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Year Citation  Score
2021 Hildebrand F, Gossmann TI, Frioux C, Özkurt E, Myers PN, Ferretti P, Kuhn M, Bahram M, Nielsen HB, Bork P. Dispersal strategies shape persistence and evolution of human gut bacteria. Cell Host & Microbe. PMID 34111423 DOI: 10.1016/j.chom.2021.05.008  1
2021 Acinas SG, Sánchez P, Salazar G, Cornejo-Castillo FM, Sebastián M, Logares R, Royo-Llonch M, Paoli L, Sunagawa S, Hingamp P, Ogata H, Lima-Mendez G, Roux S, González JM, Arrieta JM, ... ... Bork P, et al. Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Communications Biology. 4: 604. PMID 34021239 DOI: 10.1038/s42003-021-02112-2  1
2021 Brial F, Chilloux J, Nielsen T, Vieira-Silva S, Falony G, Andrikopoulos P, Olanipekun M, Hoyles L, Djouadi F, Neves AL, Rodriguez-Martinez A, Mouawad GI, Pons N, Forslund S, Le-Chatelier E, ... ... Bork P, et al. Human and preclinical studies of the host-gut microbiome co-metabolite hippurate as a marker and mediator of metabolic health. Gut. PMID 33975870 DOI: 10.1136/gutjnl-2020-323314  1
2021 Shi K, Zhang L, Yu J, Chen Z, Lai S, Zhao X, Li WG, Luo Q, Lin W, Feng J, Bork P, Zhao XM, Li F. A 12-genus bacterial signature identifies a group of severe autistic children with differential sensory behavior and brain structures. Clinical and Translational Medicine. 11: e314. PMID 33634969 DOI: 10.1002/ctm2.314  0.88
2021 Machado D, Maistrenko OM, Andrejev S, Kim Y, Bork P, Patil KR, Patil KR. Polarization of microbial communities between competitive and cooperative metabolism. Nature Ecology & Evolution. PMID 33398106 DOI: 10.1038/s41559-020-01353-4  0.4
2020 Molinaro A, Bel Lassen P, Henricsson M, Wu H, Adriouch S, Belda E, Chakaroun R, Nielsen T, Bergh PO, Rouault C, André S, Marquet F, Andreelli F, Salem JE, Assmann K, ... ... Bork P, et al. Author Correction: Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology. Nature Communications. 11: 6448. PMID 33349634 DOI: 10.1038/s41467-020-20412-9  1
2020 Trebicka J, Bork P, Krag A, Arumugam M. Utilizing the gut microbiome in decompensated cirrhosis and acute-on-chronic liver failure. Nature Reviews. Gastroenterology & Hepatology. PMID 33257833 DOI: 10.1038/s41575-020-00376-3  0.88
2020 Szklarczyk D, Gable AL, Nastou KC, Lyon D, Kirsch R, Pyysalo S, Doncheva NT, Legeay M, Fang T, Bork P, Jensen LJ, von Mering C. The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Research. PMID 33237311 DOI: 10.1093/nar/gkaa1074  0.96
2020 Molinaro A, Bel Lassen P, Henricsson M, Wu H, Adriouch S, Belda E, Chakaroun R, Nielsen T, Bergh PO, Rouault C, André S, Marquet F, Andreelli F, Salem JE, Assmann K, ... ... Bork P, et al. Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology. Nature Communications. 11: 5881. PMID 33208748 DOI: 10.1038/s41467-020-19589-w  1
2020 Bahram M, Netherway T, Frioux C, Ferretti P, Coelho LP, Geisen S, Bork P, Hildebrand F. Metagenomic assessment of the global distribution of bacteria and fungi. Environmental Microbiology. PMID 33185929 DOI: 10.1111/1462-2920.15314  1
2020 Blum M, Chang HY, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S, Richardson L, Salazar GA, Williams L, Bork P, Bridge A, et al. The InterPro protein families and domains database: 20 years on. Nucleic Acids Research. PMID 33156333 DOI: 10.1093/nar/gkaa977  0.96
2020 Letunic I, Khedkar S, Bork P. SMART: recent updates, new developments and status in 2020. Nucleic Acids Research. PMID 33104802 DOI: 10.1093/nar/gkaa937  0.96
2020 Gurumayum S, Jiang P, Hao X, Campos TL, Young ND, Korhonen PK, Gasser RB, Bork P, Zhao XM, He LJ, Chen WH. OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines. Nucleic Acids Research. PMID 33084874 DOI: 10.1093/nar/gkaa884  1
2020 Michalak M, Katzenmaier EM, Roeckel N, Woerner SM, Fuchs V, Warnken U, Yuan YP, Bork P, Neu-Yilik G, Kulozik A, von Knebel Doeberitz M, Kloor M, Kopitz J, Gebert J. (Phospho)proteomic Profiling of Microsatellite Unstable CRC Cells Reveals Alterations in Nuclear Signaling and Cholesterol Metabolism Caused by Frameshift Mutation of NMD Regulator UPF3A. International Journal of Molecular Sciences. 21. PMID 32718059 DOI: 10.3390/Ijms21155234  0.76
2020 Poisa-Beiro L, Thoma J, Landry J, Sauer S, Yamamoto A, Eckstein V, Romanov N, Raffel S, Hoffmann GF, Bork P, Benes V, Gavin AC, Tanaka M, Ho AD. Glycogen accumulation, central carbon metabolism, and aging of hematopoietic stem and progenitor cells. Scientific Reports. 10: 11597. PMID 32665666 DOI: 10.1038/S41598-020-68396-2  0.48
2020 Vieira-Silva S, Falony G, Belda E, Nielsen T, Aron-Wisnewsky J, Chakaroun R, Forslund SK, Assmann K, Valles-Colomer M, Nguyen TTD, Proost S, Prifti E, Tremaroli V, Pons N, Le Chatelier E, ... ... Bork P, et al. Statin therapy is associated with lower prevalence of gut microbiota dysbiosis. Nature. 581: 310-315. PMID 32433607 DOI: 10.1038/S41586-020-2269-X  1
2020 Sunagawa S, Acinas SG, Bork P, Bowler C, Eveillard D, Gorsky G, Guidi L, Iudicone D, Karsenti E, Lombard F, Ogata H, Pesant S, Sullivan MB, Wincker P, et al. Tara Oceans: towards global ocean ecosystems biology. Nature Reviews. Microbiology. PMID 32398798 DOI: 10.1038/S41579-020-0364-5  0.72
2020 Bahram M, Netherway T, Hildebrand F, Pritsch K, Drenkhan R, Loit K, Anslan S, Bork P, Tedersoo L. Plant nutrient-acquisition strategies drive topsoil microbiome structure and function. The New Phytologist. PMID 32279325 DOI: 10.1111/Nph.16598  1
2020 Maistrenko OM, Mende DR, Luetge M, Hildebrand F, Schmidt TSB, Li SS, Rodrigues JFM, von Mering C, Pedro Coelho L, Huerta-Cepas J, Sunagawa S, Bork P. Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity. The Isme Journal. PMID 32047279 DOI: 10.1038/S41396-020-0600-Z  1
2020 Wirbel J, Zych K, Essex M, Karcher N, Kartal E, Salazar G, Bork P, Sunagawa S, Zeller G. Abstract A40: The SIAMCAT R package enables statistical and machine learning analyses for case-control microbiome datasets Cancer Research. 80. DOI: 10.1158/1538-7445.Mvc2020-A40  0.88
2019 Marißen J, Haiß A, Meyer C, Van Rossum T, Bünte LM, Frommhold D, Gille C, Goedicke-Fritz S, Göpel W, Hudalla H, Pagel J, Pirr S, Siller B, Viemann D, Vens M, ... ... Bork P, et al. Efficacy of probiotics to prevent gut dysbiosis in preterm infants of 28+0-32+6 weeks of gestation: a randomised, placebo-controlled, double-blind, multicentre trial: the PRIMAL Clinical Study protocol. Bmj Open. 9: e032617. PMID 31753895 DOI: 10.1136/Bmjopen-2019-032617  0.44
2019 Guo T, Luna A, Rajapakse VN, Koh CC, Wu Z, Liu W, Sun Y, Gao H, Menden MP, Xu C, Calzone L, Martignetti L, Auwerx C, Buljan M, Banaei-Esfahani A, ... ... Bork P, et al. Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines. Iscience. 21: 664-680. PMID 31733513 DOI: 10.1016/J.Isci.2019.10.059  1
2019 Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh HJ, Cuenca M, Field CM, Coelho LP, Cruaud C, Engelen S, Gregory AC, Labadie K, Marec C, Pelletier E, Royo-Llonch M, ... ... Bork P, et al. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome. Cell. 179: 1068-1083.e21. PMID 31730850 DOI: 10.1016/J.Cell.2019.10.014  0.88
2019 Thomas AM, 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, ... ... Bork P, et al. Author Correction: Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nature Medicine. PMID 31664237 DOI: 10.1038/S41591-019-0663-4  1
2019 Mende DR, Letunic I, Maistrenko OM, Schmidt TSB, Milanese A, Paoli L, Hernández-Plaza A, Orakov AN, Forslund SK, Sunagawa S, Zeller G, Huerta-Cepas J, Coelho LP, Bork P. proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes. Nucleic Acids Research. PMID 31647096 DOI: 10.1093/Nar/Gkz1002  0.96
2019 Li Y, Kuhn M, Gavin AC, Bork P. Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features. Bioinformatics (Oxford, England). PMID 31605112 DOI: 10.1093/Bioinformatics/Btz736  0.96
2019 Hildebrand F, Pallen MJ, Bork P. Towards standardisation of naming novel prokaryotic taxa in the age of high-throughput microbiology. Gut. PMID 31203204 DOI: 10.1136/Gutjnl-2019-319045  1
2019 Coelho LP, Alves R, Monteiro P, Huerta-Cepas J, Freitas AT, Bork P. NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language. Microbiome. 7: 84. PMID 31159881 DOI: 10.1186/S40168-019-0684-8  0.72
2019 Gossmann TI, Shanmugasundram A, Börno S, Duvaux L, Lemaire C, Kuhl H, Klages S, Roberts LD, Schade S, Gostner JM, Hildebrand F, Vowinckel J, Bichet C, Mülleder M, Calvani E, ... ... Bork P, et al. Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity. Current Biology : Cb. PMID 31080084 DOI: 10.1016/J.Cub.2019.04.020  1
2019 Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, et al. Consent insufficient for data release-Response. Science (New York, N.Y.). 364: 446. PMID 31048484 DOI: 10.1126/Science.Aax7509  0.48
2019 Romanov N, Kuhn M, Aebersold R, Ori A, Beck M, Bork P. Disentangling Genetic and Environmental Effects on the Proteotypes of Individuals. Cell. PMID 31031010 DOI: 10.1016/J.Cell.2019.03.015  0.96
2019 Thomas AM, 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, ... ... Bork P, et al. Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nature Medicine. PMID 30936548 DOI: 10.1038/S41591-019-0405-7  1
2019 Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai R, Sunagawa S, Coelho LP, Schrotz-King P, Vogtmann E, Habermann N, ... ... Bork P, et al. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nature Medicine. PMID 30936547 DOI: 10.1038/S41591-019-0406-6  1
2019 Letunic I, Bork P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Research. PMID 30931475 DOI: 10.1093/Nar/Gkz239  0.96
2019 Milanese A, Mende DR, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, Hingamp P, Alves R, Costea PI, Coelho LP, Schmidt TSB, Almeida A, Mitchell AL, Finn RD, Huerta-Cepas J, ... Bork P, et al. Microbial abundance, activity and population genomic profiling with mOTUs2. Nature Communications. 10: 1014. PMID 30833550 DOI: 10.1038/S41467-019-08844-4  0.88
2019 Schmidt TSB, Hayward MR, Coelho LP, Li SS, Costea PI, Voigt AY, Wirbel J, Maistrenko OM, Alves RJ, Bergsten E, de Beaufort C, Sobhani I, Heintz-Buschart A, Sunagawa S, Zeller G, ... ... Bork P, et al. Extensive transmission of microbes along the gastrointestinal tract. Elife. 8. PMID 30747106 DOI: 10.7554/Elife.42693  0.88
2019 Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, et al. Toward unrestricted use of public genomic data. Science (New York, N.Y.). 363: 350-352. PMID 30679363 DOI: 10.1126/Science.Aaw1280  0.48
2019 Hildebrand F, Moitinho-Silva L, Blasche S, Jahn MTT, Gossmann TI, Heuerta Cepas J, Hercog R, Luetge M, Bahram M, Pryszlak A, Alves RJ, Waszak SM, Zhu A, Ye L, Costea PI, ... ... Bork P, et al. Antibiotics-induced monodominance of a novel gut bacterial order. Gut. PMID 30658995 DOI: 10.1136/Gutjnl-2018-317715  1
2019 Caputi L, Carradec Q, Eveillard D, Kirilovsky A, Pelletier E, Karlusich JJP, Vieira FRJ, Villar E, Chaffron S, Malviya S, Scalco E, Acinas SG, Alberti A, Aury JM, Benoiston AS, ... ... Bork P, et al. Community-Level Responses to Iron Availability in Open Ocean Plankton Ecosystems Global Biogeochemical Cycles. 33: 391-419. DOI: 10.1029/2018Gb006022  0.76
2018 Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, et al. Minimum Information about an Uncultivated Virus Genome (MIUViG). Nature Biotechnology. PMID 30556814 DOI: 10.1038/Nbt.4306  0.72
2018 Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, von Mering C. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Research. PMID 30476243 DOI: 10.1093/Nar/Gky1131  0.96
2018 Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C, Bork P. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Research. PMID 30418610 DOI: 10.1093/Nar/Gky1085  0.96
2018 Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, Brown SD, Chang HY, El-Gebali S, Fraser MI, Gough J, Haft DR, Huang H, Letunic I, Lopez R, et al. InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Research. PMID 30398656 DOI: 10.1093/Nar/Gky1100  0.96
2018 Pedersen HK, Forslund SK, Gudmundsdottir V, Petersen AØ, Hildebrand F, Hyötyläinen T, Nielsen T, Hansen T, Bork P, Ehrlich SD, Brunak S, Oresic M, Pedersen O, Nielsen HB. A computational framework to integrate high-throughput '-omics' datasets for the identification of potential mechanistic links. Nature Protocols. PMID 30382244 DOI: 10.1038/S41596-018-0064-Z  1
2018 Palleja A, Mikkelsen KH, Forslund SK, Kashani A, Allin KH, Nielsen T, Hansen TH, Liang S, Feng Q, Zhang C, Pyl PT, Coelho LP, Yang H, Wang J, Typas A, ... ... Bork P, et al. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nature Microbiology. PMID 30349083 DOI: 10.1038/S41564-018-0257-9  0.88
2018 Hennrich ML, Romanov N, Horn P, Jaeger S, Eckstein V, Steeples V, Ye F, Ding X, Poisa-Beiro L, Lai MC, Lang B, Boultwood J, Luft T, Zaugg JB, Pellagatti A, ... Bork P, et al. Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline. Nature Communications. 9: 4004. PMID 30275468 DOI: 10.1038/S41467-018-06353-4  0.48
2018 Tito RY, 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, Raes J. Population-level analysis of subtype prevalence and variation in the human gut microbiota. Gut. PMID 30171064 DOI: 10.1136/Gutjnl-2018-316106  1
2018 Jones JC, Fruciano C, Marchant J, Hildebrand F, Forslund S, Bork P, Engel P, Hughes WOH. The gut microbiome is associated with behavioural task in honey bees. Insectes Sociaux. 65: 419-429. PMID 30100619 DOI: 10.1007/S00040-018-0624-9  1
2018 Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, Bengtsson-Palme J, Anslan S, Coelho LP, Harend H, Huerta-Cepas J, Medema MH, Maltz MR, Mundra S, Olsson PA, ... ... Bork P, et al. Structure and function of the global topsoil microbiome. Nature. PMID 30069051 DOI: 10.1038/S41586-018-0386-6  1
2018 Kushugulova A, Forslund SK, Costea PI, Kozhakhmetov S, Khassenbekova Z, Urazova M, Nurgozhin T, Zhumadilov Z, Benberin V, Driessen M, Hercog R, Voigt AY, Benes V, Kandels-Lewis S, Sunagawa S, ... ... Bork P, et al. Metagenomic analysis of gut microbial communities from a Central Asian population. Bmj Open. 8: e021682. PMID 30056386 DOI: 10.1136/Bmjopen-2018-021682  0.96
2018 Ferretti P, Pasolli E, Tett A, Asnicar F, Gorfer V, Fedi S, Armanini F, Truong DT, Manara S, Zolfo M, Beghini F, Bertorelli R, De Sanctis V, Bariletti I, Canto R, ... ... Bork P, et al. Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome. Cell Host & Microbe. 24: 133-145.e5. PMID 30001516 DOI: 10.1016/J.Chom.2018.06.005  0.48
2018 Kayser K, Degenhardt F, Holzapfel S, Horpaopan S, Peters S, Spier I, Morak M, Vangala D, Rahner N, von Knebel-Doeberitz M, Schackert HK, Engel C, Büttner R, Wijnen J, Doerks T, ... Bork P, et al. Copy number variation analysis and targeted NGS in 77 families with suspected Lynch syndrome reveals novel potential causative genes. International Journal of Cancer. PMID 29987844 DOI: 10.1002/Ijc.31725  0.96
