Publications

Total: 637 publication(s)

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

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. (2019)

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

Nucleic Acids Res. doi: 10.1093/nar/gkz1002
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 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 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) 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

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) 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) 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) 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

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

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) 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) 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) 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) 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

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

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

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

Genome Med 9(1):1-13. doi: 10.1186/s13073-017-0428-y
Europe PMC | doi

Knoll RL, Forslund K, Kultima JR, Meyer CU, Kullmer U, Sunagawa S, Bork P, Gehring S. (2017)

Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition - a metagenomic analysis.

Am. J. Physiol. Gastrointest. Liver Physiol. 312(4):G327-G339. doi: 10.1152/ajpgi.00293.2016
Europe PMC | doi

Betts MJ, Wichmann O, Utz M, Andre T, Petsalaki E, Minguez P, Parca L, Roth FP, Gavin AC, Bork P, Russell RB. (2017)

Systematic identification of phosphorylation-mediated protein interaction switches.

PLoS Comput. Biol. 13(3):e1005462. doi: 10.1371/journal.pcbi.1005462
Europe PMC | doi

Wang YY, Chen WH, Xiao PP, Xie WB, Luo Q, Bork P, Zhao XM. (2017)

GEAR: A database of Genomic Elements Associated with drug Resistance.

Sci Rep 7(44085):1-8. doi: 10.1038/srep44085
Europe PMC | doi

Jouhten P, Huerta-Cepas J, Bork P, Patil KR. (2017)

Metabolic anchor reactions for robust biorefining.

Metab. Eng. 40:1-4. doi: 10.1016/j.ymben.2017.02.010
Europe PMC | doi

Minguez P, Bork P. (2017)

Bioinformatics Analysis of Functional Associations of PTMs.

Methods Mol. Biol. 1558:303-320. doi: 10.1007/978-1-4939-6783-4_14
Europe PMC | doi

Beck M, Hurt E. (2017)

The nuclear pore complex: understanding its function through structural insight.

Nat. Rev. Mol. Cell Biol. 18(2):73-89. doi: 10.1038/nrm.2016.147
Europe PMC | doi

Voigt AY, Zeller G, Bork P. (2017)

[Microbial Biomarkers for Early Cancer Detection].

Dtsch Med Wochenschr 142(4):267-274. doi: 10.1055/s-0042-110193
Europe PMC | doi

Chen WH, Lu G, Chen X, Zhao XM, Bork P. (2017)

OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines.

Nucleic Acids Res. 45(D1):D940-D944. doi: 10.1093/nar/gkw1013
Europe PMC | doi

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, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Yong SY, Mitchell AL. (2017)

InterPro in 2017-beyond protein family and domain annotations.

Nucleic Acids Res. 45(D1):D190-D199. doi: 10.1093/nar/gkw1107
Europe PMC | doi

Mende DR, Letunic I, Huerta-Cepas J, Li SS, Forslund K, Sunagawa S, Bork P. (2017)

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.

Nucleic Acids Res. 45(D1):D529-D534. doi: 10.1093/nar/gkw989
Europe PMC | doi

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. (2017)

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.

Nucleic Acids Res. 45(D1):D362-D368. doi: 10.1093/nar/gkw937
Europe PMC | doi


2016

Dauden MI, Kosinski J, Kolaj-Robin O, Desfosses A, Ori A, Faux C, Hoffmann NA, Onuma OF, Breunig KD, Beck M, Sachse C, Séraphin B, Glatt S, Müller CW. (2016)

Architecture of the yeast Elongator complex

EMBO Rep. 18(2):e201643353. doi: 10.15252/embr.201643353
Europe PMC | doi

Yelton AP, Acinas SG, Sunagawa S, Bork P, Pedrós-Alió C, Chisholm SW. (2016)

Global genetic capacity for mixotrophy in marine picocyanobacteria.

ISME J 10(12):2946-2957. doi: 10.1038/ismej.2016.64
Europe PMC | doi

Kiosze-Becker K, Ori A, Gerovac M, Heuer A, Nürenberg-Goloub E, Rashid UJ, Becker T, Beckmann R, Beck M, Tampé R. (2016)

Structure of the ribosome post-recycling complex probed by chemical cross-linking and mass spectrometry.

Nat Commun 7(13248):1-9. doi: 10.1038/ncomms13248
Europe PMC | doi

Scharaw S, Iskar M, Ori A, Boncompain G, Laketa V, Poser I, Lundberg E, Perez F, Beck M, Bork P, Pepperkok R. (2016)

The endosomal transcriptional regulator RNF11 integrates degradation and transport of EGFR.

J. Cell Biol. 215(4):543-558. doi: 10.1083/jcb.201601090
Europe PMC | doi

Beck M, Baumeister W. (2016)

Cryo-Electron Tomography: Can it Reveal the Molecular Sociology of Cells in Atomic Detail?

Trends Cell Biol. 26(11):825-837. doi: 10.1016/j.tcb.2016.08.006
Europe PMC | doi

Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, Poulos BT, Solonenko N, Lara E, Poulain J, Pesant S, Kandels-Lewis S, Dimier C, Picheral M, Searson S, Cruaud C, Alberti A, Duarte CM, Gasol JM, Vaque D, Bork P, Acinas SG, Wincker P, Sullivan MB. (2016)

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

NATURE 537(7622):689-693. doi: 10.1038/nature19366
Europe PMC | doi

Deghou S, Zeller G, Iskar M, Driessen M, Castillo M, van Noort V, Bork P. (2016)

CART - a chemical annotation retrieval toolkit.

Bioinformatics 32(18):2869-2871. doi: 10.1093/bioinformatics/btw233
Europe PMC | doi

Otsuka S, Bui KH, Schorb M, Hossain MJ, Politi AZ, Koch B, Eltsov M, Beck M, Ellenberg J. (2016)

Nuclear pore assembly proceeds by an inside-out extrusion of the nuclear envelope

Elife 5 doi: 10.7554/eLife.19071
Europe PMC | doi

Plichta DR, Juncker AS, Bertalan M, Rettedal E, Gautier L, Varela E, Manichanh C, Fouqueray C, Levenez F, Nielsen T, Dore J, Machado AMD, de Evgrafov MCR, Hansen T, Jorgensen T, Bork P, Guarner F, Pedersen O, Sommer MOA, Ehrlich SD, Sicheritz-Ponten T, Brunak S, Nielsen HB. (2016)

Transcriptional interactions suggest niche segregation among microorganisms in the human gut

Nat Microbiol 1(11):16152. doi: 10.1038/nmicrobiol.2016.152
Europe PMC | doi

Kultima JR, Coelho LP, Forslund K, Huerta-Cepas J, Li SS, Driessen M, Voigt AY, Zeller G, Sunagawa S, Bork P. (2016)

MOCAT2: a metagenomic assembly, annotation and profiling framework.

Bioinformatics 32(16):2520-2523. doi: 10.1093/bioinformatics/btw183
Europe PMC | doi

Hampoelz B, Mackmull MT, Machado P, Ronchi P, Bui KH, Schieber N, Santarella-Mellwig R, Necakov A, Andrés-Pons A, Philippe JM, Lecuit T, Schwab Y, Beck M. (2016)

Pre-assembled nuclear pores insert into the nuclear envelope during early development.

Cell 166(3):664-678. doi: 10.1016/j.cell.2016.06.015
Europe PMC | doi