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Systematic mapping of antibiotic cross-resistance and collateral sensitivity with chemical genetics.
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Nature Microbiology
2 December 2024
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The STRING database in 2025: protein networks with directionality of regulation.
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Nucleic Acids Research
18 November 2024
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Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations.
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Cell
13 November 2024
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The diversity of the microbiome impacts chronic lymphocytic leukemia development in mice and humans.
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October 2024
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Nature Communications 15
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Science Advances 10
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16 August 2024
Discovery of antimicrobial peptides in the global microbiome with machine learning.
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11 July 2024
Efficient recovery of complete gut viral genomes by combined short- and long-read sequencing.
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Advanced Science 11
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Nature Protocols 19
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March 2024
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Nature 626
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8 February 2024
SPIRE: a Searchable, Planetary-scale mIcrobiome REsource.
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5 January 2024
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Nature Communications 14
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20 September 2023
Consistency across multi-omics layers in a drug-perturbed gut microbial community.
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12 September 2023
Long-read sequencing reveals extensive DNA methylations in human gut phagenome contributed by prevalently phage-encoded methyltransferases.
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Microbiome 11
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11 August 2023
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies.
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Nature 613
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26 January 2023
The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest.
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Nucleic Acids Research 51
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6 January 2023
proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes.
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Nucleic Acids Research 51
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6 January 2023
Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses.
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Microbiome 10
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28 December 2022
Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments.
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5 December 2022
Drivers and determinants of strain dynamics following fecal microbiota transplantation.
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Nature Medicine 28
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September 2022
Biosynthetic potential of the global ocean microbiome.
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Nature 607
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7 July 2022
A faecal microbiota signature with high specificity for pancreatic cancer.
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7 June 2022
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Cell Genomics 2
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11 May 2022
Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes.
Khedkar, S., Smyshlyaev, G., Letunic, I., Maistrenko, O.M., Coelho, L.P., Orakov, A., Forslund, S.K., Hildebrand, F., Luetge, M., Schmidt, T.S.B., Barabas, O. and Bork, P.
Nucleic Acids Research 50
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8 April 2022
Meconium microbiome of very preterm infants across Germany.
Klopp, J., Ferretti, P., Meyer, C.U., Hilbert, K., Haiß, A., Marißen, J., Henneke, P., Hudalla, H., Pirr, S., Viemann, D., Zemlin, M., Forslund, S.K., Härtel, C., Bork, P., Gehring, S. and Van Rossum, T.
mSphere 7
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23 February 2022
Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics.
Pryszlak, A., Wenzel, T., Seitz, K.W., Hildebrand, F., Kartal, E., Cosenza, M.R., Benes, V., Bork, P. and Merten, C.A.
Cell Reports Methods 2
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24 January 2022
Towards the biogeography of prokaryotic genes.
Coelho, L.P., Alves, R., Del Río, Á.R., Myers, P.N., Cantalapiedra, C.P., Giner-Lamia, J., Schmidt, T.S., Mende, D.R., Orakov, A., Letunic, I., Hildebrand, F., Van Rossum, T., Forslund, S.K., Khedkar, S., Maistrenko, O.M., Pan, S., Jia, L., Ferretti, P., Sunagawa, S., Zhao, X.M., Nielsen, H.B., Huerta-Cepas, J. and Bork, P.
Nature 601
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13 January 2022
Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean.
Royo-Llonch, M., Sánchez, P., Ruiz-González, C., Salazar, G., Pedrós-Alió, C., Sebastián, M., Labadie, K., Paoli, L., M. Ibarbalz, F., Zinger, L., Churcheward, B., Chaffron, S., Eveillard, D., Karsenti, E., Sunagawa, S., Wincker, P., Karp-Boss, L., Bowler, C. and Acinas, S.G.
Nature Microbiology 6
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December 2021
Unravelling the collateral damage of antibiotics on gut bacteria.
Maier, L., Goemans, C.V., Wirbel, J., Kuhn, M., Eberl, C., Pruteanu, M., Müller, P., Garcia-Santamarina, S., Cacace, E., Zhang, B., Gekeler, C., Banerjee, T., Anderson, E.E., Milanese, A., Löber, U., Forslund, S.K., Patil, K.R., Zimmermann, M., Stecher, B., Zeller, G., Bork, P. and Typas, A.
Nature 599
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4 November 2021
A previously undescribed highly prevalent phage identified in a Danish Enteric Virome Catalog.
Van Espen, L., Bak, E.G., Beller, L., Close, L., Deboutte, W., Juel, H.B., Nielsen, T., Sinar, D., De Coninck, L., Frithioff-Bøjsøe, C., Fonvig, C.E., Jacobsen, S., Kjærgaard, M., Thiele, M., Fullam, A., Kuhn, M., Holm, J.C., Bork, P., Krag, A., Hansen, T., Arumugam, M. and Matthijnssens, J.
mSystems 6
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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., Gelincik, O., Oezcan-Wahlbrink, M., Marshall, J.D., Hernandez-Sanchez, A., Urban, K., Long, M., Cortes, E., Tosti, E., Katzenmaier, E.M., Song, Y., Elsaadi, A., Deng, N., Vilar, E., Fuchs, V., Nelius, N., Yuan, Y.P., Ahadova, A., Sei, S., Shoemaker, R.H., Umar, A., Wei, L., Liu, S., Bork, P., Edelmann, W., von Knebel Doeberitz, M., Lipkin, S.M. and Kloor, M.
Gastroenterology 161
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October 2021
Bioaccumulation of therapeutic drugs by human gut bacteria.
Klünemann, M., Andrejev, S., Blasche, S., Mateus, A., Phapale, P., Devendran, S., Vappiani, J., Simon, B., Scott, T.A., Kafkia, E., Konstantinidis, D., Zirngibl, K., Mastrorilli, E., Banzhaf, M., Mackmull, M.T., Hövelmann, F., Nesme, L., Brochado, A.R., Maier, L., Bock, T., Periwal, V., Kumar, M., Kim, Y., Tramontano, M., Schultz, C., Beck, M., Hennig, J., Zimmermann, M., Sévin, D.C., Cabreiro, F., Savitski, M.M., Bork, P., Typas, A. and Patil, K.R.
Nature 597
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23 September 2021
Coupling proteomics and metabolomics for the unsupervised identification of protein-metabolite interactions in Chaetomium thermophilum.
Li, Y., Kuhn, M., Zukowska-Kasprzyk, J., Hennrich, M.L., Kastritis, P.L., O'Reilly, F.J., Phapale, P., Beck, M., Gavin, A.C. and Bork, P.
PLoS ONE 16
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9 July 2021
Dispersal strategies shape persistence and evolution of human gut bacteria.
Hildebrand, F., Gossmann, T.I., Frioux, C., Özkurt, E., Myers, P.N., Ferretti, P., Kuhn, M., Bahram, M., Nielsen, H.B. and Bork, P.
Cell Host & Microbe 29
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14 June 2021
GUNC: detection of chimerism and contamination in prokaryotic genomes.
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Genome Biology 22
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13 June 2021
Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox.
Wirbel, J., Zych, K., Essex, M., Karcher, N., Kartal, E., Salazar, G., Bork, P., Sunagawa, S. and Zeller, G.
Genome Biology 22
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30 March 2021
OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines.
Gurumayum, S., Jiang, P., Hao, X., Campos, T.L., Young, N.D., Korhonen, P.K., Gasser, R.B., Bork, P., Zhao, X.M., He, L.J. and Chen, W.H.
Nucleic Acids Research 49
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8 January 2021
SMART: recent updates, new developments and status in 2020.
Letunic, I., Khedkar, S. and Bork, P.
Nucleic Acids Research 49
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8 January 2021
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.
Szklarczyk, D., Gable, A.L., Nastou, K.C., Lyon, D., Kirsch, R., Pyysalo, S., Doncheva, N.T., Legeay, M., Fang, T., Bork, P., Jensen, L.J. and von Mering, C.
Nucleic Acids Research 49
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8 January 2021
Metagenomic assessment of the global diversity and distribution of bacteria and fungi.
Bahram, M., Netherway, T., Frioux, C., Ferretti, P., Coelho, L.P., Geisen, S., Bork, P. and Hildebrand, F.
Environmental Microbiology 23
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January 2021
(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., Katzenmaier, E.M., Roeckel, N., Woerner, S.M., Fuchs, V., Warnken, U., Yuan, Y.P., Bork, P., Neu-Yilik, G., Kulozik, A., von Knebel Doeberitz, M., Kloor, M., Kopitz, J. and Gebert, J.
International Journal of Molecular Sciences 21
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23 July 2020
Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity.
Maistrenko, O.M., Mende, D.R., Luetge, M., Hildebrand, F., Schmidt, T.S.B., Li, S.S., Rodrigues, J.F.M., von Mering, C., Pedro Coelho, L., Huerta-Cepas, J., Sunagawa, S. and Bork, P.
ISME Journal 14
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May 2020
Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features.
Li, Y., Kuhn, M., Gavin, A.C. and Bork, P.
Bioinformatics 36
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15 February 2020
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes.
Mende, D.R., Letunic, I., Maistrenko, O.M., Schmidt, T.S.B., Milanese, A., Paoli, L., Hernández-Plaza, A., Orakov, A.N., Forslund, S.K., Sunagawa, S., Zeller, G., Huerta-Cepas, J., Coelho, L.P. and Bork, P.
Nucleic Acids Research 48
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8 January 2020
Gene expression changes and community turnover differentially shape the global ocean metatranscriptome.
Salazar, G., Paoli, L., Alberti, A., Huerta-Cepas, J., Ruscheweyh, H.J., Cuenca, M., Field, C.M., Coelho, L.P., Cruaud, C., Engelen, S., Gregory, A.C., Labadie, K., Marec, C., Pelletier, E., Royo-Llonch, M., Roux, S., Sánchez, P., Uehara, H., Zayed, A.A., Zeller, G., Carmichael, M., Dimier, C., Ferland, J., Kandels, S., Picheral, M., Pisarev, S., Poulain, J., Acinas, S.G., Babin, M., Bork, P., Bowler, C., de Vargas, C., Guidi, L., Hingamp, P., Iudicone, D., Karp-Boss, L., Karsenti, E., Ogata, H., Pesant, S., Speich, S., Sullivan, M.B., Wincker, P. and Sunagawa, S.
Cell 179
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14 November 2019
Quantitative proteome landscape of the NCI-60 cancer cell lines.
Guo, T., Luna, A., Rajapakse, V.N., Koh, C.C., Wu, Z., Liu, W., Sun, Y., Gao, H., Menden, M.P., Xu, C., Calzone, L., Martignetti, L., Auwerx, C., Buljan, M., Banaei-Esfahani, A., Ori, A., Iskar, M., Gillet, L., Bi, R., Zhang, J., Zhang, H., Yu, C., Zhong, Q., Varma, S., Schmitt, U., Qiu, P., Zhang, Q., Zhu, Y., Wild, P.J., Garnett, M.J., Bork, P., Beck, M., Liu, K., Saez-Rodriguez, J., Elloumi, F., Reinhold, W.C., Sander, C., Pommier, Y. and Aebersold, R.
iScience 21
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31 October 2019
Sample preservation and storage significantly impact taxonomic and functional profiles in metaproteomics studies of the human gut microbiome.
Hickl, O., Heintz-Buschart, A., Trautwein-Schult, A., Hercog, R., Bork, P., Wilmes, P. and Becher, D.
Microorganisms 7
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19 September 2019
Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota.
Tito, R.Y., Chaffron, S., Caenepeel, C., Lima-Mendez, G., Wang, J., Vieira-Silva, S., Falony, G., Hildebrand, F., Darzi, Y., Rymenans, L., Verspecht, C., Bork, P., Vermeire, S., Joossens, M. and Raes, J.
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7 June 2019
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language.
Coelho, L.P., Alves, R., Monteiro, P., Huerta-Cepas, J., Freitas, A.T. and Bork, P.
Microbiome 7
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3 June 2019
Ice-age climate adaptations trap the alpine marmot in a state of low genetic diversity.
Gossmann, T.I., Shanmugasundram, A., Börno, S., Duvaux, L., Lemaire, C., Kuhl, H., Klages, S., Roberts, L.D., Schade, S., Gostner, J.M., Hildebrand, F., Vowinckel, J., Bichet, C., Mülleder, M., Calvani, E., Zelezniak, A., Griffin, J.L., Bork, P., Allaine, D., Cohas, A., Welch, J.J., Timmermann, B. and Ralser, M.
Current Biology 29
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20 May 2019
Disentangling genetic and environmental effects on the proteotypes of individuals.
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16 May 2019
Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.
Wirbel, J., Pyl, P.T., Kartal, E., Zych, K., Kashani, A., Milanese, A., Fleck, J.S., Voigt, A.Y., Palleja, A., Ponnudurai, R., Sunagawa, S., Coelho, L.P., Schrotz-King, P., Vogtmann, E., Habermann, N., Niméus, E., Thomas, A.M., Manghi, P., Gandini, S., Serrano, D., Mizutani, S., Shiroma, H., Shiba, S., Shibata, T., Yachida, S., Yamada, T., Waldron, L., Naccarati, A., Segata, N., Sinha, R., Ulrich, C.M., Brenner, H., Arumugam, M., Bork, P. and Zeller, G.
Nature Medicine 25
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April 2019
Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.
Thomas, A.M., Manghi, P., Asnicar, F., Pasolli, E., Armanini, F., Zolfo, M., Beghini, F., Manara, S., Karcher, N., Pozzi, C., Gandini, S., Serrano, D., Tarallo, S., Francavilla, A., Gallo, G., Trompetto, M., Ferrero, G., Mizutani, S., Shiroma, H., Shiba, S., Shibata, T., Yachida, S., Yamada, T., Wirbel, J., Schrotz-King, P., Ulrich, C.M., Brenner, H., Arumugam, M., Bork, P., Zeller, G., Cordero, F., Dias-Neto, E., Setubal, J.C., Tett, A., Pardini, B., Rescigno, M., Waldron, L., Naccarati, A. and Segata, N.
Nature Medicine 25
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April 2019
Microbial abundance, activity and population genomic profiling with mOTUs2.
Milanese, A., Mende, D.R., Paoli, L., Salazar, G., Ruscheweyh, H.J., Cuenca, M., Hingamp, P., Alves, R., Costea, P.I., Coelho, L.P., Schmidt, T.S.B., Almeida, A., Mitchell, A.L., Finn, R.D., Huerta-Cepas, J., Bork, P., Zeller, G. and Sunagawa, S.
Nature Communications 10
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4 March 2019
Community-level responses to iron availability in open ocean plankton ecosystems.
Caputi, L., Carradec, Q., Eveillard, D., Kirilovsky, A., Pelletier, E., Pierella Karlusich, J.J., Rocha Jimenez Vieira, F., Villar, E., Chaffron, S., Malviya, S., Scalco, E., Acinas, S.G., Alberti, A., Aury, J.M., Benoiston, A.S., Bertrand, A., Biard, T., Bittner, L., Boccara, M., Brum, J.R., Brunet, C., Busseni, G., Carratalà, A., Claustre, H., Coelho, L.P., Colin, S., D'Aniello, S., Da Silva, C., Del Core, M., Doré, H., Gasparini, S., Kokoszka, F., Jamet, J.L., Lejeusne, C., Lepoivre, C., Lescot, M., Lima‐Mendez, G., Lombard, F., Lukeš, J., Maillet, N., Madoui, M.A., Martinez, E., Mazzocchi, M.G., Néou, M.B., Paz‐Yepes, J., Poulain, J., Ramondenc, S., Romagnan, J.B., Roux, S., Salvagio Manta, D., Sanges, R., Speich, S., Sprovieri, M., Sunagawa, S., Taillandier, V., Tanaka, A., Tirichine, L., Trottier, C., Uitz, J., Veluchamy, A., Veselá, J., Vincent, F., Yau, S., Kandels‐Lewis, S., Searson, S., Dimier, C., Picheral, M., Bork, P., Boss, E., Vargas, C., Follows, M.J., Grimsley, N., Guidi, L., Hingamp, P., Karsenti, E., Sordino, P., Stemmann, L., Sullivan, M.B., Tagliabue, A., Zingone, A., Garczarek, L., d'Ortenzio, F., Testor, P., Not, F., Ribera d'Alcalà, M., Wincker, P., Bowler, C. and Iudicone, D.
Global Biogeochemical Cycles 33
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March 2019
Extensive transmission of microbes along the gastrointestinal tract.
Schmidt, T.S.B., Hayward, M.R., Coelho, L.P., Li, S.S., Costea, P.I., Voigt, A.Y., Wirbel, J., Maistrenko, O.M., Alves, R.J.C., Bergsten, E., de Beaufort, C., Sobhani, I., Heintz-Buschart, A., Sunagawa, S., Zeller, G., Wilmes, P. and Bork, P.
eLife 8
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12 February 2019
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Szklarczyk, D., Gable, A.L., Lyon, D., Junge, A., Wyder, S., Huerta-Cepas, J., Simonovic, M., Doncheva, N.T., Morris, J.H., Bork, P., Jensen, L.J. and von Mering, C.
Nucleic Acids Research 47
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8 January 2019
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
Huerta-Cepas, J., Szklarczyk, D., Heller, D., Hernández-Plaza, A., Forslund, S.K., Cook, H., Mende, D.R., Letunic, I., Rattei, T., Jensen, L.J., von Mering, C. and Bork, P.
Nucleic Acids Research 47
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8 January 2019
Recovery of gut microbiota of healthy adults following antibiotic exposure.
Palleja, A., Mikkelsen, K.H., Forslund, S.K., Kashani, A., Allin, K.H., Nielsen, T., Hansen, T.H., Liang, S., Feng, Q., Zhang, C., Pyl, P.T., Coelho, L.P., Yang, H., Wang, J., Typas, A., Nielsen, M.F., Nielsen, H.B., Bork, P., Wang, J., Vilsbøll, T., Hansen, T., Knop, F.K., Arumugam, M. and Pedersen, O.
Nature Microbiology 3
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November 2018
Structure and function of the global topsoil microbiome.
Bahram, M., Hildebrand, F., Forslund, S.K., Anderson, J.L., Soudzilovskaia, N.A., Bodegom, P.M., Bengtsson-Palme, J., Anslan, S., Coelho, L.P., Harend, H., Huerta-Cepas, J., Medema, M.H., Maltz, M.R., Mundra, S., Olsson, P.A., Pent, M., Põlme, S., Sunagawa, S., Ryberg, M., Tedersoo, L. and Bork, P.
Nature 560
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9 August 2018
Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment.
Bahram, M., Anslan, S., Hildebrand, F., Bork, P. and Tedersoo, L.
Environmental Microbiology Reports 11
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August 2018
The gut microbiome is associated with behavioural task in honey bees.
Jones, J.C., Fruciano, C., Marchant, J., Hildebrand, F., Forslund, S., Bork, P., Engel, P. and Hughes, W.O.H.
Insectes Sociaux 65
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August 2018
Metagenomic analysis of gut microbial communities from a Central Asian population.
Kushugulova, A., Forslund, S.K., Costea, P.I., Kozhakhmetov, S., Khassenbekova, Z., Urazova, M., Nurgozhin, T., Zhumadilov, Z., Benberin, V., Driessen, M., Hercog, R., Voigt, A.Y., Benes, V., Kandels-Lewis, S., Sunagawa, S., Letunic, I. and Bork, P.
BMJ Open 8
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28 July 2018
Quantifying compartment-associated variations of protein abundance in proteomics data.
Parca, L., Beck, M., Bork, P. and Ori, A.
Molecular Systems Biology 14
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2 July 2018
iPath3.0: interactive pathways explorer v3.
Darzi, Y., Letunic, I., Bork, P. and Yamada, T.
Nucleic Acids Research 46
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2 July 2018
Species-specific activity of antibacterial drug combinations.
Brochado, A.R., Telzerow, A., Bobonis, J., Banzhaf, M., Mateus, A., Selkrig, J., Huth, E., Bassler, S., Zamarreño Beas, J., Zietek, M., Ng, N., Foerster, S., Ezraty, B., Py, B., Barras, F., Savitski, M.M., Bork, P., Göttig, S. and Typas, A.
Nature 559
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July 2018
Pervasive protein thermal stability variation during the cell cycle.
Becher, I., Andrés-Pons, A., Romanov, N., Stein, F., Schramm, M., Baudin, F., Helm, D., Kurzawa, N., Mateus, A., Mackmull, M.T., Typas, A., Müller, C.W., Bork, P., Beck, M. and Savitski, M.M.
Cell 173
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31 May 2018
Similarity of the dog and human gut microbiomes in gene content and response to diet.
Coelho, L.P., Kultima, J.R., Costea, P.I., Fournier, C., Pan, Y., Czarnecki-Maulden, G., Hayward, M.R., Forslund, S.K., Schmidt, T.S.B., Descombes, P., Jackson, J.R., Li, Q. and Bork, P.
Microbiome 6
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19 April 2018
Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies.
Tramontano, M., Andrejev, S., Pruteanu, M., Klünemann, M., Kuhn, M., Galardini, M., Jouhten, P., Zelezniak, A., Zeller, G., Bork, P., Typas, A. and Patil, K.R.
Nature Microbiology 3
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April 2018
Selective maternal seeding and environment shape the human gut microbiome.
Korpela, K., Costea, P., Coelho, L.P., Kandels-Lewis, S., Willemsen, G., Boomsma, D.I., Segata, N. and Bork, P.
Genome Research 28
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April 2018
Extensive impact of non-antibiotic drugs on human gut bacteria.
Maier, L., Pruteanu, M., Kuhn, M., Zeller, G., Telzerow, A., Anderson, E.E., Brochado, A.R., Fernandez, K.C., Dose, H., Mori, H., Patil, K.R., Bork, P. and Typas, A.
Nature 555
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29 March 2018
Transposase-DNA complex structures reveal mechanisms for conjugative transposition of antibiotic resistance.
Rubio-Cosials, A., Schulz, E.C., Lambertsen, L., Smyshlyaev, G., Rojas-Cordova, C., Forslund, K., Karaca, E., Bebel, A., Bork, P. and Barabas, O.
Cell 173
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22 March 2018
A global ocean atlas of eukaryotic genes.
Carradec, Q., Pelletier, E., Da Silva, C., Alberti, A., Seeleuthner, Y., Blanc-Mathieu, R., Lima-Mendez, G., Rocha, F., Tirichine, L., Labadie, K., Kirilovsky, A., Bertrand, A., Engelen, S., Madoui, M.A., Méheust, R., Poulain, J., Romac, S., Richter, D.J., Yoshikawa, G., Dimier, C., Kandels-Lewis, S., Picheral, M., Searson, S., Jaillon, O., Aury, J.M., Karsenti, E., Sullivan, M.B., Sunagawa, S., Bork, P., Not, F., Hingamp, P., Raes, J., Guidi, L., Ogata, H., De Vargas, C., Iudicone, D., Bowler, C. and Wincker, P.
Nature Communications 9
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25 January 2018
MVP: a microbe-phage interaction database.
Gao, N.L., Zhang, C., Zhang, Z., Hu, S., Lercher, M.J., Zhao, X.M., Bork, P., Liu, Z. and Chen, W.H.
Nucleic Acids Research 46
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4 January 2018
Gut microbiota composition is associated with environmental landscape in honey bees.
Jones, J.C., Fruciano, C., Hildebrand, F., Al Toufalilia, H., Balfour, N.J., Bork, P., Engel, P., Ratnieks, F.L.W. and Hughes, W.O.H.
Ecology and Evolution 8
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January 2018
Subspecies in the global human gut microbiome.
Costea, P.I., Coelho, L.P., Sunagawa, S., Munch, R., Huerta-Cepas, J., Forslund, K., Hildebrand, F., Kushugulova, A., Zeller, G. and Bork, P.
Molecular Systems Biology 13
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14 December 2017
Salt-responsive gut commensal modulates T(H)17 axis and disease.
Wilck, N., Matus, M.G., Kearney, S.M., Olesen, S.W., Forslund, K., Bartolomaeus, H., Haase, S., Mähler, A., Balogh, A., Markó, L., Vvedenskaya, O., Kleiner, F.H., Tsvetkov, D., Klug, L., Costea, P.I., Sunagawa, S., Maier, L., Rakova, N., Schatz, V., Neubert, P., Frätzer, C., Krannich, A., Gollasch, M., Grohme, D.A., Côrte-Real, B.F., Gerlach, R.G., Basic, M., Typas, A., Wu, C., Titze, J.M., Jantsch, J., Boschmann, M., Dechend, R., Kleinewietfeld, M., Kempa, S., Bork, P., Linker, R.A., Alm, E.J. and Müller, D.N.
Nature 551
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30 November 2017
Pole-to-Pole connections: similarities between arctic and antarctic microbiomes and their vulnerability to environmental change.
Kleinteich, J., Hildebrand, F., Bahram, M., Voigt, A.Y., Wood, S.A., Jungblut, A.D., Kuepper, F.C., Quesada, A., Camacho, A., Pearce, D.A., Convey, P., Vincent, W.F., Zarfl, C., Bork, P. and Dietrich, D.R.
Frontiers in Ecology and Evolution 5
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10 November 2017
Towards standards for human fecal sample processing in metagenomic studies.
Costea, P.I., Zeller, G., Sunagawa, S., Pelletier, E., Alberti, A., Levenez, F., Tramontano, M., Driessen, M., Hercog, R., Jung, F.E., Kultima, J.R., Hayward, M.R., Coelho, L.P., Allen-Vercoe, E., Bertrand, L., Blaut, M., Brown, J.R.M., Carton, T., Cools-Portier, S., Daigneault, M., Derrien, M., Druesne, A., de Vos, W.M., Finlay, B.B., Flint, H.J., Guarner, F., Hattori, M., Heilig, H., Luna, R.A., van Hylckama Vlieg, J., Junick, J., Klymiuk, I., Langella, P., Le Chatelier, Z., Mai, V., Manichanh, C., Martin, J.C., Mery, C., Morita, H., O'Toole, P.W., Orvain, C., Patil, K.R., Penders, J., Persson, S., Pons, N., Popova, M., Salonen, A., Saulnier, D., Scott, K.P., Singh, B., Slezak, K., Veiga, P., Versalovic, J., Zhao, L., Zoetendal, E.G., Ehrlich, S.D., Dore, J. and Bork, P.
Nature Biotechnology 35
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November 2017
RTK: efficient rarefaction analysis of large datasets.
Saary, P., Forslund, K., Bork, P. and Hildebrand, F.
Bioinformatics 33
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15 August 2017
Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.
Huerta-Cepas, J., Forslund, K., Coelho, L.P., Szklarczyk, D., Jensen, L.J., von Mering, C. and Bork, P.
Molecular Biology and Evolution 34
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1 August 2017
Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.
Alberti, A., Poulain, J., Engelen, S., Labadie, K., Romac, S., Ferrera, I., Albini, G., Aury, J.M., Belser, C., Bertrand, A., Cruaud, C., Da Silva, C., Dossat, C., Gavory, F., Gas, S., Guy, J., Haquelle, M., Jacoby, E., Jaillon, O., Lemainque, A., Pelletier, E., Samson, G., Wessner, M., Acinas, S.G., Royo-Llonch, M., Cornejo-Castillo, F.M., Logares, R., Fernandez-Gomez, B., Bowler, C., Cochrane, G., Amid, C., Hoopen, P.T., De Vargas, C., Grimsley, N., Desgranges, E., Kandels-Lewis, S., Ogata, H., Poulton, N., Sieracki, M.E., Stepanauskas, R., Sullivan, M.B., Brum, J.R., Duhaime, M.B., Poulos, B.T., Hurwitz, B.L., Pesant, S., Karsenti, E. and Wincker, P.
Scientific Data 4
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1 August 2017
MetaSNV: a tool for metagenomic strain level analysis.
Costea, P.I., Munch, R., Coelho, L.P., Paoli, L., Sunagawa, S. and Bork, P.