2018 Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, ... ... Bork P, et al. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology. 36: 660. PMID 29979671 DOI: 10.1038/Nbt0718-660A  0.48
2018 Brochado AR, 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, ... ... Bork P, et al. Species-specific activity of antibacterial drug combinations. Nature. PMID 29973719 DOI: 10.1038/S41586-018-0278-9  0.56
2018 Parca L, Beck M, Bork P, Ori A. Quantifying compartment-associated variations of protein abundance in proteomics data. Molecular Systems Biology. 14: e8131. PMID 29967062 DOI: 10.15252/Msb.20178131  0.52
2018 Darzi Y, Letunic I, Bork P, Yamada T. iPath3.0: interactive pathways explorer v3. Nucleic Acids Research. PMID 29718427 DOI: 10.1093/Nar/Gky299  1
2018 Becher I, Andrés-Pons A, Romanov N, Stein F, Schramm M, Baudin F, Helm D, Kurzawa N, Mateus A, Mackmull MT, Typas A, Müller CW, Bork P, Beck M, Savitski MM. Pervasive Protein Thermal Stability Variation during the Cell Cycle. Cell. PMID 29706546 DOI: 10.1016/J.Cell.2018.03.053  0.56
2018 Coelho LP, Kultima JR, Costea PI, Fournier C, Pan Y, Czarnecki-Maulden G, Hayward MR, Forslund SK, Schmidt TSB, Descombes P, Jackson JR, Li Q, Bork P. Similarity of the dog and human gut microbiomes in gene content and response to diet. Microbiome. 6: 72. PMID 29669589 DOI: 10.1186/S40168-018-0450-3  0.76
2018 Tramontano M, Andrejev S, Pruteanu M, Klünemann M, Kuhn M, Galardini M, Jouhten P, Zelezniak A, Zeller G, Bork P, Typas A, Patil KR. Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies. Nature Microbiology. 3: 514-522. PMID 29556107 DOI: 10.1038/S41564-018-0123-9  0.96
2018 Maier L, Pruteanu M, Kuhn M, Zeller G, Telzerow A, Anderson EE, Brochado AR, Fernandez KC, Dose H, Mori H, Patil KR, Bork P, Typas A. Extensive impact of non-antibiotic drugs on human gut bacteria. Nature. PMID 29555994 DOI: 10.1038/Nature25979  0.96
2018 Rubio-Cosials A, Schulz EC, Lambertsen L, Smyshlyaev G, Rojas-Cordova C, Forslund K, Karaca E, Bebel A, Bork P, Barabas O. Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance. Cell. PMID 29551265 DOI: 10.1016/J.Cell.2018.02.032  1
2018 Schmidt TSB, Raes J, Bork P. The Human Gut Microbiome: From Association to Modulation. Cell. 172: 1198-1215. PMID 29522742 DOI: 10.1016/J.Cell.2018.02.044  1
2018 Korpela K, Costea PI, Coelho LP, Kandels-Lewis S, Willemsen G, Boomsma DI, Segata N, Bork P. Selective maternal seeding and environment shape the human gut microbiome. Genome Research. PMID 29496731 DOI: 10.1101/Gr.233940.117  0.72
2018 Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, ... ... Bork P, et al. Publisher Correction: Enterotypes in the landscape of gut microbial community composition. Nature Microbiology. PMID 29440750 DOI: 10.1038/S41564-018-0114-X  1
2018 Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, ... ... Bork P, et al. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology. 36: 196. PMID 29406516 DOI: 10.1038/Nbt0218-196A  0.48
2018 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 MA, Méheust R, ... ... Bork P, et al. A global ocean atlas of eukaryotic genes. Nature Communications. 9: 373. PMID 29371626 DOI: 10.1038/S41467-017-02342-1  1
2018 Seeleuthner Y, Mondy S, Lombard V, Carradec Q, Pelletier E, Wessner M, Leconte J, Mangot JF, Poulain J, Labadie K, Logares R, Sunagawa S, de Berardinis V, Salanoubat M, Dimier C, ... ... Bork P, et al. Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans. Nature Communications. 9: 310. PMID 29358710 DOI: 10.1038/S41467-017-02235-3  0.72
2018 Jones JC, Fruciano C, Hildebrand F, Al Toufalilia H, Balfour NJ, Bork P, Engel P, Ratnieks FL, Hughes WO. Gut microbiota composition is associated with environmental landscape in honey bees. Ecology and Evolution. 8: 441-451. PMID 29321884 DOI: 10.1002/Ece3.3597  1
2018 Costea PI, Hildebrand F, Manimozhiyan A, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, ... ... Bork P, et al. Enterotypes in the landscape of gut microbial community composition. Nature Microbiology. 3: 8-16. PMID 29255284 DOI: 10.1038/S41564-017-0072-8  1
2018 Schmidt TS, Hayward MR, Coelho LP, Li SS, Costea PI, Voigt AY, Wirbel J, Maistrenko OM, Alves RJ, Bergsten E, Beaufort Cd, Sobhani I, Heintz-Buschart A, Sunagawa S, Zeller G, ... ... Bork P, et al. Author response: Extensive transmission of microbes along the gastrointestinal tract Elife. DOI: 10.7554/Elife.42693.037  0.88
2018 Kloor M, Oezcan M, Ahadova A, Yuan Y, Bork P, Sei S, Shoemaker R, Gelincik O, Lipkin S, Gebert J, Doeberitz MvK. Abstract 717: Mouse model for the development of preventive and therapeutic vaccines against microsatellite-unstable cancers Cancer Research. 78: 717-717. DOI: 10.1158/1538-7445.Am2018-717  0.64
2017 Costea PI, Coelho LP, Sunagawa S, Munch R, Huerta-Cepas J, Forslund K, Hildebrand F, Kushugulova A, Zeller G, Bork P. Subspecies in the global human gut microbiome. Molecular Systems Biology. 13: 960. PMID 29242367 DOI: 10.15252/Msb.20177589  1
2017 Gao NL, Zhang C, Zhang Z, Hu S, Lercher MJ, Zhao XM, Bork P, Liu Z, Chen WH. MVP: a microbe-phage interaction database. Nucleic Acids Research. PMID 29177508 DOI: 10.1093/Nar/Gkx1124  1
2017 Junqueira ACM, Ratan A, Acerbi E, Drautz-Moses DI, Premkrishnan BNV, Costea PI, Linz B, Purbojati RW, Paulo DF, Gaultier NE, Subramanian P, Hasan NA, Colwell RR, Bork P, Azeredo-Espin AML, et al. The microbiomes of blowflies and houseflies as bacterial transmission reservoirs. Scientific Reports. 7: 16324. PMID 29176730 DOI: 10.1038/S41598-017-16353-X  0.68
2017 Wilck N, Matus MG, Kearney SM, Olesen SW, Forslund K, Bartolomaeus H, Haase S, Mähler A, Balogh A, Markó L, Vvedenskaya O, Kleiner FH, Tsvetkov D, Klug L, Costea PI, ... ... Bork P, et al. Salt-responsive gut commensal modulates TH17 axis and disease. Nature. PMID 29143823 DOI: 10.1038/Nature24628  1
2017 Colin S, Coelho LP, Sunagawa S, Bowler C, Karsenti E, Bork P, Pepperkok R, de Vargas C. Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes. Elife. 6. PMID 29087936 DOI: 10.7554/Elife.26066  0.72
2017 Letunic I, Bork P. 20 years of the SMART protein domain annotation resource. Nucleic Acids Research. PMID 29040681 DOI: 10.1093/Nar/Gkx922  0.96
2017 Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, ... ... Bork P, et al. Towards standards for human fecal sample processing in metagenomic studies. Nature Biotechnology. PMID 28967887 DOI: 10.1038/Nbt.3960  0.88
2017 Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, ... ... Bork P, et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology. 35: 725-731. PMID 28787424 DOI: 10.1038/Nbt.3893  0.48
2017 Costea PI, Munch R, Coelho LP, Paoli L, Sunagawa S, Bork P. metaSNV: A tool for metagenomic strain level analysis. Plos One. 12: e0182392. PMID 28753663 DOI: 10.1371/Journal.Pone.0182392  0.72
2017 Kastritis PL, O'Reilly FJ, Bock T, Li Y, Rogon MZ, Buczak K, Romanov N, Betts MJ, Bui KH, Hagen WJ, Hennrich ML, Mackmull MT, Rappsilber J, Russell RB, Bork P, et al. Capturing protein communities by structural proteomics in a thermophilic eukaryote. Molecular Systems Biology. 13: 936. PMID 28743795 DOI: 10.15252/Msb.20167412  0.64
2017 Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wüllner U. Erratum to: Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients. Genome Medicine. 9: 61. PMID 28662719 DOI: 10.1186/s13073-017-0451-z  1
2017 Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Pedersen HK, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, ... ... Bork P, et al. Corrigendum: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature. 545: 116. PMID 28470190 DOI: 10.1038/Nature22318  1
2017 Huerta-Cepas J, Forslund K, Pedro Coelho L, Szklarczyk D, Juhl Jensen L, von Mering C, Bork P. Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Molecular Biology and Evolution. PMID 28460117 DOI: 10.1093/Molbev/Msx148  1
2017 Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wüllner U. Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients. Genome Medicine. 9: 39. PMID 28449715 DOI: 10.1186/S13073-017-0428-Y  1
2017 Saary P, Forslund K, Bork P, Hildebrand F. RTK: efficient rarefaction analysis of large datasets. Bioinformatics (Oxford, England). PMID 28398468 DOI: 10.1093/Bioinformatics/Btx206  1
2017 Betts MJ, Wichmann O, Utz M, Andre T, Petsalaki E, Minguez P, Parca L, Roth FP, Gavin AC, Bork P, Russell RB. Systematic identification of phosphorylation-mediated protein interaction switches. Plos Computational Biology. 13: e1005462. PMID 28346509 DOI: 10.1371/Journal.Pcbi.1005462  0.64
2017 Wang YY, Chen WH, Xiao PP, Xie WB, Luo Q, Bork P, Zhao XM. GEAR: A database of Genomic Elements Associated with drug Resistance. Scientific Reports. 7: 44085. PMID 28294141 DOI: 10.1038/Srep44085  1
2017 Voigt AY, Zeller G, Bork P. [Microbial Biomarkers for Early Cancer Detection]. Deutsche Medizinische Wochenschrift (1946). 142: 267-274. PMID 28235227 DOI: 10.1055/S-0042-110193  0.88
2017 Jouhten P, Huerta-Cepas J, Bork P, Patil KR. Metabolic anchor reactions for robust biorefining. Metabolic Engineering. 40: 1-4. PMID 28232136 DOI: 10.1016/J.Ymben.2017.02.010  0.68
2017 Minguez P, Bork P. Bioinformatics Analysis of Functional Associations of PTMs. Methods in Molecular Biology (Clifton, N.J.). 1558: 303-320. PMID 28150244 DOI: 10.1007/978-1-4939-6783-4_14  0.64
2017 Mende DR, Letunic I, Huerta-Cepas J, Li SS, Forslund K, Sunagawa S, Bork P. proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes. Nucleic Acids Research. 45: D529-D534. PMID 28053165 DOI: 10.1093/Nar/Gkw989  1
2017 Colin S, Coelho LP, Sunagawa S, Bowler C, Karsenti E, Bork P, Pepperkok R, Vargas Cd. Author response: Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes Elife. DOI: 10.7554/Elife.26066.043  0.72
2017 Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wüllner U. Erratum to: Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naive Parkinson's disease patients (vol 9, pg 39, 2017) Genome Medicine. 9: 61. DOI: 10.3929/Ethz-B-000191807  1
2016 Knoll RL, Forslund K, Kultima JR, Meyer CU, Kullmer U, Sunagawa S, Bork P, Gehring S. Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition - a metagenomic analysis. American Journal of Physiology. Gastrointestinal and Liver Physiology. ajpgi.00293.2016. PMID 28039159 DOI: 10.1152/Ajpgi.00293.2016  1
2016 Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P, Jensen LJ, von Mering C. The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Research. PMID 27924014 DOI: 10.1093/Nar/Gkw937  0.96
2016 Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, et al. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Research. PMID 27899635 DOI: 10.1093/Nar/Gkw1107  0.96
2016 Scharaw S, Iskar M, Ori A, Boncompain G, Laketa V, Poser I, Lundberg E, Perez F, Beck M, Bork P, Pepperkok R. The endosomal transcriptional regulator RNF11 integrates degradation and transport of EGFR. The Journal of Cell Biology. 215: 543-558. PMID 27872256 DOI: 10.1083/Jcb.201601090  1
2016 Chen WH, Lu G, Chen X, Zhao XM, Bork P. OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines. Nucleic Acids Research. PMID 27799467 DOI: 10.1093/Nar/Gkw1013  1
2016 Plichta DR, Juncker AS, Bertalan M, Rettedal E, Gautier L, Varela E, Manichanh C, Fouqueray C, Levenez F, Nielsen T, Doré J, Machado AM, de Evgrafov MC, Hansen T, Jørgensen T, ... Bork P, et al. Transcriptional interactions suggest niche segregation among microorganisms in the human gut. Nature Microbiology. 1: 16152. PMID 27564131 DOI: 10.1038/Nmicrobiol.2016.152  0.8
2016 Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, Nielsen T, Jensen BA, Forslund K, Hildebrand F, Prifti E, Falony G, Le Chatelier E, Levenez F, Doré J, Mattila I, Plichta DR, ... ... Bork P, et al. Human gut microbes impact host serum metabolome and insulin sensitivity. Nature. PMID 27409811 DOI: 10.1038/Nature18646  1
2016 Deghou S, Zeller G, Iskar M, Driessen M, Castillo M, van Noort V, Bork P. CART - a chemical annotation retrieval toolkit. Bioinformatics (Oxford, England). PMID 27256313 DOI: 10.1093/Bioinformatics/Btw233  1
2016 Vogtmann E, Hua X, Zeller G, Sunagawa S, Voigt AY, Hercog R, Goedert JJ, Shi J, Bork P, Sinha R. Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing. Plos One. 11: e0155362. PMID 27171425 DOI: 10.1371/Journal.Pone.0155362  1
2016 Kultima JR, Coelho LP, Forslund K, Huerta-Cepas J, Li SS, Driessen M, Voigt AY, Zeller G, Sunagawa S, Bork P. MOCAT2: a metagenomic assembly, annotation and profiling framework. Bioinformatics (Oxford, England). PMID 27153620 DOI: 10.1093/Bioinformatics/Btw183  1
2016 Saliba AE, Vonkova I, Deghou S, Ceschia S, Tischer C, Kugler KG, Bork P, Ellenberg J, Gavin AC. A protocol for the systematic and quantitative measurement of protein-lipid interactions using the liposome-microarray-based assay. Nature Protocols. 11: 1021-38. PMID 27149326 DOI: 10.1038/Nprot.2016.059  0.64
2016 Yelton AP, Acinas SG, Sunagawa S, Bork P, Pedrós-Alió C, Chisholm SW. Global genetic capacity for mixotrophy in marine picocyanobacteria. The Isme Journal. PMID 27137127 DOI: 10.1038/Ismej.2016.64  1
2016 Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas J, Nieuwdorp M, Salojärvi J, Voigt AY, Zeller G, Sunagawa S, de Vos WM, Bork P. Durable coexistence of donor and recipient strains after fecal microbiota transplantation. Science (New York, N.Y.). 352: 586-9. PMID 27126044 DOI: 10.1126/Science.Aad8852  1
2016 Chen WH, Lu G, Bork P, Hu S, Lercher MJ. Energy efficiency trade-offs drive nucleotide usage in transcribed regions. Nature Communications. 7: 11334. PMID 27098217 DOI: 10.1038/Ncomms11334  1
2016 Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Research. PMID 27095192 DOI: 10.1093/Nar/Gkw290  0.96
2016 Noguera-Julian M, Rocafort M, Guillén Y, Rivera J, Casadellà M, Nowak P, Hildebrand F, Zeller G, Parera M, Bellido R, Rodríguez C, Carrillo J, Mothe B, Coll J, Bravo I, ... ... Bork P, et al. Gut Microbiota Linked to Sexual Preference and HIV Infection. Ebiomedicine. 5: 135-46. PMID 27077120 DOI: 10.1016/J.Ebiom.2016.01.032  1
2016 Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, et al. Standardized benchmarking in the quest for orthologs. Nature Methods. PMID 27043882 DOI: 10.1038/Nmeth.3830  1
2016 Cornejo-Castillo FM, Cabello AM, Salazar G, Sánchez-Baracaldo P, Lima-Mendez G, Hingamp P, Alberti A, Sunagawa S, Bork P, de Vargas C, Raes J, Bowler C, Wincker P, Zehr JP, Gasol JM, et al. Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton. Nature Communications. 7: 11071. PMID 27002549 DOI: 10.1038/Ncomms11071  1
2016 Ori A, Iskar M, Buczak K, Kastritis P, Parca L, Andrés-Pons A, Singer S, Bork P, Beck M. Spatiotemporal variation of mammalian protein complex stoichiometries. Genome Biology. 17: 47. PMID 26975353 DOI: 10.1186/S13059-016-0912-5  1
