Browse by Research Team

2025

Patterns and drivers of diatom diversity and abundance in the global ocean.
Pierella Karlusich, J.J., Cosnier, K., Zinger, L., Henry, N., Nef, C., Bernard, G., Scalco, E., Dvorak, E., Vieira, F.R.J., Delage, E., Chaffron, S., Ovchinnikov, S., Zingone, A. and Bowler, C.
Nature Communications 16 (1): 3452. 11 April 2025

Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations.
Nishijima, S., Stankevic, E., Aasmets, O., Schmidt, T.S.B., Nagata, N., Keller, M.I., Ferretti, P., Juel, H.B., Fullam, A., Robbani, S.M., Schudoma, C., Hansen, J.K., Holm, L.A., Israelsen, M., Schierwagen, R., Torp, N., Telzerow, A., Hercog, R., Kandels, S., Hazenbrink, D.H.M., Arumugam, M., Bendtsen, F., Brøns, C., Fonvig, C.E., Holm, J.C., Nielsen, T., Pedersen, J.S., Thiele, M.S., Trebicka, J., Org, E., Krag, A., Hansen, T., Kuhn, M. and Bork, P.
Cell 188 (1): 222-236. 9 January 2025

The STRING database in 2025: protein networks with directionality of regulation.
Szklarczyk, D., Nastou, K., Koutrouli, M., Kirsch, R., Mehryary, F., Hachilif, R., Hu, D., Peluso, M.E., Huang, Q., Fang, T., Doncheva, N.T., Pyysalo, S., Bork, P., Jensen, L.J. and von Mering, C.
Nucleic Acids Research 53 (D1): D730–D737. 6 January 2025

Systematic mapping of antibiotic cross-resistance and collateral sensitivity with chemical genetics.
Sakenova, N., Cacace, E., Orakov, A., Huber, F., Varik, V., Kritikos, G., Michiels, J., Bork, P., Cossart, P., Goemans, C.V. and Typas, A.
Nature Microbiology 10 (1): 202-216. January 2025

2024

Emergence of community behaviors in the gut microbiota upon drug treatment.
Garcia-Santamarina, S., Kuhn, M., Devendran, S., Maier, L., Driessen, M., Mateus, A., Mastrorilli, E., Brochado, A.R., Savitski, M.M., Patil, K.R., Zimmermann, M., Bork, P. and Typas, A.
Cell 187 (22): 6346-6357.e20. 31 October 2024

The diversity of the microbiome impacts chronic lymphocytic leukemia development in mice and humans.
Faitova, T., Coelho, M., Da Cunha-Bang, C., Ozturk, S., Kartal, E., Bork, P., Seiffert, M. and Niemann, C.U.
Haematologica 109 (10): 3237-3250. October 2024

A catalog of small proteins from the global microbiome.
Duan, Y., Santos-Júnior, C.D., Schmidt, T.S., Fullam, A., de Almeida, B.L.S., Zhu, C., Kuhn, M., Zhao, X.M., Bork, P. and Coelho, L.P.
Nature Communications 15 (1): 7563. 31 August 2024

Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts.
Lai, S., Wang, H., Bork, P., Chen, W.H. and Zhao, X.M.
Science Advances 10 (33): eadn3316. 16 August 2024

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

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

Discovery of antimicrobial peptides in the global microbiome with machine learning.
Santos-Júnior, C.D., Torres, M.D.T., Duan, Y., Rodríguez Del Río, Á., Schmidt, T.S.B., Chong, H., Fullam, A., Kuhn, M., Zhu, C., Houseman, A., Somborski, J., Vines, A., Zhao, X.M., Bork, P., Huerta-Cepas, J., de la Fuente-Nunez, C. and Coelho, L.P.
Cell 187 (14): 3761-3778. 11 July 2024

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

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

Functional and evolutionary significance of unknown genes from uncultivated taxa.
Rodríguez Del Río, Á., Giner-Lamia, J., Cantalapiedra, C.P., Botas, J., Deng, Z., Hernández-Plaza, A., Munar-Palmer, M., Santamaría-Hernando, S., Rodríguez-Herva, J.J., Ruscheweyh, H.J., Paoli, L., Schmidt, T.S.B., Sunagawa, S., Bork, P., López-Solanilla, E., Coelho, L.P. and Huerta-Cepas, J.
Nature 626 (7998): 377-384. 8 February 2024