PLoS ONE 12
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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., Hildebrand, F., Coelho, L.P., Sunagawa, S., Bahram, M., Goeser, F., Bork, P. and Wuellner, U.
Genome Medicine 9
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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., Forslund, K., Kultima, J.R., Meyer, C.U., Kullmer, U., Sunagawa, S., Bork, P. and Gehring, S.
American Journal of Physiology Gastrointestinal and Liver Physiology 312
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1 April 2017
Metabolic anchor reactions for robust biorefining.
Jouhten, P., Huerta-Cepas, J., Bork, P. and Patil, K.R.
Metabolic Engineering 40
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March 2017
Bioinformatics analysis of functional associations of PTMs.
Minguez, P. and Bork, P.
Methods in Molecular Biology 1558
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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., Lu, G., Chen, X., Zhao, X.M. and Bork, P.
Nucleic Acids Research 45
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4 January 2017
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.
Szklarczyk, D., Morris, J.H., Cook, H., Kuhn, M., Wyder, S., Simonovic, M., Santos, A., Doncheva, N.T., Roth, A., Bork, P., Jensen, L.J. and von Mering, C.
Nucleic Acids Research 45
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4 January 2017
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.
Mende, D.R., Letunic, I., Huerta-Cepas, J., Li, S.S., Forslund, K., Sunagawa, S. and Bork, P.
Nucleic Acids Research 45
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4 January 2017
The endosomal transcriptional regulator RNF11 integrates degradation and transport of EGFR.
Scharaw, S., Iskar, M., Ori, A., Boncompain, G., Laketa, V., Poser, I., Lundberg, E., Perez, F., Beck, M., Bork, P. and Pepperkok, R.
Journal of Cell Biology 215
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21 November 2016
Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses.
Roux, S., Brum, J.R., Dutilh, B.E., Sunagawa, S., Duhaime, M.B., Loy, A., Poulos, B.T., Solonenko, N., Lara, E., Poulain, J., Pesant, S., Kandels-Lewis, S., Dimier, C., Picheral, M., Searson, S., Cruaud, C., Alberti, A., Duarte, C.M., Gasol, J.M., Vaque, D., Bork, P., Acinas, S.G., Wincker, P. and Sullivan, M.B.
Nature 537
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29 September 2016
CART - a chemical annotation retrieval toolkit.
Deghou, S., Zeller, G., Iskar, M., Driessen, M., Castillo, M., van Noort, V. and Bork, P.
Bioinformatics 32
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15 September 2016
MOCAT2: a metagenomic assembly, annotation and profiling framework.
Kultima, J.R., Coelho, L.P., Forslund, K., Huerta-Cepas, J., Li, S.S., Driessen, M., Voigt, A.Y., Zeller, G., Sunagawa, S. and Bork, P.
Bioinformatics 32
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15 August 2016
Human gut microbes impact host serum metabolome and insulin sensitivity.
Pedersen, H.K., Gudmundsdottir, V., Nielsen, H.B., Hyotylainen, T., Nielsen, T., Jensen, B.A.H., Forslund, K., Hildebrand, F., Prifti, E., Falony, G., Le Chatelier, E., Levenez, F., Doré, J., Mattila, I., Plichta, D.R., Pöhö, P., Hellgren, L.I., Arumugam, M., Sunagawa, S., Vieira-Silva, S., Jørgensen, T., Holm, J.B., Trošt, K., Kristiansen, K., Brix, S., Raes, J., Wang, J., Hansen, T., Bork, P., Brunak, S., Oresic, M., Ehrlich, S.D. and Pedersen, O.
Nature 535
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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
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8 July 2016
ETE 3: reconstruction, analysis and visualization of phylogenomic data.
Huerta-Cepas, J., Serra, F. and Bork, P.
Molecular Biology and Evolution 33
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June 2016
Colorectal cancer and the human gut microbiome: reproducibility with whole-genome shotgun sequencing.
Vogtmann, E., Hua, X., Zeller, G., Sunagawa, S., Voigt, A.Y., Hercog, R., Goedert, J.J., Shi, J., Bork, P. and Sinha, R.
PLoS ONE 11
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12 May 2016
Standardized benchmarking in the quest for orthologs.
Altenhoff, A.M., Boeckmann, B., Capella-Gutierrez, S., Dalquen, D.A., DeLuca, T., Forslund, K., Huerta-Cepas, J., Linard, B., Pereira, C., Pryszcz, L.P., Schreiber, F., da Silva, A.S., Szklarczyk, D., Train, C.M., Bork, P., Lecompte, O., von Mering, C., Xenarios, I., Sjölander, K., Jensen, L.J., Martin, M.J., Muffato, M., Gabaldón, T., Lewis, S.E., Thomas, P.D., Sonnhammer, E. and Dessimoz, C.
Nature Methods 13
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May 2016
Durable coexistence of donor and recipient strains after fecal microbiota transplantation.
Li, S.S., Zhu, A., Benes, V., Costea, P.I., Hercog, R., Hildebrand, F., Huerta-Cepas, J., Nieuwdorp, M., Salojaervi, J., Voigt, A.Y., Zeller, G., Sunagawa, S., de Vos, W.M. and Bork, P.
Science 352
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29 April 2016
Plankton networks driving carbon export in the oligotrophic ocean.
Guidi, L., Chaffron, S., Bittner, L., Eveillard, D., Larhlimi, A., Roux, S., Darzi, Y., Audic, S., Berline, L., Brum, J., Coelho, L.P., Espinoza, J.C.I., Malviya, S., Sunagawa, S., Dimier, C., Kandels-Lewis, S., Picheral, M., Poulain, J., Searson, S., Stemmann, L., Not, F., Hingamp, P., Speich, S., Follows, M., Karp-Boss, L., Boss, E., Ogata, H., Pesant, S., Weissenbach, J., Wincker, P., Acinas, S.G., Bork, P., de Vargas, C., Iudicone, D., Sullivan, M.B., Raes, J., Karsenti, E., Bowler, C. and Gorsky, G.
Nature 532
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28 April 2016
Energy efficiency trade-offs drive nucleotide usage in transcribed regions.
Chen, W.H., Lu, G., Bork, P., Hu, S. and Lercher, M.J.
Nature Communications 7
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21 April 2016
Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton.
Cornejo-Castillo, F.M., Cabello, A.M., Salazar, G., Sanchez-Baracaldo, P., Lima-Mendez, G., Hingamp, P., Alberti, A., Sunagawa, S., Bork, P., de Vargas, C., Raes, J., Bowler, C., Wincker, P., Zehr, J.P., Gasol, J.M., Massana, R. and Acinas, S.G.
Nature Communications 7
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22 March 2016
Spatiotemporal variation of mammalian protein complex stoichiometries.
Ori, A., Iskar, M., Buczak, K., Kastritis, P., Parca, L., Andres-Pons, A., Singer, S., Bork, P. and Beck, M.
Genome Biology 17
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14 March 2016
Bacterial antisense RNAs are mainly the product of transcriptional noise.
Llorens-Rico, V., Cano, J., Kamminga, T., Gil, R., Latorre, A., Chen, W.H., Bork, P., Glass, J.I., Serrano, L. and Lluch-Senar, M.
Science Advances 2
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4 March 2016
Gut microbiota linked to sexual preference and HIV infection.
Noguera-Julian, M., Rocafort, M., Guillen, Y., Rivera, J., Casadella, M., Nowak, P., Hildebrand, F., Zeller, G., Parera, M., Bellido, R., Rodriguez, C., Carrillo, J., Mothe, B., Coll, J., Bravo, I., Estany, C., Herrero, C., Saz, J., Sirera, G., Torrela, A., Navarro, J., Crespo, M., Brander, C., Negredo, E., Blanco, J., Guarner, F., Calle, M.L., Bork, P., Soennerborg, A., Clotet, B. and Paredes, R.
EBioMedicine 5
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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., van Noort, V., Lluch-Senar, M., Hennrich, M.L., Wodke, J.A.H., Yus, E., Alibes, A., Roma, G., Mende, D.R., Pesavento, C., Typas, A., Gavin, A.C., Serrano, L. and Bork, P.
Nucleic Acids Research 44
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18 February 2016
STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.
Szklarczyk, D., Santos, A., von Mering, C., Jensen, L.J., 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., Letunic, I., 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., Szklarczyk, D., Forslund, K., Cook, H., Heller, D., Walter, M.C., Rattei, T., Mende, D.R., Sunagawa, S., Kuhn, M., Jensen, L.J., von Mering, C. and Bork, P.
Nucleic Acids Research 44
(D1): D286-D293.
4 January 2016
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.
Forslund, K., Hildebrandt, F., Nielsen, T., Falony, G., Le Chatelier, E., Sunagawa, S., Prifti, E., Vieira-Silva, S., Gudmundsdottir, V., Pedersen, H.K., Arumugam, M., Kristiansen, K., Voigt, A.Y., Vestergaard, H., Hercog, R., Costea, P.I., Kultima, J.R., Li, J., Jørgensen, T., Levenez, F., Dore, J., Nielsen, H.B., Brunak, S., Raes, J., Hansen, T., Wang, J., Ehrlich, S.D., 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., Minguez, P., Bork, P., Auburger, J.J., Guilbride, D.L., 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., Toyama, B.H., Harris, M.S., Bock, T., Iskar, M., Bork, P., Ingolia, N.T., 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., Marcet-Houben, M., Rees, J.A., Forslund, K., Huerta-Cepas, J., Muffato, M., Yilmaz, P., Xenarios, I., Bork, P., 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., Faust, K., Henry, N., Decelle, J., Colin, S., Carcillo, F., Chaffron, S., Ignacio-Espinosa, J.C., Roux, S., Vincent, F., Bittner, L., Darzi, Y., Wang, J., Audic, S., Berline, L., Bontempi, G., Cabello, A.M., Coppola, L., Cornejo-Castillo, F.M., d' Ovidio, F., De Meester, L., Ferrera, I., Garet-Delmas, M.J., Guidi, L., Lara, E., Pesant, S., Royo-Llonch, M., Salazar, G., Sanchez, P., Sebastian, M., Souffreau, C., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Gorsky, G., Not, F., Ogata, H., Speich, S., Stemmann, L., Weissenbach, J., Wincker, P., Acinas, S.G., Sunagawa, S., Bork, P., Sullivan, M.B., Karsenti, E., Bowler, C., de Vargas, C. and Raes, J.
Science 348
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22 May 2015
Environmental characteristics of Agulhas rings affect interocean plankton transport.
Villar, E., Farrant, G.K., Follows, M., Garczarek, L., Speich, S., Audic, S., Bittner, L., Blanke, B., Brum, J.R., Brunet, C., Casotti, R., Chase, A., Dolan, J.R., d'Ortenzio, F., Gattuso, J.P., Grima, N., Guidi, L., Hill, C.N., Jahn, O., Jamet, J.L., Le Goff, H., Lepoivre, C., Malviya, S., Pelletier, E., Romagnan, J.B., Roux, S., Santini, S., Scalco, E., Schwenck, S.M., Tanaka, A., Testor, P., Vannier, T., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Acinas, S.G., Bork, P., Boss, E., de Vargas, C., Gorsky, G., Ogata, H., Pesant, S., Sullivan, M.B., Sunagawa, S., Wincker, P., Karsenti, E., Bowler, C., Not, F., Hingamp, P. and Iudicone, D.
Science 348
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22 May 2015
Eukaryotic plankton diversity in the sunlit ocean.
de Vargas, C., Audic, S., Henry, N., Decelle, J., Mahe, F., Logares, R., Lara, E., Berney, C., Le Bescot, N., Probert, I., Carmichael, M., Poulain, J., Romac, S., Colin, S., Aury, J.M., Bittner, L., Chaffron, S., Dunthorn, M., Engelen, S., Flegontova, O., Guidi, L., Horak, A., Jaillon, O., Lima-Mendez, G., Lukes, J., Malviya, S., Morard, R., Mulot, M., Scalco, E., Siano, R., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Acinas, S.G., Bork, P., Bowler, C., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Not, F., Ogata, H., Pesant, S., Raes, J., Sieracki, M.E., Speich, S., Stemmann, L., Sunagawa, S., Weissenbach, J., Wincker, P. and Karsenti, E.
Science 348
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22 May 2015
Patterns and ecological drivers of ocean viral communities.
Brum, J.R., Ignacio-Espinoza, J.C., Roux, S., Doulcier, G., Acinas, S.G., Alberti, A., Chaffron, S., Cruaud, C., de Vargas, C., Gasol, J.M., Gorsky, G., Gregory, A.C., Guidi, L., Hingamp, P., Iudicone, D., Not, F., Ogata, H., Pesant, S., Poulos, B.T., Schwenck, S.M., Speich, S., Dimier, C., Kandels-Lewis, S., Picheral, M., Searson, S., Bork, P., Bowler, C., Sunagawa, S., Wincker, P., Karsenti, E. and Sullivan, M.B.
Science 348
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22 May 2015
Structure and function of the global ocean microbiome.
Sunagawa, S., Coelho, L.P., Chaffron, S., Kultima, J.R., Labadie, K., Salazar, G., Djahanschiri, B., Zeller, G., Mende, D.R., Alberti, A., Cornejo-Castillo, F.M., Costea, P.I., Cruaud, C., d'Ovidio, F., Engelen, S., Ferrera, I., Gasol, J.M., Guidi, L., Hildebrand, F., Kokoszka, F., Lepoivre, C., Lima-Mendez, G., Poulain, J., Poulos, B.T., Royo-Llonch, M., Sarmento, H., Vieira-Silva, S., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Bowler, C., de Vargas, C., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Jaillon, O., Not, F., Ogata, H., Pesant, S., Speich, S., Stemmann, L., Sullivan, M.B., Weissenbach, J., Wincker, P., Karsenti, E., Raes, J., Acinas, S.G. and Bork, P.
Science 348
(6237): 1261359.
22 May 2015
Temporal and technical variability of human gut metagenomes.
Voigt, A.Y., Costea, P.I., Kultima, J.R., Li, S.S., Zeller, G., 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., Letunic, I., Parca, L., Garcia-Alonso, L., Dopazo, J., 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., Delgado, J., Chen, W.-H., Llorens-Rico, V., O'Reilly, F.J., Wodke, J.A.H., Unal, E.B., Yus, E., Martinez, S., Nichols, R.J., Ferrar, T., Vivancos, A., Schmeisky, A., Stuelke, J., van Noort, V., Gavin, A.-C., Bork, P. and Serrano, L.
Molecular Systems Biology 11
(1): 780.
21 January 2015
Potential of fecal microbiota for early-stage detection of colorectal cancer.
Zeller, G., Tap, J., Voigt, A.Y., Sunagawa, S., Kultima, J.R., Costea, P.I., Amiot, A., Boehm, J., Brunetti, F., Habermann, N., Hercog, R., Koch, M., Luciani, A., Mende, D.R., Schneider, M.A., Schrotz-King, P., Tournigand, C., Tran Van Nhieu, J., Yamada, T., Zimmermann, J., Benes, V., Kloor, M., Ulrich, C.M., von Knebel Doeberitz, M., 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., Forslund, K., Larsson, T., Powell, S., Doerks, T., 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., Schoelch, S., Iskar, M., Zeller, G., Ostertag, K., Schweitzer, C., Werner, K., Weitz, J., 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., Tito, R.Y., Voigt, A.Y., 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., Jia, H., Cai, X., Zhong, H., Feng, Q., Sunagawa, S., Arumugam, M., Kultima, J.R., Prifti, E., Nielsen, T., Juncker, A.S., Manichanh, C., Chen, B., Zhang, W., Levenez, F., Wang, J., Xu, X., Xiao, L., Liang, S., Zhang, D., Zhang, Z., Chen, W., Zhao, H., Al-Aama, J.Y., Edris, S., Yang, H., Wang, J., Hansen, T., Nielsen, H.B., Brunak, S., Kristiansen, K., Guarner, F., Pedersen, O., Dore, J., Ehrlich, S.D., 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., Almeida, M., Juncker, A.S., Rasmussen, S., Li, J., Sunagawa, S., Plichta, D.R., Gautier, L., Pedersen, A.G., Le Chatelier, E., Pelletier, E., Bonde, I., Nielsen, T., Manichanh, C., Arumugam, M., Batto, J.M., Quintanilha Dos Santos, M.B., Blom, N., Borruel, N., Burgdorf, K.S., Boumezbeur, F., Casellas, F., Dore, J., Dworzynski, P., Guarner, F., Hansen, T., Hildebrand, F., Kaas, R.S., Kennedy, S., Kristiansen, K., Kultima, J.R., Leonard, P., Levenez, F., Lund, O., Moumen, B., Le Paslier, D., Pons, N., Pedersen, O., Prifti, E., Qin, J., Raes, J., Sorensen, S., Tap, J., Tims, S., Ussery, D.W., Yamada, T., Renault, P., Sicheritz-Ponten, T., Bork, P., Wang, J., Brunak, S. and Ehrlich, S.D.
Nature Biotechnology 32
(8): 822-828.
August 2014
STITCH 4: integration of protein-chemical interactions with user data.
Kuhn, M., Szklarczyk, D., Pletscher-Frankild, S., Blicher, T.H., von Mering, C., 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., Forslund, K., Szklarczyk, D., Trachana, K., Roth, A., Huerta-Cepas, J., Gabaldon, T., Rattei, T., Creevey, C., Kuhn, M., Jensen, L.J., von Mering, C. and Bork, P.
Nucleic Acids Research 42
(1): D231-D239.
1 January 2014
Metagenomic species profiling using universal phylogenetic marker genes.
Sunagawa, S., Mende, D.R., Zeller, G., Izquierdo-Carrasco, F., Berger, S.A., Kultima, J.R., Coelho, L.P., Arumugam, M., Tap, J., Nielsen, H.B., Rasmussen, S., Brunak, S., Pedersen, O., Guarner, F., de Vos, W.M., Wang, J., Li, J., Dore, J., Ehrlich, S.D., Stamatakis, A. and Bork, P.
Nature Methods 10
(12): 1196-1199.
December 2013
Accurate and universal delineation of prokaryotic species.
Mende, D.R., Sunagawa, S., 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., Zhao, X.M., van Noort, V. and Bork, P.
PLoS Computational Biology 9
(5): e1003073.
May 2013
Consistent mutational paths predict eukaryotic thermostability.
van Noort, V., Bradatsch, B., Arumugam, M., Amlacher, S., Bange, G., Creevey, C., Falk, S., Mende, D.R., Sinning, I., Hurt, E. and Bork, P.
BMC Evolutionary Biology 13
: 7.
10 January 2013
Genomic variation landscape of the human gut microbiome.
Schloissnig, S., Arumugam, M., Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D.R., Kultima, J.R., Martin, J., Kota, K., Sunyaev, S.R., 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., Letunic, I., 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., Szklarczyk, D., Frankild, S., Kuhn, M., Simonovic, M., Roth, A., Lin, J., Minguez, P., Bork, P., 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., Zeller, G., Blattmann, P., Campillos, M., Kuhn, M., Kaminska, K.H., Runz, H., Gavin, A.C., Pepperkok, R., van Noort, V. and Bork, P.
Molecular Systems Biology 9
: 662.
2013
Systematic identification of proteins that elicit drug side effects.
Kuhn, M., Al Banchaabouchi, M., Campillos, M., Jensen, L.J., Gross, C., Gavin, A.C. and Bork, P.
Molecular Systems Biology 9
: 663.
2013
MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit.
Kultima, J.R., Sunagawa, S., Li, J., Chen, W., Chen, H., Mende, D.R., Arumugam, M., Pan, Q., Liu, B., Qin, J., Wang, J. and Bork, P.
PLoS ONE 7
(10): e47656.
17 October 2012
Deciphering a global network of functionally associated post-translational modifications.
Minguez, P., Parca, L., Diella, F., Mende, D.R., Kumar, R., Helmer-Citterich, M., Gavin, A.C., 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., Waller, A.S., Raes, J., Zelezniak, A., Perchat, N., Perret, A., Salanoubat, M., Patil, K.R., 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., van Noort, V., 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., Waller, A.S., Sunagawa, S., Jaervelin, A.I., Chan, M.M., Arumugam, M., 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., Szklarczyk, D., Trachana, K., Roth, A., Kuhn, M., Muller, J., Arnold, R., Rattei, T., Letunic, I., Doerks, T., Jensen, L.J., 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., Minguez, P., 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., Szklarczyk, D., Franceschini, A., von Mering, C., Jensen, L.J. and Bork, P.
Nucleic Acids Research 40
(Database Issue): D876-D880.
January 2012
Prediction of drug combinations by integrating molecular and pharmacological data.
Zhao, X.M., Iskar, M., Zeller, G., Kuhn, M., van Noort, V. and Bork, P.
PLoS Computational Biology 7
(12): e1002323.
29 December 2011
Identifying single copy orthologs in Metazoa.
Creevey, C.J., Muller, J., Doerks, T., Thompson, J.D., 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., Larsson, T.A., Powell, S., Chen, W.H., Doerks, T., 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., Iskar, M., Zeller, G., van Noort, V. and Bork, P.
PLoS ONE 6
(7): e22187.
13 July 2011
Enterotypes of the human gut microbiome.
Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D.R., Fernandes, G.R., Tap, J., Bruls, T., Batto, J.M., Bertalan, M., Borruel, N., Casellas, F., Fernandez, L., Gautier, L., Hansen, T., Hattori, M., Hayashi, T., Kleerebezem, M., Kurokawa, K., Leclerc, M., Levenez, F., Manichanh, C., Nielsen, H.B., Nielsen, T., Pons, N., Poulain, J., Qin, J., Sicheritz-Ponten, T., Tims, S., Torrents, D., Ugarte, E., Zoetendal, E.G., Wang, J., Guarner, F., Pedersen, O., de Vos, W.M., Brunak, S., Dore, J., Weissenbach, J., 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., Letunic, I., Yamada, T., 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., Franceschini, A., Kuhn, M., Simonovic, M., Roth, A., Minguez, P., Doerks, T., Stark, M., Muller, J., Bork, P., Jensen, L.J. and von Mering, C.
Nucleic Acids Research 39
(Database issue): D561-D568.
January 2011
A network of conserved co-occurring motifs for the regulation of alternative splicing.
Suyama, M., Harrington, E.D., Vinokourova, S., von Knebel Doeberitz, M., 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., Arumugam, M., Raes, J., Bork, P. and Relman, D.A.
Bioinformatics 26
(23): 2979-2980.
1 December 2010
SmashCommunity: A metagenomic annotation and analysis tool.
Arumugam, M., Harrington, E.D., Foerstner, K.U., Raes, J. and Bork, P.
Bioinformatics 26
(23): 2977-2978.
1 December 2010
Drug-induced regulation of target expression.
Iskar, M., Campillos, M., Kuhn, M., Jensen, L.J., 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., Luganskaja, T., Vujic-Spasic, M., Hentze, M.W., Muckenthaler, M.U., 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., Jensen, L.J., Ritchie, M.E., Toedling, J., Ning, Y., Bork, P., 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., 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., Raible, F., Tomer, R., Simakov, O., Trachana, K., Klaus, S., Snyman, H., Hannon, G.J., Bork, P. and Arendt, D.
Nature 463
(7284): 1084-1088.
25 February 2010
AQUA: Automated quality improvement for multiple sequence alignments.
Muller, J., Creevey, C.J., Thompson, J.D., 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., Herbach, N., Kerling, C., Seifert, M., Fillebeen, C., Prysch, I., Reich, J., 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., Szklarczyk, D., Franceschini, A., Campillos, M., von Mering, C., Jensen, L.J., 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., Yuan, Y.P., Benner, A., Korff, S., 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., Szklarczyk, D., Julien, P., Letunic, I., Roth, A., Kuhn, M., Powell, S., von Mering, C., Doerks, T., 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., Campillos, M., Letunic, I., Jensen, L.J. and Bork, P.
Molecular Systems Biology 6
: 343.
2010
Impact of genome reduction on bacterial metabolism and its regulation.
Yus, E., Maier, T., Michalodimitrakis, K., van Noort, V., Yamada, T., Chen, W.H., Wodke, J.A., Gueell, M., Martinez, S., Bourgeois, R., Kuehner, S., Raineri, E., Letunic, I., Kalinina, O.V., Rode, M., Herrmann, R., Gutierrez-Gallego, R., Russell, R.B., Gavin, A.C., Bork, P. and Serrano, L.
Science 326
(5957): 1263-1268.
27 November 2009
Proteome organization in a genome-reduced bacterium.
Kuehner, S., van Noort, V., Betts, M.J., Leo-Macias, A., Batisse, C., Rode, M., Yamada, T., Maier, T., Bader, S., Beltran-Alvarez, P., Castano-Diez, D., Chen, W.H., Devos, D., Gueell, M., Norambuena, T., Racke, I., Rybin, V., Schmidt, A., Yus, E., Aebersold, R., Herrmann, R., Boettcher, B., Frangakis, A.S., Russell, R.B., Serrano, L., Bork, P. and Gavin, A.C.
Science 326
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27 November 2009
Transcriptome complexity in a genome-reduced bacterium.
Gueell, M., van Noort, V., Yus, E., Chen, W.H., Leigh-Bell, J., Michalodimitrakis, K., Yamada, T., Arumugam, M., Doerks, T., Kuehner, S., Rode, M., Suyama, M., Schmidt, S., Gavin, A.C., Bork, P. and Serrano, L.
Science 326
(5957): 1268-1271.
27 November 2009
Ageing-related chromatin defects through loss of the NURD complex.
Pegoraro, G., Kubben, N., Wickert, U., Goehler, H., 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., Bernstein, H.G., Krell, D., Dobrowolny, H., Bielau, H., Steiner, J., Gos, T., Funke, S., Stauch, R., Knueppel, S. and Bogerts, B.
Brain Research 1269
: 166-175.
7 May 2009
FragIdent - automatic identification and characterisation of cDNA-fragments.
Seelow, D., Goehler, H. and Hoffmann, K.
BMC Genomics 10
: 95.
2 March 2009
ASTD: The Alternative Splicing and Transcript Diversity database.
Koscielny, G., Texier, V.L., Gopalakrishnan, C., Kumanduri, V., Riethoven, J.J., Nardone, F., Stanley, E., Fallsehr, C., Hofmann, O., Kull, M., Harrington, E., Boue, S., Eyras, E., Plass, M., Lopez, F., Ritchie, W., Moucadel, V., Ara, T., Pospisil, H., Herrmann, A., Reich, J.G., Guigo, R., Bork, P., Doeberitz, M.V., Vilo, J., Hide, W., Apweiler, R., Thanaraj, T.A. and Gautheret, D.
Genomics 93
(3): 213-220.
March 2009
Quantifying environmental adaptation of metabolic pathways in metagenomics.
Gianoulis, T.A., Raes, J., Patel, P.V., Bjornson, R., Korbel, J.O., Letunic, I., Yamada, T., Paccanaro, A., Jensen, L.J., Snyder, M., 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
Discovering functional novelty in metagenomes: examples from light-mediated processes.
Singh, A.H., Doerks, T., Letunic, I., Raes, J. and Bork, P.
Journal of Bacteriology 191
(1): 32-41.
January 2009
InterPro: the integrative protein signature database.
Hunter, S., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Das, U., Daugherty, L., Duquenne, L., Finn, R.D., Gough, J., Haft, D., Hulo, N., Kahn, D., Kelly, E., Laugraud, A., Letunic, I., Lonsdale, D., Lopez, R., Madera, M., Maslen, J., McAnulla, C., McDowall, J., Mistry, J., Mitchell, A., Mulder, N., Natale, D., Orengo, C., Quinn, A.F., Selengut, J.D., Sigrist, C.J., Thimma, M., Thomas, P.D., Valentin, F., Wilson, D., 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., 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., Kuhn, M., Stark, M., Chaffron, S., Creevey, C., Muller, J., Doerks, T., Julien, P., Roth, A., Simonovic, M., Bork, P. and von Mering, C.