2016 Lloréns-Rico V, Cano J, Kamminga T, Gil R, Latorre A, Chen WH, Bork P, Glass JI, Serrano L, Lluch-Senar M. Bacterial antisense RNAs are mainly the product of transcriptional noise. Science Advances. 2: e1501363. PMID 26973873 DOI: 10.1126/Sciadv.1501363  1
2016 Huerta-Cepas J, Serra F, Bork P. ETE 3: Reconstruction, analysis and visualization of phylogenomic data. Molecular Biology and Evolution. PMID 26921390 DOI: 10.1093/Molbev/Msw046  1
2016 Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum J, Coelho LP, Espinoza JC, Malviya S, Sunagawa S, Dimier C, ... ... Bork P, et al. Plankton networks driving carbon export in the oligotrophic ocean. Nature. PMID 26863193 DOI: 10.1038/Nature16942  1
2016 Zhang XD, Song J, Bork P, Zhao XM. The exploration of network motifs as potential drug targets from post-translational regulatory networks. Scientific Reports. 6: 20558. PMID 26853265 DOI: 10.1038/Srep20558  1
2016 Korpela K, Salonen A, Virta LJ, Kekkonen RA, Forslund K, Bork P, de Vos WM. Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children. Nature Communications. 7: 10410. PMID 26811868 DOI: 10.1038/Ncomms10410  1
2016 Chen WH, van Noort V, Lluch-Senar M, Hennrich ML, H Wodke JA, Yus E, Alibés A, Roma G, Mende DR, Pesavento C, Typas A, Gavin AC, Serrano L, Bork P. Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances. Nucleic Acids Research. PMID 26773059 DOI: 10.1093/Nar/Gkw004  1
2016 Silva-Martin N, Daudén MI, Glatt S, Hoffmann NA, Kastritis P, Bork P, Beck M, Müller CW. The Combination of X-Ray Crystallography and Cryo-Electron Microscopy Provides Insight into the Overall Architecture of the Dodecameric Rvb1/Rvb2 Complex. Plos One. 11: e0146457. PMID 26745716 DOI: 10.1371/Journal.Pone.0146457  0.36
2015 Djuika CF, Huerta-Cepas J, Przyborski JM, Deil S, Sanchez CP, Doerks T, Bork P, Lanzer M, Deponte M. Prokaryotic ancestry and gene fusion of a dual localized peroxiredoxin in malaria parasites. Microbial Cell (Graz, Austria). 2: 5-13. PMID 28357258 DOI: 10.15698/Mic2015.01.182  0.96
2015 Iskar M, Bork P, van Noort V. Discovery and validation of the antimetastatic activity of citalopram in colorectal cancer. Molecular & Cellular Oncology. 2: e975080. PMID 27308430 DOI: 10.4161/23723556.2014.975080  1
2015 Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M. Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats. Cell Systems. 1: 224-237. PMID 27135913 DOI: 10.1016/J.Cels.2015.08.012  1
2015 Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Krogh Pedersen H, Arumugam M, Kristiansen K, Yvonne Voigt A, Vestergaard H, Hercog R, ... ... Bork P, et al. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature. PMID 26633628 DOI: 10.1038/Nature15766  1
2015 Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Krogh Pedersen H, Arumugam M, Kristiansen K, Yvonne Voigt A, Vestergaard H, Hercog R, ... ... Bork P, et al. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature. PMID 26618873 DOI: 10.1038/nature15766  1
2015 Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M. STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Nucleic Acids Research. PMID 26590256 DOI: 10.1093/Nar/Gkv1277  1
2015 Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Research. PMID 26582926 DOI: 10.1093/Nar/Gkv1248  1
2015 Kuhn M, Letunic I, Jensen LJ, Bork P. The SIDER database of drugs and side effects. Nucleic Acids Research. PMID 26481350 DOI: 10.1093/Nar/Gkv1075  1
2015 Zhang C, Yin A, Li H, Wang R, Wu G, Shen J, Zhang M, Wang L, Hou Y, Ouyang H, Zhang Y, Zheng Y, Wang J, Lv X, Wang Y, ... ... Bork P, et al. Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children. Ebiomedicine. 2: 966-82. PMID 26425705 DOI: 10.1016/J.Ebiom.2015.07.007  0.52
2015 von Appen A, Kosinski J, Sparks L, Ori A, DiGuilio AL, Vollmer B, Mackmull MT, Banterle N, Parca L, Kastritis P, Buczak K, Mosalaganti S, Hagen W, Andres-Pons A, Lemke EA, ... Bork P, et al. In situ structural analysis of the human nuclear pore complex. Nature. 526: 140-3. PMID 26416747 DOI: 10.1038/Nature15381  1
2015 Shieh YW, Minguez P, Bork P, Auburger JJ, Guilbride DL, Kramer G, Bukau B. Operon structure and cotranslational subunit association direct protein assembly in bacteria. Science (New York, N.Y.). 350: 678-80. PMID 26405228 DOI: 10.1126/Science.Aac8171  1
2015 Vonkova I, Saliba AE, Deghou S, Anand K, Ceschia S, Doerks T, Galih A, Kugler KG, Maeda K, Rybin V, van Noort V, Ellenberg J, Bork P, Gavin AC. Lipid Cooperativity as a General Membrane-Recruitment Principle for PH Domains. Cell Reports. 12: 1519-30. PMID 26299969 DOI: 10.1016/J.Celrep.2015.07.054  1
2015 Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M, Yilmaz P, Xenarios I, Bork P, Lewis SE, Gabaldón T. Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream. Genome Biology and Evolution. 7: 1988-99. PMID 26133389 DOI: 10.1093/Gbe/Evv121  1
2015 Lima-Mendez G, Faust K, Henry N, Decelle J, Colin S, Carcillo F, Chaffron S, Ignacio-Espinosa JC, Roux S, Vincent F, Bittner L, Darzi Y, Wang J, Audic S, Berline L, ... ... Bork P, et al. Ocean plankton. Determinants of community structure in the global plankton interactome. Science (New York, N.Y.). 348: 1262073. PMID 25999517 DOI: 10.1126/Science.1262073  1
2015 de Vargas C, Audic S, Henry N, Decelle J, Mahé F, Logares R, Lara E, Berney C, Le Bescot N, Probert I, Carmichael M, Poulain J, Romac S, Colin S, Aury JM, ... ... Bork P, et al. Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean. Science (New York, N.Y.). 348: 1261605. PMID 25999516 DOI: 10.1126/Science.1261605  1
2015 Brum JR, Ignacio-Espinoza JC, Roux S, Doulcier G, Acinas SG, Alberti A, Chaffron S, Cruaud C, de Vargas C, Gasol JM, Gorsky G, Gregory AC, Guidi L, Hingamp P, Iudicone D, ... ... Bork P, et al. Ocean plankton. Patterns and ecological drivers of ocean viral communities. Science (New York, N.Y.). 348: 1261498. PMID 25999515 DOI: 10.1126/Science.1261498  1
2015 Villar E, Farrant GK, Follows M, Garczarek L, Speich S, Audic S, Bittner L, Blanke B, Brum JR, Brunet C, Casotti R, Chase A, Dolan JR, d'Ortenzio F, Gattuso JP, ... ... Bork P, et al. Ocean plankton. Environmental characteristics of Agulhas rings affect interocean plankton transport. Science (New York, N.Y.). 348: 1261447. PMID 25999514 DOI: 10.1126/Science.1261447  1
2015 Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, ... ... Bork P, et al. Ocean plankton. Structure and function of the global ocean microbiome. Science (New York, N.Y.). 348: 1261359. PMID 25999513 DOI: 10.1126/Science.1261359  1
2015 Bork P, Bowler C, de Vargas C, Gorsky G, Karsenti E, Wincker P. Tara Oceans. Tara Oceans studies plankton at planetary scale. Introduction. Science (New York, N.Y.). 348: 873. PMID 25999501 DOI: 10.1126/Science.Aac5605  1
2015 Sunagawa S, Karsenti E, Bowler C, Bork P. Computational eco-systems biology in Tara Oceans: translating data into knowledge. Molecular Systems Biology. 11: 809. PMID 25999085 DOI: 10.15252/Msb.20156272  0.72
2015 Zelezniak A, Andrejev S, Ponomarova O, Mende DR, Bork P, Patil KR. Metabolic dependencies drive species co-occurrence in diverse microbial communities. Proceedings of the National Academy of Sciences of the United States of America. 112: 6449-54. PMID 25941371 DOI: 10.1073/Pnas.1421834112  1
2015 Zhu A, Sunagawa S, Mende DR, Bork P. Inter-individual differences in the gene content of human gut bacterial species. Genome Biology. 16: 82. PMID 25896518 DOI: 10.1186/S13059-015-0646-9  1
2015 Voigt AY, Costea PI, Kultima JR, Li SS, Zeller G, Sunagawa S, Bork P. Temporal and technical variability of human gut metagenomes. Genome Biology. 16: 73. PMID 25888008 DOI: 10.1186/S13059-015-0639-8  1
2015 Mackmull MT, Iskar M, Parca L, Singer S, Bork P, Ori A, Beck M. Histone Deacetylase Inhibitors (HDACi) Cause the Selective Depletion of Bromodomain Containing Proteins (BCPs). Molecular & Cellular Proteomics : McP. 14: 1350-60. PMID 25755299 DOI: 10.1074/Mcp.M114.042499  1
2015 Lluch-Senar M, Delgado J, Chen WH, Lloréns-Rico V, O'Reilly FJ, Wodke JA, Unal EB, Yus E, Martínez S, Nichols RJ, Ferrar T, Vivancos A, Schmeisky A, Stülke J, van Noort V, ... ... Bork P, et al. Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium. Molecular Systems Biology. 11: 780. PMID 25609650 DOI: 10.15252/Msb.20145558  1
2015 Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, ... ... Bork P, et al. The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Research. 43: D213-21. PMID 25428371 DOI: 10.1093/Nar/Gku1243  1
2015 Betts MJ, Lu Q, Jiang Y, Drusko A, Wichmann O, Utz M, Valtierra-Gutiérrez IA, Schlesner M, Jaeger N, Jones DT, Pfister S, Lichter P, Eils R, Siebert R, Bork P, et al. Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions. Nucleic Acids Research. 43: e10. PMID 25392414 DOI: 10.1093/Nar/Gku1094  1
2015 Minguez P, Letunic I, Parca L, Garcia-Alonso L, Dopazo J, Huerta-Cepas J, Bork P. PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins. Nucleic Acids Research. 43: D494-502. PMID 25361965 DOI: 10.1093/Nar/Gku1081  1
2015 Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Research. 43: D447-52. PMID 25352553 DOI: 10.1093/Nar/Gku1003  1
2015 Letunic I, Doerks T, Bork P. SMART: recent updates, new developments and status in 2015. Nucleic Acids Research. 43: D257-60. PMID 25300481 DOI: 10.1093/Nar/Gku949  1
2015 Tedersoo L, Anslan S, Bahram M, Põlme S, Riit T, Liiv I, Kõljalg U, Kisand V, Nilsson RH, Hildebrand F, Bork P, Abarenkov K. Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi Mycokeys. 10: 1-43. DOI: 10.3897/mycokeys.10.4852  1
2015 Sunagawa S, Karsenti E, Bowler C, Bork P. Computational eco-systems biology in Tara Oceans: Translating data into knowledge Molecular Systems Biology. 11. DOI: 10.15252/msb.20156272  1
2015 Lluch-Senar M, Delgado J, Chen WH, Lloréns-Rico V, O'Reilly FJ, Wodke JAH, Unal EB, Yus E, Martínez S, Nichols RJ, Ferrar T, Vivancos A, Schmeisky A, Stülke J, Van Noort V, ... ... Bork P, et al. Defining a minimal cell: Essentiality of small ORFs and ncRNAs in a genome-reduced bacterium Molecular Systems Biology. 11. DOI: 10.15252/msb.20145558  1
2015 Noguera-Julian M, Rocafort M, Guillén Y, Rivera J, Casadellà M, Nowak P, Hildebrand F, Zeller G, Parera M, Bellido R, Rodríguez C, Carrillo J, Mothe B, Coll J, Bravo I, ... ... Bork P, et al. Gut Microbiota Linked to Sexual Preference and HIV Infection Ebiomedicine. DOI: 10.1016/j.ebiom.2016.01.032  1
2015 Zhang C, Yin A, Li H, Wang R, Wu G, Shen J, Zhang M, Wang L, Hou Y, Ouyang H, Zhang Y, Zheng Y, Wang J, Lv X, Wang Y, ... ... Bork P, et al. Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children Ebiomedicine. DOI: 10.1016/j.ebiom.2015.07.007  1
2015 Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M. Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats Cell Systems. 1: 224-237. DOI: 10.1016/j.cels.2015.08.012  1
2014 Hildebrand F, Tadeo R, Voigt AY, Bork P, Raes J. LotuS: an efficient and user-friendly OTU processing pipeline. Microbiome. 2: 30. PMID 27367037 DOI: 10.1186/2049-2618-2-30  1
2014 Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, ... ... Bork P, et al. Potential of fecal microbiota for early-stage detection of colorectal cancer. Molecular Systems Biology. 10: 766. PMID 25432777 DOI: 10.15252/Msb.20145645  1
2014 Bock T, Chen WH, Ori A, Malik N, Silva-Martin N, Huerta-Cepas J, Powell ST, Kastritis PL, Smyshlyaev G, Vonkova I, Kirkpatrick J, Doerks T, Nesme L, Baßler J, Kos M, ... ... Bork P, et al. An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum. Nucleic Acids Research. 42: 13525-33. PMID 25398899 DOI: 10.1093/Nar/Gku1147  1
2014 Trachana K, Forslund K, Larsson T, Powell S, Doerks T, von Mering C, Bork P. A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation. Plos One. 9: e111122. PMID 25369365 DOI: 10.1371/Journal.Pone.0111122  1
2014 Durdu S, Iskar M, Revenu C, Schieber N, Kunze A, Bork P, Schwab Y, Gilmour D. Luminal signalling links cell communication to tissue architecture during organogenesis. Nature. 515: 120-4. PMID 25337877 DOI: 10.1038/Nature13852  1
2014 Woerner SM, Tosti E, Yuan YP, Kloor M, Bork P, Edelmann W, Gebert J. Detection of coding microsatellite frameshift mutations in DNA mismatch repair-deficient mouse intestinal tumors. Molecular Carcinogenesis. PMID 25213383 DOI: 10.1002/Mc.22213  1
2014 Chen WH, Zhao XM, van Noort V, Bork P. Comments on "Human dominant disease genes are enriched in paralogs originating from whole genome duplication". Plos Computational Biology. 10: e1003758. PMID 25077479 DOI: 10.1371/Journal.Pcbi.1003758  1
2014 van Noort V, Schölch S, Iskar M, Zeller G, Ostertag K, Schweitzer C, Werner K, Weitz J, Koch M, Bork P. Novel drug candidates for the treatment of metastatic colorectal cancer through global inverse gene-expression profiling. Cancer Research. 74: 5690-9. PMID 25038229 DOI: 10.1158/0008-5472.Can-13-3540  1
2014 Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, ... ... Bork P, et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nature Biotechnology. 32: 822-8. PMID 24997787 DOI: 10.1038/Nbt.2939  1
2014 Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, Juncker AS, Manichanh C, Chen B, Zhang W, Levenez F, ... ... Bork P, et al. An integrated catalog of reference genes in the human gut microbiome. Nature Biotechnology. 32: 834-41. PMID 24997786 DOI: 10.1038/Nbt.2942  1
2014 Costea PI, Zeller G, Sunagawa S, Bork P. A fair comparison. Nature Methods. 11: 359. PMID 24681719 DOI: 10.1038/Nmeth.2897  1
2014 Waller AS, Yamada T, Kristensen DM, Kultima JR, Sunagawa S, Koonin EV, Bork P. Classification and quantification of bacteriophage taxa in human gut metagenomes. The Isme Journal. 8: 1391-402. PMID 24621522 DOI: 10.1038/Ismej.2014.30  1
2014 Forslund K, Sunagawa S, Coelho LP, Bork P. Metagenomic insights into the human gut resistome and the forces that shape it. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 36: 316-29. PMID 24474281 DOI: 10.1002/Bies.201300143  1
2014 Gallina AM, Bork P, Bordo D. Structural analysis of protein-ligand interactions: the binding of endogenous compounds and of synthetic drugs. Journal of Molecular Recognition : Jmr. 27: 65-72. PMID 24436123 DOI: 10.1002/Jmr.2332  1
2014 Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Research. 42: D231-9. PMID 24297252 DOI: 10.1093/Nar/Gkt1253  1
2014 Kuhn M, Szklarczyk D, Pletscher-Frankild S, Blicher TH, von Mering C, Jensen LJ, Bork P. STITCH 4: integration of protein-chemical interactions with user data. Nucleic Acids Research. 42: D401-7. PMID 24293645 DOI: 10.1093/Nar/Gkt1207  1
2014 Saliba AE, Vonkova I, Ceschia S, Findlay GM, Maeda K, Tischer C, Deghou S, van Noort V, Bork P, Pawson T, Ellenberg J, Gavin AC. A quantitative liposome microarray to systematically characterize protein-lipid interactions. Nature Methods. 11: 47-50. PMID 24270602 DOI: 10.1038/Nmeth.2734  1