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

2023

Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide.
Andrikopoulos, P., Aron-Wisnewsky, J., Chakaroun, R., Myridakis, A., Forslund, S.K., Nielsen, T., Adriouch, S., Holmes, B., Chilloux, J., Vieira-Silva, S., Falony, G., Salem, J.E., Andreelli, F., Belda, E., Kieswich, J., Chechi, K., Puig-Castellvi, F., Chevalier, M., Le Chatelier, E., Olanipekun, M.T., Hoyles, L., Alves, R., Helft, G., Isnard, R., Køber, L., Coelho, L.P., Rouault, C., Gauguier, D., Gøtze, J.P., Prifti, E., Froguel, P., Zucker, J.D., Bäckhed, F., Vestergaard, H., Hansen, T., Oppert, J.M., Blüher, M., Nielsen, J., Raes, J., Bork, P., Yaqoob, M.M., Stumvoll, M., Pedersen, O., Ehrlich, S.D., Clément, K. and Dumas, M.E.
Nature Communications 14 (1): 5843. 20 September 2023

Consistency across multi-omics layers in a drug-perturbed gut microbial community.
Wuyts, S., Alves, R., Zimmermann-Kogadeeva, M., Nishijima, S., Blasche, S., Driessen, M., Geyer, P.E, Hercog, R., Kartal, E., Maier, L., Müller, J.B., Garcia Santamarina, S., Schmidt, T.S.B., Sevin, D.C., Telzerow, A., Treit, P.V., Wenzel, T., Typas, A., Patil, K.R, Mann, M., Kuhn, M. and Bork, P.
Molecular Systems Biology 19 (9): e11525. 12 September 2023

Long-read sequencing reveals extensive DNA methylations in human gut phagenome contributed by prevalently phage-encoded methyltransferases.
Sun, C., Chen, J., Jin, M., Zhao, X., Li, Y., Dong, Y., Gao, N., Liu, Z., Bork, P., Zhao, X.M. and Chen, W.H.
Advanced Science 10 (25): 2302159. 5 September 2023

Enterotypes of the human gut mycobiome.
Lai, S., Yan, Y., Pu, Y., Lin, S., Qiu, J.G., Jiang, B.H., Keller, M.I., Wang, M., Bork, P., Chen, W.H., Zheng, Y. and Zhao, X.M.
Microbiome 11 (1): 179. 11 August 2023

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies.
Kennedy, K.M., de Goffau, M.C., Perez-Muñoz, M.E., Arrieta, M.C., Bäckhed, F., Bork, P., Braun, T., Bushman, F.D., Dore, J., de Vos, W.M., Earl, A.M., Eisen, J.A., Elovitz, M.A., Ganal-Vonarburg, S.C., Gänzle, M.G., Garrett, W.S., Hall, L.J., Hornef, M.W., Huttenhower, C., Konnikova, L., Lebeer, S., Macpherson, A.J., Massey, R.C., McHardy, A.C., Koren, O., Lawley, T.D., Ley, R.E., O'Mahony, L., O'Toole, P.W., Pamer, E.G., Parkhill, J., Raes, J., Rattei, T., Salonen, A., Segal, E., Segata, N., Shanahan, F., Sloboda, D.M., Smith, G.C.S., Sokol, H., Spector, T.D., Surette, M.G., Tannock, G.W., Walker, A.W., Yassour, M. and Walter, J.
Nature 613 (7945): 639-649. 26 January 2023

The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest.
Szklarczyk, D., Kirsch, R., Koutrouli, M., Nastou, K., Mehryary, F., Hachilif, R., Gable, A.L., Fang, T., Doncheva, N.T., Pyysalo, S., Bork, P., Jensen, L.J. and von Mering, C.
Nucleic Acids Research 51 (D1): D638-D646. 6 January 2023

proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes.
Fullam, A., Letunic, I., Schmidt, T.S.B., Ducarmon, Q.R., Karcher, N., Khedkar, S., Kuhn, M., Larralde, M., Maistrenko, O.M., Malfertheiner, L., Milanese, A., Rodrigues, J.F.M., Sanchis-López, C., Schudoma, C., Szklarczyk, D., Sunagawa, S., Zeller, G., Huerta-Cepas, J., von Mering, C., Bork, P. and Mende, D.R.
Nucleic Acids Research 51 (D1): D760-D766. 6 January 2023