Nucleic Acids Research 37
(Database Issue): D412-D416.
January 2009
A nitrile hydratase in the eukaryote monosiga brevicollis.
Foerstner, K.U., Doerks, T., Muller, J., 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., Tomancak, P., Lopez-Marti, J., Suyama, M., Bork, P., Milan, M., Torrents, D. and Manzanares, M.
Genome Biology 9
(12): R176.
16 December 2008
Modelling phagosomal lipid networks that regulate actin assembly.
Kuehnel, M., Mayorga, L.S., Dandekar, T., Thakar, J., Schwarz, R., Anes, E., 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., Liu, R., Parusel, C., Boecher, N., Schultz, J., Bork, P., Pfitzner, E., 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., Woerner, S.M., Yuan, Y.P., Bork, P., 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., Doerks, T., Creevey, C.J., Doerks, A. and Bork, P.
PLoS ONE 3
(10): e3515.
27 October 2008
Linear motif atlas for phosphorylation-dependent signaling.
Miller, M.L., Jensen, L.J., Diella, F., Jorgensen, C., Tinti, M., Li, L., Hsiung, M., Parker, S.A., Bordeaux, J., Sicheritz-Ponten, T., Olhovsky, M., Pasculescu, A., Alexander, J., Knapp, S., Blom, N., Bork, P., Li, S., Cesareni, G., Pawson, T., Turk, B.E., Yaffe, M.B., 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
Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages.
Pincus, D., Letunic, I., 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., Harrington, E.D. and Bork, P.
BMC Genomics 9
(1): 335.
15 July 2008
Drug target identification using side-effect similarity.
Campillos, M., Kuhn, M., Gavin, A.C., 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., Raes, J., Foerstner, K.U., Harrington, E.D., Dalevi, D. and Bork, P.
PLoS ONE 3
(7): e2607.
9 July 2008
KEGG Atlas mapping for global analysis of metabolic pathways.
Okuda, S., Yamada, T., Hamajima, M., Itoh, M., Katayama, T., Bork, P., Goto, S. and Kanehisa, M.
Nucleic Acids Research 36
(Web Server Issue): W423-W426.
1 July 2008
Computational lipidology: predicting lipoprotein density profiles in human blood plasma.
Huebner, K., Schwager, T., Winkler, K., Reich, J.G. and Holzhuetter, H.G.
PLoS Computational Biology 4
(5): e1000079.
23 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., Suyama, M., Pelucchi, P., Boi, S., Guffanti, A., Rizzi, E., Bork, P., Tenchini, M.L. and Ciccarelli, F.D.
BMC Genomics 9
(1): 174.
16 April 2008
Large-scale prediction of drug-target relationships.
Kuhn, M., Campillos, M., Gonzalez, P., Jensen, L.J. and Bork, P.
FEBS Letters 582
(8): 1283-1290.
9 April 2008
Predicting biological networks from genomic data.
Harrington, E.D., Jensen, L.J. and Bork, P.
FEBS Letters 582
(8): 1251-1258.
9 April 2008
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans.
King, N., Westbrook, M.J., Young, S.L., Kuo, A., Abedin, M., Chapman, J., Fairclough, S., Hellsten, U., Isogai, Y., Letunic, I., Marr, M., Pincus, D., Putnam, N., Rokas, A., Wright, K.J., Zuzow, R., Dirks, W., Good, M., Goodstein, D., Lemons, D., Li, W., Lyons, J.B., Morris, A., Nichols, S., Richter, D.J., Salamov, A., Sequencing, J.G.I., Bork, P., Lim, W.A., Manning, G., Miller, W.T., McGinnis, W., Shapiro, H., Tjian, R., 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., Tripathi, L.P., Jensen, L.J., Gahnim, M., Mason, C., Furlong, E.E., Rodrigues, V., White, K.P., 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., Berube, H., Letunic, I., Weeber, P.D., Gagneur, J., Girardot, C., Kapushesky, M., Arendt, D., Bork, P., Brazma, A., Furlong, E.E., 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., Jensen, L.J., Pasculescu, A., Olhovsky, M., Colwill, K., Bork, P., 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., von Mering, C., Campillos, M., 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., Kuhn, M., Dunkel, M., Campillos, M., Senger, C., Petsalaki, E., Ahmed, J., Urdiales, E.G., Gewiess, A., Jensen, L.J., Schneider, R., Skoblo, R., Russell, R.B., Bourne, P.E., 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., Julien, P., Kuhn, M., von Mering, C., Muller, J., Doerks, T. and Bork, P.
Nucleic Acids Research 36
(Database issue): D250-D254.
January 2008
Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat.
Kunin, V., Raes, J., Harris, J.K., Spear, J.R., Walker, J.J., Ivanova, N., von Mering, C., Bebout, B.M., Pace, N.R., Bork, P. and Hugenholtz, P.
Molecular Systems Biology 4
: 198.
2008
Genome-wide experimental determination of barriers to horizontal gene transfer.
Sorek, R., Zhu, Y., Creevey, C.J., Francino, M.P., 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., Rehwinkel, J., Stricker, M., Huntzinger, E., Yang, S.F., Doerks, T., Dorner, S., Bork, P., Boutros, M. and Izaurralde, E.
Genes & Development 21
(20): 2558-2570.
15 October 2007
Mutations in the gene encoding the 3'-5' DNA exonuclease TREX1 are associated with systemic lupus erythematosus.
Lee-Kirsch, M.A., Gong, M., Chowdhury, D., Senenko, L., Engel, K., Lee, Y.A., de Silva, U., Bailey, S.L., Witte, T., Vyse, T.J., Kere, J., Pfeiffer, C., Harvey, S., Wong, A., Koskenmies, S., Hummel, O., Rohde, K., Schmidt, R.E., Dominiczak, A.F., Gahr, M., Hollis, T., Perrino, F.W., 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., Marenholz, I., Kerscher, T., Rueschendorf, F., Esparza-Gordillo, J., Worm, M., Gruber, C., Mayr, G., Albrecht, M., Rohde, K., Schulz, H., Wahn, U., 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., Singh, A.H., Doerks, T., Letunic, I., von Mering, C., Jensen, L.J., 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., Jensen, T.S., Brunak, S., 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., Dandekar, T., Korbel, J., 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., Mattheisen, M., Dahm, S., Nuernberg, P., Roe, C., Johnson, J., Cox, N.J., Wichmann, H.E., Wienker, T.F., Schulze, J., 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., 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., Jensen, L.J., Ostheimer, G.J., van Vugt, M.A., Jorgensen, C., Miron, I.M., Diella, F., Colwill, K., Taylor, L., Elder, K., Metalnikov, P., Nguyen, V., Pasculescu, A., Jin, J., Park, J.G., Samson, L.D., Woodgett, J.R., Russell, R.B., Bork, P., 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., Kaufmann, I., Gentzel, M., Foerstner, K.U., Gantzert, A.S., Gehring, N.H., Neu-Yilik, G., Bork, P., Keller, W., Wilm, M., 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., Harrington, E.D., 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., Steffens, C., von Mering, C., Bork, P., Stahl, U. and Lang, C.
Journal of Biotechnology 130
(1): 1-10.
31 May 2007
Quantitative phylogenetic assessment of microbial communities in diverse environments.
von Mering, C., Hugenholtz, P., Raes, J., Tringe, S.G., Doerks, T., Jensen, L.J., Ward, N. and Bork, P.
Science 315
(5815): 1126-1130.
23 February 2007
Prediction of effective genome size in metagenomic samples.
Raes, J., Korbel, J.O., Lercher, M.J., 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., Boue, S., Krause, R., Jensen, L.J., Mason, C.E., Ghanim, M., White, K.P., Furlong, E.E. and Bork, P.
Molecular Systems Biology 3
: 72.
January 2007
New developments in the InterPro database.
Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Buillard, V., Cerutti, L., Copley, R., Courcelle, E., Das, U., Daugherty, L., Dibley, M., Finn, R., Fleischmann, W., Gough, J., Haft, D., Hulo, N., Hunter, S., Kahn, D., Kanapin, A., Kejariwal, A., Labarga, A., Langendijk-Genevaux, P.S., Lonsdale, D., Lopez, R., Letunic, I., Madera, M., Maslen, J., McAnulla, C., McDowall, J., Mistry, J., Mitchell, A., Nikolskaya, A.N., Orchard, S., Orengo, C., Petryszak, R., Selengut, J.D., Sigrist, C.J., Thomas, P.D., Valentin, F., Wilson, D., 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., Jensen, L.J., Kuhn, M., Chaffron, S., Doerks, T., Krueger, B., Snel, B. and Bork, P.
Nucleic Acids Research 35
(Database Issue): D358-D362.
January 2007
Opsins and clusters of sensory G-protein-coupled receptors in the sea urchin genome.
Raible, F., Tessmar-Raible, K., Arboleda, E., Kaller, T., Bork, P., Arendt, D. and Arnone, M.I.
Developmental Biology 300
(1): 461-475.
1 December 2006
Computational characterization of multiple Gag-like human proteins.
Campillos, M., Doerks, T., Shah, P.K. and Bork, P.
Trends in Genetics 22
(11): 585-589.
November 2006
Assessing systems properties of yeast mitochondria through an interaction map of the organelle.
Perocchi, F., Jensen, L.J., Gagneur, J., Ahting, U., von Mering, C., Bork, P., 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., Jensen, T.S., de Lichtenberg, U., 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., Knoblauch, H., Costanza, M.C., Luganskaja, T., Toliat, M.R., Nuernberg, P., Luft, F.C., 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., Rehwinkel, J., Doerks, T., Stark, A., 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., 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., Harrington, E., Bork, P. and Torrents, D.
PLoS Computational Biology 2
(6): e76 (627-636).
30 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., Herrmann, A., Butherus, K., Pirson, S., 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., Sahin-Toth, M., Landt, O., Chen, J.M., Kaehne, T., Drenth, J.P., Kukor, Z., Szepessy, E., Halangk, W., Dahm, S., Rohde, K., Schulz, H.U., Le Marechal, C., Akar, N., Ammann, R.W., Truninger, K., Bargetzi, M., Bhatia, E., Castellani, C., Cavestro, G.M., Cerny, M., Destro-Bisol, G., Spedini, G., Eiberg, H., Jansen, J.B., Koudova, M., Rausova, E., Macek, M., Malats, N., Real, F.X., Menzel, H.J., Moral, P., Galavotti, R., Pignatti, P.F., Rickards, O., Spicak, J., Zarnescu, N.O., Boeck, W., Gress, T.M., Friess, H., Ockenga, J., Schmidt, H., Pfuetzer, R., Loehr, M., Simon, P., Weiss, F.U., Lerch, M.M., Teich, N., Keim, V., Berg, T., Wiedenmann, B., Luck, W., Groneberg, D.A., Becker, M., Keil, T., Kage, A., Bernardova, J., Braun, M., Gueldner, C., Halangk, J., Rosendahl, J., Witt, U., Treiber, M., 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., Jensen, L.J., Jakobsen, J.S., Karzynski, M.M., Eichenlaub, M.P., 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., Aloy, P., Grandi, P., Krause, R., Boesche, M., Marzioch, M., Rau, C., Jensen, L.J., Bastuck, S., Duempelfeld, B., Edelmann, A., Heurtier, M.A., Hoffman, V., Hoefert, C., Klein, K., Hudak, M., Michon, A.M., Schelder, M., Schirle, M., Remor, M., Rudi, T., Hooper, S., Bauer, A., Bouwmeester, T., Casari, G., Drewes, G., Neubauer, G., Rick, J.M., Kuster, B., Bork, P., 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., 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., Jensen, L.J., Ouzounova, R., 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., Doerks, T., von Mehring, C., Creevey, C.J., Snel, B. and Bork, P.
Science 311
(5765): 1283-1287.
3 March 2006
Identification and analysis of evolutionarily cohesive functional modules in protein networks.
Campillos, M., von Mering, C., 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., Copley, R.R., Pils, B., Pinkert, S., Schultz, J. and Bork, P.
Nucleic Acids Research 34
(Database Issue): D257-D260.
1 January 2006
Linkage analysis of alcohol dependence using MOD scores.
Strauch, K., Fuerst, R., Rueschendorf, F., Windemuth, C., Dietter, J., Flaquer, A., 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., Tessmar-Raible, K., Osoegawa, K., Wincker, P., Jubin, C., Balavoine, G., Ferrier, D., Benes, V., de Jong, P., Weissenbach, J., 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., Keller, P., Kavagiou, Z., Jensen, L.J., Colombelli, J., Bork, P., 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., Letunic, I., Raes, J., Bork, P. and Izaurralde, E.
RNA 11
(10): 1530-1544.
October 2005
Environments shape the nucleotide composition of genomes.
Foerstner, K.U., von Mering, C., 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., Lathe, W.C. and Bork, P.
FEBS Letters 579
(24): 5281-5286.
21 September 2005
G2D: A tool for mining genes associated with disease.
Perez-Iratxeta, C., Wjst, M., 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., Rock, R., Ciccarelli, F.D., Leberfinger, C.B., Borawski, J.M., Bork, P., Wiese, S., 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., 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., Scheich, C., Sievert, V., Harttig, U., Schultz, J., Simon, B., Bork, P., Lehrach, H. and Heinemann, U.
Microbial Cell Factories 4
: 21.
5 July 2005
Extraction of transcript diversity from scientific literature.
Shah, P.K., Jensen, L.J., 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., Doerks, T., Jensen, L.J., Perez-Iratxeta, C., Kaczanowski, S., Hooper, S.D., 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., Campillos, M., Harrington, E.D., 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., Jensen, L.J., 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., Meyer, B., Fuchs, H., Stoeger, T., Eder, G., Rueschendorf, F., Heyder, J., Nuernberg, P., Hrabe de Angelis, M. and Schulz, H.
American Journal of Respiratory and Critical Care Medicine 171
: 880-888.
7 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., Dahm, S., Suk, A., Kobyliansky, E., Toliat, M.R., Ruf, N., 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., Rohde, K., Becker, C., Toliat, M., Entz, P., Suk, A., Mueller, N., Sindern, E., Haupts, M., Schimrigk, S., 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., Zdobnov, E.M., Bork, P., Pevzner, P.A. and Tesler, G.
Genome Research 15
: 98-110.
1 January 2005
Comparative metagenomics of microbial communities.
Tringe, S.G., von Mering, C., Kobayashi, A., Salamov, A.A., Chen, K., Chang, H.W., Podar, M., Short, J.M., Mathur, E.J., Detter, J.C., Bork, P., 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., Jensen, L.J., Fausboll, A., Jensen, T.S., Bork, P. and Brunak, S.
Bioinformatics 21
: 1164-1171.
1 January 2005
Complex genomic rearrangements lead to novel primate gene function.
Ciccarelli, F.D., von Mering, C., Suyama, M., Harrington, E.D., Izaurralde, E. and Bork, P.
Genome Research 15
(3): 343-351.
1 January 2005
GandrKB - ontological microarray annotation and visualization.
Schober, D., Leser, U., 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., Graves, T.A., Fulton, R.S., Fulton, L.A., Pepin, K.H., Minx, P., Wagner-McPherson, C., Layman, D., Wylie, K., Sekhon, M., Becker, M.C., Fewell, G.A., Delehaunty, K.D., Miner, T.L., Nash, W.E., Kremitzki, C., Oddy, L., Du, H., Sun, H., Bradshaw-Cordum, H., Ali, J., Carter, J., Cordes, M., Harris, A., Isak, A., van Brunt, A., Nguyen, C., Du, F., Courtney, L., Kalicki, J., Ozersky, P., Abbott, S., Armstrong, J., Belter, E.A., Caruso, L., Cedroni, M., Cotton, M., Davidson, T., Desai, A., Elliott, G., Erb, T., Fronick, C., Gaige, T., Haakenson, W., Haglund, K., Holmes, A., Harkins, R., Kim, K., Kruchowski, S.S., Strong, C.M., Grewal, N., Goyea, E., Hou, S., Levy, A., Martinka, S., Mead, K., McLellan, M.D., Meyer, R., Randall-Maher, J., Tomlinson, C., uphin-Kohlberg, S., Kozlowicz-Reilly, A., Shah, N., Swearengen-Shahid, S., Snider, J., Strong, J.T., Thompson, J., Yoakum, M., Leonard, S., Pearman, C., Trani, L., Radionenko, M., Waligorski, J.E., Wang, C., Rock, S.M., Tin-Wollam, A.M., Maupin, R., Latreille, P., Wendl, M.C., Yang, S.P., Pohl, C., Wallis, J.W., Spieth, J., Bieri, T.A., Berkowicz, N., Nelson, J.O., Osborne, J., Ding, L., Meyer, R., Sabo, A., Shotland, Y., Sinha, P., Wohldmann, P.E., Cook, L.L., Hickenbotham, M.T., Eldred, J., Williams, D., Jones, T.A., She, X., Ciccarelli, F.D., Izaurralde, E., Taylor, J., Schmutz, J., Myers, R.M., Cox, D.R., Huang, X., McPherson, J.D., Mardis, E.R., Clifton, S.W., Warren, W.C., Chinwalla, A.T., Eddy, S.R., Marra, M.A., Ovcharenko, I., Furey, T.S., Miller, W., Eichler, E.E., Bork, P., Suyama, M., Torrents, D., 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., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bradley, P., Bork, P., Bucher, P., Cerutti, L., Copley, R., Courcelle, E., Das, U., Durbin, R., Fleischmann, W., Gough, J., Haft, D., Harte, N., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lonsdale, D., Lopez, R., Letunic, I., Madera, M., Maslen, J., McDowall, J., Mitchell, A., Nikolskaya, A.N., Orchard, S., Pagni, M., Ponting, C.P., Quevillon, E., Selengut, J., Sigrist, C.J., Silventoinen, V., Studholme, D.J., Vaughan, R. and Wu, C.H.
Nucleic Acids Research 33
(Database Issue): D201-D205.
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., Heighway, J., Pearson, S., McGown, G., Thorncroft, M.R., Watson, A.J., Harrison, K.L., Lewis, S.J., Rohde, K., Barber, P.V., Povey, A.C., 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., Jensen, L.J., Snel, B., Hooper, S.D., Krupp, M., Foglierini, M., Jouffre, N., 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., Aloy, P., 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
Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes.
Doerks, T., 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., Schmidt, N., Rieger, A., Pilgram, S.M., Letunic, I., Bork, P., Soto, F., 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., von Mering, C., Bork, P. and Dandekar, T.
BioEssays 26
: 1333-1343.
1 December 2004
PASBio: predicate-argument structures for event extraction in molecular biology.
Wattarujeekrit, T., 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., Popov, A.V., Sunyaev, S., Coughlin, P., Habermann, B., Shevchenko, A., Bork, P., 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., 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., Jensen, L.J., 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., Lagarde, J., 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., Bauerfeind, A., Toliat, M.R., Becker, C., Luganskaja, T., Guenther, U.P., Rohde, K., Schuster, H., Junghans, C., Luft, F.C., Nuernberg, P. and Reich, J.G.
Human Molecular Genetics 13
(10): 993-1004.
15 May 2004
Structure-based assembly of protein complexes in yeast.
Aloy, P., Boettcher, B., Ceulemans, H., Leutwein, C., Mellwig, C., Fischer, S., Gavin, A.C., Bork, P., Superti-Furga, G., Serrano, L. and Russell, R.B.
Science 303
(5666): 2026-2029.
26 March 2004
Acropectorovertebral dysgenesis (F syndrome) maps to chromosome 2q36.
Thiele, H., McCann, C., vant Padje, S., Schwabe, G.C., Hennies, H.C., Camera, G., Opitz, J., Laxova, R., 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., Rabut, G., Ciccarelli, F.D., Herold, A., Koecher, T., Niggeweg, R., Bork, P., 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., Kupka, S., Nuernberg, P., Thiele, H., Zenner, H.R., 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., Thiele, H., Van Camp, G., Fransen, E., Apaydin, F., Aydin, O., Leistenschneider, P., Devoto, M., Zenner, H.P., Blin, N., Nuernberg, P., 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., Ryan, A., Ayhan, A., McCluggage, W.G., Feakins, R., Santibanez-Koref, M.F., Mein, C.A., Gayther, S.A. and Jacobs, I.J.
Journal of the National Cancer Institute 96
(19): 1441-1446.
1 January 2004
EASED: Extended alternatively spliced EST database.
Pospisil, H., Herrmann, A., 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
Gene annotation from scientific literature using mappings between keyword systems.
Perez, A.J., Perez-Iratxeta, C., Bork, P., 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., Andrade, M.A., Lathe, W., 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., Kenner, O., Nuernberg, P., Vogel, W. and Bartelt, B.
European Journal of Human Genetics 12
(2): 139-149.
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., Copley, R.R., Schmidt, S., Ciccarelli, F.D., Doerks, T., Schultz, J., Ponting, C.P. and Bork, P.
Nucleic Acids Research 32
(Database Issue): D142-D144.
1 January 2004
The HUPO PSI's Molecular Interaction format - a community standard for the representation of protein interaction data.
Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, R., Salwinski, L., Ceol, A., Moore, S., Orchard, S., Sarkans, U., von Mering, C., Roechert, B., Poux, S., Jung, E., Mersch, H., Kersey, P., Lappe, M., Li, Y.X., Zeng, R., Rana, D., Nikolski, M., Husi, H., Brun, C., Shanker, K., Grant, S.G.N., Sander, C., Bork, P., Zhu, W.M., Pandey, A., Brazma, A., Jacq, B., Vidal, M., Sherman, D., Legrain, P., Cesareni, G., Xenarios, L., Eisenberg, D., Steipe, B., 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., Antes, I., Basekow, R., Bork, P., Buning, C., Christensen, M., Claussen, H., Ebeling, C., Ernst, P., Gailus-Durner, V., Glatting, K.H., Gohla, R., Goessling, F., Grote, K., Heidtke, K., Herrmann, A., O'Keeffe, S., Kiesslich, O., Kolibal, S., Korbel, J.O., Lengauer, T., Liebich, I., van der Linden, M., Luz, H., Meissner, K., von Mering, C., Mevissen, H.T., Mewes, H.W., Michael, H., Mokrejs, M., Mueller, T., Pospisil, H., Rarey, M., Reich, J.G., Schneider, R., Schomburg, D., Schulze-Kremer, S., Schwarzer, K., Sommer, I., Springstubbe, S., Suhai, S., Thoppae, G., Vingron, M., Warfsmann, J., Werner, T., Wetzler, D., 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
Similarity by state/descent and genetic vector spaces: analysis of a longitudinal family study.
Stassen, H.H., 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., 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., Herrmann, A., Pankow, H. and Reich, J.
In Silico Biology 3
(1-2): 229-234.
16 December 2003
A genome-wide survey of human pseudogenes.
Torrents, D., Suyama, M., Zdobnov, E. and Bork, P.
Genome Research 13
: 2559-2567.
1 December 2003
Alternative splicing and evolution.
Boue, S., Letunic, I. and Bork, P.
BioEssays 25
: 1031-1034.
1 November 2003
Protein disorder prediction: Implications for structural proteomics.
Linding, R., Jensen, L.J., Diella, F., Bork, P., 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., 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., von Mering, C. and Bork, P.
Bioinformatics 19
: 1901-1908.
12 October 2003
Distinct methylation profiles of glioma subtypes.
Uhlmann, K., Rohde, K., Zeller, C., Szymas, J., Vogel, S., Marczinek, K., Thiel, G., 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., Moldenhauer, F., Bulik, S., 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., Windemuth, C., Hueffmeier, U., Rueschendorf, F., Stadelmann, A., Hoppe, V., Fenneker, D., Staender, M., Schmitt-Egenolf, M., Wienker, T.F., 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., Asadullah, K., Windemuth, C., Rueschendorf, F., Hueffmeier, U., Staender, M., Schmitt-Egenolf, M., Wienker, T.F., 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., 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., Linding, R., Gemund, C., Chabanis-Davidson, S., Mattingsdal, M., Cameron, S., Martin, D.M.A., Ausiello, G., Brannetti, B., Costantini, A., Ferre, F., Maselli, V., Via, A., Cesareni, G., Diella, F., Superti-Furga, G., Wyrwicz, L., Ramu, C., McGuigan, C., Gudavalli, R., Letunic, I., Bork, P., Rychlewski, L., Kuester, B., Helmer-Citterich, M., Hunter, W.N., 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., Perez, A.J., 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., Meyer, B.S., Mueller-Myhsok, B., Rueschendorf, F., Drosten, C., Laue, T., Steeg, C., Nuernberg, P. and Fleischer, B.
Genes and Immunity 4
(5): 321-325.
July 2003
Systematic discovery of analogous enzymes in thiamin biosynthesis.
Morett, E., Korbel, J., Rajan, E., Saab-Rincon, G., Olvera, L., Olvera, M., Steffen, S., 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., Jensen, T.S., 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., Zhang, H.Y., Schulz, H., Lee, Y.A., Sun, K., Bähring, S., Luft, F.C., Nürnberg, P., Reis, A., Rohde, K., Ganten, D., Hui, R.T. and Hübner, N.
Human Molecular Genetics 12
(11): 1273-1277.
1 June 2003
Information extraction from full text scientific articles: Where are the keywords?
Shah, P., Perez-Iratxeta, C., 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., 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., Knoblauch, H., Schuster, H., 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., Benner, A., Sutter, C., Schiller, M., Yuan, Y.P., Keller, G., Bork, P., 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., Tsoka, S., Andrade, M.A., Enright, A.J., Carroll, M., Poullet, P., Promponas, V., Liakopoulos, T., Palaios, G., Pasquier, C., Hamodrakas, S., Tamames, J., Yagnik, A.T., Tramontano, A., Devos, D., Blaschke, C., Valencia, A., Brett, D., Martin, D., Leroy, C., Rigoutsos, I., 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., Skovgaard, M., Sicheritz-Ponten, T., Jorgensen, M.K., Lundegaard, C., Pedersen, C.C., 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., Proukakis, C., Patel, H., Cross, H., Azam, S., Patton, M.A., 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., Gupta, R., Staerfeldt, H.H. and Brunak, S.
Bioinformatics 19
: 635-642.
22 March 2003
Increase of functional diversity by alternative splicing.
Kriventseva, E.V., Koch, I., Apweiler, R., Vingron, M., Bork, P., 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
Computational analysis of biochemical systems (book review).
Dandekar, T.
Trends in Biochemical Sciences 26
: 637-637.
1 January 2003
Genome evolution reveals biochemical networks and functional modules.
von Mering, C., Zdobnov, E.M., Tsoka, S., Ciccarelli, F.D., Pereira-Leal, J.B., 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
Impact of selection, mutation rate and genetic drift on human genetic variation.
Sunyaev, S., Kondrashov, F.A., Bork, P. and Ramensky, V.
Human Molecular Genetics 12
(24): 3325-3330.
1 January 2003
Nanoelectrospray tandem mass spectrometry and sequence similarity searching for identification of proteins from organisms with unknown genomes.