2014 Logares R, Sunagawa S, Salazar G, Cornejo-Castillo FM, Ferrera I, Sarmento H, Hingamp P, Ogata H, de Vargas C, Lima-Mendez G, Raes J, Poulain J, Jaillon O, Wincker P, Kandels-Lewis S, ... ... Bork P, et al. Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities. Environmental Microbiology. 16: 2659-71. PMID 24102695 DOI: 10.1111/1462-2920.12250  1
2014 Hildebrand F, Tito RY, Voigt AY, Bork P, Raes J. Correction to: LotuS: An efficient and user-friendly OTU processing pipeline [Microbiome, 2, (2014), 30] Microbiome. 2. DOI: 10.1186/2049-2618-2-37  1
2014 Hildebrand F, Tadeo R, Voigt AY, Bork P, Raes J. LotuS: An efficient and user-friendly OTU processing pipeline Microbiome. 2.  1
2013 Sunagawa S, Schloissnig S, Arumugam M, Forslund K, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Typas A, Weinstock GM, ... Bork P, et al. Individuality and temporal stability of the human gut microbiome. Central Asian Journal of Global Health. 2: 120. PMID 29805877 DOI: 10.5195/Cajgh.2013.120  1
2013 Beltrao P, Bork P, Krogan NJ, van Noort V. Evolution and functional cross-talk of protein post-translational modifications. Molecular Systems Biology. 9: 714. PMID 24366814 DOI: 10.1002/Msb.201304521  1
2013 Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, ... ... Bork P, et al. Metagenomic species profiling using universal phylogenetic marker genes. Nature Methods. 10: 1196-9. PMID 24141494 DOI: 10.1038/Nmeth.2693  1
2013 Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, ... ... Bork P, et al. Richness of human gut microbiome correlates with metabolic markers. Nature. 500: 541-6. PMID 23985870 DOI: 10.1038/Nature12506  1
2013 Dürnberger G, Bürckstümmer T, Huber K, Giambruno R, Doerks T, Karayel E, Burkard TR, Kaupe I, Müller AC, Schönegger A, Ecker GF, Lohninger H, Bork P, Bennett KL, Superti-Furga G, et al. Experimental characterization of the human non-sequence-specific nucleic acid interactome. Genome Biology. 14: R81. PMID 23902751 DOI: 10.1186/Gb-2013-14-7-R81  1
2013 Mende DR, Sunagawa S, Zeller G, Bork P. Accurate and universal delineation of prokaryotic species. Nature Methods. 10: 881-4. PMID 23892899 DOI: 10.1038/Nmeth.2575  1
2013 Chen WH, Zhao XM, van Noort V, Bork P. Human monogenic disease genes have frequently functionally redundant paralogs. Plos Computational Biology. 9: e1003073. PMID 23696728 DOI: 10.1371/Journal.Pcbi.1003073  1
2013 Kuhn M, Al Banchaabouchi M, Campillos M, Jensen LJ, Gross C, Gavin AC, Bork P. Systematic identification of proteins that elicit drug side effects. Molecular Systems Biology. 9: 663. PMID 23632385 DOI: 10.1038/Msb.2013.10  1
2013 Iskar M, Zeller G, Blattmann P, Campillos M, Kuhn M, Kaminska KH, Runz H, Gavin AC, Pepperkok R, van Noort V, Bork P. Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding. Molecular Systems Biology. 9: 662. PMID 23632384 DOI: 10.1038/Msb.2013.20  1
2013 Hingamp P, Grimsley N, Acinas SG, Clerissi C, Subirana L, Poulain J, Ferrera I, Sarmento H, Villar E, Lima-Mendez G, Faust K, Sunagawa S, Claverie JM, Moreau H, Desdevises Y, ... Bork P, et al. Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. The Isme Journal. 7: 1678-95. PMID 23575371 DOI: 10.1038/Ismej.2013.59  1
2013 Forslund K, Sunagawa S, Kultima JR, Mende DR, Arumugam M, Typas A, Bork P. Country-specific antibiotic use practices impact the human gut resistome. Genome Research. 23: 1163-9. PMID 23568836 DOI: 10.1101/Gr.155465.113  1
2013 Ori A, Banterle N, Iskar M, Andrés-Pons A, Escher C, Khanh Bui H, Sparks L, Solis-Mezarino V, Rinner O, Bork P, Lemke EA, Beck M. Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines. Molecular Systems Biology. 9: 648. PMID 23511206 DOI: 10.1038/Msb.2013.4  1
2013 Blaser M, Bork P, Fraser C, Knight R, Wang J. The microbiome explored: recent insights and future challenges. Nature Reviews. Microbiology. 11: 213-7. PMID 23377500 DOI: 10.1038/Nrmicro2973  1
2013 van Noort V, Bradatsch B, Arumugam M, Amlacher S, Bange G, Creevey C, Falk S, Mende DR, Sinning I, Hurt E, Bork P. Consistent mutational paths predict eukaryotic thermostability. Bmc Evolutionary Biology. 13: 7. PMID 23305080 DOI: 10.1186/1471-2148-13-7  1
2013 Kristensen DM, Waller AS, Yamada T, Bork P, Mushegian AR, Koonin EV. Orthologous gene clusters and taxon signature genes for viruses of prokaryotes. Journal of Bacteriology. 195: 941-50. PMID 23222723 DOI: 10.1128/Jb.01801-12  1
2013 Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Weinstock GM, Bork P. Genomic variation landscape of the human gut microbiome. Nature. 493: 45-50. PMID 23222524 DOI: 10.1038/Nature11711  1
2013 Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Research. 41: D808-15. PMID 23203871 DOI: 10.1093/Nar/Gks1094  1
2013 Minguez P, Letunic I, Parca L, Bork P. PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins. Nucleic Acids Research. 41: D306-11. PMID 23193284 DOI: 10.1093/Nar/Gks1230  1
2013 Pacini C, Iorio F, Gonçalves E, Iskar M, Klabunde T, Bork P, Saez-Rodriguez J. DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data. Bioinformatics (Oxford, England). 29: 132-4. PMID 23129297 DOI: 10.1093/Bioinformatics/Bts656  1
2012 Kultima JR, Sunagawa S, Li J, Chen W, Chen H, Mende DR, Arumugam M, Pan Q, Liu B, Qin J, Wang J, Bork P. MOCAT: a metagenomics assembly and gene prediction toolkit. Plos One. 7: e47656. PMID 23082188 DOI: 10.1371/Journal.Pone.0047656  1
2012 Alonso-Sáez L, Waller AS, Mende DR, Bakker K, Farnelid H, Yager PL, Lovejoy C, Tremblay JÉ, Potvin M, Heinrich F, Estrada M, Riemann L, Bork P, Pedrós-Alió C, Bertilsson S. Role for urea in nitrification by polar marine Archaea. Proceedings of the National Academy of Sciences of the United States of America. 109: 17989-94. PMID 23027926 DOI: 10.1073/Pnas.1201914109  1
2012 Minguez P, Parca L, Diella F, Mende DR, Kumar R, Helmer-Citterich M, Gavin AC, van Noort V, Bork P. Deciphering a global network of functionally associated post-translational modifications. Molecular Systems Biology. 8: 599. PMID 22806145 DOI: 10.1038/Msb.2012.31  1
2012 Yus E, Güell M, Vivancos AP, Chen WH, Lluch-Senar M, Delgado J, Gavin AC, Bork P, Serrano L. Transcription start site associated RNAs in bacteria. Molecular Systems Biology. 8: 585. PMID 22617959 DOI: 10.1038/Msb.2012.16  1
2012 Yamada T, Waller AS, Raes J, Zelezniak A, Perchat N, Perret A, Salanoubat M, Patil KR, Weissenbach J, Bork P. Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours. Molecular Systems Biology. 8: 581. PMID 22569339 DOI: 10.1038/Msb.2012.13  1
2012 Doerks T, van Noort V, Minguez P, Bork P. Annotation of the M. tuberculosis hypothetical orfeome: adding functional information to more than half of the uncharacterized proteins. Plos One. 7: e34302. PMID 22485162 DOI: 10.1371/Journal.Pone.0034302  1
2012 Mende DR, Waller AS, Sunagawa S, Järvelin AI, Chan MM, Arumugam M, Raes J, Bork P. Assessment of metagenomic assembly using simulated next generation sequencing data. Plos One. 7: e31386. PMID 22384016 DOI: 10.1371/Journal.Pone.0031386  1
2012 van Noort V, Seebacher J, Bader S, Mohammed S, Vonkova I, Betts MJ, Kühner S, Kumar R, Maier T, O'Flaherty M, Rybin V, Schmeisky A, Yus E, Stülke J, Serrano L, ... ... Bork P, et al. Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. Molecular Systems Biology. 8: 571. PMID 22373819 DOI: 10.1038/Msb.2012.4  1
2012 Chen YP, Bork P. The Tenth Asia Pacific Bioinformatics Conference (APBC 2012). Introduction. Bmc Genomics. 13: I1. PMID 22369290 DOI: 10.1186/1471-2164-13-S1-I1  1
2012 Chen WH, Trachana K, Lercher MJ, Bork P. Younger genes are less likely to be essential than older genes, and duplicates are less likely to be essential than singletons of the same age. Molecular Biology and Evolution. 29: 1703-6. PMID 22319151 DOI: 10.1093/Molbev/Mss014  1
2012 Haemmerling S, Behnisch W, Doerks T, Korbel JO, Bork P, Moog U, Hentze S, Grasshoff U, Bonin M, Rieß O, Janssen JW, Jauch A, Bartram CR, Reinhardt D, Koch KA, et al. A 15q24 microdeletion in transient myeloproliferative disease (TMD) and acute megakaryoblastic leukaemia (AMKL) implicates PML and SUMO3 in the leukaemogenesis of TMD/AMKL. British Journal of Haematology. 157: 180-7. PMID 22296450 DOI: 10.1111/J.1365-2141.2012.09028.X  1
2012 Zoetendal EG, Raes J, van den Bogert B, Arumugam M, Booijink CC, Troost FJ, Bork P, Wels M, de Vos WM, Kleerebezem M. The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. The Isme Journal. 6: 1415-26. PMID 22258098 DOI: 10.1038/Ismej.2011.212  1
2012 Iskar M, Zeller G, Zhao XM, van Noort V, Bork P. Drug discovery in the age of systems biology: the rise of computational approaches for data integration. Current Opinion in Biotechnology. 23: 609-16. PMID 22153034 DOI: 10.1016/J.Copbio.2011.11.010  1
2012 Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ, von Mering C, Bork P. eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Research. 40: D284-9. PMID 22096231 DOI: 10.1093/Nar/Gkr1060  1
2012 Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, et al. InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Research. 40: D306-12. PMID 22096229 DOI: 10.1093/Nar/Gkr948  1
2012 Kuhn M, Szklarczyk D, Franceschini A, von Mering C, Jensen LJ, Bork P. STITCH 3: zooming in on protein-chemical interactions. Nucleic Acids Research. 40: D876-80. PMID 22075997 DOI: 10.1093/Nar/Gkr1011  1
2012 Chen WH, Minguez P, Lercher MJ, Bork P. OGEE: an online gene essentiality database. Nucleic Acids Research. 40: D901-6. PMID 22075992 DOI: 10.1093/Nar/Gkr986  1
2012 Letunic I, Doerks T, Bork P. SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Research. 40: D302-5. PMID 22053084 DOI: 10.1093/Nar/Gkr931  1
2011 Zhao XM, Iskar M, Zeller G, Kuhn M, van Noort V, Bork P. Prediction of drug combinations by integrating molecular and pharmacological data. Plos Computational Biology. 7: e1002323. PMID 22219721 DOI: 10.1371/Journal.Pcbi.1002323  1
2011 Creevey CJ, Muller J, Doerks T, Thompson JD, Arendt D, Bork P. Identifying single copy orthologs in Metazoa. Plos Computational Biology. 7: e1002269. PMID 22144877 DOI: 10.1371/Journal.Pcbi.1002269  1
2011 Karsenti E, Acinas SG, Bork P, Bowler C, De Vargas C, Raes J, Sullivan M, Arendt D, Benzoni F, Claverie JM, Follows M, Gorsky G, Hingamp P, Iudicone D, Jaillon O, et al. A holistic approach to marine eco-systems biology. Plos Biology. 9: e1001177. PMID 22028628 DOI: 10.1371/Journal.Pbio.1001177  1
2011 Trachana K, Larsson TA, Powell S, Chen WH, Doerks T, Muller J, Bork P. Orthology prediction methods: a quality assessment using curated protein families. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 33: 769-80. PMID 21853451 DOI: 10.1002/Bies.201100062  1
2011 Creevey CJ, Doerks T, Fitzpatrick DA, Raes J, Bork P. Universally distributed single-copy genes indicate a constant rate of horizontal transfer. Plos One. 6: e22099. PMID 21850220 DOI: 10.1371/Journal.Pone.0022099  1
2011 Amlacher S, Sarges P, Flemming D, van Noort V, Kunze R, Devos DP, Arumugam M, Bork P, Hurt E. Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile. Cell. 146: 277-89. PMID 21784248 DOI: 10.1016/J.Cell.2011.06.039  1
2011 Brouwers L, Iskar M, Zeller G, van Noort V, Bork P. Network neighbors of drug targets contribute to drug side-effect similarity. Plos One. 6: e22187. PMID 21765950 DOI: 10.1371/Journal.Pone.0022187  1
2011 Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, ... ... Bork P, et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology. 29: 415-20. PMID 21552244 DOI: 10.1038/Nbt.1823  1
2011 Yamada T, Letunic I, Okuda S, Kanehisa M, Bork P. iPath2.0: interactive pathway explorer. Nucleic Acids Research. 39: W412-5. PMID 21546551 DOI: 10.1093/Nar/Gkr313  1
2011 Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, ... ... Bork P, et al. Enterotypes of the human gut microbiome. Nature. 473: 174-80. PMID 21508958 DOI: 10.1038/Nature09944  1
2011 Letunic I, Bork P. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Research. 39: W475-8. PMID 21470960 DOI: 10.1093/Nar/Gkr201  1
2011 Raes J, Letunic I, Yamada T, Jensen LJ, Bork P. Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data. Molecular Systems Biology. 7: 473. PMID 21407210 DOI: 10.1038/Msb.2011.6  1
2011 Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Cáceres CE, Carmel L, Casola C, Choi JH, ... ... Bork P, et al. The ecoresponsive genome of Daphnia pulex. Science (New York, N.Y.). 331: 555-61. PMID 21292972 DOI: 10.1126/Science.1197761  1
2011 Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Research. 39: D561-8. PMID 21045058 DOI: 10.1093/Nar/Gkq973  1
2011 Arumugam M, Raes J, Pelletier E, Paslier DL, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, ... ... Bork P, et al. Erratum: Enterotypes of the human gut microbiome (Nature (2011) 473 (174-180)) Nature. 474: 666-666. DOI: 10.1038/Nature10187  1
2011 Walhout AJM, Aebersold R, Meyer T, Bork P, Kirschner MW. Systems biology: What's the next challenge? Cell. 144: 837-838. DOI: 10.1016/j.cell.2011.02.040  1
2010 Gallego O, Betts MJ, Gvozdenovic-Jeremic J, Maeda K, Matetzki C, Aguilar-Gurrieri C, Beltran-Alvarez P, Bonn S, Fernández-Tornero C, Jensen LJ, Kuhn M, Trott J, Rybin V, Müller CW, Bork P, et al. A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae. Molecular Systems Biology. 6: 430. PMID 21119626 DOI: 10.1038/Msb.2010.87  1
2010 Harrington ED, Arumugam M, Raes J, Bork P, Relman DA. SmashCell: a software framework for the analysis of single-cell amplified genome sequences. Bioinformatics (Oxford, England). 26: 2979-80. PMID 20966005 DOI: 10.1093/Bioinformatics/Btq564  1
2010 Arumugam M, Harrington ED, Foerstner KU, Raes J, Bork P. SmashCommunity: a metagenomic annotation and analysis tool. Bioinformatics (Oxford, England). 26: 2977-8. PMID 20959381 DOI: 10.1093/Bioinformatics/Btq536  1
2010 Iskar M, Campillos M, Kuhn M, Jensen LJ, van Noort V, Bork P. Drug-induced regulation of target expression. Plos Computational Biology. 6. PMID 20838579 DOI: 10.1371/Journal.Pcbi.1000925  1
2010 Suyama M, Harrington ED, Vinokourova S, von Knebel Doeberitz M, Ohara O, Bork P. A network of conserved co-occurring motifs for the regulation of alternative splicing. Nucleic Acids Research. 38: 7916-26. PMID 20702423 DOI: 10.1093/Nar/Gkq705  1
2010 Jensen LJ, Bork P. Ontologies in quantitative biology: a basis for comparison, integration, and discovery. Plos Biology. 8: e1000374. PMID 20520843 DOI: 10.1371/Journal.Pbio.1000374  1
2010 Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nature Methods. 7: 248-9. PMID 20354512 DOI: 10.1038/Nmeth0410-248  1
