Publications

Total: 659 publication(s)

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, Bastard JP, Forslund S, Le Chatelier E, Falony G, Pons N, Prifti E, Quinquis B, Roume H, Vieira-Silva S, Hansen TH, Pedersen HK, Lewinter C, Sønderskov NB, MetaCardis Consortium, Køber L, Vestergaard H, Hansen T, Zucker JD, Galan P, Dumas ME, Raes J, Oppert JM, Letunic I, Nielsen J, Bork P, Ehrlich SD, Stumvoll M, Pedersen O, Aron-Wisneswky J, Clément K, Bäckhed F. (2020)

Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology.

Nat Commun 11(1) doi: 10.1038/s41467-020-19589-w
Europe PMC | doi

Bahram M, Netherway T, Frioux C, Ferretti P, Coelho LP, Geisen S, Bork P, Hildebrand F. (2020)

Metagenomic assessment of the global distribution of bacteria and fungi.

Environ Microbiol doi: 10.1111/1462-2920.15314
Europe PMC | doi

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, Gough J, Haft DH, Letunic I, Marchler-Bauer A, Mi H, Natale DA, Necci M, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A, Finn RD. (2020)

The InterPro protein families and domains database: 20 years on.

Nucleic Acids Res doi: 10.1093/nar/gkaa977
Europe PMC | doi

Letunic I, Khedkar S, Bork P. (2020)

SMART: recent updates, new developments and status in 2020.

Nucleic Acids Res doi: 10.1093/nar/gkaa937
Europe PMC | doi

Gurumayum S, Jiang P, Hao X, Campos TL, Young ND, Korhonen PK, Gasser RB, Bork P, Zhao XM, He LJ, Chen WH. (2020)

OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines.

Nucleic Acids Res doi: 10.1093/nar/gkaa884
Europe PMC | doi

Allegretti M, Zimmerli CE, Rantos V, Wilfling F, Ronchi P, Fung HKH, Lee CW, Hagen W, Turoňová B, Karius K, Börmel M, Zhang X, Müller CW, Schwab Y, Mahamid J, Pfander B, Kosinski J, Beck M. (2020)

In-cell architecture of the nuclear pore and snapshots of its turnover.

Nature doi: 10.1038/s41586-020-2670-5
Europe PMC | doi

Zhou Y, Kastritis PL, Dougherty SE, Bouvette J, Hsu AL, Burbaum L, Mosalaganti S, Pfeffer S, Hagen WJH, Förster F, Borgnia MJ, Vogel C, Beck M, Bartesaghi A, Silva GM. (2020)

Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress.

Proc Natl Acad Sci U S A 117(36):22157-22166. doi: 10.1073/pnas.2005301117
Europe PMC | doi

Turoňová B, Sikora M, Schürmann C, Hagen WJH, Welsch S, Blanc FEC, von Bülow S, Gecht M, Bagola K, Hörner C, van Zandbergen G, Landry J, de Azevedo NTD, Mosalaganti S, Schwarz A, Covino R, Mühlebach MD, Hummer G, Krijnse Locker J, Beck M. (2020)

In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges.

Science 370(6513):203-220. doi: 10.1126/science.abd5223
Europe PMC | doi

Buczak K, Kirkpatrick JM, Truckenmueller F, Santinha D, Ferreira L, Roessler S, Singer S, Beck M, Ori A. (2020)

Spatially resolved analysis of FFPE tissue proteomes by quantitative mass spectrometry.

Nat Protoc 15(9):2956-2979. doi: 10.1038/s41596-020-0356-y
Europe PMC | doi

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. (2020)

(Phospho)proteomic profiling of microsatellite unstable CRC cells reveals alterations in nuclear signaling and cholesterol metabolism caused by frameshift mutation of NMD regulator UPF3A.

Int J Mol Sci 21(15) doi: 10.3390/ijms21155234
Europe PMC | doi

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, Bastard JP, Andreelli F, Galleron N, Coelho LP, Hulot JS, Hansen TH, Pedersen HK, Lewinter C, Rouault C, Quinquis B, Salem JE, Roume H, Touch S, Søndertoft NB, Dumas ME, Touch S, Gøtze JP, Hansen T, Ehrlich SD, Galan P, Letunic I, Nielsen J, Holst JJ, Køber L, Vestergaard H, Zucker JD, Oppert JM, Stumvoll M, Bäckhed F, Clément K, Bork P, Pedersen O, Raes J. (2020)

Statin therapy is associated with lower prevalence of gut microbiota dysbiosis.

