Casari, G. and Sander, C.
Protein Science 4
(11): 2424-2428.
1 January 1995
Phylogeny reconstruction for protein sequences based on amino acid properties.
Schmidt, W.
Journal of Molecular Evolution 41
(4): 522-530.
1 January 1995
Ready for a motif submission? A proposed checklist.
Bork, P. and Ouzounis, C. and McEntyre, J.
Trends in Biochemical Sciences 20
(3): 104-104.
1 January 1995
Refinement of map position of the human GluR6 kainate receptor gene (GRIK2) and lack of association and linkage with idiopathic generalized epilepsies.
Sander, T. and Janz, D. and Ramel, C. and Ross, C.A. and Paschen, W. and Hildmann, T. and Wienker, T.F. and Bianchi, A. and Bauer, G. and Sailer, U. and Berek, K. and Neitzel, H. and Volz, A. and Ziegler, A. and Schmitz, B. and Beckmannagetta, G.
Neurology 45
(9): 1713-1720.
1 January 1995
The Functional Composition of Living Mashines.
Ouzounis, C. and Valencia, A. and Tamames, J. and Bork, P. and Sander, C.
In:
Advances in Artificial Life.
Lecture Notes in Artificial Intelligence Series ; 929
.
Springer, Berlin, Heidelberg, 843-852.
1 January 1995
The SEA module - a new extracellular domain associated with o-glycosylation.
Bork, P. and Patthy, L.
Protein Science 4
(7): 1421-1425.
1 January 1995
The cytidylyltransferase superfamily: identification of the nucleotide-binding site and fold prediction.
Bork, P. and Holm, L. and Koonin, E.V. and Sander, C.
Proteins: Structure, Function, and Genetics 22
(3): 259-266.
1 January 1995
The phenotypic spectrum related to the human epilepsy susceptibility gene ejm1.
Sander, T. and Hildmann, T. and Janz, D. and Wienker, T.F. and Neitzel, H. and Bianchi, A. and Bauer, G. and Sailer, U. and Berek, K. and Schmitz, B. and Beckmannagetta, G.
Annals of Neurology 38
(2): 210-217.
1 January 1995
Treasure your exceptions: what we can learn from autosomal-dominant inherited forms of hypertension.
Luft, F.C. and Schuster, H. and Bilginturan, N. and Wienker, T.F.
Journal of Hypertension 13
(12): 1535-1538.
1 January 1995
Variants of the angiotensin converting enzyme gene are associated with high blood pressure and myocardial infarction.
Schuster, H. and Wienker, T.F. and Luft, F.C.
In:
Atherosclerosis X; 10th International Symposium, Montreal, Quebec, Canada, October 9-14, 1994.
International Congress Series ; 1066
.
Elsevier Science Publ., Amsterdam, 862-864.
1 January 1995
1994
The WW domain: a signalling site in dystrophin.
Bork, P. and Sudol, M.
Trends in Biochemical Sciences 19
(12): 531-533.
1 December 1994
E-selectin polymorphism and atherosclerosis: an association study.
Wenzel, K. and Felix, S. and Kleber, F.X. and Brachold, R. and Menke, T. and Schattke, S. and Schulte, K.L. and Glaser, C. and Rohde, K. and Baumann, G.
Human Molecular Genetics 3
(11): 1935-1937.
1 November 1994
A novel RNA-binding motif in omnipotent suppressors of translation termination, ribosomal proteins and a ribosome modification enzyme?
Koonin, E. and Bork, P. and Sander, C.
Nucleic Acids Research 22
(11): 2166-2167.
11 June 1994
Detection of a major gene for heterocellular hereditary persistence of fetal hemoglobin after accounting for genetic modifiers.
Thein, S.L. and Sampietro, M. and Rohde, K. and Rochette, J. and Weatherall, D.J. and Lathrop, G.M. and Demenais, F.
American Journal of Human Genetics 54
(2): 214-228.
February 1994
A new family of carbon-nitrogen hydrolases.
Bork, P. and Koonin, E.
Protein Science 3
: 1344-1346.
1 January 1994
A p-loop-like motif in a widespread ATP pyrophosphatase domain: implications for the evolution of motifs and enzyme activity.
Bork, P. and Koonin, E.V.
Proteins: Structure, Function, and Genetics 20
: 347-355.
1 January 1994
Biochemical genetics of methylglyoxal dehydrogenases in the laboratory rat (Rattus norvegicus).
Bender, K. and Seibert, R.T. and Wienker, T.F. and Kren, V. and Pravenec, M. and Bissbort, S.
Biochemical Genetics 32
: 147-154.
1 January 1994
Differential display reverse transcription PCR.
Bauer, D. and Mueller, H. and Reich, J. and Riedel, H. and Ahrenkiel, V. and Warthoe, P. and Strauss, M.
BioTec 2
: 32-35.
1 January 1994
Drosophila kelch motif is derived from a common enzyme fold.
Bork, P. and Doolittle, R.F.
Journal of Molecular Biology 236
: 1277-1282.
1 January 1994
Eukaryotic translation elongation factor 1gamma contains a glutathione transferase domain - study of a diverse ancient class of proteins using motif search and structural modelling.
