Browse by Research Team

2024

Efficient recovery of complete gut viral genomes by combined short- and long-read sequencing.
Chen, J. and Sun, C. and Dong, Y. and Jin, M. and Lai, S. and Jia, L. and Zhao, X. and Wang, H. and Gao, N.L. and Bork, P. and Liu, Z. and Chen, W.H. and Zhao, X.M.
Advanced Science 11 (13): 2305818. 3 April 2024

High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities.
Müller, P. and de la Cuesta-Zuluaga, J. and Kuhn, M. and Baghai Arassi, M. and Treis, T. and Blasche, S. and Zimmermann, M. and Bork, P. and Patil, K.R. and Typas, A. and Garcia-Santamarina, S. and Maier, L.
Nature Protocols 19 (3): 668-699. March 2024

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 Munar-Palmer, M. and Santamaría-Hernando, S. and Rodríguez-Herva, J.J. and Ruscheweyh, H.J. and Paoli, L. and Schmidt, T.S.B. and Sunagawa, S. and Bork, P. and López-Solanilla, E. and Coelho, L.P. and Huerta-Cepas, J.
Nature 626 (7998): 377-384. 8 February 2024

SPIRE: a Searchable, Planetary-scale mIcrobiome REsource.
Schmidt, T.S.B. and Fullam, A. and Ferretti, P. and Orakov, A. and Maistrenko, O.M. and Ruscheweyh, H.J. and Letunic, I. and Duan, Y. and Van Rossum, T. and Sunagawa, S. and Mende, D.R. and Finn, R.D. and Kuhn, M. and Pedro Coelho, L. and Bork, P.
Nucleic Acids Research 52 (D1): D777-D783. 5 January 2024

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

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Gibbs, R.A. and Weinstock, G.M. and Metzker, M.L. and Muzny, D.M. and Sodergren, E.J. and Scherer, S. and Scott, G. and Steffen, D. and Worley, K.C. and Burch, P.E. and Okwuonu, G. and Hines, S. and Lewis, L. and DeRamo, C. and Delgado, O. and Dugan-Rocha, S. and Miner, G. and Morgan, M. and Hawes, A. and Gill, R. and Holt, R.A. and Adams, M.D. and Amanatides, P.G. and Baden-Tillson, H. and Barnstead, M. and Chin, S. and Evans, C.A. and Ferriera, S. and Fosler, C. and Glodek, A. and Gu, Z. and Jennings, D. and Kraft, C.L. and Nguyen, T. and Pfannkoch, C.M. and Sitter, C. and Sutton, G.G. and Venter, J.C. and Woodage, T. and Smith, D. and Lee, H.M. and Gustafson, E. and Cahill, P. and Kana, A. and Doucette-Stamm, L. and Weinstock, K. and Fechtel, K. and Weiss, R.B. and Dunn, D.M. and Green, E.D. and Blakesley, R.W. and Bouffard, G.G. and de Jong, P.J. and Osoegawa, K. and Zhu, B. and Marra, M. and Schein, J. and Bosdet, I. and Fjell, C. and Jones, S. and Krzywinski, M. and Mathewson, C. and Siddiqui, A. and Wye, N. and McPherson, J. and Zhao, S. and Fraser, C.M. and Shetty, J. and Shatsman, S. and Geer, K. and Chen, Y. and Abramzon, S. and Nierman, W.C. and Havlak, P.H. and Chen, R. and Durbin, K.J. and Egan, A. and Ren, Y. and Song, X.Z. and Li, B. and Liu, Y. and Qin, X. and Cawley, S. and Worley, K.C. and Cooney, A.J. and D'Souza, L.M. and Martin, K. and Wu, J.Q. and Gonzalez-Garay, M.L. and Jackson, A.R. and Kalafus, K.J. and McLeod, M.P. and Milosavljevic, A. and Virk, D. and Volkov, A. and Wheeler, D.A. and Zhang, Z. and Bailey, J.A. and Eichler, E.E. and Tuzun, E. and Birney, E. and Mongin, E. and Ureta-Vidal, A. and Woodwark, C. and Zdobnov, E. and Bork, P. and Suyama, M. and Torrents, D. and Alexandersson, M. and Trask, B.J. and Young, J.M. and Huang, H. and Wang, H. and Xing, H. and Daniels, S. and Gietzen, D. and Schmidt, J. and Stevens, K. and Vitt, U. and Wingrove, J. and Camara, F. and Alba, M.M. and Abril, J.F. and Guigo, R. and Smit, A. and Dubchak, I. and Rubin, E.M. and Couronne, O. and Poliakov, A. and Hübner, N. and Ganten, D. and Goesele, C. and Hummel, O. and Kreitler, T. and Lee, Y.A. and Monti, J. and Schulz, H. and Zimdahl, H. and Himmelbauer, H. and Lehrach, H. and Jacob, H.J. and Bromberg, S. and Gullings-Handley, J. and Jensen-Seaman, M.I. and Kwitek, A.E. and Lazar, J. and Pasko, D. and Tonellato, P.J. and Twigger, S. and Ponting, C.P. and Duarte, J.M. and Rice, S. and Goodstadt, L. and Beatson, S.A. and Emes, R.D. and Winter, E.E. and Webber, C. and Brandt, P. and Nyakatura, G. and Adetobi, M. and Chiaromonte, F. and Elnitski, L. and Eswara, P. and Hardison, R.C. and Hou, M. and Kolbe, D. and Makova, K. and Miller, W. and Nekrutenko, A. and Riemer, C. and Schwartz, S. and Taylor, J. and Yang, S. and Zhang, Y. and Lindpaintner, K. and Andrews, T.D. and Caccamo, M. and Clamp, M. and Clarke, L. and Curwen, V. and Durbin, R. and Eyras, E. and Searle, S.M. and Cooper, G.M. and Batzoglou, S. and Brudno, M. and Sidow, A. and Stone, E.A. and Venter, J.C. and Payseur, B.A. and Bourque, G. and Lopez-Otin, C. and Puente, X.S. and Chakrabarti, K. and Chatterji, S. and Dewey, C. and Pachter, L. and Bray, N. and Yap, V.B. and Caspi, A. and Tesler, G. and Pevzner, P.A. and Haussler, D. and Roskin, K.M. and Baertsch, R. and Clawson, H. and Furey, T.S. and Hinrichs, A.S. and Karolchik, D. and Kent, W.J. and Rosenbloom, K.R. and Trumbower, H. and Weirauch, M. and Cooper, D.N. and Stenson, P.D. and Ma, B. and Brent, M. and Arumugam, M. and Shteynberg, D. and Copley, R.R. and Taylor, M.S. and Riethman, H. and Mudunuri, U. and Peterson, J. and Guyer, M. and Felsenfeld, A. and Old, S. and Mockrin, S. and Collins, F.
Nature 428 (6982): 493-521. 1 April 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 Nürnberg, P. and Reis, A. and Rohde, K. and Ganten, D. and Hui, R.T. and Hübner, 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