Nature 581(7808):310-315. doi: 10.1038/s41586-020-2269-x
Europe PMC | doi

Van Rossum T, Ferretti P, Maistrenko OM, Bork P. (2020)

Diversity within species: interpreting strains in microbiomes.

Nat. Rev. Microbiol. 18(9) doi: 10.1038/s41579-020-0368-1
Europe PMC | doi

Sunagawa S, Acinas SG, Bork P, Bowler C, Tara Oceans Coordinators, Eveillard D, Gorsky G, Guidi L, Iudicone D, Karsenti E, Lombard F, Ogata H, Pesant S, Sullivan MB, Wincker P, de Vargas C. (2020)

Tara Oceans: towards global ocean ecosystems biology.

Nat. Rev. Microbiol. 18(8) doi: 10.1038/s41579-020-0364-5
Europe PMC | doi

Bahram M, Netherway T, Hildebrand F, Pritsch K, Drenkhan R, Loit K, Anslan S, Bork P, Tedersoo L. (2020)

Plant nutrient-acquisition strategies drive topsoil microbiome structure and function.

New Phytol 227(4) doi: 10.1111/nph.16598
Europe PMC | doi

Lee CW, Wilfling F, Ronchi P, Allegretti M, Mosalaganti S, Jentsch S, Beck M, Pfander B. (2020)

Selective autophagy degrades nuclear pore complexes.

Nat. Cell Biol. 22(2):159-166. doi: 10.1038/s41556-019-0459-2
Europe PMC | doi

Turoňová B, Hagen WJH, Obr M, Mosalaganti S, Beugelink JW, Zimmerli CE, Kräusslich HG, Beck M. (2020)

Benchmarking tomographic acquisition schemes for high-resolution structural biology.

Nat Commun 11(1) doi: 10.1038/s41467-020-14535-2
Europe PMC | doi

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. (2020)

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity.

ISME J 14(5):1247-1259. doi: 10.1038/s41396-020-0600-z
Europe PMC | doi

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. (2020)

proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes.

Nucleic Acids Res. 48(D1):D621-D625. doi: 10.1093/nar/gkz1002
Europe PMC | doi

Lee B-G, Merkel F, Allegretti M, Hassler M, Cawood C, Lecomte L, O'Reilly FJ, Sinn LR, Gutierrez-Escribano P, Kschonsak M, Bravo S, Nakane T, Rappsilber J, Aragon L, Beck M, Löwe J, Haering CH. (2020)

Cryo-EM structures of holo condensin reveal a subunit flip-flop mechanism.

Nat Struct Mol Biol 27(8):743-751. doi: 10.1038/s41594-020-0457-x
Europe PMC | doi

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. (2020)

Glycogen accumulation, central carbon metabolism, and aging of hematopoietic stem and progenitor cells.

Sci Rep 10(1) doi: 10.1038/s41598-020-68396-2
Europe PMC | doi


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, Herting E, König I, Gehring S, Zemlin M, Henneke P, Bork P, Härtel C, Härtel C. (2019)

Efficacy of Bifidobacterium longum, B. infantis and Lactobacillus acidophilus 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(11) doi: 10.1136/bmjopen-2019-032617
Europe PMC | doi

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, Sánchez P, Roux S, Zayed AA, Uehara H, Carmichael M, Zeller G, Ferland J, Dimier C, Picheral M, Kandels S, Poulain J, Pisarev S, Acinas SG, Poulain J, Bork P, Babin M, Guidi L, Hingamp P, Bowler C, de Vargas C, Karsenti E, Ogata H, Iudicone D, Karp-Boss L, Sullivan MB, Wincker P, Pesant S, Speich S, Sunagawa S. (2019)

Gene expression changes and community turnover differentially shape the global ocean metatranscriptome.

Cell 179(5):1068-1083.e21. doi: 10.1016/j.cell.2019.10.014
Europe PMC | doi

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, Iskar M, Ori A, Bi R, Gillet L, Zhang H, Zhang J, Zhong Q, Yu C, Schmitt U, Varma S, Zhang Q, Qiu P, Wild PJ, Zhu Y, Bork P, Garnett MJ, Saez-Rodriguez J, Elloumi F, Beck M, Liu K, Pommier Y, Aebersold R, Reinhold WC, Sander C. (2019)

Quantitative proteome landscape of the NCI-60 cancer cell lines.

iScience 21:664-680. doi: 10.1016/j.isci.2019.10.059
Europe PMC | doi

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, Trompetto M, , Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N. (2019)

Author correction: metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.