2010 Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, ... ... Bork P, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 464: 59-65. PMID 20203603 DOI: 10.1038/Nature08821  1
2010 Granovskaia MV, Jensen LJ, Ritchie ME, Toedling J, Ning Y, Bork P, Huber W, Steinmetz LM. High-resolution transcription atlas of the mitotic cell cycle in budding yeast. Genome Biology. 11: R24. PMID 20193063 DOI: 10.1186/Gb-2010-11-3-R24  1
2010 Trachana K, Jensen LJ, Bork P. Evolution and regulation of cellular periodic processes: a role for paralogues. Embo Reports. 11: 233-8. PMID 20168326 DOI: 10.1038/Embor.2010.9  1
2010 Christodoulou F, Raible F, Tomer R, Simakov O, Trachana K, Klaus S, Snyman H, Hannon GJ, Bork P, Arendt D. Ancient animal microRNAs and the evolution of tissue identity. Nature. 463: 1084-8. PMID 20118916 DOI: 10.1038/Nature08744  1
2010 Kuhn M, Campillos M, Letunic I, Jensen LJ, Bork P. A side effect resource to capture phenotypic effects of drugs. Molecular Systems Biology. 6: 343. PMID 20087340 DOI: 10.1038/Msb.2009.98  1
2010 Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, ... ... Bork P, et al. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science (New York, N.Y.). 327: 343-8. PMID 20075255 DOI: 10.1126/Science.1178028  1
2010 Muller J, Creevey CJ, Thompson JD, Arendt D, Bork P. AQUA: automated quality improvement for multiple sequence alignments. Bioinformatics (Oxford, England). 26: 263-5. PMID 19926669 DOI: 10.1093/Bioinformatics/Btp651  1
2010 Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Research. 38: D190-5. PMID 19900971 DOI: 10.1093/Nar/Gkp951  1
2010 Kuhn M, Szklarczyk D, Franceschini A, Campillos M, von Mering C, Jensen LJ, Beyer A, Bork P. STITCH 2: an interaction network database for small molecules and proteins. Nucleic Acids Research. 38: D552-6. PMID 19897548 DOI: 10.1093/Nar/Gkp937  1
2010 Woerner SM, Yuan YP, Benner A, Korff S, von Knebel Doeberitz M, Bork P. SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology. Nucleic Acids Research. 38: D682-9. PMID 19820113 DOI: 10.1093/Nar/Gkp839  1
2010 Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, ... ... Bork P, et al. The “Minimum Information about an ENvironmental Sequence” (MIENS) specification Nature Precedings. 5: 1-1. DOI: 10.1038/Npre.2010.5252.1  1
2009 Güell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kühner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P, et al. Transcriptome complexity in a genome-reduced bacterium. Science (New York, N.Y.). 326: 1268-71. PMID 19965477 DOI: 10.1126/Science.1176951  1
2009 Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, Chen WH, Wodke JA, Güell M, Martínez S, Bourgeois R, Kühner S, Raineri E, Letunic I, Kalinina OV, Rode M, ... ... Bork P, et al. Impact of genome reduction on bacterial metabolism and its regulation. Science (New York, N.Y.). 326: 1263-8. PMID 19965476 DOI: 10.1126/Science.1177263  1
2009 Kühner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castaño-Diez D, Chen WH, Devos D, Güell M, Norambuena T, ... ... Bork P, et al. Proteome organization in a genome-reduced bacterium. Science (New York, N.Y.). 326: 1235-40. PMID 19965468 DOI: 10.1126/Science.1176343  1
2009 Yamada T, Bork P. Evolution of biomolecular networks: lessons from metabolic and protein interactions. Nature Reviews. Molecular Cell Biology. 10: 791-803. PMID 19851337 DOI: 10.1038/Nrm2787  1
2009 Juncker AS, Jensen LJ, Pierleoni A, Bernsel A, Tress ML, Bork P, von Heijne G, Valencia A, Ouzounis CA, Casadio R, Brunak S. Sequence-based feature prediction and annotation of proteins. Genome Biology. 10: 206. PMID 19226438 DOI: 10.1186/Gb-2009-10-2-206  1
2009 Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P, Gerstein MB. Quantifying environmental adaptation of metabolic pathways in metagenomics. Proceedings of the National Academy of Sciences of the United States of America. 106: 1374-9. PMID 19164758 DOI: 10.1073/Pnas.0808022106  1
2009 Koscielny G, Le Texier V, Gopalakrishnan C, Kumanduri V, Riethoven JJ, Nardone F, Stanley E, Fallsehr C, Hofmann O, Kull M, Harrington E, Boué S, Eyras E, Plass M, Lopez F, ... ... Bork P, et al. ASTD: The Alternative Splicing and Transcript Diversity database. Genomics. 93: 213-20. PMID 19059335 DOI: 10.1016/J.Ygeno.2008.11.003  1
2009 Letunic I, Doerks T, Bork P. SMART 6: recent updates and new developments. Nucleic Acids Research. 37: D229-32. PMID 18978020 DOI: 10.1093/Nar/Gkn808  1
2009 Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C. STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Research. 37: D412-6. PMID 18940858 DOI: 10.1093/Nar/Gkn760  1
2009 Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, et al. InterPro: the integrative protein signature database. Nucleic Acids Research. 37: D211-5. PMID 18940856 DOI: 10.1093/Nar/Gkn785  1
2009 Singh AH, Doerks T, Letunic I, Raes J, Bork P. Discovering functional novelty in metagenomes: examples from light-mediated processes. Journal of Bacteriology. 191: 32-41. PMID 18849420 DOI: 10.1128/Jb.01084-08  1
2008 Foerstner KU, Doerks T, Muller J, Raes J, Bork P. A nitrile hydratase in the eukaryote Monosiga brevicollis. Plos One. 3: e3976. PMID 19096720 DOI: 10.1371/Journal.Pone.0003976  1
2008 Quijano C, Tomancak P, Lopez-Marti J, Suyama M, Bork P, Milan M, Torrents D, Manzanares M. Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution. Genome Biology. 9: R176. PMID 19087263 DOI: 10.1186/Gb-2008-9-12-R176  1
2008 Perotti C, Liu R, Parusel CT, Böcher N, Schultz J, Bork P, Pfitzner E, Groner B, Shemanko CS. Heat shock protein-90-alpha, a prolactin-STAT5 target gene identified in breast cancer cells, is involved in apoptosis regulation. Breast Cancer Research : Bcr. 10: R94. PMID 19014541 DOI: 10.1186/Bcr2193  1
2008 Korff S, Woerner SM, Yuan YP, Bork P, von Knebel Doeberitz M, Gebert J. Frameshift mutations in coding repeats of protein tyrosine phosphatase genes in colorectal tumors with microsatellite instability. Bmc Cancer. 8: 329. PMID 19000305 DOI: 10.1186/1471-2407-8-329  1
2008 Foerstner KU, Doerks T, Creevey CJ, Doerks A, Bork P. A computational screen for type I polyketide synthases in metagenomics shotgun data. Plos One. 3: e3515. PMID 18953415 DOI: 10.1371/Journal.Pone.0003515  1
2008 Jensen LJ, Bork P. Biochemistry. Not comparable, but complementary. Science (New York, N.Y.). 322: 56-7. PMID 18832636 DOI: 10.1126/Science.1164801  1
2008 Miller ML, Jensen LJ, Diella F, Jørgensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Pasculescu A, Alexander J, Knapp S, Blom N, ... Bork P, et al. Linear motif atlas for phosphorylation-dependent signaling. Science Signaling. 1: ra2. PMID 18765831 DOI: 10.1126/Scisignal.1159433  1
2008 Harrington ED, Bork P. Sircah: a tool for the detection and visualization of alternative transcripts. Bioinformatics (Oxford, England). 24: 1959-60. PMID 18635569 DOI: 10.1093/Bioinformatics/Btn361  1
2008 Pallejà A, Harrington ED, Bork P. Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions? Bmc Genomics. 9: 335. PMID 18627618 DOI: 10.1186/1471-2164-9-335  1
2008 Campillos M, Kuhn M, Gavin AC, Jensen LJ, Bork P. Drug target identification using side-effect similarity. Science (New York, N.Y.). 321: 263-6. PMID 18621671 DOI: 10.1126/Science.1158140  1
2008 Hooper SD, Raes J, Foerstner KU, Harrington ED, Dalevi D, Bork P. A molecular study of microbe transfer between distant environments. Plos One. 3: e2607. PMID 18612393 DOI: 10.1371/Journal.Pone.0002607  1
2008 Pincus D, Letunic I, Bork P, Lim WA. Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages. Proceedings of the National Academy of Sciences of the United States of America. 105: 9680-4. PMID 18599463 DOI: 10.1073/Pnas.0803161105  1
2008 Jensen LJ, de Lichtenberg U, Jensen TS, Brunak S, Bork P. Circular reasoning rather than cyclic expression. Genome Biology. 9: 403. PMID 18598377 DOI: 10.1186/Gb-2008-9-6-403  1
2008 Raes J, Bork P. Molecular eco-systems biology: towards an understanding of community function. Nature Reviews. Microbiology. 6: 693-9. PMID 18587409 DOI: 10.1038/Nrmicro1935  1
2008 Kunin V, Raes J, Harris JK, Spear JR, Walker JJ, Ivanova N, von Mering C, Bebout BM, Pace NR, Bork P, Hugenholtz P. Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Molecular Systems Biology. 4: 198. PMID 18523433 DOI: 10.1038/Msb.2008.35  1
2008 Okuda S, Yamada T, Hamajima M, Itoh M, Katayama T, Bork P, Goto S, Kanehisa M. KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Research. 36: W423-6. PMID 18477636 DOI: 10.1093/Nar/Gkn282  1
2008 Soldà G, Suyama M, Pelucchi P, Boi S, Guffanti A, Rizzi E, Bork P, Tenchini ML, Ciccarelli FD. Non-random retention of protein-coding overlapping genes in Metazoa. Bmc Genomics. 9: 174. PMID 18416813 DOI: 10.1186/1471-2164-9-174  1
2008 Richards S, Gibbs RA, Weinstock GM, Brown SJ, Denell R, Beeman RW, Gibbs R, Beeman RW, Brown SJ, Bucher G, Friedrich M, Grimmelikhuijzen CJ, Klingler M, Lorenzen M, ... ... Bork P, ... ... Bork P, et al. The genome of the model beetle and pest Tribolium castaneum. Nature. 452: 949-55. PMID 18362917 DOI: 10.1038/Nature06784  0.64
2008 Harrington ED, Jensen LJ, Bork P. Predicting biological networks from genomic data. Febs Letters. 582: 1251-8. PMID 18294967 DOI: 10.1016/J.Febslet.2008.02.033  1
2008 Kuhn M, Campillos M, González P, Jensen LJ, Bork P. Large-scale prediction of drug-target relationships. Febs Letters. 582: 1283-90. PMID 18291108 DOI: 10.1016/J.Febslet.2008.02.024  1
2008 Letunic I, Yamada T, Kanehisa M, Bork P. iPath: interactive exploration of biochemical pathways and networks. Trends in Biochemical Sciences. 33: 101-3. PMID 18276143 DOI: 10.1016/J.Tibs.2008.01.001  1
2008 King N, Westbrook MJ, Young SL, Kuo A, Abedin M, Chapman J, Fairclough S, Hellsten U, Isogai Y, Letunic I, Marr M, Pincus D, Putnam N, Rokas A, Wright KJ, ... ... Bork P, et al. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature. 451: 783-8. PMID 18273011 DOI: 10.1038/Nature06617  1
2008 Kuhn M, von Mering C, Campillos M, Jensen LJ, Bork P. STITCH: interaction networks of chemicals and proteins. Nucleic Acids Research. 36: D684-8. PMID 18084021 DOI: 10.1093/Nar/Gkm795  1
2008 Shah PK, Tripathi LP, Jensen LJ, Gahnim M, Mason C, Furlong EE, Rodrigues V, White KP, Bork P, Sowdhamini R. Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families. Gene. 407: 199-215. PMID 17996400 DOI: 10.1016/J.Gene.2007.10.012  1
2008 Linding R, Jensen LJ, Pasculescu A, Olhovsky M, Colwill K, Bork P, Yaffe MB, Pawson T. NetworKIN: a resource for exploring cellular phosphorylation networks. Nucleic Acids Research. 36: D695-9. PMID 17981841 DOI: 10.1093/Nar/Gkm902  1
2008 Günther S, Kuhn M, Dunkel M, Campillos M, Senger C, Petsalaki E, Ahmed J, Urdiales EG, Gewiess A, Jensen LJ, Schneider R, Skoblo R, Russell RB, Bourne PE, Bork P, et al. SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Research. 36: D919-22. PMID 17942422 DOI: 10.1093/Nar/Gkm862  1
2008 Jensen LJ, Julien P, Kuhn M, von Mering C, Muller J, Doerks T, Bork P. eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Research. 36: D250-4. PMID 17942413 DOI: 10.1093/Nar/Gkm796  1
2008 Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong EE, Wittbrodt J, Henrich T. 4DXpress: a database for cross-species expression pattern comparisons. Nucleic Acids Research. 36: D847-53. PMID 17916571 DOI: 10.1093/Nar/Gkm797  1
2008 Jensen LJ, Lichtenberg Ud, Jensen TS, Brunak S, Bork P. Just-in-time assembly of cell-cycle protein complexes Nature Precedings. DOI: 10.1038/Npre.2008.2273.1  0.96
2008 Jensen LJ, Kuhn M, Stark M, Chaffron S, Mering Cv, Bork P. STRING and STITCH: known and predicted interactions between proteins and chemicals Nature Precedings. 3: 1-1. DOI: 10.1038/Npre.2008.2265.1  0.96
2008 Frishman D, Albrecht M, Blankenburg H, Bork P, Harrington ED, Hermjakob H, Juhl Jensen L, Juan DA, Lengauer T, Pagel P, Schachter V, Valencia A. Protein-protein interactions: Analysis and prediction Modern Genome Annotation: the Biosapiens Network. 353-410. DOI: 10.1007/978-3-211-75123-7_17  1
2008 Yeats C, Orengo C, Veuthey AL, Boeckmann B, Jensen LJ, Valencia A, Rausell A, Bork P. Modern genome annotation: The BioSapiens network Modern Genome Annotation: the Biosapiens Network. 213-238. DOI: 10.1007/978-3-211-75123-7_11  1
2008 Haudry Y, Ong CK, Ettwiller L, Berube H, Letunic I, Kapushesky M, Weeber PD, Wang X, Gagneur J, Girardot C, Arendt D, Bork P, Brazma A, Furlong E, Wittbrodt J, et al. Comparing and analysing gene expression patterns across animal species using 4DXpress Series On Advances in Bioinformatics and Computational Biology. 6: 373-382.  1
2007 Sorek R, Zhu Y, Creevey CJ, Francino MP, Bork P, Rubin EM. Genome-wide experimental determination of barriers to horizontal gene transfer. Science (New York, N.Y.). 318: 1449-52. PMID 17947550 DOI: 10.1126/Science.1147112  1
2007 Raes J, Foerstner KU, Bork P. Get the most out of your metagenome: computational analysis of environmental sequence data. Current Opinion in Microbiology. 10: 490-8. PMID 17936679 DOI: 10.1016/J.Mib.2007.09.001  1
2007 Eulalio A, Rehwinkel J, Stricker M, Huntzinger E, Yang SF, Doerks T, Dorner S, Bork P, Boutros M, Izaurralde E. Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing. Genes & Development. 21: 2558-70. PMID 17901217 DOI: 10.1101/Gad.443107  1
2007 Harrington ED, Singh AH, Doerks T, Letunic I, von Mering C, Jensen LJ, Raes J, Bork P. Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Proceedings of the National Academy of Sciences of the United States of America. 104: 13913-8. PMID 17717083 DOI: 10.1073/Pnas.0702636104  1
2007 de Lichtenberg U, Jensen TS, Brunak S, Bork P, Jensen LJ. Evolution of cell cycle control: same molecular machines, different regulation. Cell Cycle (Georgetown, Tex.). 6: 1819-25. PMID 17671420 DOI: 10.4161/Cc.6.15.4537  1
2007 Raes J, Harrington ED, Singh AH, Bork P. Protein function space: viewing the limits or limited by our view? Current Opinion in Structural Biology. 17: 362-9. PMID 17574832 DOI: 10.1016/J.Sbi.2007.05.010  1
2007 Linding R, Jensen LJ, Ostheimer GJ, van Vugt MA, Jørgensen C, Miron IM, Diella F, Colwill K, Taylor L, Elder K, Metalnikov P, Nguyen V, Pasculescu A, Jin J, Park JG, ... ... Bork P, et al. Systematic discovery of in vivo phosphorylation networks. Cell. 129: 1415-26. PMID 17570479 DOI: 10.1016/J.Cell.2007.05.052  1
2007 Perez-Iratxeta C, Bork P, Andrade-Navarro MA. Update of the G2D tool for prioritization of gene candidates to inherited diseases. Nucleic Acids Research. 35: W212-6. PMID 17478516 DOI: 10.1093/nar/gkm223  1
2007 Pachkov M, Dandekar T, Korbel J, Bork P, Schuster S. Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism. Gene. 396: 215-25. PMID 17467928 DOI: 10.1016/J.Gene.2007.02.033  1