Koonin, E.V. and Mushegian, A.R. and Tatusov, R.L. and Altschul, S.F. and Bryant, S.H. and Bork, P. and Valencia, A.
Protein Science 3
: 2045-2054.
1 January 1994
FMN- or DNA-binding?
Koonin, E. and Bork, P.
Trends in Biochemical Sciences 19
: 234-235.
1 January 1994
From genome sequences to protein function.
Bork, P. and Ouzounis, C. and Sander, C.
Current Opinion in Structural Biology 4
: 393-403.
1 January 1994
Genequiz: a workbench for sequence analysis.
Scharf, M. and Schneider, R. and Casari, G. and Bork, P. and Valencia, A. and Ouzounis, C. and Sander, C.
In:
Proceedings of the International Conference Itell.Syst.Mol.Biol.
AAAI Press, California, 348-353.
1 January 1994
The immunoglobulin fold - Structural classification, sequence patterns and common core.
Bork, P. and Holm, L. and Sander, C.
Journal of Molecular Biology 242
: 309-320.
1 January 1994
The modular structure of NifU proteins.
Ouzounis, C. and Bork, P. and Sander, C.
Trends in Biochemical Sciences 19
: 199-200.
1 January 1994
The use of loss of constitutional heterozygosity data to ascertain the location of predisposing genes in cancer families.
Teare, M.D. and Rohde, K. and Santibanez-Koref, M.F.
Journal of Medical Genetics 31
: 448-452.
1 January 1994
Tracing the spread of fibronectin type III domains in bacterial glycohydrolases.
Little, E. and Bork, P. and Doolittle, R.F.
Journal of Molecular Evolution 39
: 631-643.
1 January 1994
Vergleichende Untersuchungen des Klostridien-Tumor-Testes an Hunden und Pferden.
Fabricius, E.M. and Dietz, O. and Schneeweiss, U. and Schmidt, W. and Wildner, G.P. and Baumann, G. and Benedix, A. and Weisbrich, C.
Monatshefte fuer Veterinaermedizin 49
: 151-157.
1 January 1994
Yeast chromosome III: new gene functions.
Koonin, E. and Bork, P. and Sander, C.
EMBO Journal 13
: 493-503.
1 January 1994
1993
Hundreds of ankyrin-like repeats in functionally diverse proteins: mobile modules that cross phyla horizontally?
Bork, P.
Proteins: Structure, Function, and Bioinformatics 17
(4): 363-374.
December 1993
Les proteines, molecules modulaires.
Doolittle, R.F. and Bork, P.
Pour la Science 194
: 52-59.
December 1993
Identification of differentially expressed mRNA species by an improved display technique (DDRT-PCR).
Bauer, D. and Mueller, H. and Reich, J. and Riedel, H. and Ahrenkiel, V. and Warthoe, P. and Strauss, M.
Nucleic Acids Research 21
(18): 4272-4280.
11 September 1993
The modular architecture of a new family of growth regulators related to connective tissue growth factor.
Bork, P.
FEBS Letters 327
(2): 125-130.
26 July 1993
Linkage analysis in German breast cancer families with early onset of the disease, using highly polymorphic markers from the chromosome 17q11-q24 region.
Zimmermann, W. and Bender, E. and Rohde, K. and Reis, A. and Wiseman, R. and Futreal, A. and Krause, H. and Prokoph, H. and Werner, S. and Scherneck, S.
American Journal of Human Genetics 52
(4): 789-791.
April 1993
An expanding family of helicases within the "DEAD/H" superfamily.
Bork, P. and Koonin, E.
Nucleic Acids Research 21
(3): 751-752.
11 February 1993
3-aminobenzamide protects the mouse thymocytes in vitro from dexamethasone-mediated apoptotic cell death and cytolysis without changing DNA strand breakage.
Hoshino, J. and Beckmann, G. and Kroeger, H.
Journal of Steroid Biochemistry and Molecular Biology 44
: 113-119.
1 January 1993
A fast, sensitive pattern-matching approach for protein sequences.
Rohde, K. and Bork, P.
Computer Applications in the Biosciences 9
: 183-189.
1 January 1993
A hybrid protein kinase - RNase in an interferon-induced pathway.
Bork, P. and Sander, C.
FEBS Letters 334
: 149-152.
1 January 1993
A trefoil domain in the major rabbit zona-pellucida protein.
Bork, P.
Protein Science 2
: 669-670.
1 January 1993
An adhesive domain detected in functionally diverse receptors.
Beckmann, G. and Bork, P.
Trends in Biochemical Sciences 18
: 40-41.
1 January 1993
Convergent evolution of similar enzymatic function on different protein folds: the hexokinase, ribokinase and galactokinase families of sugar kinases.
Bork, P. and Sander, C. and Valencia, A.
Protein Science 2
: 31-40.
1 January 1993
Entschluesselung von Proteinfunktion mit Hilfe des Computers: Erkennung und Interpretation entfernter Sequenzaehnlichkeiten.
Bork, P.
In:
Informatik in den Biowissenschaften. (Informatik aktuell).
Springer, Berlin [u.a.], 67-78.