Nat Med 25(12) doi: 10.1038/s41591-019-0663-4
Europe PMC | doi

Hampoelz B, Schwarz A, Ronchi P, Bragulat-Teixidor H, Tischer C, Gaspar I, Ephrussi A, Schwab Y, Beck M. (2019)

Nuclear pores assemble from Nucleoporin condensates during oogenesis.

Cell 179(3):671-686.e17. doi: 10.1016/j.cell.2019.09.022
Europe PMC | doi

Li Y, Kuhn M, Gavin AC, Bork P. (2019)

Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features.

Bioinformatics 36(4):1213-1218. doi: 10.1093/bioinformatics/btz736
Europe PMC | doi

Hickl O, Heintz-Buschart A, Trautwein-Schult A, Hercog R, Bork P, Wilmes P, Becher D. (2019)

Sample preservation and storage significantly impact taxonomic and functional profiles in metaproteomics studies of the human gut microbiome.

Microorganisms 7(9) doi: 10.3390/microorganisms7090367
Europe PMC | doi

Schwarz A, Beck M. (2019)

The benefits of cotranslational assembly: a structural perspective.

Trends Cell Biol. 29(10) doi: 10.1016/j.tcb.2019.07.006
Europe PMC | doi

Hildebrand F, Pallen MJ, Bork P. (2019)

Towards standardisation of naming novel prokaryotic taxa in the age of high-throughput microbiology.

Gut 69(7) doi: 10.1136/gutjnl-2019-319045
Europe PMC | doi

Coelho LP, Alves R, Monteiro P, Huerta-Cepas J, Freitas AT, Bork P. (2019)

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language.

Microbiome 7(1) doi: 10.1186/s40168-019-0684-8
Europe PMC | doi

Holzer K, Ori A, Cooke A, Dauch D, Drucker E, Riemenschneider P, Andres-Pons A, DiGuilio AL, Mackmull MT, Baßler J, Roessler S, Breuhahn K, Zender L, Glavy JS, Dombrowski F, Hurt E, Schirmacher P, Beck M, Singer S. (2019)

Nucleoporin Nup155 is part of the p53 network in liver cancer.

Nat Commun 10(1) doi: 10.1038/s41467-019-10133-z
Europe PMC | doi

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, Griffin JL, Zelezniak A, Allaine D, Bork P, Welch JJ, Cohas A, Ralser M, Timmermann B. (2019)

Ice-age climate adaptations trap the alpine marmot in a state of low genetic diversity.

Curr. Biol. 29(10):1712-1720.e7. doi: 10.1016/j.cub.2019.04.020
Europe PMC | doi

Hampoelz B, Andres-Pons A, Kastritis P, Beck M. (2019)

Structure and assembly of the nuclear pore complex.

Annu Rev Biophys 48:515-536. doi: 10.1146/annurev-biophys-052118-115308
Europe PMC | doi

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, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Munoz AR, Roberts RJ, Rossello-Mora R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I, Xenarios I, Whitman WB. (2019)

Consent insufficient for data release–Response.

Science 364(6439):446. doi: 10.1126/science.aax7509
Europe PMC | doi

Thaller DJ, Allegretti M, Borah S, Ronchi P, Beck M, Lusk CP. (2019)

An ESCRT-LEM protein surveillance system is poised to directly monitor the nuclear envelope and nuclear transport system.

Elife 8 doi: 10.7554/eLife.45284
Europe PMC | doi

Romanov N, Kuhn M, Aebersold R, Ori A, Beck M, Bork P. (2019)

Disentangling genetic and environmental effects on the proteotypes of individuals.

Cell 177(5):1308-1318.e10. doi: 10.1016/j.cell.2019.03.015
Europe PMC | doi

Gregory AC, Zayed AA, Conceição-Neto N, Temperton B, Bolduc B, Alberti A, Ardyna M, Arkhipova K, Carmichael M, Cruaud C, Dimier C, Domínguez-Huerta G, Ferland J, Kandels S, Liu Y, Pesant S, Marec C, Pisarev S, Picheral M, Tremblay JÉ, Poulain J, Vik D, Vik D, Bowler C, Babin M, de Vargas C, Culley AI, Iudicone D, Dutilh BE, Roux S, Karp-Boss L, Sullivan MB, Sunagawa S, Wincker P. (2019)

Marine DNA viral macro- and microdiversity from pole to pole.