Shevchenko, A., Sunyaev, S., Liska, A., 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., Unterholzner, L., Ciccarelli, F.D., 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., Huynen, M., Jaeggi, D., Schmidt, S., 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., Fulton, R.S., Fulton, L.A., Graves, T.A., Pepin, K.H., Wagner-McPherson, C., Layman, D., Maas, J., Jaeger, S., Walker, R., Wylie, K., Sekhon, M., Becker, M.C., O'Laughlin, M.D., Schaller, M.E., Fewell, G.A., Delehaunty, K.D., Miner, T.L., Nash, W.E., Cordes, M., Du, H., Sun, H., Edwards, J., Bradshaw-Cordum, H., Ali, J., Andrews, S., Isak, A., VanBrunt, A., Nguyen, C., Du, F.Y., Lamar, B., Courtney, L., Kalicki, J., Ozersky, P., Bielicki, L., Scott, K., Holmes, A., Harkins, R., Harris, A., Strong, C.M., Hou, S.F., Tomlinson, C., Dauphin-Kohlberg, S., Kozlowicz-Reilly, A., Leonard, S., Rohlfing, T., Rock, S.M., Tin-Wollam, A.M., Abbott, A., Minx, P., Maupin, R., Strowmatt, C., Latreille, P., Miller, N., Johnson, D., Murray, J., Woessner, J.P., Wendl, M.C., Yang, S.P., Schultz, B.R., Wallis, J.W., Spieth, J., Bieri, T.A., Nelson, J.O., Berkowicz, N., Wohldmann, P.E., Cook, L.L., Hickenbotham, M.T., Eldred, J., Williams, D., Bedell, J.A., Mardis, E.R., Clifton, S.W., Chissoe, S.L., Marra, M.A., Raymond, C., Haugen, E., Gillett, W., Zhou, Y., James, R., Phelps, K., Iadanoto, S., Bubb, K., Simms, E., Levy, R., Clendenning, J., Kaul, R., Kent, W.J., Furey, T.S., Baertsch, R.A., Brent, M.R., Keibler, E., Flicek, P., Bork, P., Suyama, M., Bailey, J.A., Portnoy, M.E., Torrents, D., Chinwalla, A.T., Gish, W.R., Eddy, S.R., McPherson, J.D., Olson, M.V., Eichler, E.E., Green, E.D., 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., Apweiler, R., Attwood, T.K., Bairoch, A., Barrell, D., Bateman, A., Binns, D., Biswas, M., Bradley, P., Bork, P., Bucher, P., Copley, R.R., Courcelle, E., Das, U., Durbin, R., Falquet, L., Fleischmann, W., Griffiths-Jones, S., Haft, D., Harte, N., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lopez, R., Letunic, I., Lonsdale, D., Silventoinen, V., Orchard, S.E., Pagni, M., Peyruc, D., Ponting, C.P., Selengut, J.D., Servant, F., Sigrist, C.J.A., Vaughan, R. and Zdobnov, E.M.
Nucleic Acids Research 31
(1): 315-318.
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
Praediktive Diagnostik und genetisches Design: Ein Blick in die Zukunft.
Reich, J.
Zeitschrift fuer Biopolitik 2
(2): 89-98.
2003
Metabolic network structure determines key aspects of functionality and regulation.
Stelling, J., Klamt, S., Bettenbrock, K., Schuster, S. and Gilles, E.D.
Nature 420
(6912): 190-193.
14 November 2002
Mechanisms of carcinogenicity/chemotherapy by O(6)-methylguanine.
Margison, G.P., Santibanez-Koref, M.F. and Povey, A.C.
Mutagenesis 17
(6): 483-487.
November 2002
Power and sample size calculations for case-control genetic association tests when errors are present: Application to single nucleotide polymorphisms.
Gordon, D., Finch, S.J., Nothnagel, M. and Ott, J.
Human Heredity 54
(1): 22-33.
November 2002
The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract.
Schell, M.A., Karmirantzou, M., Snel, B., Vilanova, D., Berger, B., Pessi, G., Zwahlen, M.C., Desiere, F., Bork, P., Delley, M., Pridmore, R.D. and Arigoni, F.
Proceedings of the National Academy of Sciences of the United States of America 99
(22): 14422-14427.
29 October 2002
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster.
Zdobnov, E.M., von Mering, C., Letunic, I., Torrents, D., Suyama, M., Copley, R.R., Christophides, G.K., Thomasova, D., Holt, R.A., Subramanian, G.M., Mueller, H.M., Dimopoulos, G., Law, J.H., Wells, M.A., Birney, E., Charlab, R., Halpern, A.L., Kokoza, E., Kraft, C.L., Lai, Z., Lewis, S., Louis, C., Barillas-Mury, C., Nusskern, D., Rubin, G.M., Salzberg, S.L., Sutton, G.G., Topalis, P., Wides, R., Wincker, P., Yandell, M., Collins, F.H., Ribeiro, J., Gelbart, W.M., Kafatos, F.C. and Bork, P.
Science 298
(5591): 149-159.
4 October 2002
The genome sequence of the malaria mosquito Anopheles gambiae.
Holt, R.A., Subramanian, G.M., Halpern, A., Sutton, G.G., Charlab, R., Nusskern, D.R., Wincker, P., Clark, A.G., Ribeiro, J.M.C., Wides, R., Salzberg, S.L., Loftus, B., Yandell, M., Majoros, W.H., Rusch, D.B., Lai, Z.W., Kraft, C.L., Abril, J.F., Anthouard, V., Arensburger, P., Atkinson, P.W., Baden, H., de Berardinis, V., Baldwin, D., Benes, V., Biedler, J., Blass, C., Bolanos, R., Boscus, D., Barnstead, M., Cai, S., Center, A., Chatuverdi, K., Christophides, G.K., Chrystal, M.A., Clamp, M., Cravchik, A., Curwen, V., Dana, A., Delcher, A., Dew, I., Evans, C.A., Flanigan, M., Grundschober-Freimoser, A., Friedli, L., Gu, Z.P., Guan, P., Guigo, R., Hillenmeyer, M.E., Hladun, S.L., Hogan, J.R., Hong, Y.S., Hoover, J., Jaillon, O., Ke, Z.X., Kodira, C., Kokoza, E., Koutsos, A., Letunic, I., Levitsky, A., Liang, Y., Lin, J.J., Lobo, N.F., Lopez, J.R., Malek, J.A., McIntosh, T.C., Meister, S., Miller, J., Mobarry, C., Mongin, E., Murphy, S.D., O'Brochta, D.A., Pfannkoch, C., Qi, R., Regier, M.A., Remington, K., Shao, H.G., Sharakhova, M.V., Sitter, C.D., Shetty, J., Smith, T.J., Strong, R., Sun, J.T., Thomasova, D., Ton, L.Q., Topalis, P., Tu, Z.J., Unger, M.F., Walenz, B., Wang, A.H., Wang, J., Wang, M., Wang, X.L., Woodford, K.J., Wortman, J.R., Wu, M., Yao, A., Zdobnov, E.M., Zhang, H.Y., Zhao, Q., Zhao, S.Y., Zhu, S.P.C., Zhimulev, I., Coluzzi, M., della Torre, A., Roth, C.W., Louis, C., Kalush, F., Mural, R.J., Myers, E.W., Adams, M.D., Smith, H.O., Broder, S., Gardner, M.J., Fraser, C.M., Birney, E., Bork, P., Brey, P.T., Venter, J.C., Weissenbach, J., Kafatos, F.C., Collins, F.H. and Hoffman, S.L.
Science 298
(5591): 129-149.
4 October 2002
Association of the 867Asp variant of the human anion exchanger 3 gene with common subtypes of idiopathic generalized epilepsy.
Sander, T., Toliat, M.R., Heils, A., Leschik, G., Becker, C., Rueschendorf, F., Rohde, K., Mundlos, S. and Nuernberg, P.
Epilepsy Research 51
(3): 249-255.
1 October 2002
Comparative analysis of protein interaction networks.
Bork, P.
Bioinformatics 18 Suppl 2
: S64.
1 October 2002
Discussion: Conservation of gene co-regulation in prokaryotes and eukaryotes.
Snel, B., Bork, P. and Huynen, M.
Trends in Biotechnology 20
(10): 410.
1 October 2002
Periodic catatonia: confirmation of linkage to chromosome 15 and further evidence for genetic heterogeneity.
Stoeber, G., Seelow, D., Rueschendorf, F., Ekici, A., Beckmann, H. and Reis, A.
Human Genetics 111
(4-5): 323-330.
October 2002
Treatment of multifunctional enzymes in metabolic pathway analysis.
Schuster, S. and Zevedei-Oancea, I.
Biophysical Chemistry 99
(1): 63-75.
3 September 2002
Human non-synonymous SNPs: server and survey.
Ramensky, V., Bork, P. and Sunyaev, S.
Nucleic Acids Research 30
(17): 3894-3900.
1 September 2002
InterPro: an integrated documentation resource for protein families, domains and functional sites.
Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Biswas, M., Bradley, P., Bork, P., Bucher, P., Copley, R., Courcelle, E., Durbin, R., Falquet, L., Fleischmann, W., Gouzy, J., Griffith-Jones, S., Haft, D., Hermjakob, H., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lopez, R., Letunic, I., Orchard, S., Pagni, M., Peyruc, D., Ponting, C.P., Servant, F. and Sigrist, C.J.
Briefings in Bioinformatics 3
: 225-235.
1 September 2002
Structure of transfection-active histone H1/DNA complexes.
Lucius, H., Haberland, A., Zaitsev, S., Dalluege, R., Schneider, M. and Boettger, M.
Molecular Biology Reports 28
(3): 157-165.
September 2002
NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria.
Andrade, M.A., Ciccarelli, F.D., Perez-Iratxeta, C. and Bork, P.
Genome Biology 3
(9): research0047.
15 August 2002
Applying metabolic pathway analysis to make good use of methanol.
Schuster, S. and Klamt, S.
Trends in Biotechnology 20
(8): 322-322.
1 August 2002
SPG20 is mutated in Troyer syndrome, an hereditary spastic paraplegia.
Patel, H., Cross, H., Proukakis, C., Hershberger, R., Bork, P., Ciccarelli, F.D., Patton, M.A., McKusick, V.A. and Crosby, A.H.
Nature Genetics 31
: 347-348.
1 August 2002
Predicting protein cellular localization using a domain projection method.
Mott, R., Schultz, J., Bork, P. and Ponting, C.P.
Genome Research 12
(8): 1168-1174.
August 2002
Reaction routes in biochemical reaction systems: Algebraic properties, validated calculation procedure and example from nucleotide metabolism.
Schuster, S., Hilgetag, C., Woods, J.H. and Fell, D.A.
Journal of Mathematical Biology 45
(2): 153-181.
August 2002
Association of genes to genetically inherited diseases using data mining.
Perez-Iratxeta, C., Bork, P. and Andrade, M.A.
Nature Genetics 31
(3): 316-319.
July 2002
Common exon duplication in animals and its role in alternative splicing.
Letunic, I., Copley, R.R. and Bork, P.
Human Molecular Genetics 11
: 1561-1567.
15 June 2002
Comparative genomic analysis in the region of a major Plasmodium-refractoriness locus of Anopheles gambiae.
Thomasova, D., Ton, L.Q., Copley, R.R., Zdobnov, E.M., Wang, X., Hong, Y.S., Sim, C., Bork, P., Kafatos, F.C. and Collins, F.H.
Proceedings of the National Academy of Sciences of the United States of America 99
: 8179-8184.
11 June 2002
Common haplotypes in five genes influence genetic variance of LDL and HDL cholesterol in the general population.
Knoblauch, H., Bauerfeind, A., Kraehenbuehl, C., Daury, A., Rohde, K., Bejanin, S., Essioux, L., Schuster, H., Luft, F.C. and Reich, J.
Human Molecular Genetics 11
(12): 1477-1485.
1 June 2002
Computing fuzzy associations for the analysis of biological literature.
Perez-Iratxeta, C., Keer, H.S., Bork, P. and Andrade, M.A.
Biotechniques 32
(6): 1380-1385.
June 2002
Proteinkomplexe und Netzwerke: Neue Herausforderungen fuer die Proteomik.
von Mering, C. and Bork, P.
GenomXpress 2002
(2): 2-4.
June 2002
Comparative assessment of large-scale data sets of protein-protein interactions.
von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S.G., Fields, S. and Bork, P.
Nature 417
(6887): 399-403.
23 May 2002
Mapping of gene loci for nephronophthisis type 4 and Senior-Loken syndrome, to chromosome 1p36.
Schuermann, M.J., Otto, E., Becker, A., Saar, K., Rueschendorf, F., Polak, B.C., Ala-Mello, S., Hoefele, J., Wiedensohler, A., Haller, M., Omran, H., Nuernberg, P. and Hildebrandt, F.
American Journal of Human Genetics 70
(5): 1240-1246.
May 2002
Identification of attenuation and antitermination regulation in prokaryotes.
Lathe, W.C., Suyama, M. and Bork, P.
Genome Biology 3
: preprint0003.1.
30 April 2002
The identification of functional modules from the genomic association of genes.
Snel, B., Bork, P. and Huynen, M.A.
Proceedings of the National Academy of Sciences of the United States of America 99
: 5890-5895.
30 April 2002
BSD: a novel domain in transcription factors and synapse-associated proteins.
Doerks, T., Huber, S., Buchner, E. and Bork, P.
Trends in Biochemical Sciences 27
(4): 168-170.
1 April 2002
A versatile structural domain analysis server using profile weight matrices.
Schmidt, S., Bork, P. and Dandekar, T.
Journal of Chemical Information and Computer Sciences 42
(2): 405-407.
March 2002
Integration of genome data and protein structures: prediction of protein folds, protein interactions and 'molecular phenotypes' of single nucleotide polymorphisms (Reprinted from Current Opinion in Structural Biology, vol 11, pg 125-130, 2001).
Sunyaev, S.R., Lathe, W. and Bork, P.
Trends in Genetics
(Suppl. March): S19-S24.
March 2002
Functional organization of the yeast proteome by systematic analysis of protein complexes.
Gavin, A.C., Boesche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J.M., Michon, A.M., Cruciat, C.M., Remor, M., Hoefert, C., Schelder, M., Brajenovic, M., Ruffner, H., Merino, A., Klein, K., Hudak, M., Dickson, D., Rudi, T., Gnau, V., Bauch, A., Bastuck, S., Huhse, B., Leutwein, C., Heurtier, M.A., Copley, R.R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P., Seraphin, B., Kuester, B., Neubauer, G. and Superti-Furga, G.
Nature 415
(6868): 141-147.
10 January 2002
A complex prediction: three-dimensional model of the yeast exosome.
Aloy, P., Ciccarelli, F.D., Leutwein, C., Gavin, A.C., Superti-Furga, G., Bork, P., Boettcher, B. and Russell, R.B.
EMBO Reports 3
: 628-635.
1 January 2002
A self-organizing model for the development of orientation selectivity and ocular dominance patterns in the visual nervous system.
Muro, E.M., Andrade, M.A. and Moran, F.
Neural Network World 12
(4): 319-332.
1 January 2002
AMOP, a protein module aternativelly spliced in cancer cells.
Ciccarelli, F.D., Doerks, T. and Bork, P.
Trends in Biochemical Sciences 27
: 113-115.
1 January 2002
Alternative splicing and genome complexity.
Brett, D., Pospisil, H., Valcarel, J., Reich, J. and Bork, P.
Nature Genetics 30
(1): 29-30.
1 January 2002
CASH - a beta-helix domain widespread among carbohydrate-binding proteins.
Ciccarelli, F.D., Copley, R.R., Doerks, T., Russell, R.B. and Bork, P.
Trends in Biochemical Sciences 27
(2): 59-62.
1 January 2002
Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria.
Klamt, S., Schuster, S. and Gilles, E.D.
Biotechnology and Bioengineering 77
(7): 734-751.
1 January 2002
Calculating as many fluxes as possible in underdetermined metabolic networks.
Klamt, S. and Schuster, S.
Molecular Biology Reports 29
(1-2): 243-248.
1 January 2002
Exclusion of the neuronal nicotinic acetylcholine receptor alpha 7 subunit gene as a candidate for catatonic schizophrenia in a large family supporting the chromosome 15q13-22 locus.
Meyer, J., Ortega, G., Schraut, K., Nuernberg, G., Rueschendorf, F., Saar, K., Moessner, R., Wienker, T.F., Reis, A., Stoeber, G. and Lesch, K.P.
Molecular Psychiatry 7
: 220-223.
1 January 2002
Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae.
Schuster, S., Pfeiffer, T., Moldenhauer, F., Koch, I. and Dandekar, T.
Bioinformatics 18
(2): 351-361.
1 January 2002
Genomes in flux: The evolution of archaeal and proteobacterial gene content.
Snel, B., Bork, P. and Huynen, M.A.
Genome Research 12
(1): 17-25.
1 January 2002
HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources.
Fredman, D., Siegfried, M., Yuan, Y.P., Bork, P., Lehvaslaiho, H. and Brookes, A.J.
Nucleic Acids Research 30
(1): 387-391.
1 January 2002
Identification and characterization of UEV3, a human cDNA with similarities to inactive E2 ubiquitin-conjugating enzymes.
Kloor, M., Bork, P., Duwe, A., Klaes, R., Doeberitz, M.V. and Ridder, R.
Biochimica et Biophysica Acta - Gene Structure and Expression 1579
: 219-224.
1 January 2002
Immunity-related genes and gene families in Anopheles gambiae.
Christophides, G.K., Zdobnov, E., Barillas-Mury, C., Birney, E., Blandin, S., Blass, C., Brey, P.T., Collins, F.H., Danielli, A., Dimopoulos, G., Hetru, C., Hoa, N., Hoffmann, J.A., Kanzok, S.M., Letunic, I., Levashina, E.A., Loukeris, T.G., Lycett, G., Meister, S., Michel, K., Mueller, H.M., Osta, M.A., Paskewitz, S.M., Reichhart, J.M., Rzhetsky, A., Troxler, L., Vernick, K.D., Vlachou, D., Volz, J., von Mering, C., Xu, J.N., Zheng, L.B., Bork, P. and Kafatos, F.C.
Science 298
: 159-165.
1 January 2002
Recent improvements to the SMART domain-based sequence annotation resource.
Letunic, I., Goodstadt, L., Dickens, N.J., Doerks, T., Schultz, J., Mott, R., Ciccarelli, F., Copley, R.R., Ponting, C.P. and Bork, P.
Nucleic Acids Research 30
(1): 242-244.
1 January 2002
STAT6 as an asthma candidate gene: polymorphism-screening, association and haplotype analysis in a Caucasian sib-pair study.
Duetsch, G., Illig, T., Loesgen, S., Rohde, K., Klopp, N., Herbon, N., Gohlke, H., Altmueller, J. and Wjst, M.
Human Molecular Genetics 11
(6): 613-621.
1 January 2002
Systematic identification of novel protein domain families associated with nuclear functions.
Doerks, T., Copley, R.R., Schultz, J., Ponting, C.P. and Bork, P.
Genome Research 12
(1): 47-56.
1 January 2002
Use of network analysis of metabolic systems in bioengineering.
Schuster, S., Klamt, S., Weckwerth, W., Moldenhauer, F. and Pfeiffer, T.
Bioprocess and Biosystems Engineering 24
(6): 363-372.
1 January 2002
Microarrays, Genexpressionsanalyse und Bioinformatik.
Schober, D.
Biospektrum 8
(3): 307-310.
2002
The Spir actin organizers are involved in vesicle transport processes.
Kerkhoff, E., Simpson, J.C., Leberfinger, C.B., Otto, I.M., Doerks, T., Bork, P., Rapp, U.R., Raabe, T. and Pepperkok, R.
Current Biology 11
: 1963-1968.
11 December 2001
Novel protein domains and repeats in Drosophila melanogaster: insights into structure, function, and evolution.
Ponting, C.P., Mott, R., Bork, P. and Copley, R.R.
Genome Research 11
: 1996-2008.
1 December 2001
Medical target prediction from genome sequence: combining different sequence analysis algorithms with expert knowledge and input from artificial intelligence approaches.
Dandekar, T., Du, F., Schirmer, R.H. and Schmidt, S.
Computers and Chemistry 26
(1): 15-21.
December 2001
The phosphoglucose isomerase from the hyperthermophilic archaeon Pyrococcus furiosus is a unique glycolytic enzyme that belongs to the cupin superfamily.
Verhees, C.H., Huynen, M.A., Ward, D.E., Schiltz, E., de Vos, W.M. and van der Oost, J.
Journal of Biological Chemistry 276
(44): 40926-40932.
2 November 2001
When genetic distance matters: measuring genetic differentiation at microsatellite loci in whole-genome scans of recent and incipient mosquito species.
Wang, R., Zheng, L., Toure, Y.T., Dandekar, T. and Kafatos, F.C.
Proceedings of the National Academy of Sciences of the United States of America 98
(19): 10769-10774.
11 September 2001
Protons and sodium ions acting as intracellular carrier pigeons?
Schuster, S.
Trends in Biotechnology 19
(9): 330-330.
1 September 2001
Structure--function characterization of cellulose synthase: relationship to other glycosyltransferases.
Saxena, I.M., Brown, R.M. and Dandekar, T.
Phytochemistry 57
: 1135-1148.
1 August 2001
A rapid bioinformatic method identifies novel genes with direct clinical relevance to colon cancer.
Brett, D., Kemmner, W., Koch, G., Roefzaad, C., Gross, S. and Schlag, P.M.
Oncogene 20
(33): 4581-4585.
27 July 2001
What can silent mutations tell us?
Schuster, S.
Trends in Biotechnology 19
(7): 242-242.
1 July 2001
A combination of the F-box motif and kelch repeats defines a large Arabidopsis family of F-box proteins.
Andrade, M.A., Gonzalez-Guzman, M., Serrano, R. and Rodriguez, P.L.
Plant Molecular Biology 46
(5): 603-614.
July 2001
Inversions and the dynamics of eukaryotic gene order.
Huynen, M.A., Snel, B. and Bork, P.
Trends in Genetics 17
(6): 304-306.
1 June 2001
A compartment model to calculate time-dependent concentration profiles of topically applied chemical compounds in the anterior compartments of the rabbit eye.
Pospisil, H. and Holzhuetter, H.G.
Alternatives to Laboratory Animals 29
: 347-365.
3 May 2001
Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching.
Shevchenko, A., Sunyaev, S., Loboda, A., Shevchenko, A., Bork, P., Ens, W. and Standing, K.G.
Analytical Chemistry 73
(9): 1917-1926.
1 May 2001
Solvent entropy-driven searching for protein modeling examined and tested in simplified models.
Koenig, R. and Dandekar, T.
Protein Engineering 14
: 329-335.
1 May 2001
Simulation of plasticity in the adult visual cortex.
Andrade-Navarro, M.A., Muro, E.M. and Moran, F.
Biological Cybernetics 84
(6): 445-451.
May 2001
Towards the genetic basis of periodic catatonia: pedigree sample for genome scan I and II.
Stoeber, G., Pfuhlmann, B., Nuernberg, G., Schmidtke, A., Reis, A., Franzek, E. and Wienker, T.F.
European Archives of Psychiatry and Clinical Neuroscience 251
(Suppl 1): I25-I30.
May 2001
Molecular characterization of a cDNA encoding functional human CLK4 kinase and localization to chromosome 5q35 [correction of 4q35].
Schultz, J., Jones, T., Bork, P., Sheer, D., Blencke, S., Steyrer, S., Wellbrock, U., Bevec, D., Ullrich, A. and Wallasch, C.
Genomics 71
: 368-370.
1 February 2001
A novel form of "central pouchlike" cataract, with sutural opacities, maps to chromosome 15q21-22.
Vanita, A., Singh, J.R., Sarhadi, V.K., Singh, D., Reis, A., Rueschendorf, F., Becker-Follmann, J., Jung, M. and Sperling, K.
American Journal of Human Genetics 68
(2): 509-514.
February 2001
The black-pearl gene of Drosophila defines a novel conserved protein family and is required for larval growth and survival.
Becker, S., Gehrsitz, A., Bork, P., Buchner, S. and Buchner, E.
Gene 262
: 15-22.
10 January 2001
Fundamental Study - Enumerating all connected maximal common subgraphs in two graphs.
Koch, I.
Theoretical Computer Science 250
(1-2): 1-30.
6 January 2001
Assignment of PGL3 to chromosome 1 (q21-q23) in a family with autosomal dominant non-chromaffin paraganglioma.
Niemann, S., Becker-Follmann, J., Nuernberg, G., Rueschendorf, F., Sieweke, N., Huegens-Penzel, M., Traupe, H., Wienker, T.F., Reis, A. and Mueller, U.
American Journal of Medical Genetics 98
(1): 32-36.
1 January 2001
Bifurcation analysis of calcium oscillations: time-scale separation, canards, and frequency lowering.
Schuster, S. and Marhl, M.
Journal of Biological Systems 9
(4): 291-314.
1 January 2001
Characterization of a mutation in the lens-specific MP70 encoding gene of the mouse leading to a dominant cataract.
Graw, J., Loster, J., Soewarto, D., Fuchs, H., Meyer, B., Reis, A., Wolf, E., Balling, R. and de Angelis, M.H.
Experimental Eye Research 73
(6): 867-876.
1 January 2001
Cooperation and competition in the evolution of ATP-producing pathways.
Pfeiffer, T., Schuster, S. and Bonhoeffer, S.
Science 292
: 504-507.
1 January 2001
DDT - a novel domain in different transcription and chromosome remodeling factors.
Doerks, T., Copley, R. and Bork, P.
Trends in Biochemical Sciences 26
: 145-146.
1 January 2001
Evolution of prokaryotic gene order: genome rearrangements in closely related species.
Suyama, M. and Bork, P.
Trends in Genetics 17
(1): 10-13.
1 January 2001
Evolution of tuf genes: ancient duplication, differential loss and gene conversion.
Lathe, W.C. and Bork, P.
FEBS Letters 502
(3): 113-116.
1 January 2001
Fine mapping and single nucleotide polymorphism association results of candidate genes for asthma and related phenotypes.
Immervoll, T., Loesgen, S., Duetsch, G., Gohlke, H., Herbon, N., Klugbauer, S., Dempfle, A., Bickeboeller, H., Becker-Follmann, J., Rueschendorf, F., Saar, K., Reis, A., Wichmann, H.E. and Wjst, M.
Human Mutation 18
: 327-336.
1 January 2001
Frameshift peptide-derived T-cell epitopes: a source of novel tumor-specific antigens.
Linnebacher, M., Gebert, J., Rudy, W., Woerner, S., Yuan, Y.P. and von Knebel-Doeberitz, M.
International Journal of Cancer 93
(1): 6-11.
1 January 2001
Genome speak.
Bork, P. and Copley, R.
Nature 409
: 815.
1 January 2001
Haplotyping and estimation of haplotype frequencies for closely linked biallelic multilocus genetic phenotypes including nuclear family information.
Rohde, K. and Fuerst, R.
Human Mutation 17
(4): 289-295.
1 January 2001
Hydrogenosomes: convergent adaptations of mitochondria to anaerobic environments.
Hackstein, J.H.P., Akhmanova, A.S., Voncken, F., van Hoek, A., Alen, T., Boxma, B., Moon-van der Staay, S.Y., Staay, G., Leunissen, J., Huynen, M.A., Rosenberg, J. and Veenhuis, M.
Zoology 104
: 290-302.
1 January 2001
Identification of cellular interactions in RNA and protein molecules.
Dandekar, T., Du, F. and Bertram, H.
Nonlinear Analysis Theory Methods & Applications 47
: 225-234.
1 January 2001
Integration of genome data and protein structures: prediction of protein folds, protein interactions and 'molecular phenotypes' of single nucleotide polymorphisms.
Sunyaev, S.R., Lathe, W. and Bork, P.
Current Opinion in Structural Biology 11
(1): 125-130.
1 January 2001
Localisation of a gene for an autosomal recessive syndrome of macrocephaly, multiple epiphyseal dysplasia, and distinctive facies to chromosome 15q26.
Bayoumi, R., Saar, K., Lee, Y.A., Nuernberg, G., Reis, A., Nur-E-Kamal, M. and Al Gazali, L.I.
Journal of Medical Genetics 38
(6): 369-373.
1 January 2001
Post-translational GPI lipid anchor modification of proteins in kingdoms of life: analysis of protein sequence data from complete genomes.
Eisenhaber, B., Bork, P. and Eisenhaber, F.
Protein Engineering 14
(1): 17-25.
1 January 2001
Prediction of deleterious human alleles.
Sunyaev, S.R., Ramensky, V., Koch, I., Lathe, W., Kondrashov, A.S. and Bork, P.
Human Molecular Genetics 10
(6): 591-597.
1 January 2001
Refinement of the gene locus for autosomal dominant medullary cystic kidney disease type 1 (MCKD1) and construction of a physical and partial transcriptional map of the region.