2007 Danckwardt S, Kaufmann I, Gentzel M, Foerstner KU, Gantzert AS, Gehring NH, Neu-Yilik G, Bork P, Keller W, Wilm M, Hentze MW, Kulozik AE. Splicing factors stimulate polyadenylation via USEs at non-canonical 3' end formation signals. The Embo Journal. 26: 2658-69. PMID 17464285 DOI: 10.1038/Sj.Emboj.7601699  1
2007 Boettner M, Steffens C, von Mering C, Bork P, Stahl U, Lang C. Sequence-based factors influencing the expression of heterologous genes in the yeast Pichia pastoris--A comparative view on 79 human genes. Journal of Biotechnology. 130: 1-10. PMID 17389146 DOI: 10.1016/J.Jbiotec.2007.02.019  1
2007 von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N, Bork P. Quantitative phylogenetic assessment of microbial communities in diverse environments. Science (New York, N.Y.). 315: 1126-30. PMID 17272687 DOI: 10.1126/Science.1133420  1
2007 Hooper SD, Boué S, Krause R, Jensen LJ, Mason CE, Ghanim M, White KP, Furlong EE, Bork P. Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis. Molecular Systems Biology. 3: 72. PMID 17224916 DOI: 10.1038/Msb4100112  1
2007 Raes J, Korbel JO, Lercher MJ, von Mering C, Bork P. Prediction of effective genome size in metagenomic samples. Genome Biology. 8: R10. PMID 17224063 DOI: 10.1186/Gb-2007-8-1-R10  1
2007 Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, et al. New developments in the InterPro database. Nucleic Acids Research. 35: D224-8. PMID 17202162 DOI: 10.1093/Nar/Gkl841  1
2007 von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Krüger B, Snel B, Bork P. STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Research. 35: D358-62. PMID 17098935 DOI: 10.1093/Nar/Gkl825  1
2007 Zdobnov EM, Bork P. Quantification of insect genome divergence. Trends in Genetics : Tig. 23: 16-20. PMID 17097187 DOI: 10.1016/J.Tig.2006.10.004  1
2007 Letunic I, Bork P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics (Oxford, England). 23: 127-8. PMID 17050570 DOI: 10.1093/Bioinformatics/Btl529  1
2006 . Insights into social insects from the genome of the honeybee Apis mellifera. Nature. 443: 931-49. PMID 17073008 DOI: 10.1038/Nature05260  1
2006 Raible F, Tessmar-Raible K, Arboleda E, Kaller T, Bork P, Arendt D, Arnone MI. Opsins and clusters of sensory G-protein-coupled receptors in the sea urchin genome. Developmental Biology. 300: 461-75. PMID 17067569 DOI: 10.1016/J.Ydbio.2006.08.070  1
2006 Perocchi F, Jensen LJ, Gagneur J, Ahting U, von Mering C, Bork P, Prokisch H, Steinmetz LM. Assessing systems properties of yeast mitochondria through an interaction map of the organelle. Plos Genetics. 2: e170. PMID 17054397 DOI: 10.1371/Journal.Pgen.0020170  1
2006 Jensen LJ, Jensen TS, de Lichtenberg U, Brunak S, Bork P. Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature. 443: 594-7. PMID 17006448 DOI: 10.1038/Nature05186  1
2006 Campillos M, Doerks T, Shah PK, Bork P. Computational characterization of multiple Gag-like human proteins. Trends in Genetics : Tig. 22: 585-9. PMID 16979784 DOI: 10.1016/J.Tig.2006.09.006  1
2006 Suyama M, Harrington E, Bork P, Torrents D. Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes. Plos Computational Biology. 2: e76. PMID 16846249 DOI: 10.1371/Journal.Pcbi.0020076  1
2006 Suyama M, Torrents D, Bork P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Research. 34: W609-12. PMID 16845082 DOI: 10.1093/Nar/Gkl315  1
2006 Behm-Ansmant I, Rehwinkel J, Doerks T, Stark A, Bork P, Izaurralde E. mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Genes & Development. 20: 1885-98. PMID 16815998 DOI: 10.1101/Gad.1424106  1
2006 Sandmann T, Jensen LJ, Jakobsen JS, Karzynski MM, Eichenlaub MP, Bork P, Furlong EE. A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development. Developmental Cell. 10: 797-807. PMID 16740481 DOI: 10.1016/J.Devcel.2006.04.009  0.96
2006 Foerstner KU, von Mering C, Bork P. Comparative analysis of environmental sequences: potential and challenges. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 361: 519-23. PMID 16524840 DOI: 10.1098/Rstb.2005.1809  1
2006 Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. Toward automatic reconstruction of a highly resolved tree of life. Science (New York, N.Y.). 311: 1283-7. PMID 16513982 DOI: 10.1126/Science.1123061  1
2006 Yanai I, Korbel JO, Boue S, McWeeney SK, Bork P, Lercher MJ. Similar gene expression profiles do not imply similar tissue functions. Trends in Genetics : Tig. 22: 132-8. PMID 16480787 DOI: 10.1016/J.Tig.2006.01.006  1
2006 Campillos M, von Mering C, Jensen LJ, Bork P. Identification and analysis of evolutionarily cohesive functional modules in protein networks. Genome Research. 16: 374-82. PMID 16449501 DOI: 10.1101/Gr.4336406  1
2006 Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dümpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, ... ... Bork P, et al. Proteome survey reveals modularity of the yeast cell machinery. Nature. 440: 631-6. PMID 16429126 DOI: 10.1038/Nature04532  1
2006 Jensen LJ, Saric J, Bork P. Literature mining for the biologist: from information retrieval to biological discovery. Nature Reviews. Genetics. 7: 119-29. PMID 16418747 DOI: 10.1038/Nrg1768  0.96
2006 Shah PK, Bork P. LSAT: learning about alternative transcripts in MEDLINE. Bioinformatics (Oxford, England). 22: 857-65. PMID 16410322 DOI: 10.1093/Bioinformatics/Btk044  1
2006 Letunic I, Copley RR, Pils B, Pinkert S, Schultz J, Bork P. SMART 5: domains in the context of genomes and networks. Nucleic Acids Research. 34: D257-60. PMID 16381859 DOI: 10.1093/Nar/Gkj079  1
2006 Saric J, Jensen LJ, Ouzounova R, Rojas I, Bork P. Extraction of regulatory gene/protein networks from Medline. Bioinformatics (Oxford, England). 22: 645-50. PMID 16046493 DOI: 10.1093/Bioinformatics/Bti597  0.96
2005 Raible F, Tessmar-Raible K, Osoegawa K, Wincker P, Jubin C, Balavoine G, Ferrier D, Benes V, de Jong P, Weissenbach J, Bork P, Arendt D. Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii. Science (New York, N.Y.). 310: 1325-6. PMID 16311335 DOI: 10.1126/Science.1119089  1
2005 Taxis C, Keller P, Kavagiou Z, Jensen LJ, Colombelli J, Bork P, Stelzer EH, Knop M. Spore number control and breeding in Saccharomyces cerevisiae: a key role for a self-organizing system. The Journal of Cell Biology. 171: 627-40. PMID 16286509 DOI: 10.1083/Jcb.200507168  1
2005 Foerstner KU, von Mering C, Hooper SD, Bork P. Environments shape the nucleotide composition of genomes. Embo Reports. 6: 1208-13. PMID 16200051 DOI: 10.1038/Sj.Embor.7400538  1
2005 Rehwinkel J, Letunic I, Raes J, Bork P, Izaurralde E. Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets. Rna (New York, N.Y.). 11: 1530-44. PMID 16199763 DOI: 10.1261/Rna.2160905  1
2005 Hooper SD, Bork P. Medusa: a simple tool for interaction graph analysis. Bioinformatics (Oxford, England). 21: 4432-3. PMID 16188923 DOI: 10.1093/Bioinformatics/Bti696  1
2005 Suyama M, Lathe WC, Bork P. Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii. Febs Letters. 579: 5281-6. PMID 16182294 DOI: 10.1016/J.Febslet.2005.08.051  1
2005 Mikkelsen TS, Hillier LW, Eichler EE, Zody MC, Jaffe DB, Yang S, Enard W, Hellmann I, Lindblad-Toh K, Altheide TK, Archidiacono N, Bork P, Butler J, Chang JL, Cheng Z, et al. Initial sequence of the chimpanzee genome and comparison with the human genome Nature. 437: 69-87. PMID 16136131 DOI: 10.1038/Nature04072  1
2005 Perez-Iratxeta C, Wjst M, Bork P, Andrade MA. G2D: a tool for mining genes associated with disease. Bmc Genetics. 6: 45. PMID 16115313 DOI: 10.1186/1471-2156-6-45  1
2005 Shah PK, Jensen LJ, Boué S, Bork P. Extraction of transcript diversity from scientific literature. Plos Computational Biology. 1: e10. PMID 16103899 DOI: 10.1371/Journal.Pcbi.0010010  1
2005 Mees A, Rock R, Ciccarelli FD, Leberfinger CB, Borawski JM, Bork P, Wiese S, Gessler M, Kerkhoff E. Very-KIND is a novel nervous system specific guanine nucleotide exchange factor for Ras GTPases. Gene Expression Patterns : Gep. 6: 79-85. PMID 16099729 DOI: 10.1016/J.Modgep.2005.04.015  1
2005 Tenhaken R, Doerks T, Bork P. DCD - a novel plant specific domain in proteins involved in development and programmed cell death. Bmc Bioinformatics. 6: 169. PMID 16008837 DOI: 10.1186/1471-2105-6-169  1
2005 Büssow K, Scheich C, Sievert V, Harttig U, Schultz J, Simon B, Bork P, Lehrach H, Heinemann U. Structural genomics of human proteins--target selection and generation of a public catalogue of expression clones. Microbial Cell Factories. 4: 21. PMID 15998469 DOI: 10.1186/1475-2859-4-21  0.72
2005 Zdobnov EM, von Mering C, Letunic I, Bork P. Consistency of genome-based methods in measuring Metazoan evolution. Febs Letters. 579: 3355-61. PMID 15943981 DOI: 10.1016/J.Febslet.2005.04.006  1
2005 Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM. Comparative metagenomics of microbial communities. Science (New York, N.Y.). 308: 554-7. PMID 15845853 DOI: 10.1126/Science.1107851  1
2005 Shah PK, Aloy P, Bork P, Russell RB. Structural similarity to bridge sequence space: finding new families on the bridges. Protein Science : a Publication of the Protein Society. 14: 1305-14. PMID 15840833 DOI: 10.1110/Ps.041187405  1
2005 Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D, Wylie K, Sekhon M, Becker MC, Fewell GA, Delehaunty KD, Miner TL, Nash WE, ... ... Bork P, et al. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature. 434: 724-31. PMID 15815621 DOI: 10.1038/Nature03466  1
2005 Korbel JO, Doerks T, Jensen LJ, Perez-Iratxeta C, Kaczanowski S, Hooper SD, Andrade MA, Bork P. Systematic association of genes to phenotypes by genome and literature mining. Plos Biology. 3: e134. PMID 15799710 DOI: 10.1371/Journal.Pbio.0030134  1
2005 Zdobnov EM, Campillos M, Harrington ED, Torrents D, Bork P. Protein coding potential of retroviruses and other transposable elements in vertebrate genomes. Nucleic Acids Research. 33: 946-54. PMID 15716312 DOI: 10.1093/Nar/Gki236  1
2005 Ciccarelli FD, von Mering C, Suyama M, Harrington ED, Izaurralde E, Bork P. Complex genomic rearrangements lead to novel primate gene function. Genome Research. 15: 343-51. PMID 15710750 DOI: 10.1101/Gr.3266405  1
2005 de Lichtenberg U, Jensen LJ, Brunak S, Bork P. Dynamic complex formation during the yeast cell cycle. Science (New York, N.Y.). 307: 724-7. PMID 15692050 DOI: 10.1126/Science.1105103  1
2005 von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA, Bork P. STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Research. 33: D433-7. PMID 15608232 DOI: 10.1093/Nar/Gki005  1
2005 Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, et al. InterPro, progress and status in 2005. Nucleic Acids Research. 33: D201-5. PMID 15608177 DOI: 10.1093/Nar/Gki106  1
2005 Ciccarelli FD, Bork P. The WHy domain mediates the response to desiccation in plants and bacteria. Bioinformatics (Oxford, England). 21: 1304-7. PMID 15598830 DOI: 10.1093/Bioinformatics/Bti221  1
2005 Bourque G, Zdobnov EM, Bork P, Pevzner PA, Tesler G. Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Research. 15: 98-110. PMID 15590940 DOI: 10.1101/Gr.3002305  1
2005 de Lichtenberg U, Jensen LJ, Fausbøll A, Jensen TS, Bork P, Brunak S. Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics (Oxford, England). 21: 1164-71. PMID 15513999 DOI: 10.1093/Bioinformatics/Bti093  1
2004 Koehl A, Schmidt N, Rieger A, Pilgram SM, Letunic I, Bork P, Soto F, Friauf E, Nothwang HG. Gene expression profiling of the rat superior olivary complex using serial analysis of gene expression. The European Journal of Neuroscience. 20: 3244-58. PMID 15610157 DOI: 10.1111/J.1460-9568.2004.03791.X  1
2004 . Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 432: 695-716. PMID 15592404 DOI: 10.1038/Nature03154  1
2004 Doerks T, von Mering C, Bork P. Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes. Nucleic Acids Research. 32: 6321-6. PMID 15576358 DOI: 10.1093/Nar/Gkh973  1
2004 Krause R, von Mering C, Bork P, Dandekar T. Shared components of protein complexes--versatile building blocks or biochemical artefacts? Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 26: 1333-43. PMID 15551274 DOI: 10.1002/Bies.20141  1
2004 Liska AJ, Popov AV, Sunyaev S, Coughlin P, Habermann B, Shevchenko A, Bork P, Karsenti E, Shevchenko A. Homology-based functional proteomics by mass spectrometry: application to the Xenopus microtubule-associated proteome. Proteomics. 4: 2707-21. PMID 15352245 DOI: 10.1002/Pmic.200300813  1
2004 Korbel JO, Jensen LJ, von Mering C, Bork P. Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs. Nature Biotechnology. 22: 911-7. PMID 15229555 DOI: 10.1038/Nbt988  1
2004 Jensen LJ, Lagarde J, von Mering C, Bork P. ArrayProspector: a web resource of functional associations inferred from microarray expression data. Nucleic Acids Research. 32: W445-8. PMID 15215427 DOI: 10.1093/Nar/Gkh407  1
2004 Bork P, Jensen LJ, von Mering C, Ramani AK, Lee I, Marcotte EM. Protein interaction networks from yeast to human. Current Opinion in Structural Biology. 14: 292-9. PMID 15193308 DOI: 10.1016/J.Sbi.2004.05.003  1
2004 Pérez AJ, Perez-Iratxeta C, Bork P, Thode G, Andrade MA. Gene annotation from scientific literature using mappings between keyword systems. Bioinformatics (Oxford, England). 20: 2084-91. PMID 15059832 DOI: 10.1093/Bioinformatics/Bth207  1
2004 Doerks T, Andrade MA, Lathe W, von Mering C, Bork P. Global analysis of bacterial transcription factors to predict cellular target processes. Trends in Genetics : Tig. 20: 126-31. PMID 15049306 DOI: 10.1016/J.Tig.2004.01.006  1
2004 Aloy P, Böttcher B, Ceulemans H, Leutwein C, Mellwig C, Fischer S, Gavin AC, Bork P, Superti-Furga G, Serrano L, Russell RB. Structure-based assembly of protein complexes in yeast. Science (New York, N.Y.). 303: 2026-9. PMID 15044803 DOI: 10.1126/Science.1092645  1
2004 Suyama M, Torrents D, Bork P. BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments. Bioinformatics (Oxford, England). 20: 1968-70. PMID 15037510 DOI: 10.1093/Bioinformatics/Bth172  1
2004 Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, ... ... Bork P, et al. The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nature Biotechnology. 22: 177-83. PMID 14755292 DOI: 10.1038/Nbt926  1
2004 Crass T, Antes I, Basekow R, Bork P, Buning C, Christensen M, Claussen H, Ebeling C, Ernst P, Gailus-Durner V, Glatting KH, Gohla R, Gössling F, Grote K, Heidtke K, et al. The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. Bioinformatics (Oxford, England). 20: 268-70. PMID 14734319 DOI: 10.1093/Bioinformatics/Btg398  1
2004 Forler D, Rabut G, Ciccarelli FD, Herold A, Köcher T, Niggeweg R, Bork P, Ellenberg J, Izaurralde E. RanBP2/Nup358 provides a major binding site for NXF1-p15 dimers at the nuclear pore complex and functions in nuclear mRNA export. Molecular and Cellular Biology. 24: 1155-67. PMID 14729961 DOI: 10.1128/Mcb.24.3.1155-1167.2004  1