Cell 177(5):1109-1123.e14. doi: 10.1016/j.cell.2019.03.040
Europe PMC | doi

Letunic I, Bork P. (2019)

Interactive Tree Of Life (iTOL) v4: recent updates and new developments.

Nucleic Acids Res. 47(W1):W256-W259. doi: 10.1093/nar/gkz239
Europe PMC | doi

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, Trompetto M, , Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N. (2019)

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.

Nat. Med. 25(4) doi: 10.1038/s41591-019-0405-7
Europe PMC | doi

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, Niméus E, Thomas AM, Manghi P, Gandini S, Serrano D, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Waldron L, Naccarati A, Segata N, Sinha R, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G. (2019)

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.

Nat. Med. 25(4) doi: 10.1038/s41591-019-0406-6
Europe PMC | doi

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, Zeller G, Sunagawa S. (2019)

Microbial abundance, activity and population genomic profiling with mOTUs2.

Nat Commun 10(1) doi: 10.1038/s41467-019-08844-4
Europe PMC | doi

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, Bertrand A, Biard T, Bittner L, Boccara M, Brum JR, Brunet C, Busseni G, Carratala A, Claustre H, Coelho LP, Colin S, D'Aniello S, Da Silva C, Del Core M, Dore H, Gasparini S, Kokoszka F, Jamet JL, Lejeusne C, Lepoivre C, Lescot M, Lima-Mendez G, Lombard F, Lukes J, Maillet N, Madoui MA, Martinez E, Mazzocchi MG, Neou MB, Paz-Yepes J, Poulain J, Ramondenc S, Romagnan JB, Roux S, Manta DS, Sanges R, Speich S, Sprovieri M, Sunagawa S, Taillandier V, Tanaka A, Tirichine L, Trottier C, Uitz J, Veluchamy A, Vesela J, Vincent F, Yau S, Kandels-Lewis S, Searson S, Dimier C, Picheral M, Bork P, Boss E, De Vargas C, Follows MJ, Grimsley N, Guidi L, Hingamp P, Karsenti E, Sordino P, Stemmann L, Sullivan MB, Tagliabue A, Zingone A, Garczarek L, d'Ortenzio F, Testor P, Not F, d'Alcala MR, Wincker P, Bowler C, Iudicone D, Gorsky G, Jaillon O, Karp-Boss L, Krzic U, Ogata H, Pesant S, Raes J, Reynaud EG, Sardet C, Sieracki M, Velayoudon D, Weissenbach J, Weissenbach J, Sieracki M, Velayoudon D. (2019)

Community-Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Global Biochem Cycle 33(3):391-419. doi: 10.1029/2018GB006022
doi

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, Wilmes P, Bork P. (2019)

Extensive transmission of microbes along the gastrointestinal tract.

Elife 8 doi: 10.7554/eLife.42693
Europe PMC | doi

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, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Munoz AR, Roberts RJ, Rossello-Mora R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I, Xenarios I, Whitman WB. (2019)

Toward unrestricted use of public genomic data.

Science 363(6425):350-352. doi: 10.1126/science.aaw1280
Europe PMC | doi

Hildebrand F, Moitinho-Silva L, Blasche S, Jahn MTT, Gossmann TI, Huerta Cepas J, Hercog R, Luetge M, Bahram M, Pryszlak A, Alves RJ, Waszak SM, Zhu A, Ye L, Costea PI, Belzer C, Aalvink S, Sunagawa S, Forslund SK, Merten C, Hentschel U, Benes V, Patil KR, Bork P. (2019)

Antibiotics-induced monodominance of a novel gut bacterial order.

Gut 68(10):1781-1790. doi: 10.1136/gutjnl-2018-317715
Europe PMC | doi

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. (2019)

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.