2022

Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses.
Kunath, B.J., Hickl, O., Queirós, P., Martin-Gallausiaux, C., Lebrun, L.A., Halder, R., Laczny, C.C., Schmidt, T.S.B., Hayward, M.R., Becher, D., Heintz-Buschart, A., de Beaufort, C., Bork, P., May, P. and Wilmes, P.
Microbiome 10 (1): 243. 28 December 2022

Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments.
Ruscheweyh, H.J., Milanese, A., Paoli, L., Karcher, N., Clayssen, Q., Keller, M.I., Wirbel, J., Bork, P., Mende, D.R., Zeller, G. and Sunagawa, S.
Microbiome 10 (1): 212. 5 December 2022

Dissecting the intracellular pancreatic tumor microbiome at single-cell level.
Schmidt, T.S.B. and Bork, P.
Cancer Cell 40 (10): 1083-1085. 10 October 2022

Drivers and determinants of strain dynamics following fecal microbiota transplantation.
Schmidt, T.S.B., 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., Thielemann, R., von Stetten, M., Van Rossum, T., Benes, V., Borody, T.J., de Vos, W.M., Ponsioen, C.Y., Nieuwdorp, M. and Bork, P.
Nature Medicine 28 (9): 1902-1912. September 2022

Biosynthetic potential of the global ocean microbiome.
Paoli, L., Ruscheweyh, H.J., Forneris, C.C., Hubrich, F., Kautsar, S., Bhushan, A., Lotti, A., Clayssen, Q., Salazar, G., Milanese, A., Carlström, C.I., Papadopoulou, C., Gehrig, D., Karasikov, M., Mustafa, H., Larralde, M., Carroll, L.M., Sánchez, P., Zayed, A.A., Cronin, D.R., Acinas, S.G., Bork, P., Bowler, C., Delmont, T.O., Gasol, J.M., Gossert, A.D., Kahles, A., Sullivan, M.B., Wincker, P., Zeller, G., Robinson, S.L., Piel, J. and Sunagawa, S.
Nature 607 (7917): 111-118. 7 July 2022

A faecal microbiota signature with high specificity for pancreatic cancer.
Kartal, E., Schmidt, T.S.B., Molina-Montes, E., Rodríguez-Perales, S., Wirbel, J., Maistrenko, O.M., Akanni, W.A., Alashkar Alhamwe, B., Alves, R.J., Carrato, A., Erasmus, H.P., Estudillo, L., Finkelmeier, F., Fullam, A., Glazek, A.M., Gómez-Rubio, P., Hercog, R., Jung, F., Kandels, S., Kersting, S., Langheinrich, M., Márquez, M., Molero, X., Orakov, A., Van Rossum, T., Torres-Ruiz, R., Telzerow, A., Zych, K., Benes, V., Zeller, G., Trebicka, J., Real, F.X., Malats, N. and Bork, P.
Gut 71 (7): 1359-1372. 7 June 2022

Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean.
Delmont, T.O., Gaia, M., Hinsinger, D.D., Frémont, P., Vanni, C., Fernandez-Guerra, A., Eren, A.M., Kourlaiev, A., d'Agata, L., Clayssen, Q., Villar, E., Labadie, K., Cruaud, C., Poulain, J., Da Silva, C., Wessner, M., Noel, B., Aury, J.M., de Vargas, C., Bowler, C., Karsenti, E., Pelletier, E., Wincker, P. and Jaillon, O.
Cell Genomics 2 (5): 100123. 11 May 2022

Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes.
Khedkar, S., 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 (6): 3155-3168. 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 (1): e0080821. 23 February 2022

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

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 (1): 100137. 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 (7892): 252-256. 13 January 2022