Fuchshuber, A., Kroiss, S., Karle, S., Berthold, S., Huck, K., Burton, C., Rahman, N., Koptides, M., Deltas, C., Otto, E., Rueschendorf, F., Feest, T. and Hildebrandt, F.
Genomics 72
(3): 278-284.
1 January 2001
Systematic identification of genes with coding microsatellites mutated in DNA mismatch repair-deficient cancer cells.
Woerner, S.M., Gebert, J., Yuan, Y.P., Sutter, C., Ridder, R., Bork, P. and von Knebel-Doeberitz, M.
International Journal of Cancer 93
(1): 12-19.
1 January 2001
The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly.
Huynen, M.A., Snel, B., Bork, P. and Gibson, T.J.
Human Molecular Genetics 10
(21): 2463-2468.
1 January 2001
Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences.
Iyer, L.M., Aravind, L., Bork, P., Hofmann, K., Mushegian, A.R., Zhulin, I.B. and Koonin, E.V.
Genome Biology 2
(12): RESEARCH0051.
2001
The large-scale organization of metabolic networks.
Dandekar, T. and Schuster, S.
Chemtracts 14
: 137-141.
2001
TAP (NXF1) belongs to a multigene family of putative RNA export factors with a conserved modular architecture.
Herold, A., Suyama, M., Rodrigues, J.P., Braun, I.C., Kutay, U., Carmo-Fonseca, M., Bork, P. and Izaurralde, E.
Molecular and Cellular Biology 20
: 8996-9008.
1 December 2000
Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III.
Gonczy, P., Echeverri, G., Oegema, K., Coulson, A., Jones, S.J., Copley, R.R., Duperon, J., Oegema, J., Brehm, M., Cassin, E., Hannak, E., Kirkham, M., Pichler, S., Flohrs, K., Goessen, A., Leidel, S., Alleaume, A.M., Martin, C., Ozlu, N., Bork, P. and Hyman, A.A.
Nature 408
(6810): 331-336.
16 November 2000
Homology among (betaalpha)8barrels: implications for the evolution of metabolic pathways.
Copley, R.R. and Bork, P.
Journal of Molecular Biology 303
: 627-641.
3 November 2000
A complete enumeration and classification of two-locus disease models.
Li, W.T. and Reich, J.
Human Heredity 50
(6): 334-349.
1 November 2000
Splitting schizophrenia: Periodic catatonia-susceptibility locus on chromosome 15q15.
Stoeber, G., Saar, K., Rueschendorf, F., Meyer, J., Nuernberg, G., Jatzke, S., Franzek, E., Reis, A., Lesch, K.P., Wienker, T.F. and Beckmann, H.
American Journal of Human Genetics 67
: 1201-1207.
1 November 2000
Gene context conservation of a higher order than operons.
Lathe, W.C., Snel, B. and Bork, P.
Trends in Biochemical Sciences 25
(10): 474-479.
1 October 2000
Genomewide scan in German families reveals evidence for a novel psoriasis-susceptibility locus on chromosome 19p13.
Lee, Y.A., Rueschendorf, F., Windemuth, C., Schmitt-Egenolf, M., Stadelmann, A., Nuernberg, G., Staender, M., Wienker, T.F., Reis, A. and Traupe, H.
American Journal of Human Genetics 67
(4): 1020-1024.
1 October 2000
Multiple sclerosis associated amino acids of polymorphic regions relevant for the HLA antigen binding are confined to HLA-DR2.
Zipp, F., Windemuth, C., Pankow, H., Dichgans, J., Wienker, T.F., Martin, R. and Mueller, C.
Human Immunology 61
(10): 1021-1030.
1 October 2000
STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene.
Snel, B., Lehmann, G., Bork, P. and Huynen, M.A.
Nucleic Acids Research 28
(18): 3442-3444.
15 September 2000
Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.
Dandekar, T., Huynen, M.A., Regula, J., Ueberle, B., Zimmermann, C.U., Andrade, M.A., Doerks, T., Sanches-Pulido, L., Snel, B., Suyama, M., Yuan, Y.P., Herrmann, R. and Bork, P.
Nucleic Acids Research 28
(17): 3278-3288.
1 September 2000
Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences.
Huynen, M., Snel, B., Lathe, W. and Bork, P.
Genome Research 10
(8): 1204-1210.
1 August 2000
SNP frequencies in human genes - an excess of rare alleles and differing modes of selection.
Sunyaev, S.R., Lathe, W.C., Ramensky, V.E. and Bork, P.
Trends in Genetics 16
(8): 335-337.
1 August 2000
The 3'-untranslated region of the human estrogen receptor alpha gene mediates rapid messenger ribonucleic acid turnover.
Kenealy, M.R., Flouriot, G., Sonntag-Buck, V., Dandekar, T., Brand, H. and Gannon, F.
Endocrinology 141
(8): 2805-2813.
August 2000
DNA recognition, strand selectivity, and cleavage mode during integrase family site-specific recombination.
Tribble, G., Ahn, Y.T., Lee, J., Dandekar, T. and Jayaram, M.
Journal of Biological Chemistry 275
(29): 22255-22267.
21 July 2000
A tumor suppressor locus in familial and sporadic chordoma maps to 1p36.
Miozzo, M., Dalpra, L., Riva, P., Volonte, M., Macciardi, F., Pericotti, S., Tibiletti, M.G., Cerati, M., Rohde, K., Larizza, L. and Conti, A.M.F.
International Journal of Cancer 87
(1): 68-72.
1 July 2000
Automated annotation of GPI anchor sites: case study C-elegans.
Eisenhaber, B., Bork, P., Yuan, Y.P., Loeffler, G. and Eisenhaber, F.
Trends in Biochemical Sciences 25
(7): 340-341.
1 July 2000
L27, a novel heterodimerization domain in receptor targeting proteins Lin-2 and Lin-7.
Doerks, T., Bork, P., Kamberov, E., Makarova, O., Muecke, S. and Margolis, B.
Trends in Biochemical Sciences 25
: 317-318.
1 July 2000
NAIL - Network Analysis Interface for Linking HMMER results.
Sanchez-Pulido, L., Yuan, Y.P., Andrade, M.A. and Bork, P.
Bioinformatics 16
(7): 656-657.
1 July 2000
Prediction of structural domains of TAP reveals details of its interaction with p15 and nucleoporins.
Suyama, M., Doerks, T., Braun, I.C., Sattler, M., Izaurralde, E. and Bork, P.
EMBO Reports 1
(1): 53-58.
1 July 2000
Anopheles gambiae pilot gene discovery project: Identification of mosquito innate immunity genes from expressed sequence tags generated from immune-competent cell lines.
Dimopoulos, G., Casavant, T.L., Chang, S.R., Scheetz, T., Roberts, C., Donohue, M., Schultz, J., Benes, V., Bork, P., Ansorge, W., Soares, M.B. and Kafatos, F.C.
Proceedings of the National Academy of Sciences of the United States of America 97
(12): 6619-6624.
6 June 2000
Exploitation of gene context.
Huynen, M.A., Snel, B., Lathe, W. and Bork, P.
Current Opinion in Structural Biology 10
(3): 366-370.
1 June 2000
More than 1,000 putative new human signalling proteins revealed by EST data mining.
Schultz, J., Doerks, T., Ponting, C.P., Copley, R.R. and Bork, P.
Nature Genetics 25
(2): 201-204.
1 June 2000
Crystal structures of the membrane-binding C2 domain of human coagulation factor V structure of the C2 domain of human factor VIII at 1.5 A resolution.
Dandekar, T.
Chemtracts 13
(6): 398-401.
June 2000
Homology-based method for identification of protein repeats using statistical significance estimates.
Andrade, M.A., Ponting, C.P., Gibson, T.J. and Bork, P.
Journal of Molecular Biology 298
(3): 521-537.
5 May 2000
The p150-Spir protein provides a link between c-Jun N-terminal kinase function and actin reorganization.
Otto, I.M., Raabe, T., Rennefahrt, U.E., Bork, P., Rapp, U.R. and Kerkhoff, E.
Current Biology 10
: 345-348.
23 March 2000
A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks.
Schuster, S., Fell, D.A. and Dandekar, T.
Nature Biotechnology 18
(3): 326-332.
1 March 2000
Stochastic sensing of organic analytes by a pore-forming protein containing a molecular adapter.
Schultzberg, M., Boulin, C. and Dandekar, T.
Chemtracts 13
(3): 198-202.
March 2000
Cellular information transfer regarded from a stoichiometry and control analysis perspective.
Schuster, S., Kholodenko, B.N. and Westerhoff, H.V.
Biosystems 55
(1-3): 73-81.
1 February 2000
Discovery, scoring and utilization of human single nucleotide polymorphisms: a multidisciplinary problem.
Isaksson, A., Landegren, U., Syvanen, A.C., Bork, P., Stein, C., Ortigao, F. and Brookes, A.J.
European Journal of Human Genetics 8
: 154-156.
1 February 2000
Isolated familial somatotropinomas: Establishment of linkage to chromosome 11q13.1-11q13.3 and evidence for a potential second locus at chromosome 2p16-12.
Gadelha, M.R., Une, K.N., Rohde, K., Vaisman, M., Kineman, R.D. and Frohman, L.A.
Journal of Clinical Endocrinology and Metabolism 85
(2): 707-714.
1 February 2000
The GeneQuiz web server: protein functional analysis through the Web.
Hoersch, S., Leroy, C., Brown, N.P., Andrade, M.A. and Sander, C.
Trends in Biochemical Sciences 25
(1): 33-35.
28 January 2000
A cholesterol-lowering gene maps to chromosome 13q.
Knoblauch, H., Mueller-Myhsok, B., Busjahn, A., Avi, L.B., Bähring, S., Baron, H., Heath, S.C., Uhlmann, R., Faulhaber, H.D., Shpitzen, S., Aydin, A., Reshef, A., Rosenthal, M., Eliav, O., Muhl, A., Lowe, A., Schurr, D., Harats, D., Jeschke, E., Friedlander, Y., Schuster, H., Luft, F.C. and Leitersdorf, E.
American Journal of Human Genetics 66
(1): 157-166.
1 January 2000
A pathway model of lipid metabolism to predict the effect of genetic variability on lipid levels.
Knoblauch, H., Schuster, H., Luft, J.C. and Reich, J.
Journal of Molecular Medicine 78
: 507-515.
1 January 2000
EST comparison indicates 38% of human mRNAs contain possible alternative splice forms.
Brett, D., Hanke, J., Lehmann, G., Haase, S., Delbrueck, S., Krueger, S., Reich, J. and Bork, P.
FEBS Letters 474
(1): 83-86.
1 January 2000
HGBASE: a database of SNPs and other variations in and around human genes.
Brookes, A.J., Lehvaslaiho, H., Siegfried, M., Boehm, J.G., Yuan, Y.P., Sarkar, C.M., Bork, P. and Ortigao, F.
Nucleic Acids Research 28
(1): 356-360.
1 January 2000
REF, an evolutionary conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export.
Stutz, F., Bachi, A., Doerks, T., Braun, I.C., Seraphin, B., Wilm, P., Bork, P. and Izaurralde, E.
RNA 6
: 638-638.
1 January 2000
SMART: a web-based tool for the study of genetically mobile domains.
Schultz, J., Copley, R.R., Doerks, T., Ponting, C.P. and Bork, P.
Nucleic Acids Research 28
(1): 231-234.
1 January 2000
Comparative genome analysis: exploiting the context of genes to infer evolution and predict function.
Bork, P., Snel, B., Lehmann, G., Suyama, M., Dandekar, T., Lathe, W. and Huynen, M.
Computational Biology 1
: 281-294.
2000
The three-dimensional structure of the HRDC domain and implications for the Werner and Bloom syndrome proteins.
Liu, Z., Macias, M.J., Bottomley, M.J., Stier, G., Linge, J.P., Nilges, M., Bork, P. and Sattler, M.
Structure with Folding & Design 7
: 1557-1566.
15 December 1999
A genetic framework for floral patterning.
Koch, G. and Dandekar, T.
Chemtracts 12
(13): 956-959.
December 1999
RNA-catalysed nucleotide synthesis.
Koch, G. and Dandekar, T.
Chemtracts 12
(13): 938-943.
December 1999
Refined genetic algorithm simulations to model proteins.
Koenig, R. and Dandekar, T.
Journal of Molecular Modeling 5
(12): 317-324.
December 1999
Lateral gene transfer, genome surveys, and the phylogeny of prokaryotes.
Huynen, M.A., Snel, B. and Bork, P.
Science 286
(5444): 1443a.
19 November 1999
Pore-forming peptides of Entamoeba dispar : similarity and divergence to amoebapores in structure, expression and activity.
Nickel, R., Ott, C., Dandekar, T. and Leippe, M.
European Journal of Biochemistry 265
(3): 1002-1007.
1 November 1999
Functional classes in the three domains of life.
Andrade, M.A., Ouzounis, C., Sander, C., Tamames, J. and Valencia, A.
Journal of Molecular Evolution 49
(5): 551-557.
November 1999
Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes.
Sunyaev, S.R., Hanke, J., Aydin, A., Wirkner, U., Zastrow, I., Reich, J. and Bork, P.
Journal of Molecular Medicine 77
(11): 754-760.
November 1999
Solution structure of the receptor tyrosine kinase EphB2 SAM domain and identification of two distinct homotypic interaction sites.
Smalla, M., Schmieder, P., Kelly, M., Ter Laak, A., Krause, G., Ball, L., Wahl, M., Bork, P. and Oschkinat, H.
Protein Science 8
: 1954-1961.
1 October 1999
Prediction of potential GPI-modification sites in proprotein sequences.
Eisenhaber, B., Bork, P. and Eisenhaber, F.
Journal of Molecular Biology 292
: 741-758.
24 September 1999
Quality-of-life assessment in the old using the WHOQOL 100: differences between patients with senile dementia and patients with cancer.
Struttmann, T., Fabro, M., Romieu, G., de Roquefeuil, G., Touchon, J., Dandekar, T. and Ritchie, K.
International Psychogeriatrics 11
: 273-279.
1 September 1999
Mutation of the mouse klotho gene leads to a syndrome resembling ageing. Condensation and commentary.
Sharma, K., Kelly, L. and Dandekar, T.
Chemtracts 12
(10): 703-707.
September 1999
Domain organization of Mac-2 binding protein and its oligomerization to linear and ring-like structures.
Mueller, S.A., Sasaki, T., Bork, P., Wolpensinger, B., Schulthess, T., Timpl, R., Engel, A. and Engel, J.
Journal of Molecular Biology 291
: 801-813.
27 August 1999
Neutral evolution of mutational robustness.
van Nimwegen, E., Crutchfield, J.P. and Huynen, M.
Proceedings of the National Academy of Sciences of the United States of America 96
: 9716-9720.
17 August 1999
Characterization of polymorphisms in the promoter of the human angiotensin II subtype 1 (AT1) receptor gene.
Erdmann, J., Riedel, K., Rohde, K., Folgmann, I., Wienker, T.F., Fleck, E. and Regitz-Zagrosek, V.
Annals of Human Genetics 63 Part 4
: 369-374.
1 July 1999
Domains in plexins: links to integrins and transcription factors.
Bork, P., Doerks, T., Springer, T.A. and Snel, B.
Trends in Biochemical Sciences 24
: 261-263.
1 July 1999
Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries.
Eisenhaber, F. and Bork, P.
Bioinformatics 15
: 528-535.
1 July 1999
[An approach to the inverse folding problem based on the multiple alignment].
Sunyaev, S.R., Eisenhaber, F. and Tumanyan, V.G.
Biofizika 44
(4): 620-623.
July 1999
Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer.
Ponting, C.P., Aravind, L., Schultz, J., Bork, P. and Koonin, E.V.
Journal of Molecular Biology 289
: 729-745.
18 June 1999
A novel transactivation domain in parkin.
Morett, E. and Bork, P.
Trends in Biochemical Sciences 24
: 229-231.
1 June 1999
Metabolic pathway analysis: Basic concepts and scientific applications in the post-genomic era.
Schilling, C.H., Schuster, S., Palsson, B.O. and Heinrich, R.
Biotechnology Progress 15
(3): 296-303.
1 May 1999
PSIC: profile extraction from sequence alignments with position-specific counts of independent observations.
Sunyaev, S.R., Eisenhaber, F., Rodchenkov, I.V., Eisenhaber, B., Tumanyan, V.G. and Kuznetsov, E.N.
Protein Engineering 12
: 387-394.
1 May 1999
Automated genome sequence analysis and annotation.
Andrade, M.A., Brown, N.P., Leroy, C., Hoersch, S., de Daruvar, A., Reich, C., Franchini, A., Tamames, J., Valencia, A., Ouzounis, C. and Sander, C.
Bioinformatics 15
(5): 391-412.
May 1999
Analyzing the interplay between secondary and tertiary structure predictions in folding simulations with a genetic algorithm.
Dandekar, T. and Du, F.
Journal of Molecular Modeling 5
(4): 78-89.
1 April 1999
Improving genetic algorithms for protein folding simulations by systematic crossover.
Koenig, R. and Dandekar, T.
Biosystems 50
(1): 17-25.
April 1999
Microinjected glutathione reductase crystals as indicators of the redox status in living cells.
Keese, M.A., Saffrich, R., Dandekar, T., Becker, K. and Schirmer, R.H.
FEBS Letters 447
(2-3): 135-138.
26 March 1999
Fine mapping of the antigen-antibody interaction of scFv215, a recombinant antibody inhibiting RNA polymerase II from Drosophila melanogaster.
Liu, Z., Song, D., Kramer, A., Martin, A.C., Dandekar, T., Schneider-Mergener, J., Bautz, E.K. and Duebel, S.
Journal of Molecular Recognition 12
(2): 103-111.
24 March 1999
The mahogany protein is a receptor involved in suppression of obesity.
Nagle, D.L., McGrail, S.H., Vitale, J., Wolf, E.A., Dussault, B.J., DiRocco, L., Holmgren, L., Montagno, J., Bork, P., Huszar, D., Fairchild-Huntress, V., Ge, P., Keilty, J., Ebeling, C., Baldini, L., Gilchrist, J., Burn, P., Carlson, G.A. and Moore, K.J.
Nature 398
: 148-152.
11 March 1999
Exploring the metabolic and genetic control of gene expression on a genomic scale.
Koenig, R. and Dandekar, T.
Chemtracts 12
(3): 148-152.
March 1999
Mice lacking bombesin receptor subtype-3 develop metabolic defects and obesity (Condensation and commentary).
Kelly, L., Sharma, K. and Dandekar, T.
Chemtracts 12
: 223-228.
March 1999
Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering.
Schuster, S., Dandekar, T. and Fell, D.A.
Trends in Biotechnology 17
(2): 53-60.
1 February 1999
A point of entry into genomics.
Bork, P. and Huynen, M.
Nature Genetics 23
: 273-273.
1 January 1999
Associative database of protein sequences.
Hanke, J., Lehmann, G., Bork, P. and Reich, J.
Bioinformatics 15
: 741-748.
1 January 1999
Genome phylogeny based on gene content.
Snel, B., Bork, P. and Huynen, M.A.
Nature Genetics 21
: 108-110.
1 January 1999
METATOOL: for studying metabolic networks.
Pfeiffer, T., Sanchez-Valdenebro, I., Nuno, J.C., Montero, F. and Schuster, S.
Bioinformatics 15
: 251-257.
1 January 1999
Modular control analysis of slipping enzymes.
Schuster, S. and Westerhoff, H.V.
Biosystems 49
: 1-15.
1 January 1999
Pathway alignment: application to the comparative analysis of glycolytic enzymes.
Dandekar, T., Schuster, S., Snel, B., Huynen, M. and Bork, P.
Biochemical Journal 343
: 115-124.
1 January 1999
Protein families in multicellular organisms.
Copley, R.R., Schultz, J., Ponting, C.P. and Bork, P.
Current Opinion in Structural Biology 9
: 408-415.
1 January 1999
SMART: identification and annotation of domains from signalling and extracellular protein sequences.
Ponting, C.P., Schultz, J., Milpetz, F. and Bork, P.
Nucleic Acids Research 27
(1): 229-232.
1 January 1999
Studies on the stoichiometric structure of enzymatic reaction systems.
Schuster, S.
Theory in Biosciences 118
: 125-139.
1 January 1999
Use and limitations of modular metabolic control analysis in medicine and biotechnology.
Schuster, S.
Metabolic Engineering 1
: 232-242.
1 January 1999
Altern und Sterben - evolutionsbiologische und soziobiologische Begruendungen.
Dandekar, T.
Praxis der Naturwissenschaften - Biologie 48
: 1-16.
1999
Bioinformatik.
Bork, P.
Biospektrum 5
(3/1999): 172.
1999
Homology-based gene prediction using neural nets.
Cai, Y.D. and Bork, P.
Analytical Biochemistry 265
: 269-274.
15 December 1998
Genomic organization of a 225-kb region in Xq28 containing the gene for X-linked myotubular myopathy (MTM1) and a related gene (MTMR1).
Kioschis, P., Wiemann, S., Heiss, N.S., Francis, F., Goetz, C., Poustka, A., Taudien, S., Platzer, M., Wiehe, T., Beckmann, G., Weber, J., Nordsiek, G. and Rosenthal, A.
Genomics 54
: 256-266.
1 December 1998
Identical variant TSG101 transcripts in soft tissue sarcomas and various non-neoplastic tissues.
Willeke, F., Ridder, R., Bork, P., Klaes, R., Mechtersheimer, G., Schwarzbach, M., Zimmer, D., Kloor, M., Lehnert, T., Herfarth, C. and Knebel-Doeberitz, M.
Molecular Carcinogenesis 23
: 195-200.
1 December 1998
Phylogenetic analysis of nucleotide sequences: an algebraic approach.
Schmidt, W.
Mathematical Biosciences 154
: 39-55.
1 December 1998
Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase.
Eisenhaber, B., Bork, P. and Eisenhaber, F.
Protein Engineering 11
: 1155-1161.
1 December 1998
A pyrimidine-rich exonic splicing suppressor binds multiple RNA splicing factors and inhibits spliceosome assembly.
Zheng, Z.M., Huynen, M. and Baker, C.C.
Proceedings of the National Academy of Sciences of the United States of America 95
(24): 14088-14093.
24 November 1998
Conservation of gene order: a fingerprint of proteins that physically interact.
Dandekar, T., Snel, B., Huynen, M. and Bork, P.
Trends in Biochemical Sciences 23
(9): 324-328.
1 September 1998
Multi-locus nonparametric linkage analysis of complex trait loci with neural networks.
Lucek, P., Hanke, J., Reich, J., Solla, S.A. and Ott, J.
Human Heredity 48
: 275-284.
1 September 1998
Automatic detection of conserved RNA structure elements in complete RNA virus genomes.
Hofacker, I.L., Fekete, M., Flamm, C., Huynen, M.A., Rauscher, S., Stolorz, P.E. and Stadler, P.F.
Nucleic Acids Research 26
(16): 3825-3836.
15 August 1998
Evolution of new protein function: recombinational enhancer Fis originated by horizontal gene transfer from the transcriptional regulator NtrC.
Morett, E. and Bork, P.
FEBS Letters 433
: 108-112.
14 August 1998
Measuring genome evolution.
Huynen, M.A. and Bork, P.
Proceedings of the National Academy of Sciences of the United States of America 95
(11): 5849-5856.
26 May 1998
SMART, a simple modular architecture research tool: Identification of signaling domains.
Schultz, J., Milpetz, F., Bork, P. and Ponting, C.P.
Proceedings of the National Academy of Sciences of the United States of America 95
(11): 5857-5864.
26 May 1998
Differential gene expression in mammary carcinoma cell lines: identification of DRIM, a new gene down-regulated in metastasis.
Schwirzke, M., Gnirke, A., Bork, P., Tarin, D. and Weidle, U.H.
Anticancer Research 18
: 1409-1421.
1 May 1998
Nibrin, a novel DNA double-strand break repair protein, is mutated in Nijmegen breakage syndrome.
Varon, R., Vissinga, C., Platzer, M., Cerosaletti, K.M., Chrzanowska, K.H., Saar, K., Beckmann, G., Seemanova, E., Cooper, P.R., Nowak, N.J., Stumm, M., Weemaes, C.M.R., Gatti, R.A., Wilson, R.K., Digweed, M., Rosenthal, A., Sperling, K., Concannon, P. and Reis, A.
Cell 93
(3): 467-476.
1 May 1998
The frequency distribution of gene family sizes in complete genomes.
Huynen, M.A. and van Nimwegen, E.
Molecular Biology and Evolution 15
(5): 583-589.
1 May 1998
Processing of the precursors to small nucleolar RNAs and rRNAs requires common components.
Petfalski, E., Dandekar, T., Henry, Y. and Tollervey, D.
Molecular and Cellular Biology 18
(3): 1181-1189.
March 1998
Characterization of targeting domains by sequence analysis: glycogen-binding domains in protein phosphatases.
Bork, P., Dandekar, T., Eisenhaber, F. and Huynen, M.
Journal of Molecular Medicine 76
: 77-79.
1 February 1998
Are knowledge-based potentials derived from protein structure sets discriminative with respect to amino acid types?
Sunyaev, S.R., Eisenhaber, F., Argos, P., Kuznetsov, E.N. and Tumanyan, V.G.
Proteins: Structure, Function, and Bioinformatics 31
: 225-246.
1 January 1998
Characterization of naturally occurring myosin heavy chain antisense mRNA in rat heart.
Luther, H.P., Haase, H., Hohaus, A., Beckmann, G., Reich, J. and Morano, I.
Journal of Cellular Biochemistry 70
: 110-120.
1 January 1998
Conformational stability studies of the pleckstrin DEP domain: definition of the domain boundaries.
Kharrat, A., Millevoi, S., Baraldi, E., Ponting, C.P., Bork, P. and Pastore, A.
Biochimica et Biophysica Acta 1385
: 157-164.
1 January 1998
Control analysis of metabolic systems involving quasi- equilibrium reactions.
Kholodenko, B.N., Schuster, S., Garcia, J., Westerhoff, H.V. and Cascante, M.
Biochimica et Biophysica Acta 1379
: 337-352.
1 January 1998
Determination of the fold of the core protein of Hepatitis B virus by electron cryomicroscopy.
Dandekar, T. and Argos, P.
Chemtracts 11
: 161-165.
1 January 1998
Differential genome analysis applied to the species-specific features of Helicobacter pylori.
Huynen, M., Dandekar, T. and Bork, P.
FEBS Letters 426
: 1-5.
1 January 1998
Frame: detection of genomic sequencing errors.
Brown, N.P., Sander, C. and Bork, P.
Bioinformatics 14
: 367-371.
1 January 1998
Homology-based fold predictions for Mycoplasma genitalium proteins.
Huynen, M., Doerks, T., Eisenhaber, F., Orengo, C., Sunyaev, S.R., Yuan, Y.P. and Bork, P.
Journal of Molecular Biology 280
: 323-326.
1 January 1998
Mammalian protein homologous to VAT-1 of torpedo californica: isolation from Ehrlich Ascites Tumor cells, biochemical characterization and organization of its gene.
Hayess, K., Kraft, R., Sachsinger, J., Janke, J., Jandrig, B., Beckmann, G., Rohde, K. and Benndorf, R.
Journal of Cellular Biochemistry 69
: 304-315.
1 January 1998
Merging extracellular domains: Fold prediction for laminin G- like and amino-terminal thrombospondin-like modules based on homology to pentraxins.
Beckmann, G., Hanke, J., Bork, P. and Reich, J.
Journal of Molecular Biology 275
: 725-730.
1 January 1998
Mitochondria as an important factor in the maintenance of constant amplitudes of cytosolic calcium oscillations.
Marhl, M., Schuster, S. and Brumen, M.
Biophysical Chemistry 71
: 125-132.
1 January 1998
Modelling oscillations of calcium and endoplasmic reticulum transmembrane potential role of the signalling and buffering proteins and of the size of the Ca2+ sequestering ER subcompartments.