Nucleic Acids Res. 47(D1):D309-D314. doi: 10.1093/nar/gky1085
Europe PMC | doi

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, Madeira F, Luciani A, Mi H, Marchler-Bauer A, Necci M, Natale DA, Orengo C, Nuka G, Paysan-Lafosse T, Pandurangan AP, Potter SC, Pesseat S, Rawlings ND, Qureshi MA, Richardson LJ, Redaschi N, Sangrador-Vegas A, Sigrist CJA, Rivoire C, Salazar GA, Thanki N, Thomas PD, Sillitoe I, Sutton GG, Tosatto SCE, Yong SY, Finn RD. (2019)

InterPro in 2019: improving coverage, classification and access to protein sequence annotations.

Nucleic Acids Res. 47(D1):D351-D360. doi: 10.1093/nar/gky1100
Europe PMC | doi

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. (2019)

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.

Nucleic Acids Res. 47(D1):D607-D613. doi: 10.1093/nar/gky1131
Europe PMC | doi


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, Daly RA, Cochrane GR, Duhaime MB, Desnues C, Enault F, Emerson JB, Hingamp P, Fuhrman JA, Hurwitz BL, Hugenholtz P, Labonté JM, Ivanova NN, Malmstrom RR, Lee KB, Mizrachi IK, Martinez-Garcia M, Petit MA, Putonti C, Ogata H, Páez-Espino D, Rodriguez-Valera F, Rosario K, Rattei T, Reyes A, Steward GF, Sullivan MB, Schriml L, Schulz F, Temperton B, Tringe SG, Sunagawa S, Suttle CA, Wilhelm SW, Whiteson KL, Webster NS, Thurber RV, Yilmaz P, Wrighton KC, Woyke T, Wommack KE, Allen LZ, Yutin N, Young MJ, Yoshida T, Eloe-Fadrosh EA, Kyrpides NC. (2018)

Minimum Information about an Uncultivated Virus Genome (MIUViG).

Nat. Biotechnol. 37(1) doi: 10.1038/nbt.4306
Europe PMC | doi

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, Moebus S, Bork P, Fischer S, Herms S, Aretz S, Hoffmann P, Steinke-Lange V. (2018)

Copy number variation analysis and targeted NGS in 77 families with suspected Lynch syndrome reveals novel potential causative genes.

Int. J. Cancer 143(11) doi: 10.1002/ijc.31725
Europe PMC | doi

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, Nielsen HB, Nielsen MF, Wang J, Bork P, Hansen T, Vilsbøll T, Arumugam M, Knop FK, Pedersen O. (2018)

Recovery of gut microbiota of healthy adults following antibiotic exposure.

Nat Microbiol 3(11) doi: 10.1038/s41564-018-0257-9
Europe PMC | doi

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. (2018)

A computational framework to integrate high-throughput '-omics' datasets for the identification of potential mechanistic links.

Nat Protoc 13(12) doi: 10.1038/s41596-018-0064-z
Europe PMC | doi

Beck M, Mosalaganti S, Kosinski J. (2018)

From the resolution revolution to evolution: structural insights into the evolutionary relationships between vesicle coats and the nuclear pore.

Curr. Opin. Struct. Biol. 52:32-40. doi: 10.1016/j.sbi.2018.07.012
Europe PMC | doi

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, Aloy P, Bork P, Gavin AC, Ho AD. (2018)

Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline.

Nat Commun 9(1) doi: 10.1038/s41467-018-06353-4
Europe PMC | doi

Bedarf JR, Hildebrand F, Goeser F, Bork P, Wüllner U. (2018)

Das Darmmikrobiom bei der Parkinson-Krankheit.

Nervenarzt 90(2):160-166. doi: 10.1007/s00115-018-0601-6
Europe PMC | doi

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. (2018)

Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota.

Gut 68(7):1180-1189. doi: 10.1136/gutjnl-2018-316106
Europe PMC | doi

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, Põlme S, Pent M, Ryberg M, Sunagawa S, Tedersoo L, Bork P. (2018)

Structure and function of the global topsoil microbiome.

Nature 560(7717):233-237. doi: 10.1038/s41586-018-0386-6
Europe PMC | doi

Bahram M, Anslan S, Hildebrand F, Bork P, Tedersoo L. (2018)

Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment.

Environ Microbiol Rep 11(4):487-494. doi: 10.1111/1758-2229.12684
Europe PMC | doi

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, Letunic I, Bork P. (2018)

Metagenomic analysis of gut microbial communities from a Central Asian population.

BMJ Open 8(7) doi: 10.1136/bmjopen-2018-021682
Europe PMC | doi

Kehrer J, Kuss C, Andres-Pons A, Reustle A, Dahan N, Devos D, Kudryashev M, Beck M, Mair GR, Frischknecht F. (2018)

Nuclear pore complex components in the malaria parasite Plasmodium berghei.