2021

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 (12): 1561-1574. 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 : 120-124. 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 (5): e00382-21. 26 October 2021

Recurrent frameshift neoantigen vaccine elicits protective immunity with reduced tumor burden and improved overall survival in a Lynch syndrome mouse model.
Gebert, J., 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 (4): 288-1302.e13. October 2021

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

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 : 533-538. 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 (7): e0254429. 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 (7): 1167-1176. 14 June 2021

GUNC: detection of chimerism and contamination in prokaryotic genomes.
Orakov, A., Fullam, A., Coelho, L.P., Khedkar, S., Szklarczyk, D., Mende, D.R., Schmidt, T.S.B. and Bork, P.
Genome Biology 22 (1): 178. 13 June 2021

Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox.
Wirbel, J., Zych, K., Essex, M., Karcher, N., Kartal, E., Salazar, G., Bork, P., Sunagawa, S. and Zeller, G.
Genome Biology 22 (1): 93. 30 March 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

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 (D1): D998-D1003. 8 January 2021

SMART: recent updates, new developments and status in 2020.
Letunic, I., Khedkar, S. and Bork, P.
Nucleic Acids Research 49 (D1): D458-D460. 8 January 2021

The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.
Szklarczyk, D., 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 (D): D605-D612. 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 (1): 316-326. January 2021

2020

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

(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 (15): 5234. 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 (5): 1247-1259. 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 (4): 1213-1218. 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 (D1): D621-D625. 8 January 2020

2019

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 (5): 1068-1083. 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 : 664-680. 31 October 2019

Sample preservation and storage significantly impact taxonomic and functional profiles in metaproteomics studies of the human gut microbiome.
Hickl, O., Heintz-Buschart, A., Trautwein-Schult, A., Hercog, R., Bork, P., Wilmes, P. and Becher, D.
Microorganisms 7 (9): 367. 19 September 2019

Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota.
Tito, R.Y., 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.
Gut 68 (7): 1180-1189. 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 (1): 84. 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 (10): 1712-1720. 20 May 2019

Disentangling genetic and environmental effects on the proteotypes of individuals.
Romanov, N., Kuhn, M., Aebersold, R., Ori, A., Beck, M. and Bork, P.
Cell 177 (5): 1308-1318. 16 May 2019

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.
Wirbel, J., 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 (4): 679-689. April 2019

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.
Thomas, A.M., 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 (4): 667-678. 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 (1): 1014. 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 (3): 391-419. 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 : e42693. 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 (D1): D607-D613. 8 January 2019

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
Huerta-Cepas, J., 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 (D1): D309-D314. 8 January 2019

2018

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 : 1255-1265. 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 (7717): 233-237. 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 (4): 487-494. 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 (3): 419-429. 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 (7): e021682. 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 (7): e8131. 2 July 2018

iPath3.0: interactive pathways explorer v3.
Darzi, Y., Letunic, I., Bork, P. and Yamada, T.
Nucleic Acids Research 46 (W1): W510-W513. 2 July 2018

Species-specific activity of antibacterial drug combinations.
Brochado, A.R., 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 (7713): 259-263. 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 (6): 1495-1507. 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 (1): 72. 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 (3): 514-522. 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 (4): 561-568. 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 (7698): 623-628. 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 (1): 208-220. 22 March 2018

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

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 (1): 373. 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 (D1): D700-D707. 4 January 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

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 (1): 441-451. January 2018

2017

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 (12): 960. 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 (7682): 585-589. 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 : 137. 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 (11): 1069-1076. November 2017

RTK: efficient rarefaction analysis of large datasets.
Saary, P., Forslund, K., Bork, P. and Hildebrand, F.
Bioinformatics 33 (16): 2594-2595. 15 August 2017

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.
Huerta-Cepas, J., Forslund, K., Coelho, L.P., Szklarczyk, D., Jensen, L.J., von Mering, C. and Bork, P.
Molecular Biology and Evolution 34 (8): 2115-2122. 1 August 2017

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.
Alberti, A., 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 : 170093. 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 (7): e0182392. 28 July 2017

Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naive Parkinson's disease patients.
Bedarf, J.R., Hildebrand, F., Coelho, L.P., Sunagawa, S., Bahram, M., Goeser, F., Bork, P. and Wuellner, U.
Genome Medicine 9 (1): 39. 28 April 2017

Gut microbiota differs between children with inflammatory bowel disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis.
Knoll, R.L., 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 (4): G327-G339. 1 April 2017

Metabolic anchor reactions for robust biorefining.
Jouhten, P., Huerta-Cepas, J., Bork, P. and Patil, K.R.
Metabolic Engineering 40 : 1-4. March 2017

Bioinformatics analysis of functional associations of PTMs.
Minguez, P. and Bork, P.
Methods in Molecular Biology 1558 (1558): 303-320. 2 February 2017

OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines.
Chen, W.H., Lu, G., Chen, X., Zhao, X.M. and Bork, P.
Nucleic Acids Research 45 (D1): D940-D944. 4 January 2017

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.
Szklarczyk, D., 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 (D1): D362-D368. 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 (D1): D529-D534. 4 January 2017

2016

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 (4): 543-558. 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 (7622): 689-693. 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 (18): 2869-2871. 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 (16): 2520-2523. 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 (7612): 376-381. 21 July 2016

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees.
Letunic, I. and Bork, P.
Nucleic Acids Research 44 (W1): W242-W245. 8 July 2016

ETE 3: reconstruction, analysis and visualization of phylogenomic data.
Huerta-Cepas, J., Serra, F. and Bork, P.
Molecular Biology and Evolution 33 (6): 1635-1638. June 2016

Colorectal cancer and the human gut microbiome: reproducibility with whole-genome shotgun sequencing.
Vogtmann, E., Hua, X., Zeller, G., Sunagawa, S., Voigt, A.Y., Hercog, R., Goedert, J.J., Shi, J., Bork, P. and Sinha, R.
PLoS ONE 11 (5): e0155362. 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 (5): 425-430. 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 (6285): 586-589. 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 (7600): 465-470. 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 : 11334. 21 April 2016

Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton.
Cornejo-Castillo, F.M., 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 : 11071. 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 (1): 47. 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 (3): e1501363. 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 : 135-146. March 2016

Integration of multi-omics data of a genome-reduced bacterium: prevalence of post-transcriptional regulation and its correlation with protein abundances.
Chen, W.H., 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 (3): 1192-1202. 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

2015

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 (6237): 1262073. 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 (6237): 1261447. 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 (6237): 1261605. 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 (6237): 1261498. 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

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

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

2014

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

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

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

2013

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

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

2012

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

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

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

2011

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

2010

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

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

2009

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 (5957): 1235-1240. 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

Evolution of biomolecular networks - lessons from metabolic and protein interactions.
Yamada, T. and Bork, P.
Nature Reviews Molecular Cell Biology 10 (11): 791-803. November 2009

Ageing-related chromatin defects through loss of the NURD complex.
Pegoraro, G., 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

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

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

2008

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

Biochemistry. Not comparable, but complementary.
Jensen, L.J. and Bork, P.
Science 322 (5898): 56-57. 3 October 2008

Linear motif atlas for phosphorylation-dependent signaling.
Miller, M.L., 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

Molecular eco-systems biology: towards an understanding of community function.
Raes, J. and Bork, P.
Nature Reviews Microbiology 6 (9): 693-699. September 2008

Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages.
Pincus, D., 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

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

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

Genetiker in Berlin-Buch [Geneticists in Berlin-Buch].
Max-Delbrueck-Centrum fuer Molekulare Medizin, MDC, ed.
Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin. May 2008

Max Delbrueck - der Physiker. Und die Grundlegung der Biologie [Max Delbrueck - the Physicist. Laying the Foundation of Biology].
Reich, J.
In: Genetiker in Berlin-Buch [Geneticists in Berlin-Buch]. Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, 12-22. May 2008

The genome of the model beetle and pest tribolium castaneum.