1 January 1993
Epidermal growth factor-like modules.
Campbell, I.D. and Bork, P.
Current Opinion in Structural Biology 3
(3): 385-392.
1 January 1993
Evolutionarily mobile modules in proteins.
Doolittle, R.F. and Bork, P.
Scientific American 269
: 50-56.
1 January 1993
Exopolyphosphate phosphatase and guanosine pentaphosphate phosphatase belong to the sugar kinase/actin/hsp70 superfamily.
Reizer, J. and Reizer, A. and Saier, M.H. and Bork, P. and Sander, C.
Trends in Biochemical Sciences 18
: 247-248.
1 January 1993
Fibronectin type III modules in the receptor phosphatase CD45 and tapeworm antigens.
Bork, P. and Doolittle, R.F.
Protein Science 2
: 1185-1187.
1 January 1993
Loss of constitutional heterozygosity on chromosome 11p in human ovarian cancer. Positive correlation with grade of differentiation.
Kiechle-Schwarz, M. and Bauknecht, T. and Wienker, T.F. and Walz, L. and Pfleiderer, A.
Cancer 72
: 2423-2432.
1 January 1993
Mobile Protein-Module: evolutionaer jung oder alt?
Doolittle, R.F. and Bork, P.
Spektrum der Wissenschaft 12
: 40-47.
1 January 1993
Molecular modelling of the norrie disease protein predicts a cystine knot growth factor tertiary structure.
Meitinger, T. and Meindl, A. and Bork, P. and Rost, B. and Sander, C. and Haasemann, M. and Murken, J.
Nature Genetics 5
: 376-380.
1 January 1993
On the genetics of mandibular prognathism: analysis of large European noble families.
Wolff, G. and Wienker, T.F. and Sander, H.
Journal of Medical Genetics 30
: 112-116.
1 January 1993
Prokaryotic members of a new family of putative helicases with similarity to transcripton activator SNF2.
Kolsto, A.B. and Bork, P. and Kvaloy, K. and Lindback, T. and Gronstadt, A. and Kristensen, T. and Sander, C.
Journal of Molecular Biology 230
: 684-688.
1 January 1993
Quantitative investigations into the elimination of in vitro- obtained spores of the non-pathogenic clostridium butyricum strain CNRZ 528, and their persistence in organs of different species following intravenous spore administration.
Fabricius, E.M. and Schneeweiss, U. and Schau, H.P. and Schmidt, W. and Benedix, A.
Research in Microbiology 144
: 741-753.
1 January 1993
Rotamers - to be or not to be? - An analysis of amino acid side-chains conformations in globular proteins.
Schrauber, H. and Eisenhaber, F. and Argos, P.
Journal of Molecular Biology 230
: 592-612.
1 January 1993
T-cell receptor variable genes and genetic susceptibility to celiac disease: an association and linkage study.
Roschmann, E. and Wienker, T.F. and Gerok, W. and Volk, B.A.
Gastroenterology 105
: 1790-1796.
1 January 1993
The CUB domain: A widespread module in developmentally regulated proteins.
Bork, P. and Beckmann, G.
Journal of Molecular Biology 231
: 539-545.
1 January 1993
1992
An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins.
Bork, P. and Sander, C. and Valencia, A.
Proceedings of the National Academy of Sciences of the United States of America 89
(16): 7290-7294.
15 August 1992
A large domain common to sperm receptors (Zp2 and Zp3) and TGF-beta type III receptor.
Bork, P. and Sander, C.
FEBS Letters 300
: 237-240.
1 January 1992
A module of DnaJ heat shock proteins found in malaria parasites.
Bork, P. and Sander, C. and Valencia, A. and Bukau, B.
Trends in Biochemical Sciences 17
: 129-129.
1 January 1992
C curve fitting and modeling for scientists and engineers.
Reich, J.
McGraw-Hill, New York [u.a.].
1 January 1992
Cloning of a gene from Bacillus cereus with homology to the mreb gene of Echerichia coli.
Nahara, A. and Naterstad, K. and Kristensen, T. and Lopez, R. and Bork, P. and Kolsto, A.B.
Gene 122
: 181-185.
1 January 1992
Comprehensive sequence analysis of the 182 predicted ORFs of yeast chromosome III.
Bork, P. and Ouzounis, C. and Sander, C. and Scharf, M. and Schneider, R. and Sonnhammer, E.
Protein Science 1
: 1677-1690.
1 January 1992
Mobile modules and motifs.
Bork, P.
Current Opinion in Structural Biology 2
: 413-421.
1 January 1992
Proposed acquisition of an animal protein domain by bacteria.
Bork, P. and Doolittle, R.F.
Proceedings of the National Academy of Sciences of the United States of America 89
: 8990-8994.
1 January 1992
The modular architecture of vertebrate collagens.
Bork, P.
FEBS Letters 307
: 49-54.
1 January 1992
What's in a genome?
Bork, P. and Ouzounis, C. and Sander, C. and Scharf, M. and Schneider, R. and Sonnhammer, E.
Nature 358
: 287.
1 January 1992
This list was generated on Tue Sep 26 02:19:01 2023 CEST.