Marhl, M., Schuster, S., Brumen, M. and Heinrich, R.
Bioelectrochemistry and Bioenergetics 46
: 79-90.
1 January 1998
Modelling the interrelation between the transmembrane potential and pH difference across membranes with electrogenic proton transport upon build-up of the proton-motive force.
Schuster, S., Ouhabi, R., Rigoulet, M. and Mazat, J.P.
Bioelectrochemistry and Bioenergetics 45
: 181-192.
1 January 1998
Predicting functions from protein sequences - where are the bottlenecks?
Bork, P. and Koonin, E.V.
Nature Genetics 18
: 313-318.
1 January 1998
Protein annotation: detective work for function prediction.
Doerks, T., Bairoch, A. and Bork, P.
Trends in Genetics 14
: 248-250.
1 January 1998
Structural basis for the binding of a globular antifreeze to ice.
Dandekar, T. and Argos, P.
Chemtracts 11
: 229-232.
1 January 1998
Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches.
Dandekar, T., Beyer, K., Bork, P., Kenealy, M.R., Pantopoulos, K., Hentze, M., Sonntag-Buck, V., Flouriot, G., Gannon, F., Keller, W. and Schreiber, S.
Bioinformatics 14
: 271-278.
1 January 1998
The modelling of metabolic systems. Structure, control and optimality.
Heinrich, R. and Schuster, S.
Biosystems 47
: 61-77.
1 January 1998
Towards detection of orthologues in sequence databases.
Yuan, Y.P., Eulenstein, O., Vingron, M. and Bork, P.
Bioinformatics 14
: 285-289.
1 January 1998
Isolation and molecular characterization of a surface-bound proteinase of Entamoeba histolytica.
Jacobs, T., Bruchhaus, I., Dandekar, T., Tannich, E. and Leippe, M.
Molecular Microbiology 27
(2): 269-276.
January 1998
Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families.
Andrade, M.A. and Valencia, A.
Bioinformatics 14
(7): 600-607.
1998
Gene families: the taxonomy of protein paralogs and chimeras.
Henikoff, S., Greene, E.A., Pietrokovski, S., Bork, P., Attwood, T.K. and Hood, L.
Science 278
(5338): 609-614.
24 October 1997
Probabilistic evaluation of similarity between pairs of three-dimensional protein structures utilizing temperature factors.
Carugo, O. and Eisenhaber, F.
Journal of Applied Crystallography 30
(5/1): 547-549.
1 October 1997
Refined mapping of the epilepsy susceptibility locus EJM1 on chromosome 6.
Sander, T., Bockenkamp, B., Hildmann, T., Blasczyk, R., Kretz, R., Wienker, T.F., Volz, A., Schmitz, B., Beckmannagetta, G., Riess, O., Epplen, J.T., Janz, D. and Ziegler, A.
Neurology 49
(3): 842-847.
1 September 1997
Localization of the gene causing keratolytic winter erythema to chromosome 8p22-p23, and evidence for a founder effect in south african afrikaans-speakers.
Starfield, M., Hennies, H.C., Jung, M., Jenkins, T., Wienker, T.F., Hull, P., Spurdle, A., Kuester, W., Ramsay, M. and Reis, A.
American Journal of Human Genetics 61
(2): 370-378.
August 1997
A novel class of RanGTP binding proteins.
Goerlich, D., Dabrowski, M., Bischoff, F.R., Kutay, U., Bork, P., Hartmann, E., Prehn, S. and Izaurralde, E.
Journal of Cell Biology 138
(1): 65-80.
14 July 1997
A genome wide search for susceptibility loci in three european malignant hyperthermia pedigrees.
Robinson, R.I., Monnier, N., Wolz, W., Jung, M., Reis, A., Nuernberg, G., Curran, J.L., Monsieurs, K., Stieglitz, P., Heytens, L., Fricker, R., Vanbroeckhoven, C., Deufel, T., Hopkins, P.M., Lunardi, J. and Mueller, C.R.
Human Molecular Genetics 6
(6): 953-961.
June 1997
The gene for the ataxia telangiectasia variant, nijmegen breakage syndrome, maps to a 1 cm interval on chromosome 8q21.
Saar, K., Chrzanowska, K.H., Stumm, M., Jung, M., Nuernberg, G., Wienker, T.F., Seemanova, E., Wegner, R.D., Reis, A. and Sperling, K.
American Journal of Human Genetics 60
(3): 605-610.
March 1997
Strong indication for a breast cancer susceptibility gene on chromosome 8p12-p22: linkage analysis in german breast cancer families.
Seitz, S., Rohde, K., Bender, E., Nothnagel, A., Koelble, K., Schlag, P.M. and Scherneck, S.
Oncogene 14
(6): 741-743.
13 February 1997
A putative nucleic acid-binding domain in Werner's and Bloom's syndrome helicases.
Morozov, V., Mushegian, A.R., Koonin, E.V. and Bork, P.
Trends in Biochemical Sciences 22
: 417-418.
1 January 1997
A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins.
Bork, P., Hofmann, K., Bucher, P., Neuwald, A., Altschul, S.F. and Koonin, E.V.
FASEB Journal 11
(1): 68-76.
1 January 1997
Allelic association of juvenile absence epilepsy with a glur5 kainate receptor gene (grik1) polymorphism.
Sander, T., Hildmann, T., Kretz, R., Fuerst, R., Sailer, U., Bauer, G., Schmitz, B., Beck-Mannagetta, G., Wienker, T.F. and Janz, D.
American Journal of Medical Genetics 74
: 416-421.
1 January 1997
Analysis of genetic linkage and somatic loss of heterozygosity in affected pairs of first-degree relatives.
Rohde, K., Teare, M.D. and Koref, M.S.
American Journal of Human Genetics 61
: 418-422.
1 January 1997
Applying experimental data to protein fold prediction with the genetic algorithm.
Dandekar, T. and Argos, P.
Protein Engineering 10
: 877-893.
1 January 1997
Artificial neural network method for predicting the specificity of GalNAc-transferase.
Cai, Y.D., Yu, H. and Chou, K.C.
Journal of Protein Chemistry 16
: 689-700.
1 January 1997
Assessing the reliability of RNA folding using statistical mechanics.
Huynen, M.A., Guttel, R. and Konings, D.A.M.
Journal of Molecular Biology 267
: 1104-1112.
1 January 1997
BRCA1 mutations and phenotype.
Grade, K., Hoeffken, K., Kath, R., Nothnagel, A., Bender, E. and Scherneck, S.
Journal of Cancer Research and Clinical Oncology 123
: 69-70.
1 January 1997
Bioinformatics and molecular medicine: introduction and call for papers.
Bork, P.
Journal of Molecular Medicine 75
: 3-4.
1 January 1997
Comparative genome analysis: From sequences to functions.
Bork, P.
Developments in Industrial Microbiology 34
: 21-23.
1 January 1997
Deletion mapping and linkage analysis provide strong indication for the involvement of the human chromosome region 8p12-p22 in breast carcinogenesis.
Seitz, S., Rohde, K., Bender, E., Nothnagel, A., Pidde, H., Ullrich, O.M., El-Zehairy, A., Haensch, W., Jandrig, B., Koelble, K., Schlag, P.M. and Scherneck, S.
British Journal of Cancer 76
: 983-991.
1 January 1997
Genome maps 8. Building gene families. Wall chart.
Greene, E.A., Pietrokovski, S., Henikoff, S., Bork, P., Attwood, T.K., Hood, L. and Bairoch, A.
Science 278
: 615-626.
1 January 1997
Improving protein structure prediction by new strategies: experimental insights and the genetic algorithm.
Dandekar, T.
Journal of Molecular Modeling 3
: 312-314.
1 January 1997
Localisation of a gene for Papillon-Lefevre syndrome to chromosome 11q14-q21 by homozygosity mapping.
Laass, M.W., Hennies, H.C., Preis, S., Stevens, H.P., Jung, M., Leigh, I.M., Wienker, T.F. and Reis, A.
Human Genetics 101
: 376-382.
1 January 1997
Localization of the gene for Wieacker Wolff syndrome in the pericentromeric region of the X chromosome.
Kloos, D.U., Jakubiczka, S., Wienker, T.F., Wolff, G. and Wieacker, P.
Human Genetics 100
: 426-430.
1 January 1997
Molecular modeling of amoebapore and nk lysin: a four-alpha-helix bundle motif of cytolytic peptides from distantly related organisms.
Dandekar, T. and Leippe, M.
Folding & Design 2
: 47-52.
1 January 1997
Neurovascular compression at the ventrolateral medulla in autosomal dominant hypertension and brachydactyly.
Naraghi, R., Schuster, H., Toka, H.R., Bähring, S., Toka, O., Oeztekin, O., Bilginturan, N., Knoblauch, H., Wienker, T.F., Busjahn, A., Haller, H., Fahlbusch, R. and Luft, F.C.
Stroke 28
: 1749-1754.
1 January 1997
On the classification and evolution of protein modules.
Hegyi, H. and Bork, P.
Journal of Protein Chemistry 16
: 545-551.
1 January 1997
Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs.
Mushegian, A.R., Bassett, D.E., Boguski, M.S., Bork, P. and Koonin, E.V.
Proceedings of the National Academy of Sciences of the United States of America 94
: 5831-5836.
1 January 1997
Probing Flp: a new approach to analyze the structure of a DNA recognizing protein by combining the genetic algorithm, mutagenesis and non-canonical DNA target sites.
Saxena, P., Whang, I., Voziyanov, Y., Harkey, C., Argos, P., Jayaram, M. and Dandekar, T.
Biochimica et Biophysica Acta 1340
: 187-204.
1 January 1997
RNA ligands selected by cleavage stimulation factor (CstF) contain distinct sequence motifs that function as downstream elements in 3' end processing of pre-mRNA.
Beyer, K., Dandekar, T. and Keller, W.
Journal of Biological Chemistry 272
: 26769-26779.
1 January 1997
Relationship of polymorphisms in the renin angiotensin system and in e selectin of patients with early severe coronary heart disease.
Wenzel, K., Blackburn, A., Ernst, M., Affeldt, M., Hanke, R., Baumann, G., Felix, S.B., Kleber, F.X., Rohde, K., Glaser, C. and Speer, A.
Journal of Molecular Medicine 75
: 57-61.
1 January 1997
SAM as a protein interaction domain involved in developmental regulation.
Schultz, J., Ponting, C., Hofmann, K. and Bork, P.
Protein Science 6
: 249-253.
1 January 1997
SPRY domains in ryanodine receptors (Ca2+ release channels).
Ponting, C., Schultz, J. and Bork, P.
Trends in Biochemical Sciences 22
: 193-194.
1 January 1997
The breast cancer gene product TSG101: a regulator of ubiquitination?
Ponting, C.P., Cai, Y.D. and Bork, P.
Journal of Molecular Medicine 75
: 467-469.
1 January 1997
The sequence alerting server-a new WEB server.
Hegyi, H., Lai, J. and Bork, P.
Computer Applications in the Biosciences 13
: 619-620.
1 January 1997
Use of a modified binding model for the investigation of affinity dependence on antibody concentration in immunoassay systems.
Strohner, P., Sarrach, D. and Reich, J.
Journal of Immunological Methods 203
: 113-122.
1 January 1997
Linkage of the gene for the triple a syndrome to chromosome 12q13 near the type II keratin gene cluster.
Weber, A., Wienker, T.F., Jung, M., Easton, D., Dean, H.J., Heinrichs, C., Reis, A. and Clark, A.J.L.
Human Molecular Genetics 5
(12): 2061-2066.
1 December 1996
Structure and distribution of modules in extracellular proteins.
Bork, P., Downing, A.K., Kieffer, B. and Campbell, I.D.
Quaterly Reviews of Biophysics 29
(2): 119-167.
1 May 1996
A distance measure based on binary character data and its application to phylogeny reconstruction.
Schmidt, W. and Mueller, E.C.
Bulletin of Mathematical Biology 58
: 449-469.
1 January 1996
Ancient duplication of dna polymerase inferred from analysis of complete bacterial genomes.
Koonin, E.V. and Bork, P.
Trends in Biochemical Sciences 21
(4): 128-129.
1 January 1996
Angiotensin converting enzyme and heart chymase gene polymorphisms in hypertrophic cardiomyopathy.
Pfeufer, A., Osterziel, K.J., Urata, H., Borck, G., Schuster, H., Wienker, T.F., Dietz, R. and Luft, F.C.
American Journal of Cardiology 78
: 362-364.
1 January 1996
Autosomal dominant hypertension and brachydactyly in a turkish kindred resembles essential hypertension.
Schuster, H., Wienker, T.F., Toka, H.R., Bähring, S., Jeschke, E., Toka, O., Busjahn, A., Hempel, A., Tahlhammer, C., Oelkers, W., Kunze, J., Bilginturan, N., Haller, H. and Luft, F.C.
Hypertension 28
: 1085-1092.
1 January 1996
BRCA1 mutations in German breast-cancer families.
Jandrig, B., Grade, K., Seitz, S., Waindzoch, B., Mueller, M., Bender, E., Nothnagel, A., Rohde, K., Schlag, P.M., Kath, R., Hoeffken, K. and Scherneck, S.
International Journal of Cancer 68
: 188-192.
1 January 1996
Common subtypes of idiopathic generalized epilepsies: lack of linkage to d20s19 close to candidate loci (ebn1, eegv1) on chromosome 20.
Sander, T., Hildmann, T., Wienker, T.F., Ramel, C., Beckmannagetta, G., Bianchi, A., Sailer, U., Berek, K., Bauer, G., Neitzel, H., Schmitz, B., Durner, M., Johnson, K.J. and Janz, D.
American Journal of Medical Genetics 67
(1): 31-39.
1 January 1996
Comparison of CD45 extracellular domain sequences from divergent vertebate species suggests the conservation of three fibronectin type III domains.
Okumura, M., Matthew, R.J., Robb, B., Litmann, G.W., Bork, P. and Thomas, M.L.
Journal of Immunology 157
: 1569-1575.
1 January 1996
DNA polymorphisms in adhesion molecule genes: a new risk factor for early atherosclerosis.
Wenzel, K., Ernst, M., Rohde, K., Baumann, G. and Speer, A.
Human Genetics 97
(1): 15-20.
1 January 1996
Exclusion of linkage between idiopathic generalized epilepsies and the GABAA receptor alpha1 and gamma2 subunit gene cluster on chromosome 5.
Sander, T., Hildmann, T., Janz, D., Wienker, T.F., Bianchi, A., Bauer, G., Sailer, U., Scaramelli, A., Neitzel, H., Schmitz, B., Bailey, M.E.S., Beckmannagetta, G., Johnson, K.J. and Darlison, M.G.
Epilepsy Research 23
(3): 235-244.
1 January 1996
Friedreich's ataxia protein: phylogenetic evidence for mitochondrial dysfunction.
Gibson, T., Koonin, E.V., Musco, G., Pastore, A. and Bork, P.
Trends in Neurosciences 19
: 465-468.
1 January 1996
Glycoprotein mediated cell binding of lectin coated liposomes.
Schaefer, H., Stahn, R., Schreiber, J. and Schmidt, W.
Journal of Liposome Research 6
: 479-496.
1 January 1996
Go hunting in sequence databases but watch out for the traps.
Bork, P. and Bairoch, A.
Trends in Genetics 12
: 425-427.
1 January 1996
Identification and mutation analysis of the complete gene for the Chediak-Higashi syndrome.
Nagle, D.L., Karim, M., Woolf, E.A., Holmgren, L., Bork, P., Misumi, D., McGrail, D., Dussault, J.R., Duyk, G., Spritz, R.A. and Moore, K.J.
Nature Genetics 14
: 307-312.
1 January 1996
Identification of residues within the shc phosphotyrosine binding phosphotyrosine interaction domain crucial for phosphopeptide interaction.
Yajnik, V., Blaikie, P., Bork, P. and Margolis, B.
Journal of Biological Chemistry 271
(4): 1813-1816.
1 January 1996
Kohonen map as visualization tool for the analysis of protein sequences: multiple alignments, domains and segments of secondary structures.
Hanke, J. and Reich, J.
Computer Applications in the Biosciences 12
: 447-454.
1 January 1996
Metabolism and evolution of Haemophilus influenzae deduced from a whole genome comparison with Escherichia coli.
Tatusov, R.L., Mushegian, A.R., Bork, P., Brown, N.P., Hayes, W.S., Borodovsky, M., Rudd, K.E. and Koonin, E.V.
Current Biology 6
(3): 279-291.
1 January 1996
On the classification of modular proteins.
Henrissat, B. and Bork, P.
Protein Engineering 9
: 725-726.
1 January 1996
Pleckstrin's repeat performance: a novel domain in g protein signaling.
Ponting, C.P. and Bork, P.
Trends in Biochemical Sciences 21
: 245-246.
1 January 1996
Protein sequence motifs.
Bork, P. and Koonin, E.V.
Current Opinion in Structural Biology 6
: 366-376.
1 January 1996
Role of T cell receptor delta gene in susceptibility to celiac disease.
Roschmann, E., Wienker, T.F. and Volk, B.A.
Journal of Molecular Medicine 74
(2): 93-98.
1 January 1996
Self-organizing hierarchic networks for pattern recognition in protein sequence.
Hanke, J., Beckmann, G., Bork, P. and Reich, J.
Protein Science 5
: 72-82.
1 January 1996
Sperm-egg binding protein or proto-oncogene?
Bork, P.
Science 271
(5254): 1431-1432.
1 January 1996
Structural motifs of the pkd1 protein.
Lohning, C., Pohlschmidt, M., Glucksmannkuis, M.A., Duyk, G., Bork, P., Schneider, M.O., Reeders, S.T. and Frischauf, A.M.
Nephrology Dialysis Transplantation 11 Suppl.
: 2-4.
1 January 1996
The protein phosphatase 2C (PP2C) superfamily: detection of bacterial homologues.
Bork, P., Brown, N.P., Hegyi, H. and Schultz, J.
Protein Science 5
: 1421-1425.
1 January 1996
Von Genomsequenzen zu Proteinfunktionen.
Bork, P.
Informationstechnik und technische Informatik 5
: 20-26.
1 January 1996
Polycystic kidney disease: the complete structure of the PKD1 gene and its protein.
Gluecksmann-Kuis, M.A., Tayber, O., Woolf, E.A., Bougueleret, L., Deng, N.H., Alperin, G.D., Iris, F., Hawkins, F., Munro, C., Lakey, N., Duyk, G., Schneider, M.C., Geng, L., Zhang, F., Zhao, Z.H., Torosian, S., Zhou, J., Reeders, S.T., Bork, P., Pohlschmidt, M., Lohning, C., Kraus, B., Nowicka, U., Leung, A.L.S. and Frischauf, A.M.
Cell 81
(2): 289-298.
21 April 1995
A program using loss-of-constitutional- heterozygosity data to ascertain the location of predisposing genes in cancer families.
Rohde, K., Teare, M.D., Scherneck, S. and Santibanez-Koref, M.F.
Human Heredity 45
: 337-345.
1 January 1995
An angiotensin-converting enzyme gene variant is associated with acute myocardial infarction in women but not in men.
Schuster, H., Wienker, T.F., Stremmler, U., Noll, B., Steinmetz, A. and Luft, F.C.
American Journal of Cardiology 76
(8): 601-603.
1 January 1995
Analysis of marker genes contributing to coeliac disease susceptibility.
Roschmann, E., Wienker, T.F., Gerok, W. and Volk, A.
Advances in Experimental Medicine and Biology 371 B
: 1339-1343.
1 January 1995
Characterization of a novel protein-binding module - the WW domain.
Sudol, M., Chen, H.I., Bourgeret, C., Einbond, A. and Bork, P.
FEBS Letters 369
(1): 67-71.
1 January 1995
Characterization of the mammalian YAP (Yes-associated protein) gene and its role in defining a novel module - the WW domain.
Sudol, M., Bork, P., Einbond, A., Kastury, K., Druck, T., Negrini, M., Huebner, K. and Lehman, D.
Journal of Biological Chemistry 270
: 14733-14741.
1 January 1995
Divergent evolution of a beta/alpha-barrel subclass: detection of numerous phosphate-binding sites by motif search.
Bork, P., Gellerich, J., Groth, H., Hooft, R. and Martin, F.
Protein Science 4
: 268-274.
1 January 1995
Exploring the Mycoplasma capricolum genome: a small bacterium reveals its physiology.
Bork, P., Ouzounis, C., Casari, G., Schneider, R., Sander, C., Dolan, M., Gilbert, W. and Gillevet, P.M.
Molecular Microbiology 16
: 955-967.
1 January 1995
Klonierung des Brustkrebsgens BRCA1. Stellungnahme erarbeitet durch eine adhoc-Gruppe im Rahmen des "Gesamtprogramms zur Krebsbekaempfung".
Chang-Claude, J., Hundsdoerfer, G., Jonat, W., Scherneck, S. and Wienker, T.F.
Frauenarzt 36
(5): 572-574.
1 January 1995
More WW domains.
Bork, P. and Sudol, M.
Trends in Biochemical Sciences 20
: 54-54.
1 January 1995
New protein functions in yeast chromosome VIII.
Ouzounis, C., Bork, P., Casari, G. and Sander, C.
Protein Science 4
(11): 2424-2428.
1 January 1995
Phylogeny reconstruction for protein sequences based on amino acid properties.
Schmidt, W.
Journal of Molecular Evolution 41
(4): 522-530.
1 January 1995
Ready for a motif submission? A proposed checklist.
Bork, P., Ouzounis, C. and McEntyre, J.
Trends in Biochemical Sciences 20
(3): 104-104.
1 January 1995
Refinement of map position of the human GluR6 kainate receptor gene (GRIK2) and lack of association and linkage with idiopathic generalized epilepsies.
Sander, T., Janz, D., Ramel, C., Ross, C.A., Paschen, W., Hildmann, T., Wienker, T.F., Bianchi, A., Bauer, G., Sailer, U., Berek, K., Neitzel, H., Volz, A., Ziegler, A., Schmitz, B. and Beckmannagetta, G.
Neurology 45
(9): 1713-1720.
1 January 1995
The SEA module - a new extracellular domain associated with o-glycosylation.
Bork, P. and Patthy, L.
Protein Science 4
(7): 1421-1425.
1 January 1995
The cytidylyltransferase superfamily: identification of the nucleotide-binding site and fold prediction.
Bork, P., Holm, L., Koonin, E.V. and Sander, C.
Proteins: Structure, Function, and Genetics 22
(3): 259-266.
1 January 1995
The phenotypic spectrum related to the human epilepsy susceptibility gene ejm1.
Sander, T., Hildmann, T., Janz, D., Wienker, T.F., Neitzel, H., Bianchi, A., Bauer, G., Sailer, U., Berek, K., Schmitz, B. and Beckmannagetta, G.
Annals of Neurology 38
(2): 210-217.
1 January 1995
Treasure your exceptions: what we can learn from autosomal-dominant inherited forms of hypertension.
Luft, F.C., Schuster, H., Bilginturan, N. and Wienker, T.F.
Journal of Hypertension 13
(12): 1535-1538.
1 January 1995
The WW domain: a signalling site in dystrophin.
Bork, P. and Sudol, M.
Trends in Biochemical Sciences 19
(12): 531-533.
1 December 1994
E-selectin polymorphism and atherosclerosis: an association study.
Wenzel, K., Felix, S., Kleber, F.X., Brachold, R., Menke, T., Schattke, S., Schulte, K.L., Glaser, C., Rohde, K. and Baumann, G.
Human Molecular Genetics 3
(11): 1935-1937.
1 November 1994
A novel RNA-binding motif in omnipotent suppressors of translation termination, ribosomal proteins and a ribosome modification enzyme?
Koonin, E., Bork, P. and Sander, C.
Nucleic Acids Research 22
(11): 2166-2167.
11 June 1994
Detection of a major gene for heterocellular hereditary persistence of fetal hemoglobin after accounting for genetic modifiers.
Thein, S.L., Sampietro, M., Rohde, K., Rochette, J., Weatherall, D.J., Lathrop, G.M. and Demenais, F.
American Journal of Human Genetics 54
(2): 214-228.
February 1994
A new family of carbon-nitrogen hydrolases.
Bork, P. and Koonin, E.
Protein Science 3
: 1344-1346.
1 January 1994
A p-loop-like motif in a widespread ATP pyrophosphatase domain: implications for the evolution of motifs and enzyme activity.
Bork, P. and Koonin, E.V.
Proteins: Structure, Function, and Genetics 20
: 347-355.
1 January 1994
Biochemical genetics of methylglyoxal dehydrogenases in the laboratory rat (Rattus norvegicus).
Bender, K., Seibert, R.T., Wienker, T.F., Kren, V., Pravenec, M. and Bissbort, S.
Biochemical Genetics 32
: 147-154.
1 January 1994
Differential display reverse transcription PCR.
Bauer, D., Mueller, H., Reich, J., Riedel, H., Ahrenkiel, V., Warthoe, P. and Strauss, M.
BioTec 2
: 32-35.
1 January 1994
Drosophila kelch motif is derived from a common enzyme fold.
Bork, P. and Doolittle, R.F.
Journal of Molecular Biology 236
: 1277-1282.
1 January 1994
Eukaryotic translation elongation factor 1gamma contains a glutathione transferase domain - study of a diverse ancient class of proteins using motif search and structural modelling.
Koonin, E.V., Mushegian, A.R., Tatusov, R.L., Altschul, S.F., Bryant, S.H., Bork, P. and Valencia, A.
Protein Science 3
: 2045-2054.
1 January 1994
From genome sequences to protein function.
Bork, P., Ouzounis, C. and Sander, C.
Current Opinion in Structural Biology 4
: 393-403.
1 January 1994
The use of loss of constitutional heterozygosity data to ascertain the location of predisposing genes in cancer families.
Teare, M.D., Rohde, K. and Santibanez-Koref, M.F.
Journal of Medical Genetics 31
: 448-452.
1 January 1994
Tracing the spread of fibronectin type III domains in bacterial glycohydrolases.
Little, E., Bork, P. and Doolittle, R.F.
Journal of Molecular Evolution 39
: 631-643.
1 January 1994
Vergleichende Untersuchungen des Klostridien-Tumor-Testes an Hunden und Pferden.
Fabricius, E.M., Dietz, O., Schneeweiss, U., Schmidt, W., Wildner, G.P., Baumann, G., Benedix, A. and Weisbrich, C.
Monatshefte fuer Veterinaermedizin 49
: 151-157.
1 January 1994
Yeast chromosome III: new gene functions.
Koonin, E., Bork, P. and Sander, C.
EMBO Journal 13
: 493-503.
1 January 1994
Hundreds of ankyrin-like repeats in functionally diverse proteins: mobile modules that cross phyla horizontally?
Bork, P.
Proteins: Structure, Function, and Bioinformatics 17
(4): 363-374.
December 1993
Les proteines, molecules modulaires.
Doolittle, R.F. and Bork, P.
Pour la Science 194
: 52-59.
December 1993
Identification of differentially expressed mRNA species by an improved display technique (DDRT-PCR).
Bauer, D., Mueller, H., Reich, J., Riedel, H., Ahrenkiel, V., Warthoe, P. and Strauss, M.
Nucleic Acids Research 21
(18): 4272-4280.
11 September 1993
Linkage analysis in German breast cancer families with early onset of the disease, using highly polymorphic markers from the chromosome 17q11-q24 region.
Zimmermann, W., Bender, E., Rohde, K., Reis, A., Wiseman, R., Futreal, A., Krause, H., Prokoph, H., Werner, S. and Scherneck, S.
American Journal of Human Genetics 52
(4): 789-791.
April 1993
An expanding family of helicases within the "DEAD/H" superfamily.
Bork, P. and Koonin, E.
Nucleic Acids Research 21
(3): 751-752.
11 February 1993
3-aminobenzamide protects the mouse thymocytes in vitro from dexamethasone-mediated apoptotic cell death and cytolysis without changing DNA strand breakage.