Sci Rep 8(1) doi: 10.1038/s41598-018-29590-5
Europe PMC | doi

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, Cologna M, Clementi R, Cusumano G, Crifò T, Innamorati C, Gottardi S, Postai D, Masè C, Duranti S, Savoi D, Mancabelli L, Lugli GA, Ferrario C, Turroni F, Mangifesta M, Milani C, Yassour M, Vlamakis H, Anzalone R, Viappiani A, Koren O, Tateo S, Xavier R, Collado CM, Ventura M, Huttenhower C, Soffiati M, Pedrotti A, Bork P, Segata N. (2018)

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome.

Cell Host Microbe 24(1):133-145.e5. doi: 10.1016/j.chom.2018.06.005
Europe PMC | doi

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, Savitski MM, Göttig S, Typas A. (2018)

Species-specific activity of antibacterial drug combinations.

Nature 559(7713):259-263. doi: 10.1038/s41586-018-0278-9
Europe PMC | doi

Darzi Y, Letunic I, Bork P, Yamada T. (2018)

iPath3.0: interactive pathways explorer v3.

Nucleic Acids Res. 46(W1) doi: 10.1093/nar/gky299
Europe PMC | doi

Parca L, Beck M, Bork P, Ori A. (2018)

Quantifying compartment-associated variations of protein abundance in proteomics data.

Mol. Syst. Biol. 14(7) doi: 10.15252/msb.20178131
Europe PMC | doi

Mosalaganti S, Kosinski J, Albert S, Schaffer M, Strenkert D, Salomé PA, Merchant SS, Plitzko JM, Baumeister W, Engel BD, Beck M. (2018)

In situ architecture of the algal nuclear pore complex.

Nat Commun 9(1) doi: 10.1038/s41467-018-04739-y
Europe PMC | doi

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. (2018)

Pervasive Protein Thermal Stability Variation during the Cell Cycle.

Cell 173(6) doi: 10.1016/j.cell.2018.03.053
Europe PMC | doi

Jones JC, Fruciano C, Marchant J, Hildebrand F, Forslund S, Bork P, Engel P, Hughes WOH. (2018)

The gut microbiome is associated with behavioural task in honey bees.

Insectes Soc 65(3):419-429. doi: 10.1007/s00040-018-0624-9
Europe PMC | doi

Buczak K, Ori A, Kirkpatrick JM, Holzer K, Dauch D, Roessler S, Endris V, Lasitschka F, Parca L, Schmidt A, Zender L, Schirmacher P, Krijgsveld J, Singer S, Beck M. (2018)

Spatial tissue proteomics quantifies inter- and intra-tumor heterogeneity in hepatocellular carcinoma.

Mol Cell Proteomics 17(4) doi: 10.1074/mcp.RA117.000189
Europe PMC | doi

Korpela K, Costea PI, Coelho LP, Kandels-Lewis S, Willemsen G, Boomsma DI, Segata N, Bork P. (2018)

Selective maternal seeding and environment shape the human gut microbiome.

Genome Res. 28(4) doi: 10.1101/gr.233940.117
Europe PMC | doi

Tramontano M, Andrejev S, Pruteanu M, Klünemann M, Kuhn M, Galardini M, Jouhten P, Zelezniak A, Zeller G, Bork P, Typas A, Patil KR. (2018)

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies.

Nat Microbiol 3(4) doi: 10.1038/s41564-018-0123-9
Europe PMC | doi

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. (2018)

Similarity of the dog and human gut microbiomes in gene content and response to diet.

Microbiome 6(1) doi: 10.1186/s40168-018-0450-3
Europe PMC | doi

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. (2018)

Extensive impact of non-antibiotic drugs on human gut bacteria.

Nature 555(7698) doi: 10.1038/nature25979
Europe PMC | doi

Rubio-Cosials A, Schulz EC, Lambertsen L, Smyshlyaev G, Rojas-Cordova C, Forslund K, Karaca E, Bebel A, Bork P, Barabas O. (2018)

Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance.

Cell 173(1):208-220.e20. doi: 10.1016/j.cell.2018.02.032
Europe PMC | doi

Schmidt TSB, Raes J, Bork P. (2018)

The Human Gut Microbiome: From Association to Modulation.