Nature 452 (7190): 949-955. 24 April 2008

Non-random retention of protein-coding overlapping genes in Metazoa.
Solda', G., 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

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

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

In gratitude: Charlie.
Reich, J.
Beginnings 28 (4): 39. 2008

Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat.
Kunin, V., 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

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

2007

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

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

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

Ein kurzer Essay zur politischen Lage beim Stammzellgesetz [A short essay on the political situation concerning the stem cell law].
Reich, J.
Biospektrum 13 (3): 227. May 2007

Quantitative phylogenetic assessment of microbial communities in diverse environments.
von Mering, C., 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

2006

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

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

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

Insights into social insects from the genome of the honeybee Apis mellifera.

Nature 443 (7114): 931-949. 26 October 2006

Assessing systems properties of yeast mitochondria through an interaction map of the organelle.
Perocchi, F., 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

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

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

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

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

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

2005

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

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

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

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

The definition of multilocus haplotype blocks and common diseases.
Nothnagel, M.
UNSPECIFIED thesis, UNSPECIFIED. 6 January 2005

A theoretical framework for detecting signal transfer routes in signalling networks.
Zevedei-Oancea, I. and Schuster, S.
Computers & Chemical Engineering 29 (3): 597-617. 1 January 2005

Association of ANKH gene polymorphisms with radiographic hand bone size and geometry in a Chuvasha population.
Malkin, I., 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

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

Ein Repr㲥ntationsformat zur standardisierten Beschreibung und wissensbasierten Modellierung genomischer Expressionsdaten (Dissertation, Humboldt Universit㲬 Berlin, 2005).
Schober, D.
UNSPECIFIED thesis, UNSPECIFIED. 1 January 2005

GandrKB - ontological microarray annotation and visualization.
Schober, D., 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

Is there biological research beyond Systems Biology? A comparative analysis of terms.
Bork, P.
Molecular Systems Biology 1 : 2005.0012 (Article Number). 1 January 2005

Lack of association of the G protein-coupled receptor for asthma susceptibility gene with atopic dermatitis.
Soederhaell, C., 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

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

Towards cellular systems in 4D.
Bork, P. and Serrano, L.
Cell 121 : 507-509. 1 January 2005

2004

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
Hillier, L.W., 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

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

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

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

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

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

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

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

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

Metabolic pathway analysis in biotechnology.
Schuster, S.
In: Metabolic Engineering in the Post Genomic Era. Horizon Bioscience, Wymondham, 181-208. ISBN 0-9545232-2-9 1 January 2004

Quality analysis and integration of large-scale molecular data sets.
Jensen, L.J. and Bork, P.
Drug Discovery Today: TARGETS 3 : 51-56. 1 January 2004

SMART 4.0: towards genomic data integration.
Letunic, I., 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

Sequences and topology. Genes and structures in context.
Bork, P. and Orengo, C.A.
Current Opinion in Structural Biology 14 : 261-263. 1 January 2004

Splice variants of gene expression - A source for diversity of the human proteome.
Reich, J.G. and Pospisil, H.
In: XII International Congress on Genes, Gene Families, and Isozymes : Berlin, Germany, July 19 - 24, 2003. Monduzzi, Bologna, 3-9. ISBN 88-758-7006-3 1 January 2004

The HUPO PSI's Molecular Interaction format - a community standard for the representation of protein interaction data.
Hermjakob, H., 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

2003

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

Biosensor (neuer Bauart).
Dandekar, T.
DE4338732A1 ; DE4338732C2. 11 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

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

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

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

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

Bioinformatics in the post-sequence era.
Kanehisa, M. and Bork, P.
Nature Genetics 33 : 305-310. 1 January 2003

Computational analysis of biochemical systems (book review).
Dandekar, T.
Trends in Biochemical Sciences 26 : 637-637. 1 January 2003

Detection and characterization of pseudogenes.
Torrents, D., Suyama, M. and Bork, P.
In: Bioinformatics and Genomes : Current Perspectives. Horizon Scientific Press, Wymondham, 197-209. ISBN 1-898486-47-6 1 January 2003

Function prediction and protein networks.
Huynen, M.A., Snel, B., von Mering, C. and Bork, P.
Current Opinion in Cell Biology 15 : 191-198. 1 January 2003

Genome evolution reveals biochemical networks and functional modules.
von Mering, C., 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

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

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

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

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

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

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.
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