Hoshino, J., Beckmann, G. and Kroeger, H.
Journal of Steroid Biochemistry and Molecular Biology 44
: 113-119.
1 January 1993
A fast, sensitive pattern-matching approach for protein sequences.
Rohde, K. and Bork, P.
Computer Applications in the Biosciences 9
: 183-189.
1 January 1993
A hybrid protein kinase - RNase in an interferon-induced pathway.
Bork, P. and Sander, C.
FEBS Letters 334
: 149-152.
1 January 1993
A trefoil domain in the major rabbit zona-pellucida protein.
Bork, P.
Protein Science 2
: 669-670.
1 January 1993
An adhesive domain detected in functionally diverse receptors.
Beckmann, G. and Bork, P.
Trends in Biochemical Sciences 18
: 40-41.
1 January 1993
Convergent evolution of similar enzymatic function on different protein folds: the hexokinase, ribokinase and galactokinase families of sugar kinases.
Bork, P., Sander, C. and Valencia, A.
Protein Science 2
: 31-40.
1 January 1993
Epidermal growth factor-like modules.
Campbell, I.D. and Bork, P.
Current Opinion in Structural Biology 3
(3): 385-392.
1 January 1993
Evolutionarily mobile modules in proteins.
Doolittle, R.F. and Bork, P.
Scientific American 269
: 50-56.
1 January 1993
Exopolyphosphate phosphatase and guanosine pentaphosphate phosphatase belong to the sugar kinase/actin/hsp70 superfamily.
Reizer, J., Reizer, A., Saier, M.H., Bork, P. and Sander, C.
Trends in Biochemical Sciences 18
: 247-248.
1 January 1993
Fibronectin type III modules in the receptor phosphatase CD45 and tapeworm antigens.
Bork, P. and Doolittle, R.F.
Protein Science 2
: 1185-1187.
1 January 1993
Loss of constitutional heterozygosity on chromosome 11p in human ovarian cancer. Positive correlation with grade of differentiation.
Kiechle-Schwarz, M., Bauknecht, T., Wienker, T.F., Walz, L. and Pfleiderer, A.
Cancer 72
: 2423-2432.
1 January 1993
Mobile Protein-Module: evolutionaer jung oder alt?
Doolittle, R.F. and Bork, P.
Spektrum der Wissenschaft 12
: 40-47.
1 January 1993
Molecular modelling of the norrie disease protein predicts a cystine knot growth factor tertiary structure.
Meitinger, T., Meindl, A., Bork, P., Rost, B., Sander, C., Haasemann, M. and Murken, J.
Nature Genetics 5
: 376-380.
1 January 1993
On the genetics of mandibular prognathism: analysis of large European noble families.
Wolff, G., Wienker, T.F. and Sander, H.
Journal of Medical Genetics 30
: 112-116.
1 January 1993
Prokaryotic members of a new family of putative helicases with similarity to transcripton activator SNF2.
Kolsto, A.B., Bork, P., Kvaloy, K., Lindback, T., Gronstadt, A., Kristensen, T. and Sander, C.
Journal of Molecular Biology 230
: 684-688.
1 January 1993
Quantitative investigations into the elimination of in vitro- obtained spores of the non-pathogenic clostridium butyricum strain CNRZ 528, and their persistence in organs of different species following intravenous spore administration.
Fabricius, E.M., Schneeweiss, U., Schau, H.P., Schmidt, W. and Benedix, A.
Research in Microbiology 144
: 741-753.
1 January 1993
Rotamers - to be or not to be? - An analysis of amino acid side-chains conformations in globular proteins.
Schrauber, H., Eisenhaber, F. and Argos, P.
Journal of Molecular Biology 230
: 592-612.
1 January 1993
T-cell receptor variable genes and genetic susceptibility to celiac disease: an association and linkage study.
Roschmann, E., Wienker, T.F., Gerok, W. and Volk, B.A.
Gastroenterology 105
: 1790-1796.
1 January 1993
The CUB domain: A widespread module in developmentally regulated proteins.
Bork, P. and Beckmann, G.
Journal of Molecular Biology 231
: 539-545.
1 January 1993
An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins.
Bork, P., Sander, C. and Valencia, A.
Proceedings of the National Academy of Sciences of the United States of America 89
(16): 7290-7294.
15 August 1992
A large domain common to sperm receptors (Zp2 and Zp3) and TGF-beta type III receptor.
Bork, P. and Sander, C.
FEBS Letters 300
: 237-240.
1 January 1992
A module of DnaJ heat shock proteins found in malaria parasites.
Bork, P., Sander, C., Valencia, A. and Bukau, B.
Trends in Biochemical Sciences 17
: 129-129.
1 January 1992
Cloning of a gene from Bacillus cereus with homology to the mreb gene of Echerichia coli.
Nahara, A., Naterstad, K., Kristensen, T., Lopez, R., Bork, P. and Kolsto, A.B.
Gene 122
: 181-185.
1 January 1992
Comprehensive sequence analysis of the 182 predicted ORFs of yeast chromosome III.
Bork, P., Ouzounis, C., Sander, C., Scharf, M., Schneider, R. and Sonnhammer, E.
Protein Science 1
: 1677-1690.
1 January 1992
Mobile modules and motifs.
Bork, P.
Current Opinion in Structural Biology 2
: 413-421.
1 January 1992
Proposed acquisition of an animal protein domain by bacteria.
Bork, P. and Doolittle, R.F.
Proceedings of the National Academy of Sciences of the United States of America 89
: 8990-8994.
1 January 1992
The modular architecture of vertebrate collagens.
Bork, P.
FEBS Letters 307
: 49-54.
1 January 1992
Book Section
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
Modern genome annotation: The BioSapiens network.
Yeats, C., Orengo, C., Veuthey, A.L., Boeckmann, B., Jensen, L.J., Valencia, A., 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., Albrecht, M., Blankenburg, H., Bork, P., Harrington, E.D., Hermjakob, H., Jensen, L.J., Juan, D.A., Lengauer, T., Pagel, P., Schachter, V. and Valencia, A.
In:
Modern Genome Annotation.
Springer, 353-410.
ISBN 978-3-211-75122-0
2008
Compositional asymmetries and predicted origins of replication of the Saccharomyces cerevisiae genome.
Korbel, J.O., Assmus, H., 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
Extracting regulatory gene expression networks from PubMed.
Saric, J., Jensen, L.J., Ouzounova, R., 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
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
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
Detection and characterization of pseudogenes.
Torrents, D., 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
High rate of gene displacement in vitamine biosynthetic pathways.
Morett, E., Saab-Rincon, G., Merino, E., Bork, P., Rajan, E., 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
Making predictions about robustness and flexibility from metabolic network structure.
Schuster, S., 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
An essay on individual sequence variation in Expressed Sequence Tags(ESTs).
Reich, J., Brett, D. and Hanke, J.
In:
Genomics and Proteomics: Functional and Computational Aspects.
Springer, 83-94.
ISBN 978-0-306-46312-9
2002
Minimal T-Invariants in biochemical petri nets.
Schuster, S. and Moldenhauer, F.
In:
Modellierung und Simulation Metabolischer Netzwerke.
Universitaet Magdeburg, Fakultaet fuer Informatik, Magdeburg, 3-10.
May 2000
METATOOL: eine Software zur Analyse und Vorhersage metabolischer Stoffwechselwege.
Moldenhauer, F., Lange, M., Hofestaedt, R. and Schuster, S.
In:
Modellierung und Simulation metabolischer Netzwerke : DFG-Workshop im Rahmen des DFG-Schwerpunktes Informatikmethoden zur Analyse und Interpretation großer genomischer Datenmengen ; 19. - 20. Mai 2000 in Magdeburg, Otto-von-Guericke-Universitaet.
Preprint / Otto-von-Guericke-Universitaet Magdeburg, Fakultaet fuer Informatik ; 2000,10
.
Otto-von-Guericke-Univ., Fakultaet fuer Informatik, Magdeburg, 34-38.
1 January 2000
Recent developments in metabolic pathway analysis and their potential implications for biotechnology and medicine.
Schuster, S., Dandekar, T., Mauch, K., Reuss, M. and Fell, D.
In:
Technological and Medical Implications of Metabolic Control Analysis.
Kluwer Acad. Publ., Dordrecht, 57-66.
1 January 2000
Structural analysis of metabolic networks: elementary flux modes, analgy to Petri Nets, and application to Mycoplasma pneumoniae.
Schuster, S., Pfeiffer, T., Moldenhauer, F., Koch, I. and Dandekar, T.
In:
German Conference on Bioinformatics 2000 : Proceedings of the German Conference on Bioinformatics, October 5 - 7, 2000, Heidelberg.
Logos-Verl., Berlin, 115-120.
ISBN 3-89722-498-4
1 January 2000
Topological analysis of metabolic networks. Application to the metabolism of Mycoplasma pneumoniae.
Pfeiffer, T., Dandekar, T., Moldenhauer, F. and Schuster, S.
In:
Bio Thermo Kinetics. Animating the Cellular Map.
Univ.Press, Stellenbosch, 229-234.
1 January 2000
Exploitation of gene context to infer evolution and to predict function.
Bork, P., Snel, B., Lehmann, G., Suyama, M., Dandekar, T., Lathe, W. and Huynen, M.
In:
Comparative Genomics : Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families.
Computational Biology ; 1
.
Kluwer, Dordrecht, 281-294.
ISBN 0-7923-6583-6 ; 0-7923-6584-4
2000
Structural analysis of metabolic networks: elementary flux modes, analogy to petri nets, and application to Mycoplasma pneumoniae.
Schuster, S., Pfeiffer, T., Moldenhauer, F., Koch, I. and Dandekar, T.
In:
GCB 2000 : Proceedings of the German Conference on Bioinformatics, October 5 - 7, 2000, Heidelberg.
Logos, Berlin, 115-120.
ISBN 3-89722-498-4
2000
Using time-dependent petri nets for the analysis of metabolic networks.
Heiner, M., Koch, I. and Schuster, S.
In:
Modellierung und Simulation Metabolischer Netzwerke.
Universitaet Magdeburg, Fakultaet fuer Informatik, Magdeburg, 15-21.
2000
Die genomische Struktur des ATM-Gens und Hinweise auf die Moeglichkeit umfangreicher Deletionen.
Platzer, M., Wiehe, T., Rohde, K., Sandoval, N. and Rosenthal, A.
In:
Ataxia teleangiectatica.
Medizinische Genetik, Muenchen, 17-19.
10 October 1999
Genome comparisons to monitor molecular evolution.
Bork, P., Dandekar, T., Snel, B. and Huynen, M.A.
In:
Microbial Evolution and Infection : 50th Congress of the Deutsche Gesellschaft fuer Hygiene und Mikrobiologie (DGHM) and the 25th Annual Meeting of the Deutsche Gesellschaft fuer Infektiologie (DGI).
Einhorn-Presse Verlag, Reinbek, 80-92.
ISBN 3-88756-811-7
1 July 1999
Applying logic programming to derive novel functional information of genomes.
Bansal, A. and Bork, P.
In:
Practical Aspects of Declarative Languages : First International Workshop, PADL'99 ; San Antonio, Texas, USA, January 18 - 19, 1999 ; Proceedings.
Lecture Notes in Computer Sciences ; 1551
.
Springer, Berlin [u.a.], 275-289.
ISBN 3-540-65527-1
1 January 1999
Automatic extraction of biological information from scientific text: protein-protein interactions.
Blaschke, C., Andrade, M.A., Ouzounis, C. and Valencia, A.
In:
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB'99) : Heidelberg, Germany, August 6 - 10, 1999.
ISMB Conference Series ; 7
.
AAAI Press, Menlo Park, Calif., 60-67.
ISBN 1-57735-083-9
1 January 1999
Position-specific annotation of protein function based on multiple homologs.
Andrade, M.A.
In:
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB'99) : Heidelberg, Germany, August 6 - 10, 1999.
ISMB Conference Series ; 7
.
AAAI Press, Menlo Park, Calif., 28-33.
ISBN 1-57735-083-9
1 January 1999
Sequence analysis.
Gibson, T. and Bork, P.
In:
Encyclopedia of Molecular Biology.
Wiley Biotechnology Encyclopedias
.
Wiley, New York [u.a.], 2320-2324.
ISBN 0-471-15302-8
1 January 1999
Elementary modes analysis ilustrated with human red cell metabolism.
Schuster, S., Fell, D.A., Pfeiffer, T., Dandekar, T. and Bork, P.
In:
Bio Thermokinetics in the Post Genomic Era.
Chalmers, Goeteborg, 332-339.
1 January 1998
Influence of calcium binding to proteins on calcium oscillation. A mathematical model.
Schuster, S., Marhl, M., Brumen, M. and Heinrich, R.
In:
Information Processing in Cells and Tissues.
Plenum Press, New York, 137-150.
1 January 1998
Questions about RNA secondary structures in HIV and HPV.
Huynen, M.A. and Konings, D.A.M.
In:
Viral Regulatory Structures and their Degeneracy.
Addison Wesley Longman, Massachusetts, 143-162.
1 January 1998
Sequence and structure of proteins.
Eisenhaber, F. and Bork, P.
In:
On Recombinant Proteins, Monoclonal Antibodies and Therapeutic Genes.
Biotechnology ; 5
.
Wiley-VCH, Weinheim, 43-86.
1998
Evidence of two components of repair of radiation damage in pig skin: Analysis of quantal response data based on a compartmental dose-response model.
Schmidt, W.
In:
Modelling in Clinical Radiobiology.
Albert-Ludwigs-University Freiburg, Freiburg, 92-102.
1 January 1997
Bioinformatik: Proteinsequenzen und Sekundaerstruktur-Vorhersagen.
Rohde, K.
In:
Methoden in der Proteinanalytik.
Springer, Berlin, 311-333.
1 January 1996
The Functional Composition of Living Mashines.
Ouzounis, C., Valencia, A., Tamames, J., Bork, P. and Sander, C.
In:
Advances in Artificial Life.
Lecture Notes in Artificial Intelligence Series ; 929
.
Springer, Berlin, Heidelberg, 843-852.
1 January 1995
Variants of the angiotensin converting enzyme gene are associated with high blood pressure and myocardial infarction.
Schuster, H., Wienker, T.F. and Luft, F.C.
In:
Atherosclerosis X; 10th International Symposium, Montreal, Quebec, Canada, October 9-14, 1994.
International Congress Series ; 1066
.
Elsevier Science Publ., Amsterdam, 862-864.
1 January 1995
Genequiz: a workbench for sequence analysis.
Scharf, M., Schneider, R., Casari, G., Bork, P., Valencia, A., Ouzounis, C. and Sander, C.
In:
Proceedings of the International Conference Itell.Syst.Mol.Biol.
AAAI Press, California, 348-353.
1 January 1994
Entschluesselung von Proteinfunktion mit Hilfe des Computers: Erkennung und Interpretation entfernter Sequenzaehnlichkeiten.
Bork, P.
In:
Informatik in den Biowissenschaften. (Informatik aktuell).
Springer, Berlin [u.a.], 67-78.
1 January 1993
Book
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
Stammzellforschung und Zelltherapie. Stand des Wissens und der Rahmenbedingungen in Deutschland / Supplement zum Gentechnologiebericht.
Wobus, A.M., Hucho, F., van den Daele, W., Koechy, K., Reich, J., Rheinberger, H.J., Mueller-Roeber, B., Sperling, K., Boysen, M., Koelsch, M., 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
Es wird ein Mensch gemacht. Moeglichkeit und Grenzen der Gentechnik.
Reich, J.
Rowohlt, Berlin.
ISBN 3871344710
2003
Ein graphentheoretischer Ansatz zum paarweisen und multiplen Vergleich von Proteinstrukturen.
Koch, I.
Wissenschaft und Technik, Berlin.
ISBN 3-89685-446-1
1 January 1998
Regulatory RNA.
Dandekar, T. and Sharma, K.
Springer, Heidelberg.
ISBN 3-540-64343-5
1 January 1998
C curve fitting and modeling for scientists and engineers.
Reich, J.
McGraw-Hill, New York [u.a.].
1 January 1992
Thesis
The definition of multilocus haplotype blocks and common diseases.
Nothnagel, M.
UNSPECIFIED thesis, UNSPECIFIED.
6 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
Ein graphentheoretischer Ansatz zum paarweisen und multiplen Vergleich von Proteinstrukturen.
Koch, I.
UNSPECIFIED thesis, UNSPECIFIED.
1 January 1997
Patent
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., Reich, J.G., Luft, F.C., Knoblauch, H., Bauerfeind, A., Luganskaja, T. and Rohde, K.
EP1566449.
24 August 2005
Biosensor (neuer Bauart).
Dandekar, T.
DE4338732A1 ; DE4338732C2.
11 December 2003
Neuartige selektive Beschichtungsmethode fuer die Oberflaechenbehandlung (z.B. von Sensoren und Leiterplatinen).
Koenig, R. and Dandekar, T.
DE19833683A1.
3 February 2000
Verbesserter einschichtiger Biosensor.
Dandekar, T. and Boulin, C.
DE19721698A1.
26 November 1998
Review
Review: Opportunities and barriers for omics-based biomarker discovery in steatotic liver diseases.
Thiele, M., Villesen, I.., Niu, L., Johansen, S., Sulek, K., Nishijima, S., Van Espen, L., Keller, M., Israelsen, M., Suvitaival, T., de Zawadzki, A., Juel, H.B., Brol, M.J., Stinson, S.E., Huang, Y., Alvarez Silva, M.C., Kuhn, M., Anastasiadou, E., Leeming, D.J., Karsdal, M., Matthijnssens, J., Arumugam, M., Dalgaard, L.T., Legido-Quigley, C., Mann, M., Trebicka, J., Bork, P., Jensen, L.J., Hansen, T. and Krag, A.
Journal of Hepatology 81
(2): 345-359.
August 2024
Diversity within species: interpreting strains in microbiomes.
Van Rossum, T., Ferretti, P., Maistrenko, O.M. and Bork, P.
Nature Reviews Microbiology 18
: 491-506.
September 2020
Tara Oceans: towards global ocean ecosystems biology.
Sunagawa, S., Acinas, S.G., Bork, P., Bowler, C., Eveillard, D., Gorsky, G., Guidi, L., Iudicone, D., Karsenti, E., Lombard, F., Ogata, H., Pesant, S., Sullivan, M.B., Wincker, P. and de Vargas, C.
Nature Reviews Microbiology 18
(8): 428-445.
August 2020
The human gut microbiome: from association to modulation.
Schmidt, T.S.B., Raes, J. and Bork, P.
Cell 172
(6): 1198-1215.
8 March 2018
Enterotypes in the landscape of gut microbial community composition.
Costea, P.I., Hildebrand, F., Manimozhiyan, A., Baeckhed, F., Blaser, M.J., Bushman, F.D., de Vos, W.M., Ehrlich, S.D., Fraser, C.M., Hattori, M., Huttenhower, C., Jeffery, I.B., Knights, D., Lewis, J.D., Ley, R.E., Ochman, H., O'Toole, P.W., Quince, C., Relman, D.A., Shanahan, F., Sunagawa, S., Wang, J., Weinstock, G.M., Wu, G.D., Zeller, G., Zhao, L., Raes, J., Knight, R. and Bork, P.
Nature Microbiology 3
(1): 8-16.
January 2018
Evolution and functional cross-talk of protein post-translational modifications.
Beltrao, P., Bork, P., Krogan, N.J. and van Noort, V.
Molecular Systems Biology 9
: 714.
22 December 2013
Drug discovery in the age of systems biology: the rise of computational approaches for data integration.
Iskar, M., Zeller, G., Zhao, X.M., van Noort, V. and Bork, P.
Current Opinion in Biotechnology 23
(4): 609-616.
August 2012
Neue Wege der Stammzellforschung: Reprogrammierung von differenzierten Koerperzellen [New methods in stem cell research: reprogramming of differentiated body cells].
Beier, H.M., Fehse, B., Friedrich, B., Goetz, M., Hansmann, I., Hucho, F., Koechy, K., Mueller-Roeber, B., Rheinberger, H.J., Reich, J., Ropers, H.H., Schoeler, H.R., Schoene-Seifert, B., Sperling, K., Tanner, K., Taupitz, J. and Wobus, A.M.
Journal fuer Reproduktionsmedizin und Endokrinologie 7
(2): 68-77.
2010
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
Sequence-based feature prediction and annotation of proteins.
Juncker, A.S., Jensen, L.J., Pierleoni, A., Bernsel, A., Tress, M.L., Bork, P., von Heijne, G., Valencia, A., Ouzounis, C.A., Casadio, R. and Brunak, S.
Genome Biology 10
(2): 206.
2 February 2009
Molecular eco-systems biology: towards an understanding of community function.
Raes, J. and Bork, P.
Nature Reviews Microbiology 6
(9): 693-699.
September 2008
Get the most out of your metagenome: computational analysis of environmental sequence data.
Raes, J., Foerstner, K.U. and Bork, P.
Current Opinion in Microbiology 10
(5): 490-498.
October 2007
The tumour-Clostridium phenomenon: 50 years of developmental research.
Schmidt, W., Fabricius, E.M. and Schneeweiss, U.
International Journal of Oncology 29
(6): 1479-1492.
1 December 2006
Insights into social insects from the genome of the honeybee Apis mellifera.
Nature 443
(7114): 931-949.
26 October 2006
Literature mining for the biologist: from information retrieval to biological discovery.
Jensen, L.J., Saric, J. and Bork, P.
Nature Reviews Genetics 7
(2): 119-129.
February 2006
Initial sequence of the chimpanzee genome and comparison with the human genome.
Mikkelsen, T.S., Hillier, L.W., Eichler, E.E., Zody, M.C., Jaffe, D.B., Yang, S.P., Enard, W., Hellmann, I., Lindblad-Toh, K., Altheide, T.K., Archidiacono, N., Bork, P., Butler, J., Chang, J.L., Cheng, Z., Chinwalla, A.T., de Jong, P., Delehaunty, K.D., Fronick, C.C., Fulton, L.L., Gilad, Y., Glusman, G., Gnerre, S., Graves, T.A., Hayakawa, T., Hayden, K.E., Huang, X.Q., Ji, H.K., Kent, W.J., King, M.C., Kulbokas, E.J., Lee, M.K., Liu, G., Lopez-Otin, C., Makova, K.D., Man, O., Mardis, E.R., Mauceli, E., Miner, T.L., Nash, W.E., Nelson, J.O., Paeaebo, S., Patterson, N.J., Pohl, C.S., Pollard, K.S., Pruefer, K., Puente, X.S., Reich, D., Rocchi, M., Rosenbloom, K., Ruvolo, M., Richter, D.J., Schaffner, S.F., Smit, A.F.A., Smith, S.M., Suyama, M., Taylor, J., Torrents, D., Tuzun, E., Varki, A., Velasco, G., Ventura, M., Wallis, J.W., Wendl, M.C., Wilson, R.K., Lander, E.S. and Waterston, R.H.
Nature 437
(7055): 69-87.
1 September 2005
Consistency of genome-based methods in measuring Metazoan evolution.
Zdobnov, E.M., von Mering, C., Letunic, I. and Bork, P.
FEBS Letters 579
: 3355-3361.
1 January 2005
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
Hillier, L.W., Miller, W., Birney, E., Warren, W., Hardison, R.C., Ponting, C.P., Bork, P., Burt, D.W., Groenen, M.A.M., Delany, M.E., Dodgson, J.B., Chinwalla, A.T., Cliften, P.F., Clifton, S.W., Delehaunty, K.D., Fronick, C., Fulton, R.S., Graves, T.A., Kremitzki, C., Layman, D., Magrini, V., McPherson, J.D., Miner, T.L., Minx, P., Nash, W.E., Nhan, M.N., Nelson, J.O., Oddy, L.G., Pohl, C.S., Randall-Maher, J., Smith, S.M., Wallis, J.W., Yang, S.P., Romanov, M.N., Rondelli, C.M., Paton, B., Smith, J., Morrice, D., Daniels, L., Tempest, H.G., Robertson, L., Masabanda, J.S., Griffin, D.K., Vignal, A., Fillon, V., Jacobbson, L., Kerje, S., Andersson, L., Crooijmans, R.P.M., Aerts, J., van der Poel, J.J., Ellegren, H., Caldwell, R.B., Hubbard, S.J., Grafham, D.V., Kierzek, A.M., McLaren, S.R., Overton, I.M., Arakawa, H., Beattie, K.J., Bezzubov, Y., Boardman, P.E., Bonfield, J.K., Croning, M.D.R., Davies, R.M., Francis, M.D., Humphray, S.J., Scott, C.E., Taylor, R.G., Tickle, C., Brown, W.R.A., Rogers, J., Buerstedde, J.M., Wilson, S.A., Stubbs, L., Ovcharenko, I., Gordon, L., Lucas, S., Miller, M.M., Inoko, H., Shiina, T., Kaufman, J., Salomonsen, J., Skjoedt, K., Wong, G.K.S., Wang, J., Liu, B., Wang, J., Yu, J., Yang, H.M., Nefedov, M., Koriabine, M., de Jong, P.J., Goodstadt, L., Webber, C., Dickens, N.J., Letunic, I., Suyama, M., Torrents, D., von Mering, C., Zdobnov, E.M., Makova, K., Nekrutenko, A., Elnitski, L., Eswara, P., King, D.C., Yang, S., Tyekucheva, S., Radakrishnan, A., Harris, R.S., Chiaromonte, F., Taylor, J., He, J.B., Rijnkels, M., Griffiths-Jones, S., Ureta-Vidal, A., Hoffman, M.M., Severin, J., Searle, S.M.J., Law, A.S., Speed, D., Waddington, D., Cheng, Z., Tuzun, E., Eichler, E., Bao, Z.R., Flicek, P., Shteynberg, D.D., Brent, M.R., Bye, J.M., Huckle, E.J., Chatterji, S., Dewey, C., Pachter, L., Kouranov, A., Mourelatos, Z., Hatzigeorgiou, A.G., Paterson, A.H., Ivarie, R., Brandstrom, M., Axelsson, E., Backstrom, N., Berlin, S., Webster, M.T., Pourquie, O., Reymond, A., Ucla, C., Antonarakis, S.E., Long, M.Y., Emerson, J.J., Betran, E., Dupanloup, I., Kaessmann, H., Hinrichs, A.S., Bejerano, G., Furey, T.S., Harte, R.A., Raney, B., Siepel, A., Kent, W.J., Haussler, D., Eyras, E., Castelo, R., Abril, J.F., Castellano, S., Camara, F., Parra, G., Guigo, R., Bourque, G., Tesler, G., Pevzner, P.A., Smit, A., Fulton, L.A., Mardis, E.R. and Wilson, R.K.
Nature 432
(7018): 695-716.