Cell 172(6):1198-1215. doi: 10.1016/j.cell.2018.02.044
Europe PMC | doi

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, Birren B, Malmstrom RR, Bork P, Podar M, Garrity GM, Weinstock GM, Yooseph S, Dodsworth JA, Glöckner FO, Sutton G, Nelson WC, Gilbert JA, Jungbluth SP, Hallam SJ, Tighe S, Ettema TJG, Baker BJ, Rattei T, Konstantinidis KT, Liu WT, McMahon KD, Fierer N, Eisen JA, Hedlund B, Cochrane G, Karsch-Mizrachi I, Knight R, Finn R, Rinke C, Lapidus A, Tyson GW, Rinke C, Eren AM, Parks DH, Yilmaz P, Meyer F, Woyke T, Hugenholtz P, Banfield JF, Schriml L. (2018)

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Nat. Biotechnol. 36(2) doi: 10.1038/nbt0218-196a
Europe PMC | doi

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, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P. (2018)

Publisher Correction: Enterotypes in the landscape of gut microbial community composition.

Nat Microbiol 3(3):388. doi: 10.1038/s41564-018-0114-x
Europe PMC | doi

Mathieson T, Franken H, Kosinski J, Kurzawa N, Zinn N, Sweetman G, Poeckel D, Ratnu VS, Schramm M, Becher I, Steidel M, Noh KM, Bergamini G, Beck M, Bantscheff M, Savitski MM. (2018)

Systematic analysis of protein turnover in primary cells.

Nat Commun 9(1):689. doi: 10.1038/s41467-018-03106-1
Europe PMC | doi

Jones JC, Fruciano C, Hildebrand F, Al Toufalilia H, Balfour NJ, Bork P, Engel P, Ratnieks FL, Hughes WO. (2018)

Gut microbiota composition is associated with environmental landscape in honey bees.

Ecol Evol 8(1):441-451. doi: 10.1002/ece3.3597
Europe PMC | doi

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, Poulain J, Romac S, Richter DJ, Yoshikawa G, Dimier C, Kandels-Lewis S, Picheral M, Searson S, Searson S, Jaillon O, Aury JM, Karsenti E, Sullivan MB, Sunagawa S, Bork P, Not F, Hingamp P, Raes J, Guidi L, Ogata H, de Vargas C, Iudicone D, Bowler C, Wincker P. (2018)

A global ocean atlas of eukaryotic genes.

Nat Commun 9(1) doi: 10.1038/s41467-017-02342-1
Europe PMC | doi

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, Kandels-Lewis S, Picheral M, Searson S, Searson S, Pesant S, Poulton N, Stepanauskas R, Bork P, Bowler C, Hingamp P, Sullivan MB, Iudicone D, Massana R, Aury JM, Henrissat B, Karsenti E, Jaillon O, Sieracki M, de Vargas C, Wincker P. (2018)

Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans.

Nat Commun 9(1) doi: 10.1038/s41467-017-02235-3
Europe PMC | doi

Gao NL, Zhang C, Zhang Z, Hu S, Lercher MJ, Zhao XM, Bork P, Liu Z, Chen WH. (2018)

MVP: a microbe-phage interaction database.

Nucleic Acids Res. 46(D1):D700-D707. doi: 10.1093/nar/gkx1124
Europe PMC | doi

Letunic I, Bork P. (2018)

20 years of the SMART protein domain annotation resource.

Nucleic Acids Res. 46(D1):D493-D496. doi: 10.1093/nar/gkx922
Europe PMC | doi

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, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P. (2018)

Enterotypes in the landscape of gut microbial community composition.

Nat Microbiol 3(1):8-16. doi: 10.1038/s41564-017-0072-8
Europe PMC | doi

Otsuka S, Steyer AM, Schorb M, Hériché JK, Hossain MJ, Sethi S, Kueblbeck M, Schwab Y, Beck M, Ellenberg J. (2018)

Postmitotic nuclear pore assembly proceeds by radial dilation of small membrane openings

Nat. Struct. Mol. Biol. 25(1):21-28. doi: 10.1038/s41594-017-0001-9
Europe PMC | doi


2017

Albert S, Schaffer M, Beck F, Mosalaganti S, Asano S, Thomas HF, Plitzko JM, Beck M, Baumeister W, Engel BD. (2017)

Proteasomes tether to two distinct sites at the nuclear pore complex.