2004 Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP, Bork P. SMART 4.0: towards genomic data integration. Nucleic Acids Research. 32: D142-4. PMID 14681379 DOI: 10.1093/Nar/Gkh088  1
2003 Waterston RH, Hillier LW, Fulton LA, Fulton RS, Graves TA, Pepin KH, Bork P, Suyama M, Torrents D, Chinwalla AT, Mardis ER, McPherson JD, Wilson RK. The human genome: genes, pseudogenes, and variation on chromosome 7. Cold Spring Harbor Symposia On Quantitative Biology. 68: 13-22. PMID 15338598 DOI: 10.1101/Sqb.2003.68.13  1
2003 Perez-Iratxeta C, Astola N, Ciccarelli FD, Sha PK, Bork P, Andrade MA. A protocol for the update of references to scientific literature in biological databases. Applied Bioinformatics. 2: 189-91. PMID 15130808  1
2003 Ciccarelli FD, Izaurralde E, Bork P. The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold. Bmc Bioinformatics. 4: 64. PMID 14687415 DOI: 10.1186/1471-2105-4-64  1
2003 von Mering C, Zdobnov EM, Tsoka S, Ciccarelli FD, Pereira-Leal JB, Ouzounis CA, Bork P. Genome evolution reveals biochemical networks and functional modules. Proceedings of the National Academy of Sciences of the United States of America. 100: 15428-33. PMID 14673105 DOI: 10.1073/Pnas.2136809100  1
2003 Torrents D, Suyama M, Zdobnov E, Bork P. A genome-wide survey of human pseudogenes. Genome Research. 13: 2559-67. PMID 14656963 DOI: 10.1101/Gr.1455503  1
2003 Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB. Protein disorder prediction: implications for structural proteomics. Structure (London, England : 1993). 11: 1453-9. PMID 14604535 DOI: 10.1016/J.Str.2003.10.002  1
2003 Boue S, Letunic I, Bork P. Alternative splicing and evolution. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 25: 1031-4. PMID 14579243 DOI: 10.1002/Bies.10371  1
2003 Sunyaev S, Kondrashov FA, Bork P, Ramensky V. Impact of selection, mutation rate and genetic drift on human genetic variation. Human Molecular Genetics. 12: 3325-30. PMID 14570704 DOI: 10.1093/Hmg/Ddg359  1
2003 Krause R, von Mering C, Bork P. A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens. Bioinformatics (Oxford, England). 19: 1901-8. PMID 14555622 DOI: 10.1093/Bioinformatics/Btg344  1
2003 Gatfield D, Unterholzner L, Ciccarelli FD, Bork P, Izaurralde E. Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways. The Embo Journal. 22: 3960-70. PMID 12881430 DOI: 10.1093/Emboj/Cdg371  1
2003 Ciccarelli FD, Bork P, Kerkhoff E. The KIND module: a putative signalling domain evolved from the C lobe of the protein kinase fold. Trends in Biochemical Sciences. 28: 349-52. PMID 12877999 DOI: 10.1016/S0968-0004(03)00116-6  1
2003 Schmidt S, Sunyaev S, Bork P, Dandekar T. Metabolites: a helping hand for pathway evolution? Trends in Biochemical Sciences. 28: 336-41. PMID 12826406 DOI: 10.1016/S0968-0004(03)00114-2  1
2003 Perez-Iratxeta C, Pérez AJ, Bork P, Andrade MA. Update on XplorMed: A web server for exploring scientific literature. Nucleic Acids Research. 31: 3866-8. PMID 12824439 DOI: 10.1093/Nar/Gkg538  1
2003 Puntervoll P, Linding R, Gemünd C, Chabanis-Davidson S, Mattingsdal M, Cameron S, Martin DM, Ausiello G, Brannetti B, Costantini A, Ferrè F, Maselli V, Via A, Cesareni G, Diella F, ... ... Bork P, et al. ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Research. 31: 3625-30. PMID 12824381 DOI: 10.1093/Nar/Gkg545  1
2003 Morett E, Korbel JO, Rajan E, Saab-Rincon G, Olvera L, Olvera M, Schmidt S, Snel B, Bork P. Systematic discovery of analogous enzymes in thiamin biosynthesis. Nature Biotechnology. 21: 790-5. PMID 12794638 DOI: 10.1038/Nbt834  1
2003 Shah PK, Perez-Iratxeta C, Bork P, Andrade MA. Information extraction from full text scientific articles: where are the keywords? Bmc Bioinformatics. 4: 20. PMID 12775220 DOI: 10.1186/1471-2105-4-20  1
2003 Netzel R, Perez-Iratxeta C, Bork P, Andrade MA. The way we write. Embo Reports. 4: 446-51. PMID 12728240 DOI: 10.1038/Sj.Embor.Embor833  1
2003 Woerner SM, Benner A, Sutter C, Schiller M, Yuan YP, Keller G, Bork P, Doeberitz Mv, Gebert JF. Pathogenesis of DNA repair-deficient cancers: a statistical meta-analysis of putative Real Common Target genes. Oncogene. 22: 2226-35. PMID 12700659 DOI: 10.1038/Sj.Onc.1206421  1
2003 Ciccarelli FD, Proukakis C, Patel H, Cross H, Azam S, Patton MA, Bork P, Crosby AH. The identification of a conserved domain in both spartin and spastin, mutated in hereditary spastic paraplegia. Genomics. 81: 437-41. PMID 12676568 DOI: 10.1016/S0888-7543(03)00011-9  1
2003 Huynen MA, Snel B, von Mering C, Bork P. Function prediction and protein networks. Current Opinion in Cell Biology. 15: 191-8. PMID 12648675 DOI: 10.1016/S0955-0674(03)00009-7  1
2003 Kriventseva EV, Koch I, Apweiler R, Vingron M, Bork P, Gelfand MS, Sunyaev S. Increase of functional diversity by alternative splicing. Trends in Genetics : Tig. 19: 124-8. PMID 12615003 DOI: 10.1016/S0168-9525(03)00023-4  1
2003 Kanehisa M, Bork P. Bioinformatics in the post-sequence era. Nature Genetics. 33: 305-10. PMID 12610540 DOI: 10.1038/Ng1109  1
2003 Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley RR, Courcelle E, Das U, Durbin R, et al. The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Research. 31: 315-8. PMID 12520011 DOI: 10.1093/Nar/Gkg046  1
2003 von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B. STRING: a database of predicted functional associations between proteins. Nucleic Acids Research. 31: 258-61. PMID 12519996 DOI: 10.1093/Nar/Gkg034  1
2003 Shevchenko A, Sunyaev S, Liska A, Bork P, Shevchenko A. Nanoelectrospray tandem mass spectrometry and sequence similarity searching for identification of proteins from organisms with unknown genomes. Methods in Molecular Biology (Clifton, N.J.). 211: 221-34. PMID 12489434 DOI: 10.1385/1-59259-342-9:221  1
2002 Perez-Iratxeta C, Bork P, Andrade MA. Exploring MEDLINE abstracts with XplorMed. Drugs of Today (Barcelona, Spain : 1998). 38: 381-9. PMID 12532176 DOI: 10.1358/Dot.2002.38.6.678344  1
2002 Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, ... ... Bork P, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420: 520-62. PMID 12466850 DOI: 10.1038/Nature01262  1
2002 Copley RR, Ponting CP, Schultz J, Bork P. Sequence analysis of multidomain proteins: past perspectives and future directions. Advances in Protein Chemistry. 61: 75-98. PMID 12461821 DOI: 10.1016/S0065-3233(02)61002-2  1
2002 Kloor M, Bork P, Duwe A, Klaes R, von Knebel Doeberitz M, Ridder R. Identification and characterization of UEV3, a human cDNA with similarities to inactive E2 ubiquitin-conjugating enzymes. Biochimica Et Biophysica Acta. 1579: 219-24. PMID 12427560 DOI: 10.1016/S0167-4781(02)00543-2  0.32
2002 Schell MA, Karmirantzou M, Snel B, Vilanova D, Berger B, Pessi G, Zwahlen MC, Desiere F, Bork P, Delley M, Pridmore RD, Arigoni F. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proceedings of the National Academy of Sciences of the United States of America. 99: 14422-7. PMID 12381787 DOI: 10.1073/Pnas.212527599  1
2002 Christophides GK, Zdobnov E, Barillas-Mury C, Birney E, Blandin S, Blass C, Brey PT, Collins FH, Danielli A, Dimopoulos G, Hetru C, Hoa NT, Hoffmann JA, Kanzok SM, Letunic I, ... ... Bork P, et al. Immunity-related genes and gene families in Anopheles gambiae. Science (New York, N.Y.). 298: 159-65. PMID 12364793 DOI: 10.1126/Science.1077136  1
2002 Zdobnov EM, von Mering C, Letunic I, Torrents D, Suyama M, Copley RR, Christophides GK, Thomasova D, Holt RA, Subramanian GM, Mueller HM, Dimopoulos G, Law JH, Wells MA, Birney E, ... ... Bork P, et al. Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (New York, N.Y.). 298: 149-59. PMID 12364792 DOI: 10.1126/Science.1077061  1
2002 Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, ... ... Bork P, et al. The genome sequence of the malaria mosquito Anopheles gambiae. Science (New York, N.Y.). 298: 129-49. PMID 12364791 DOI: 10.1126/Science.1076181  1
2002 Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley R, Courcelle E, Durbin R, Falquet L, Fleischmann W, et al. InterPro: an integrated documentation resource for protein families, domains and functional sites. Briefings in Bioinformatics. 3: 225-35. PMID 12230031 DOI: 10.1093/Bib/3.3.225  1
2002 Andrade MA, Ciccarelli FD, Perez-Iratxeta C, Bork P. NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria. Genome Biology. 3: RESEARCH0047. PMID 12225586 DOI: 10.1186/Gb-2002-3-9-Research0047  1
2002 Ramensky V, Bork P, Sunyaev S. Human non-synonymous SNPs: server and survey. Nucleic Acids Research. 30: 3894-900. PMID 12202775 DOI: 10.1093/Nar/Gkf493  0.44
2002 Mott R, Schultz J, Bork P, Ponting CP. Predicting protein cellular localization using a domain projection method. Genome Research. 12: 1168-74. PMID 12176924 DOI: 10.1101/Gr.96802  1
2002 Patel H, Cross H, Proukakis C, Hershberger R, Bork P, Ciccarelli FD, Patton MA, McKusick VA, Crosby AH. SPG20 is mutated in Troyer syndrome, an hereditary spastic paraplegia. Nature Genetics. 31: 347-8. PMID 12134148 DOI: 10.1038/Ng937  1
2002 Aloy P, Ciccarelli FD, Leutwein C, Gavin AC, Superti-Furga G, Bork P, Bottcher B, Russell RB. A complex prediction: three-dimensional model of the yeast exosome. Embo Reports. 3: 628-35. PMID 12101094 DOI: 10.1093/Embo-Reports/Kvf135  1
2002 von Mering C, Bork P. Teamed up for transcription. Nature. 417: 797-8. PMID 12075329 DOI: 10.1038/417797A  1
2002 Perez-Iratxeta C, Keer HS, Bork P, Andrade MA. Computing fuzzy associations for the analysis of biological literature. Biotechniques. 32: 1380-2, 1384-5. PMID 12074170 DOI: 10.2144/02326Bc03  1
2002 Thomasova D, Ton LQ, Copley RR, Zdobnov EM, Wang X, Hong YS, Sim C, Bork P, Kafatos FC, Collins FH. Comparative genomic analysis in the region of a major Plasmodium-refractoriness locus of Anopheles gambiae. Proceedings of the National Academy of Sciences of the United States of America. 99: 8179-84. PMID 12060762 DOI: 10.1073/Pnas.082235599  1
2002 Letunic I, Copley RR, Bork P. Common exon duplication in animals and its role in alternative splicing. Human Molecular Genetics. 11: 1561-7. PMID 12045209 DOI: 10.1093/Hmg/11.13.1561  1
2002 Perez-Iratxeta C, Bork P, Andrade MA. Association of genes to genetically inherited diseases using data mining. Nature Genetics. 31: 316-9. PMID 12006977 DOI: 10.1038/Ng895  1
2002 von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature. 417: 399-403. PMID 12000970 DOI: 10.1038/Nature750  1
2002 Snel B, Bork P, Huynen MA. The identification of functional modules from the genomic association of genes. Proceedings of the National Academy of Sciences of the United States of America. 99: 5890-5. PMID 11983890 DOI: 10.1073/Pnas.092632599  1
2002 Doerks T, Huber S, Buchner E, Bork P. BSD: a novel domain in transcription factors and synapse-associated proteins. Trends in Biochemical Sciences. 27: 168-70. PMID 11943536 DOI: 10.1016/S0968-0004(01)02042-4  1
2002 Copley RR, Doerks T, Letunic I, Bork P. Protein domain analysis in the era of complete genomes. Febs Letters. 513: 129-34. PMID 11911892 DOI: 10.1016/S0014-5793(01)03289-6  1
2002 Schmidt S, Bork P, Dandekar T. A versatile structural domain analysis server using profile weight matrices. Journal of Chemical Information and Computer Sciences. 42: 405-7. PMID 11911710 DOI: 10.1021/Ci010374R  1
2002 Ciccarelli FD, Doerks T, Bork P. AMOP, a protein module alternatively spliced in cancer cells. Trends in Biochemical Sciences. 27: 113-5. PMID 11893501 DOI: 10.1016/S0968-0004(01)02049-7  1
2002 Korbel JO, Snel B, Huynen MA, Bork P. SHOT: a web server for the construction of genome phylogenies. Trends in Genetics : Tig. 18: 158-62. PMID 11858840 DOI: 10.1016/S0168-9525(01)02597-5  1
2002 Ciccarelli FD, Copley RR, Doerks T, Russell RB, Bork P. CASH--a beta-helix domain widespread among carbohydrate-binding proteins. Trends in Biochemical Sciences. 27: 59-62. PMID 11852237 DOI: 10.1016/S0968-0004(01)02046-1  1
2002 Copley RR, Letunic I, Bork P. Genome and protein evolution in eukaryotes. Current Opinion in Chemical Biology. 6: 39-45. PMID 11827821 DOI: 10.1016/S1367-5931(01)00278-2  1
2002 Gavin AC, Bösche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Remor M, Höfert C, Schelder M, Brajenovic M, Ruffner H, ... ... Bork P, et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 415: 141-7. PMID 11805826 DOI: 10.1038/415141A  1
2002 Doerks T, Copley RR, Schultz J, Ponting CP, Bork P. Systematic identification of novel protein domain families associated with nuclear functions. Genome Research. 12: 47-56. PMID 11779830 DOI: 10.1101/Gr.203201  1
2002 Snel B, Bork P, Huynen MA. Genomes in flux: the evolution of archaeal and proteobacterial gene content. Genome Research. 12: 17-25. PMID 11779827 DOI: 10.1101/Gr.176501  1
2002 Fredman D, Siegfried M, Yuan YP, Bork P, Lehväslaiho H, Brookes AJ. HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources. Nucleic Acids Research. 30: 387-91. PMID 11752345 DOI: 10.1093/Nar/30.1.387  1
2002 Letunic I, Goodstadt L, Dickens NJ, Doerks T, Schultz J, Mott R, Ciccarelli F, Copley RR, Ponting CP, Bork P. Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Research. 30: 242-4. PMID 11752305 DOI: 10.1093/Nar/30.1.242  1
2002 Brett D, Pospisil H, Valcárcel J, Reich J, Bork P. Alternative splicing and genome complexity. Nature Genetics. 30: 29-30. PMID 11743582 DOI: 10.1038/Ng803  1
2002 Morett E, Korbel JO, Rajan E, Saab-Rincon G, Olveral L, Olveral M, Schmidt S, Snel B, Bork P. Discovery of Analogous Enzymes in Thiamin Biosynthesis by Anticorrelation Genome Informatics. 13: 365-366. DOI: 10.11234/Gi1990.13.365  1
2001 Iyer LM, Aravind L, Bork P, Hofmann K, Mushegian AR, Zhulin IB, Koonin EV. Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences. Genome Biology. 2: RESEARCH0051. PMID 11790254 DOI: 10.1186/Gb-2001-2-12-Research0051  1
2001 Kerkhoff E, Simpson JC, Leberfinger CB, Otto IM, Doerks T, Bork P, Rapp UR, Raabe T, Pepperkok R. The Spir actin organizers are involved in vesicle transport processes. Current Biology : Cb. 11: 1963-8. PMID 11747823 DOI: 10.1016/S0960-9822(01)00602-9  1
2001 Ponting CP, Mott R, Bork P, Copley RR. Novel protein domains and repeats in Drosophila melanogaster: insights into structure, function, and evolution. Genome Research. 11: 1996-2008. PMID 11731489 DOI: 10.1101/Gr.198701  1
2001 Huynen MA, Snel B, Bork P, Gibson TJ. The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly. Human Molecular Genetics. 10: 2463-8. PMID 11689493 DOI: 10.1093/Hmg/10.21.2463  1
2001 Lathe WC, Bork P. Evolution of tuf genes: ancient duplication, differential loss and gene conversion. Febs Letters. 502: 113-6. PMID 11583110 DOI: 10.1016/S0014-5793(01)02639-4  1
2001 Perez-Iratxeta C, Bork P, Andrade MA. XplorMed: a tool for exploring MEDLINE abstracts. Trends in Biochemical Sciences. 26: 573-5. PMID 11551795 DOI: 10.1016/S0968-0004(01)01926-0  1