9 December 2004
Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Gibbs, R.A., Weinstock, G.M., Metzker, M.L., Muzny, D.M., Sodergren, E.J., Scherer, S., Scott, G., Steffen, D., Worley, K.C., Burch, P.E., Okwuonu, G., Hines, S., Lewis, L., DeRamo, C., Delgado, O., Dugan-Rocha, S., Miner, G., Morgan, M., Hawes, A., Gill, R., Holt, R.A., Adams, M.D., Amanatides, P.G., Baden-Tillson, H., Barnstead, M., Chin, S., Evans, C.A., Ferriera, S., Fosler, C., Glodek, A., Gu, Z., Jennings, D., Kraft, C.L., Nguyen, T., Pfannkoch, C.M., Sitter, C., Sutton, G.G., Venter, J.C., Woodage, T., Smith, D., Lee, H.M., Gustafson, E., Cahill, P., Kana, A., Doucette-Stamm, L., Weinstock, K., Fechtel, K., Weiss, R.B., Dunn, D.M., Green, E.D., Blakesley, R.W., Bouffard, G.G., de Jong, P.J., Osoegawa, K., Zhu, B., Marra, M., Schein, J., Bosdet, I., Fjell, C., Jones, S., Krzywinski, M., Mathewson, C., Siddiqui, A., Wye, N., McPherson, J., Zhao, S., Fraser, C.M., Shetty, J., Shatsman, S., Geer, K., Chen, Y., Abramzon, S., Nierman, W.C., Havlak, P.H., Chen, R., Durbin, K.J., Egan, A., Ren, Y., Song, X.Z., Li, B., Liu, Y., Qin, X., Cawley, S., Worley, K.C., Cooney, A.J., D'Souza, L.M., Martin, K., Wu, J.Q., Gonzalez-Garay, M.L., Jackson, A.R., Kalafus, K.J., McLeod, M.P., Milosavljevic, A., Virk, D., Volkov, A., Wheeler, D.A., Zhang, Z., Bailey, J.A., Eichler, E.E., Tuzun, E., Birney, E., Mongin, E., Ureta-Vidal, A., Woodwark, C., Zdobnov, E., Bork, P., Suyama, M., Torrents, D., Alexandersson, M., Trask, B.J., Young, J.M., Huang, H., Wang, H., Xing, H., Daniels, S., Gietzen, D., Schmidt, J., Stevens, K., Vitt, U., Wingrove, J., Camara, F., Alba, M.M., Abril, J.F., Guigo, R., Smit, A., Dubchak, I., Rubin, E.M., Couronne, O., Poliakov, A., Hübner, N., Ganten, D., Goesele, C., Hummel, O., Kreitler, T., Lee, Y.A., Monti, J., Schulz, H., Zimdahl, H., Himmelbauer, H., Lehrach, H., Jacob, H.J., Bromberg, S., Gullings-Handley, J., Jensen-Seaman, M.I., Kwitek, A.E., Lazar, J., Pasko, D., Tonellato, P.J., Twigger, S., Ponting, C.P., Duarte, J.M., Rice, S., Goodstadt, L., Beatson, S.A., Emes, R.D., Winter, E.E., Webber, C., Brandt, P., Nyakatura, G., Adetobi, M., Chiaromonte, F., Elnitski, L., Eswara, P., Hardison, R.C., Hou, M., Kolbe, D., Makova, K., Miller, W., Nekrutenko, A., Riemer, C., Schwartz, S., Taylor, J., Yang, S., Zhang, Y., Lindpaintner, K., Andrews, T.D., Caccamo, M., Clamp, M., Clarke, L., Curwen, V., Durbin, R., Eyras, E., Searle, S.M., Cooper, G.M., Batzoglou, S., Brudno, M., Sidow, A., Stone, E.A., Venter, J.C., Payseur, B.A., Bourque, G., Lopez-Otin, C., Puente, X.S., Chakrabarti, K., Chatterji, S., Dewey, C., Pachter, L., Bray, N., Yap, V.B., Caspi, A., Tesler, G., Pevzner, P.A., Haussler, D., Roskin, K.M., Baertsch, R., Clawson, H., Furey, T.S., Hinrichs, A.S., Karolchik, D., Kent, W.J., Rosenbloom, K.R., Trumbower, H., Weirauch, M., Cooper, D.N., Stenson, P.D., Ma, B., Brent, M., Arumugam, M., Shteynberg, D., Copley, R.R., Taylor, M.S., Riethman, H., Mudunuri, U., Peterson, J., Guyer, M., Felsenfeld, A., Old, S., Mockrin, S. and Collins, F.
Nature 428
(6982): 493-521.
1 April 2004
Metabolites: a helping hand for pathway evolution?
Schmidt, S., Sunyaev, S., Bork, P. and Dandekar, T.
Trends in Biochemical Sciences 28
(6): 336-341.
June 2003
Bioinformatics in the post-sequence era.
Kanehisa, M. and Bork, P.
Nature Genetics 33
: 305-310.
1 January 2003
Function prediction and protein networks.
Huynen, M.A., Snel, B., von Mering, C. and Bork, P.
Current Opinion in Cell Biology 15
: 191-198.
1 January 2003
Initial sequencing and comparative analysis of the mouse genome.
Waterston, R.H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J.F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P., Antonarakis, S.E., Attwood, J., Baertsch, R., Bailey, J., Barlow, K., Beck, S., Berry, E., Birren, B., Bloom, T., Bork, P., Botcherby, M., Bray, N., Brent, M.R., Brown, D.G., Brown, S.D., Bult, C., Burton, J., Butler, J., Campbell, R.D., Carninci, P., Cawley, S., Chiaromonte, F., Chinwalla, A.T., Church, D.M., Clamp, M., Clee, C., Collins, F.S., Cook, L.L., Copley, R.R., Coulson, A., Couronne, O., Cuff, J., Curwen, V., Cutts, T., Daly, M., David, R., Davies, J., Delehaunty, K.D., Deri, J., Dermitzakis, E.T., Dewey, C., Dickens, N.J., Diekhans, M., Dodge, S., Dubchak, I., Dunn, D.M., Eddy, S.R., Elnitski, L., Emes, R.D., Eswara, P., Eyras, E., Felsenfeld, A., Fewell, G.A., Flicek, P., Foley, K., Frankel, W.N., Fulton, L.A., Fulton, R.S., Furey, T.S., Gage, D., Gibbs, R.A., Glusman, G., Gnerre, S., Goldman, N., Goodstadt, L., Grafham, D., Graves, T.A., Green, E.D., Gregory, S., Guigo, R., Guyer, M., Hardison, R.C., Haussler, D., Hayashizaki, Y., Hillier, L.W., Hinrichs, A., Hlavina, W., Holzer, T., Hsu, F., Hua, A., Hubbard, T., Hunt, A., Jackson, I., Jaffe, D.B., Johnson, L.S., Jones, M., Jones, T.A., Joy, A., Kamal, M., Karlsson, E.K., Karolchik, D., Kasprzyk, A., Kawai, J., Keibler, E., Kells, C., Kent, W.J., Kirby, A., Kolbe, D.L., Korf, I., Kucherlapati, R.S., Kulbokas, E.J., Kulp, D., Landers, T., Leger, J.P., Leonard, S., Letunic, I., LeVine, R., Li, J., Li, M., Lloyd, C., Lucas, S., Ma, B., Maglott, D.R., Mardis, E.R., Matthews, L., Mauceli, E., Mayer, J.H., McCarthy, M., McCombie, W.R., McLaren, S., McLay, K., McPherson, J.D., Meldrim, J., Meredith, B., Mesirov, J.P., Miller, W., Miner, T.L., Mongin, E., Montgomery, K.T., Morgan, M., Mott, R., Mullikin, J.C., Muzny, D.M., Nash, W.E., Nelson, J.O., Nhan, M.N., Nicol, R., Ning, Z., Nusbaum, C., O'Connor, M.J., Okazaki, Y., Oliver, K., Overton-Larty, E., Pachter, L., Parra, G., Pepin, K.H., Peterson, J., Pevzner, P., Plumb, R., Pohl, C.S., Poliakov, A., Ponce, T.C., Ponting, C.P., Potter, S., Quail, M., Reymond, A., Roe, B.A., Roskin, K.M., Rubin, E.M., Rust, A.G., Santos, R., Sapojnikov, V., Schultz, B., Schultz, J., Schwartz, M.S., Schwartz, S., Scott, C., Seaman, S., Searle, S., Sharpe, T., Sheridan, A., Shownkeen, R., Sims, S., Singer, J.B., Slater, G., Smit, A., Smith, D.R., Spencer, B., Stabenau, A., Stange-Thomann, N., Sugnet, C., Suyama, M., Tesler, G., Thompson, J., Torrents, D., Trevaskis, E., Tromp, J., Ucla, C., Ureta-Vidal, A., Vinson, J.P., von Niederhausern, A.C., Wade, C.M., Wall, M., Weber, R.J., Weiss, R.B., Wendl, M.C., West, A.P., Wetterstrand, K., Wheeler, R., Whelan, S., Wierzbowski, J., Willey, D., Williams, S., Wilson, R.K., Winter, E., Worley, K.C., Wyman, D., Yang, S., Yang, S.P., Zdobnov, E.M., Zody, M.C. and Lander, E.S.
Nature 420
(6915): 520-562.
5 December 2002
DNA testing for familial hypercholesterolemia: improving disease recognition and patient care.
Vergopoulos, A., Knoblauch, H. and Schuster, H.
American Journal of Pharmacogenomics 2
(4): 253-262.
December 2002
The rhodanese/Cdc25 phosphatase superfamily. Sequence-structure-function relations.
Bordo, D. and Bork, P.
EMBO Reports 3
: 741-746.
1 August 2002
Exploring Medline abstracts with XplorMed.
Perez-Iratxeta, C., Bork, P. and Andrade, M.A.
Drugs of Today 38
: 381-389.
1 June 2002
SHOT: a web server for the construction of genome phylogenies.
Korbel, J.O., Snel, B., Huynen, M.A. and Bork, P.
Trends in Genetics 18
: 158-162.
1 March 2002
Genome and protein evolution in eukaryotes.
Copley, R.R., Letunic, I. and Bork, P.
Current Opinion in Chemical Biology 6
: 39-45.
1 January 2002
Modelling of simple and complex calcium oscillations - From single-cell responses to intercellular signalling.
Schuster, S., Marhl, M. and Hoefer, T.
European Journal of Biochemistry 269
(5): 1333-1355.
1 January 2002
O6-alkylguanine-DNA alkyltransferase: role in carcinogenesis and chemotherapy.
Margison, G.P. and Santibanez-Koref, M.F.
BioEssays 24
(3): 255-266.
1 January 2002
Protein domain analysis in the era of complete genomes.
Copley, R.R., Doerks, T., Letunic, I. and Bork, P.
FEBS Letters 513
(1): 129-134.
1 January 2002
Statistical gene mapping of traits in humans--hypertension as a complex trait: is it amenable to genetic analysis?
Nothnagel, M. and Ott, J.
Seminars in Nephrology 22, 2
: 105-114.
1 January 2002
Sequence analysis of multidomain proteins: Past perspectives and future directions.
Copley, R.R., Ponting, C.P., Schultz, J. and Bork, P.
Advances in Protein Chemistry 61
: 75-98.
2002
Initial sequencing and analysis of the human genome.
Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., Funke, R., Gage, D., Harris, K., Heaford, A., Howland, J., Kann, L., Lehoczky, J., LeVine, R., McEwan, P., McKernan, K., Meldrim, J., Mesirov, J.P., Miranda, C., Morris, W., Naylor, J., Raymond, C., Rosetti, M., Santos, R., Sheridan, A., Sougnez, C., Stange-Thomann, N., Stojanovic, N., Subramanian, A., Wyman, D., Rogers, J., Sulston, J., Ainscough, R., Beck, S., Bentley, D., Burton, J., Clee, C., Carter, N., Coulson, A., Deadman, R., Deloukas, P., Dunham, A., Dunham, I., Durbin, R., French, L., Grafham, D., Gregory, S., Hubbard, T., Humphray, S., Hunt, A., Jones, M., Lloyd, C., McMurray, A., Matthews, L., Mercer, S., Milne, S., Mullikin, J.C., Mungall, A., Plumb, R., Ross, M., Shownkeen, R., Sims, S., Waterston, R.H., Wilson, R.K., Hillier, L.W., McPherson, J.D., Marra, M.A., Mardis, E.R., Fulton, L.A., Chinwalla, A.T., Pepin, K.H., Gish, W.R., Chissoe, S.L., Wendl, M.C., Delehaunty, K.D., Miner, T.L., Delehaunty, A., Kramer, J.B., Cook, L.L., Fulton, R.S., Johnson, D.L., Minx, P.J., Clifton, S.W., Hawkins, T., Branscomb, E., Predki, P., Richardson, P., Wenning, S., Slezak, T., Doggett, N., Cheng, J.F., Olsen, A., Lucas, S., Elkin, C., Uberbacher, E., Frazier, M., Gibbs, R.A., Muzny, D.M., Scherer, S.E., Bouck, J.B., Sodergren, E.J., Worley, K.C., Rives, C.M., Gorrell, J.H., Metzker, M.L., Naylor, S.L., Kucherlapati, R.S., Nelson, D.L., Weinstock, G.M., Sakaki, Y., Fujiyama, A., Hattori, M., Yada, T., Toyoda, A., Itoh, T., Kawagoe, C., Watanabe, H., Totoki, Y., Taylor, T., Weissenbach, J., Heilig, R., Saurin, W., Artiguenave, F., Brottier, P., Bruls, T., Pelletier, E., Robert, C., Wincker, P., Rosenthal, A., Platzer, M., Nyakatura, G., Taudien, S., Rump, A., Yang, H.M., Yu, J., Wang, J., Huang, G.Y., Gu, J., Hood, L., Rowen, L., Madan, A., Qin, S.Z., Davis, R.W., Federspiel, N.A., Abola, A.P., Proctor, M.J., Myers, R.M., Schmutz, J., Dickson, M., Grimwood, J., Cox, D.R. and Olson, M.V.
Nature 409
(6822): 860-921.
15 February 2001
Comparison of ARM and HEAT protein repeats.
Andrade, M.A., Petosa, C., O'Donoghue, S.I., Mueller, C.W. and Bork, P.
Journal of Molecular Biology 309
(1): 1-18.
1 January 2001
Protein repeats: Structures, functions, and evolution.
Andrade, M.A., Perez-Iratxeta, C. and Ponting, C.P.
Journal of Structural Biology 134
(2-3): 117-131.
1 January 2001
Automated extraction of information in molecular biology.
Andrade, M.A. and Bork, P.
FEBS Letters 476
(1-2): 12-17.
30 June 2000
Evolution of domain families.
Ponting, C.P., Schultz, J., Copley, R., Andrade, M.A. and Bork, P.
Advances in Protein Chemistry 54
: 185-244.
1 January 2000
Gene and context: Integrative approaches to genome analysis.
Huynen, M.A. and Snel, B.
Advances in Protein Chemistry 54
: 345-379.
1 January 2000
Individual variation in protein-coding sequences of human genome.
Sunyaev, S., Hanke, J., Brett, D., Aydin, A., Zastrow, I., Lathe, W., Bork, P. and Reich, J.
Advances in Protein Chemistry 54
: 409-437.
2000
Variation and evolution of the citric-acid cycle: a genomic perspective.
Huynen, M.A., Dandekar, T. and Bork, P.
Trends in Microbiology 7
(7): 281-291.
9 July 1999
Predicting function: From genes to genomes and back.
Bork, P., Dandekar, T., Diaz-Lazcoz, Y., Eisenhaber, F., Huynen, M. and Yuan, Y.P.
Journal of Molecular Biology 283
: 707-725.
6 November 1998
Computational methods for the prediction of protein folds.
Dandekar, T. and Koenig, R.
Biochimica et Biophysica Acta 1343
: 1-15.
14 November 1997
Cytoplasmic signalling domains: the next generation.
Bork, P., Schultz, J. and Ponting, C.P.
Trends in Biochemical Sciences 22
: 296-298.
1 January 1997
Applying motif and profile searches.
Bork, P. and Gibson, T.
Methods in Enzymology 266
: 162-184.
1 January 1996
The immunoglobulin fold - Structural classification, sequence patterns and common core.
Bork, P., Holm, L. and Sander, C.
Journal of Molecular Biology 242
: 309-320.
1 January 1994
The modular architecture of a new family of growth regulators related to connective tissue growth factor.
Bork, P.
FEBS Letters 327
(2): 125-130.
26 July 1993
Letter
Circular reasoning rather than cyclic expression.
Jensen, L.J., de Lichtenberg, U., Jensen, T.S., Brunak, S. and Bork, P.
Genome Biology 9
(6): 403.
23 June 2008
iPath: interactive exploration of biochemical pathways and networks.
Letunic, I., Yamada, T., Kanehisa, M. and Bork, P.
Trends in Biochemical Sciences 33
(3): 101-103.
March 2008
In gratitude: Charlie.
Reich, J.
Beginnings 28
(4): 39.
2008
Lack of association of the G protein-coupled receptor for asthma susceptibility gene with atopic dermatitis.
Soederhaell, C., Marenholz, I., Nickel, R., Grueber, C., Kehrt, R., Rohde, K., Griffioen, R.W., Meglio, P., Tarani, L., Gustafsson, D., Hoffmann, U., Gerstner, B., Mueller, S., Wahn, U. and Lee, Y.A.
Journal of Allergy and Clinical Immunology 116
(1): 220-221.
1 January 2005
Estimating rates of alternative splicing in mammals and invertebrates.
Harrington, E.D., Boue, S., Valcarcel, J., Reich, J.G. and Bork, P.
Nature Genetics 36
(9): 916-917.
1 January 2004
Worldwide scientific publishing activity.
Perez-Iratxeta, C. and Andrade, M.A.
Science 297
(5581): 519-519.
26 July 2002
Genome sequences and great expectations.
Iliopoulos, I., Tsoka, S., Andrade, M.A., Janssen, P., Audit, B., Tramontano, A., Valencia, A., Leroy, C., Sander, C. and Ouzounis, C.A.
Genome Biology 2
(1): Interactions0001.1-Interactions0001.3.
1 January 2001
A mitochondrial ancestry of the hydrogenosomes of Nyctotherus ovalis.
van Hoek, A.H.A.M., Akhmanova, A.S., Huynen, M.A. and Hackstein, J.H.P.
Molecular Biology and Evolution 17
(1): 202-206.
1 January 2000
Phospholipases A2 and Wnts are unlikely to share a common ancestor.
Copley, R.R., Ponting, C.P. and Bork, P.
Current Biology 9
: R718-R719.
7 October 1999
A latrophilin/CL-1-like GPS domain in polycystin-1.
Ponting, C.P., Hofmann, K. and Bork, P.
Current Biology 9
(16): R585-R588.
26 August 1999
No Sec7-homology domain in guanine-nucleotide-exchange factors that act on Ras and Rho.
Ponting, C.P., Bork, P., Schultz, J. and Aravind, L.
Trends in Biochemical Sciences 24
: 177-178.
1 May 1999
Deletion at 12p in a japanese child with brachydactyly overlaps the assigned locus of brachydactyly with hypertension in a turkish family.
Bähring, S., Nagai, T., Toka, H.R., Nitz, I., Toka, O., Aydin, A., Muhl, A., Wienker, T.F., Schuster, H. and Luft, F.C.
American Journal of Human Genetics 60
: 732-735.
1 January 1997
Differential genome display.
Huynen, M.A., Diaz-Lazcoz, Y. and Bork, P.
Trends in Genetics 13
: 389-390.
1 January 1997
Secreted fringe like signaling molecules may be glycosyltransferases.
Yuan, Y.P., Schultz, J., Mlodzik, M. and Bork, P.
Cell 88
: 9-11.
1 January 1997
BRCA1 protein products ... Functional motifs...
Koonin, E.V., Altschul, S.F. and Bork, P.
Nature Genetics 13
(3): 266-268.
1 July 1996
Internal repeats in the BRCA2 protein sequence.
Bork, P., Blomberg, N. and Nilges, M.
Nature Genetics 13
: 22-23.
1 January 1996
Non-orthologous gene displacement.
Koonin, E.V., Mushegian, A.R. and Bork, P.
Trends in Genetics 12
: 334-336.
1 January 1996
Severe autosomal dominant hypertension and brachydactyly in a unique turkish kindred maps to human chromosome 12.
Schuster, H., Wienker, T.F., Bähring, S., Bilginturan, N., Toka, H.R., Neitzel, H., Jeschke, E., Toka, O., Gilbert, D., Lowe, A., Ott, J., Haller, H. and Luft, F.C.
Nature Genetics 13
(1): 98-100.
1 January 1996
Heat repeats in Huntington's disease protein.
Andrade, M.A. and Bork, P.
Nature Genetics 11
(2): 115-116.
1 October 1995
A comment on "Can measurement of potential doubling time (TPOT) be compared between laboratories ? A quality control study".
Schmidt, W.
Cytometry 21
: 218-219.
1 January 1995
A phosphotyrosine interaction domain.
Bork, P. and Margolis, B.
Cell 80
(5): 693-694.
1 January 1995
Challenging times for bioinformatics.
Casari, G., Andrade, M.A., Bork, P., Daruvar, A., Ouzounis, C., Schneider, R., Tamames, J., Valencia, A. and Sander, C.
Nature 376
: 647-648.
1 January 1995
FMN- or DNA-binding?
Koonin, E. and Bork, P.
Trends in Biochemical Sciences 19
: 234-235.
1 January 1994
The modular structure of NifU proteins.
Ouzounis, C., Bork, P. and Sander, C.
Trends in Biochemical Sciences 19
: 199-200.
1 January 1994
What's in a genome?
Bork, P., Ouzounis, C., Sander, C., Scharf, M., Schneider, R. and Sonnhammer, E.
Nature 358
: 287.
1 January 1992
Editorial
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
Computational eco-systems biology in Tara Oceans: translating data into knowledge.
Sunagawa, S., Karsenti, E., Bowler, C. and Bork, P.
Molecular Systems Biology 11
(5): 809.
21 May 2015
Comments on "Human dominant disease genes are enriched in paralogs originating from whole genome duplication".
Chen, W.H., Zhao, X.M., van Noort, V. and Bork, P.
PLoS Computational Biology 10
(7): e1003758.
31 July 2014
Biochemistry. Not comparable, but complementary.
Jensen, L.J. and Bork, P.
Science 322
(5898): 56-57.
3 October 2008
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
Similar gene expression profiles do not imply similar tissue functions.
Yanai, I., Korbel, J.O., Boue, S., McWeeney, S.K., Bork, P. and Lercher, M.J.
Trends in Genetics 22
(3): 132-138.
March 2006
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
Towards cellular systems in 4D.
Bork, P. and Serrano, L.
Cell 121
: 507-509.
1 January 2005
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
A second large family with catatonic schizophrenia supports the region distally of CHRNA7 on chromosome 15q14-15.
Meyer, J., Rueschendorf, F. and Lesch, K.P.
Molecular Psychiatry 8
: 259-260.
1 March 2003
The way we write - Country-specific variations of the English language in the biomedical literature.
Netzel, R., Perez-Iratxeta, C., Bork, P. and Andrade, M.A.
EMBO Reports 4
: 446-451.
1 January 2003
Genome organization: Teamed up for transcription.
von Mering, C. and Bork, P.
Nature 417
(6891): 797-798.
20 June 2002
Embryonic stem cells - The debate in Germany.
Reich, J.G.
Science 296
(5566): 265-265.
12 April 2002
Modularity in the gain and loss of genes: applications for function prediction.
Ettema, T., van der Oost, J. and Huynen, M.
Trends in Genetics 17
(9): 485-487.
September 2001
Flux determination by isotopomer balancing - a successful application of theory to experiment.
Schuster, S.
Trends in Biotechnology 19
(3): 85.
1 March 2001
The draft sequences. Filling in the gaps.
Bork, P. and Copley, R.
Nature 409
(6822): 818-820.
15 February 2001
XplorMed: a tool for exploring MEDLINE abstracts.
Perez-Iratxeta, C., Bork, P. and Andrade, M.A.
Trends in Biochemical Sciences 26
(9): 573-575.
1 January 2001
Breeding of Escherichia coli based in colour - commentary.
Schuster, S.
Trends in Biotechnology 18
(11): 442.
1 November 2000
GRAM, a novel domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins.
Doerks, T., Strauss, M., Brendel, M. and Bork, P.
Trends in Biochemical Sciences 25
(10): 483-485.
1 October 2000
EST analysis online: WWW tools for detection of SNPs and alternative splice forms.
Brett, D., Lehmann, G., Hanke, J., Gross, S., Reich, J. and Bork, P.
Trends in Genetics 16
(9): 416-418.
1 September 2000
Biotechnology in silicio. Metabolic proteomics of Haemophilus influenzae : commentary.
Schuster, S.
Trends in Biotechnology 18
(8): 328-328.
1 August 2000
Sequences and topology. Genome and proteome informatics - Editorial overview.
Bork, P. and Eisenberg, D.
Current Opinion in Structural Biology 10
(3): 341-342.
1 June 2000
Towards a structural basis of human non-synonymous single nucleotide polymorphisms.
Sunyaev, S.R., Ramensky, V. and Bork, P.
Trends in Genetics 16
(5): 198-200.
1 May 2000
Powers and pitfalls in sequence analysis: The 70% hurdle.
Bork, P.
Genome Research 10
(4): 398-400.
1 April 2000
Genome evolution - gene fusion versus gene fission.
Snel, B., Bork, P. and Huynen, M.
Trends in Genetics 16
: 9-11.
1 January 2000
Preface: Protein sequence analysis.
Bork, P.
Advances in Protein Chemistry 54
: xi-xv.
1 January 2000
View from the east.
Reich, J.G.
Science 286
(5442): 1087-1087.
5 November 1999
Alternative splicing of human genes - more the rule than the exception?
Hanke, J., Brett, D., Zastrow, I., Aydin, A., Delbrueck, S., Lehmann, G., Luft, F.C., Reich, J. and Bork, P.
Trends in Genetics 15
: 389-390.
1 October 1999
Sequences and topology deriving biological knowledge from genomic sequences.
Bork, P. and Eisenberg, D.
Current Opinion in Structural Biology 8
: 331-332.
1 January 1998
Wanted: subcellular localization of proteins based on sequence.
Eisenhaber, F. and Bork, P.
Trends in Cell Biology 8
: 169-170.
1 January 1998
Free radicals and memory loss.
Dandekar, T.
Redox Report 3
: 71-73.
1 January 1997
Exon shuffling and other ways of module exchange: comment.
Bork, P.
Matrix Biology 15
: 311-312.
1 January 1996
Comment
Mapping the combinatorial regulation by transcription factors.
Schuster, S.
Trends in Biotechnology 20
(1): 5-6.
1 January 2002
Preprint
Refined enterotyping reveals dysbiosis in global fecal metagenomes.
Keller, M.I., Nishijima, S., Podlesny, D., Kim, C.Y., Robbani, S.M., Schudoma, C., Fullam, A., Richter, J., Letunic, I., Akanni, W., Orakov, A., Schmidt, T.S., Marotta, F., Trebicka, J., Kuhn, M., Van Rossum, T. and Bork, P.
bioRxiv
: 2024.08.13.607711v2.
14 August 2024
C. difficile is overdiagnosed in adults and a commensal in infants.
Ferretti, P., Wirbel, J., Maistrenko, O.M., Van Rossum, T., Alves, R., Fullam, A., Akanni, W., Schudoma, C., Schwarz, A., Thielemann, R., Thomas, L., Kuhn, M., Zeller, G., Schmidt, T.S.B. and Bork, P.
bioRxiv
: 2022.02.16.480740v1.
18 February 2022
Drivers and determinants of strain dynamics following faecal microbiota transplantation.
Schmidt, T.S.B., Li, S.S., Maistrenko, O.M., Akanni, W., Coelho, L.P., Dolai, S., Fullam, A., Glazek, A.M., Hercog, R., Herrema, H., Jung, F., Kandels, S., Orakov, A., Van Rossum, T., Benes, V., Borody, T.J., de Vos, W.M., Ponsioen, C.Y., Nieuwdorp, M. and Bork, P.
bioRxiv
: 2021.09.30.462010.
30 September 2021
Uncharted biosynthetic potential of the ocean microbiome.
Paoli, L., Ruscheweyh, H.J., Forneris, C.C., Kautsar, S., Clayssen, Q., Salazar, G., Milanese, A., Gehrig, D., Larralde, M., Carroll, L.M., Sánchez, P., Zayed, A.A., Cronin, D.R., Acinas, S.G., Bork, P., Bowler, C., Delmont, T.O., Sullivan, M.B., Wincker, P., Zeller, G., Robinson, S.L., Piel, J. and Sunagawa, S.
bioRxiv
: 2021.03.24.436479.
24 March 2021
Other
Stops genejockeys being taken for a ride.
Eisenhaber, F.
Elsevier.
1 September 1998
This list was generated on Sat Dec 21 19:29:01 2024 UTC.
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