Proc. Natl. Acad. Sci. U.S.A. 114(52) doi: 10.1073/pnas.1716305114
Europe PMC | doi

Mackmull MT, Klaus B, Heinze I, Chokkalingam M, Beyer A, Russell RB, Ori A, Beck M. (2017)

Landscape of nuclear transport receptor cargo specificity.

Mol. Syst. Biol. 13(12) doi: 10.15252/msb.20177608
Europe PMC | doi

Costea PI, Coelho LP, Sunagawa S, Munch R, Huerta-Cepas J, Forslund K, Hildebrand F, Kushugulova A, Zeller G, Bork P. (2017)

Subspecies in the global human gut microbiome.

Mol. Syst. Biol. 13(12) doi: 10.15252/msb.20177589
Europe PMC | doi

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, Sunagawa S, Maier L, Rakova N, Schatz V, Neubert P, Frätzer C, Krannich A, Gollasch M, Grohme DA, Côrte-Real BF, Gerlach RG, Basic M, Typas A, Wu C, Titze JM, Jantsch J, Boschmann M, Dechend R, Kleinewietfeld M, Kempa S, Bork P, Linker RA, Alm EJ, Müller DN. (2017)

Salt-responsive gut commensal modulates TH17 axis and disease.

Nature 551(7682):585-589. doi: 10.1038/nature24628
Europe PMC | doi

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, Bryant DA, Schuster SC. (2017)

The microbiomes of blowflies and houseflies as bacterial transmission reservoirs.

Sci Rep 7(1) doi: 10.1038/s41598-017-16353-x
Europe PMC | doi

Beck M, Schirmacher P, Singer S. (2017)

Alterations of the nuclear transport system in hepatocellular carcinoma - New basis for therapeutic strategies.

J Hepatol 67(5):1051-1061. doi: 10.1016/j.jhep.2017.06.021
Europe PMC | doi

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, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna RA, van Hylckama Vlieg J, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal EG, Ehrlich SD, Dore J, Bork P. (2017)

Towards standards for human fecal sample processing in metagenomic studies.

Nat Biotechnol. 35(11) doi: 10.1038/nbt.3960
Europe PMC | doi

Colin S, Coelho LP, Sunagawa S, Bowler C, Karsenti E, Bork P, Pepperkok R, de Vargas C. (2017)

Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes.

Elife 6 doi: 10.7554/eLife.26066
Europe PMC | doi

Teimer R, Kosinski J, von Appen A, Beck M, Hurt E. (2017)

A short linear motif in scaffold Nup145C connects Y-complex with pre-assembled outer ring Nup82 complex.

Nat Commun 8(1):107. doi: 10.1038/s41467-017-01160-9
Europe PMC | doi

Sadian Y, Tafur L, Kosinski J, Jakobi AJ, Wetzel R, Buczak K, Hagen WJ, Beck M, Sachse C, Müller CW. (2017)

Structural insights into transcription initiation by yeast RNA polymerase I.

EMBO J 36(18) doi: 10.15252/embj.201796958
Europe PMC | doi

Saary P, Forslund K, Bork P, Hildebrand F. (2017)

RTK: efficient rarefaction analysis of large datasets.

Bioinformatics 33(16) doi: 10.1093/bioinformatics/btx206
Europe PMC | doi

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, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Rinke C, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. (2017)

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Nat. Biotechnol. 35(8):725-731. doi: 10.1038/nbt.3893
Europe PMC | doi

Huerta-Cepas J, Forslund K, Pedro Coelho L, Szklarczyk D, Juhl Jensen L, von Mering C, Bork P. (2017)

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.

Mol Biol Evol 34(8):2115-2122. doi: 10.1093/molbev/msx148
Europe PMC | doi

Costea PI, Munch R, Coelho LP, Paoli L, Sunagawa S, Bork P. (2017)

metaSNV: A tool for metagenomic strain level analysis.

PLoS One 12(7) doi: 10.1371/journal.pone.0182392
Europe PMC | doi

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, Beck M, Gavin AC. (2017)

Capturing protein communities by structural proteomics in a thermophilic eukaryote.

Mol Syst Biol 13(7):936. doi: 10.15252/msb.20167412
Europe PMC | doi

Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wüllner U. (2017)

Erratum to: Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients.

Genome Med 9(1):61. doi: 10.1186/s13073-017-0451-z
Europe PMC | doi