2001 Andrade MA, Petosa C, O'Donoghue SI, Müller CW, Bork P. Comparison of ARM and HEAT protein repeats. Journal of Molecular Biology. 309: 1-18. PMID 11491282 DOI: 10.1006/Jmbi.2001.4624  1
2001 Woerner SM, Gebert J, Yuan YP, Sutter C, Ridder R, Bork P, von Knebel Doeberitz M. Systematic identification of genes with coding microsatellites mutated in DNA mismatch repair-deficient cancer cells. International Journal of Cancer. Journal International Du Cancer. 93: 12-9. PMID 11391615 DOI: 10.1002/Ijc.1299  1
2001 Linnebacher M, Gebert J, Rudy W, Woerner S, Yuan YP, Bork P, von Knebel Doeberitz M. Frameshift peptide-derived T-cell epitopes: a source of novel tumor-specific antigens. International Journal of Cancer. Journal International Du Cancer. 93: 6-11. PMID 11391614 DOI: 10.1002/Ijc.1298  1
2001 Huynen MA, Snel B, Bork P. Inversions and the dynamics of eukaryotic gene order. Trends in Genetics : Tig. 17: 304-6. PMID 11377779 DOI: 10.1016/S0168-9525(01)02302-2  1
2001 Shevchenko A, Sunyaev S, Loboda A, Shevchenko A, Bork P, Ens W, Standing KG. Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching. Analytical Chemistry. 73: 1917-26. PMID 11354471 DOI: 10.1021/AC0013709  0.44
2001 Eisenhaber B, Bork P, Eisenhaber F. Post-translational GPI lipid anchor modification of proteins in kingdoms of life: analysis of protein sequence data from complete genomes. Protein Engineering. 14: 17-25. PMID 11287675 DOI: 10.1093/Protein/14.1.17  1
2001 Doerks T, Copley R, Bork P. DDT -- a novel domain in different transcription and chromosome remodeling factors. Trends in Biochemical Sciences. 26: 145-6. PMID 11246006 DOI: 10.1016/S0968-0004(00)01769-2  1
2001 Bork P, Copley R. Genome speak. Nature. 409: 815. PMID 11241984 DOI: 10.1038/35057269  0.56
2001 Bork P, Copley R. The draft sequences. Filling in the gaps. Nature. 409: 818-20. PMID 11236994 DOI: 10.1038/35057274  1
2001 Sunyaev S, Ramensky V, Koch I, Lathe W, Kondrashov AS, Bork P. Prediction of deleterious human alleles. Human Molecular Genetics. 10: 591-7. PMID 11230178 DOI: 10.1093/Hmg/10.6.591  1
2001 Sunyaev S, Lathe W, Bork P. Integration of genome data and protein structures: prediction of protein folds, protein interactions and "molecular phenotypes" of single nucleotide polymorphisms. Current Opinion in Structural Biology. 11: 125-30. PMID 11179902 DOI: 10.1016/S0959-440X(00)00175-5  1
2001 Becker S, Gehrsitz A, Bork P, Buchner S, Buchner E. The black-pearl gene of Drosophila defines a novel conserved protein family and is required for larval growth and survival. Gene. 262: 15-22. PMID 11179663 DOI: 10.1016/S0378-1119(00)00548-5  1
2001 Schultz J, Jones T, Bork P, Sheer D, Blencke S, Steyrer S, Wellbrock U, Bevec D, Ullrich A, Wallasch C. Molecular characterization of a cDNA encoding functional human CLK4 kinase and localization to chromosome 5q35 [correction of 4q35]. Genomics. 71: 368-70. PMID 11170754 DOI: 10.1006/Geno.2000.6447  1
2001 Suyama M, Bork P. Evolution of prokaryotic gene order: genome rearrangements in closely related species. Trends in Genetics : Tig. 17: 10-3. PMID 11163906 DOI: 10.1016/S0168-9525(00)02159-4  1
2001 Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, Fitzhugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, ... ... Bork P, et al. Erratum: Initial sequencing and analysis of the human genome: International Human Genome Sequencing Consortium (Nature (2001) 409 (860-921)) Nature. 412: 565-566. DOI: 10.1038/35087627  0.96
2000 Suyama M, Doerks T, Braun IC, Sattler M, Izaurralde E, Bork P. Prediction of structural domains of TAP reveals details of its interaction with p15 and nucleoporins. Embo Reports. 1: 53-8. PMID 11256625 DOI: 10.1093/Embo-Reports/Kvd009  1
2000 Gönczy P, Echeverri C, Oegema K, Coulson A, Jones SJ, Copley RR, Duperon J, Oegema J, Brehm M, Cassin E, Hannak E, Kirkham M, Pichler S, Flohrs K, Goessen A, ... ... Bork P, et al. Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature. 408: 331-6. PMID 11099034 DOI: 10.1038/35042526  1
2000 Herold A, Suyama M, Rodrigues JP, Braun IC, Kutay U, Carmo-Fonseca M, Bork P, Izaurralde E. TAP (NXF1) belongs to a multigene family of putative RNA export factors with a conserved modular architecture. Molecular and Cellular Biology. 20: 8996-9008. PMID 11073998 DOI: 10.1128/Mcb.20.23.8996-9008.2000  1
2000 Copley RR, Bork P. Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways. Journal of Molecular Biology. 303: 627-41. PMID 11054297 DOI: 10.1006/Jmbi.2000.4152  1
2000 Doerks T, Strauss M, Brendel M, Bork P. GRAM, a novel domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins. Trends in Biochemical Sciences. 25: 483-5. PMID 11050430 DOI: 10.1016/S0968-0004(00)01664-9  1
2000 Lathe WC, Snel B, Bork P. Gene context conservation of a higher order than operons. Trends in Biochemical Sciences. 25: 474-9. PMID 11050428 DOI: 10.1016/S0968-0004(00)01663-7  1
2000 Sánchez-Pulido L, Yuan YP, Andrade MA, Bork P. NAIL-Network Analysis Interface for Linking HMMER results. Bioinformatics (Oxford, England). 16: 656-7. PMID 11038338 DOI: 10.1093/Bioinformatics/16.7.656  1
2000 Snel B, Lehmann G, Bork P, Huynen MA. STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Research. 28: 3442-4. PMID 10982861 DOI: 10.1093/Nar/28.18.3442  1
2000 Brett D, Lehmann G, Hanke J, Gross S, Reich J, Bork P. EST analysis online: WWW tools for detection of SNPs and alternative splice forms. Trends in Genetics : Tig. 16: 416-8. PMID 10973071 DOI: 10.1016/S0168-9525(00)02089-8  1
2000 Huynen M, Snel B, Lathe W, Bork P. Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Research. 10: 1204-10. PMID 10958638 DOI: 10.1101/Gr.10.8.1204  1
2000 Dandekar T, Huynen M, Regula JT, Ueberle B, Zimmermann CU, Andrade MA, Doerks T, Sánchez-Pulido L, Snel B, Suyama M, Yuan YP, Herrmann R, Bork P. Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames. Nucleic Acids Research. 28: 3278-88. PMID 10954595 DOI: 10.1093/Nar/28.17.3278  1
2000 Sunyaev SR, Lathe WC, Ramensky VE, Bork P. SNP frequencies in human genes an excess of rare alleles and differing modes of selection. Trends in Genetics : Tig. 16: 335-7. PMID 10904261 DOI: 10.1016/S0168-9525(00)02058-8  1
2000 Andrade MA, Bork P. Automated extraction of information in molecular biology. Febs Letters. 476: 12-7. PMID 10878241 DOI: 10.1016/S0014-5793(00)01661-6  1
2000 Eisenhaber B, Bork P, Yuan Y, Löffler G, Eisenhaber F. Automated annotation of GPI anchor sites: case study C. elegans. Trends in Biochemical Sciences. 25: 340-1. PMID 10871885 DOI: 10.1016/S0968-0004(00)01601-7  1
2000 Doerks T, Bork P, Kamberov E, Makarova O, Muecke S, Margolis B. L27, a novel heterodimerization domain in receptor targeting proteins Lin-2 and Lin-7. Trends in Biochemical Sciences. 25: 317-8. PMID 10871881 DOI: 10.1016/S0968-0004(00)01599-1  0.96
2000 Huynen M, Snel B, Lathe W, Bork P. Exploitation of gene context. Current Opinion in Structural Biology. 10: 366-70. PMID 10851194 DOI: 10.1016/S0959-440X(00)00098-1  1
2000 Dimopoulos G, Casavant TL, Chang S, Scheetz T, Roberts C, Donohue M, Schultz J, Benes V, Bork P, Ansorge W, Soares MB, Kafatos FC. Anopheles gambiae pilot gene discovery project: identification of mosquito innate immunity genes from expressed sequence tags generated from immune-competent cell lines. Proceedings of the National Academy of Sciences of the United States of America. 97: 6619-24. PMID 10841561 DOI: 10.1073/Pnas.97.12.6619  1
2000 Schultz J, Doerks T, Ponting CP, Copley RR, Bork P. More than 1,000 putative new human signalling proteins revealed by EST data mining. Nature Genetics. 25: 201-4. PMID 10835637 DOI: 10.1038/76069  1
2000 Sunyaev S, Hanke J, Brett D, Aydin A, Zastrow I, Lathe W, Bork P, Reich J. Individual variation in protein-coding sequences of human genome. Advances in Protein Chemistry. 54: 409-37. PMID 10829234 DOI: 10.1016/S0065-3233(00)54012-1  1
2000 Ponting CP, Schultz J, Copley RR, Andrade MA, Bork P. Evolution of domain families. Advances in Protein Chemistry. 54: 185-244. PMID 10829229 DOI: 10.1016/S0065-3233(00)54007-8  1
2000 Brett D, Hanke J, Lehmann G, Haase S, Delbrück S, Krueger S, Reich J, Bork P. EST comparison indicates 38% of human mRNAs contain possible alternative splice forms. Febs Letters. 474: 83-6. PMID 10828456 DOI: 10.1016/S0014-5793(00)01581-7  1
2000 Stutz F, Bachi A, Doerks T, Braun IC, Séraphin B, Wilm M, Bork P, Izaurralde E. REF, an evolutionary conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export. Rna (New York, N.Y.). 6: 638-50. PMID 10786854 DOI: 10.1017/S1355838200000078  1
2000 Sunyaev S, Ramensky V, Bork P. Towards a structural basis of human non-synonymous single nucleotide polymorphisms. Trends in Genetics : Tig. 16: 198-200. PMID 10782110 DOI: 10.1016/S0168-9525(00)01988-0  0.44
2000 Andrade MA, Ponting CP, Gibson TJ, Bork P. Homology-based method for identification of protein repeats using statistical significance estimates. Journal of Molecular Biology. 298: 521-37. PMID 10772867 DOI: 10.1006/Jmbi.2000.3684  1
2000 Isaksson A, Landegren U, Syvänen AC, Bork P, Stein C, Ortigao F, Brookes AJ. Discovery, scoring and utilization of human single nucleotide polymorphisms: a multidisciplinary problem. European Journal of Human Genetics : Ejhg. 8: 154-6. PMID 10757651 DOI: 10.1038/Sj.Ejhg.5200424  0.4
2000 Otto IM, Raabe T, Rennefahrt UE, Bork P, Rapp UR, Kerkhoff E. The p150-Spir protein provides a link between c-Jun N-terminal kinase function and actin reorganization. Current Biology : Cb. 10: 345-8. PMID 10744979 DOI: 10.1016/S0960-9822(00)00388-2  0.36
2000 Snel B, Bork P, Huynen M. Genome evolution. Gene fusion versus gene fission. Trends in Genetics : Tig. 16: 9-11. PMID 10637623 DOI: 10.1016/S0168-9525(99)01924-1  1
2000 Brookes AJ, Lehväslaiho H, Siegfried M, Boehm JG, Yuan YP, Sarkar CM, Bork P, Ortigao F. HGBASE: a database of SNPs and other variations in and around human genes. Nucleic Acids Research. 28: 356-60. PMID 10592273 DOI: 10.1093/Nar/28.1.356  1
2000 Schultz J, Copley RR, Doerks T, Ponting CP, Bork P. SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Research. 28: 231-4. PMID 10592234 DOI: 10.1093/Nar/28.1.231  1
1999 Copley RR, Ponting CP, Bork P. Phospholipases A2 and Wnts are unlikely to share a common ancestor. Current Biology : Cb. 9: R718-9. PMID 10712041 DOI: 10.1016/S0960-9822(99)80466-7  1
1999 Liu Z, Macias MJ, Bottomley MJ, Stier G, Linge JP, Nilges M, Bork P, Sattler M. The three-dimensional structure of the HRDC domain and implications for the Werner and Bloom syndrome proteins. Structure (London, England : 1993). 7: 1557-66. PMID 10647186 DOI: 10.1016/S0969-2126(00)88346-X  0.52
1999 Sunyaev S, Hanke J, Aydin A, Wirkner U, Zastrow I, Reich J, Bork P. Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes. Journal of Molecular Medicine (Berlin, Germany). 77: 754-60. PMID 10619435 DOI: 10.1007/S001099900059  1
1999 Bork P, Huynen M. A point of entry into genomics Nature Genetics. 23: 273-273. PMID 10545945 DOI: 10.1038/15453  0.88
1999 Barnes MR, Russell RB, Copley RR, Ponting CP, Bork P, Cumberledge S, Reichsman F, Moore HM. A lipid-binding domain in Wnt: a case of mistaken identity? Current Biology : Cb. 9: R717-9. PMID 10531014 DOI: 10.1016/S0960-9822(99)80465-5  0.72
1999 Hanke J, Brett D, Zastrow I, Aydin A, Delbrück S, Lehmann G, Luft F, Reich J, Bork P. Alternative splicing of human genes: more the rule than the exception? Trends in Genetics : Tig. 15: 389-90. PMID 10498933 DOI: 10.1016/S0168-9525(99)01830-2  1
1999 Hanke J, Lehmann G, Bork P, Reich JG. Associative database of protein sequences. Bioinformatics (Oxford, England). 15: 741-8. PMID 10498774 DOI: 10.1093/Bioinformatics/15.9.741  1
1999 Eisenhaber B, Bork P, Eisenhaber F. Prediction of potential GPI-modification sites in proprotein sequences. Journal of Molecular Biology. 292: 741-58. PMID 10497036 DOI: 10.1006/Jmbi.1999.3069  1
1999 Dandekar T, Schuster S, Snel B, Huynen M, Bork P. Pathway alignment: application to the comparative analysis of glycolytic enzymes. The Biochemical Journal. 343: 115-24. PMID 10493919 DOI: 10.1042/Bj3430115  1
1999 Eisenhaber F, Bork P. Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries. Bioinformatics (Oxford, England). 15: 528-35. PMID 10487860  1
1999 Ponting CP, Hofmann K, Bork P. A latrophilin/CL-1-like GPS domain in polycystin-1. Current Biology : Cb. 9: R585-8. PMID 10469603 DOI: 10.1016/S0960-9822(99)80379-0  0.96
1999 Huynen MA, Dandekar T, Bork P. Variation and evolution of the citric-acid cycle: a genomic perspective. Trends in Microbiology. 7: 281-91. PMID 10390638 DOI: 10.1016/S0966-842X(99)01539-5  1
1999 Bork P, Doerks T, Springer TA, Snel B. Domains in plexins: links to integrins and transcription factors. Trends in Biochemical Sciences. 24: 261-3. PMID 10390613 DOI: 10.1016/S0968-0004(99)01416-4  1
1999 Ponting CP, Aravind L, Schultz J, Bork P, Koonin EV. Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer. Journal of Molecular Biology. 289: 729-45. PMID 10369758 DOI: 10.1006/Jmbi.1999.2827  0.96
1999 Morett E, Bork P. A novel transactivation domain in parkin. Trends in Biochemical Sciences. 24: 229-31. PMID 10366851 DOI: 10.1016/S0968-0004(99)01381-X  1
1999 Copley RR, Schultz J, Ponting CP, Bork P. Protein families in multicellular organisms. Current Opinion in Structural Biology. 9: 408-15. PMID 10361098 DOI: 10.1016/S0959-440X(99)80055-4  1
1999 Ponting CP, Bork P, Schultz J, Aravind L. No Sec7-homology domain in guanine-nucleotide-exchange factors that act on Ras and Rho. Trends in Biochemical Sciences. 24: 177-8. PMID 10322430 DOI: 10.1016/S0968-0004(99)01379-1  0.96
1999 Snel B, Bork P, Huynen MA. Genome phylogeny based on gene content. Nature Genetics. 21: 108-10. PMID 9916801 DOI: 10.1038/5052  1
1999 Ponting CP, Schultz J, Milpetz F, Bork P. SMART: identification and annotation of domains from signalling and extracellular protein sequences. Nucleic Acids Research. 27: 229-32. PMID 9847187 DOI: 10.1093/Nar/27.1.229  0.96
1998 Eisenhaber B, Bork P, Eisenhaber F. Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase. Protein Engineering. 11: 1155-61. PMID 9930665 DOI: 10.1093/Protein/11.12.1155  1
1998 Cai Y, Bork P. Homology-based gene prediction using neural nets. Analytical Biochemistry. 265: 269-74. PMID 9882402 DOI: 10.1006/Abio.1998.2876  1
1998 Willeke F, Ridder R, Bork P, Klaes R, Mechtersheimer G, Schwarzbach M, Zimmer D, Kloor M, Lehnert T, Herfarth C, von Knebel Doeberitz M. Identical variant TSG101 transcripts in soft tissue sarcomas and various non-neoplastic tissues. Molecular Carcinogenesis. 23: 195-200. PMID 9869447 DOI: 10.1002/(Sici)1098-2744(199812)23:4<195::Aid-Mc1>3.0.Co;2-G  0.32
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