Publications

Total: 644 publication(s)

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, 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 doi: 10.1002/ijc.31725
Europe PMC | doi

Qu K, Glass B, Doležal M, Schur FKM, Murciano B, Rein A, Rumlová M, Ruml T, Kräusslich HG, Briggs JAG. (2018)

Structure and architecture of immature and mature murine leukemia virus capsids.

Proc Natl Acad Sci U S A doi: 10.1073/pnas.1811580115
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. (2018)

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

Nucleic Acids Res. doi: 10.1093/nar/gky1131
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. (2018)

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

Nucleic Acids Res. 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. (2018)

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

Nucleic Acids Res. doi: 10.1093/nar/gky1100
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 doi: 10.1038/s41596-018-0064-z
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 doi: 10.1038/s41564-018-0257-9
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

Kovtun O, Leneva N, Bykov YS, Ariotti N, Teasdale RD, Schaffer M, Engel BD, Owen DJ, Briggs JAG, Collins BM. (2018)

Structure of the membrane-assembled retromer coat determined by cryo-electron tomography.

Nature 561(7724) doi: 10.1038/s41586-018-0526-z
Europe PMC | doi

Mattei S, Tan A, Glass B, Müller B, Kräusslich HG, Briggs JAG. (2018)

High-resolution structures of HIV-1 Gag cleavage mutants determine structural switch for virus maturation.

Proc. Natl. Acad. Sci. U.S.A. 115(40) doi: 10.1073/pnas.1811237115
Europe PMC | doi

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

Das Darmmikrobiom bei der Parkinson-Krankheit.

Nervenarzt 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 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 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

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

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

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

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

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

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

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

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

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

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

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


2017

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

Jones JC, Fruciano C, Hildebrand F, Al Toufalilia H, Balfour NJ, Bork P, Engel P, Ratnieks FL, Hughes WO. (2017)

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

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

Pak AJ, Grime JMA, Sengupta P, Chen AK, Durumeric AEP, Srivastava A, Yeager M, Briggs JAG, Lippincott-Schwartz J, Voth GA. (2017)

Immature HIV-1 lattice assembly dynamics are regulated by scaffolding from nucleic acid and the plasma membrane.

Proc Natl Acad Sci U S A 114(47):E10056-E10065. doi: 10.1073/pnas.1706600114
Europe PMC | doi

Bykov YS, Schaffer M, Dodonova SO, Albert S, Plitzko JM, Baumeister W, Engel BD, Briggs JA. (2017)

The structure of the COPI coat determined within the cell.

Elife 6 doi: 10.7554/eLife.32493
Europe PMC | doi

Wan W, Kolesnikova L, Clarke M, Koehler A, Noda T, Becker S, Briggs JAG. (2017)

Structure and assembly of the Ebola virus nucleocapsid

Nature 551(7680):394-397. doi: 10.1038/nature24490
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

Adell MAY, Migliano SM, Upadhyayula S, Bykov YS, Sprenger S, Pakdel M, Vogel GF, Jih G, Skillern W, Behrouzi R, Babst M, Schmidt O, Hess MW, Briggs JA, Kirchhausen T, Teis D. (2017)

Recruitment dynamics of ESCRT-III and Vps4 to endosomes and implications for reverse membrane budding.

Elife 6 doi: 10.7554/eLife.31652
Europe PMC | doi

Lauber C, Seitz S, Mattei S, Suh A, Beck J, Herstein J, Börold J, Salzburger W, Kaderali L, Briggs JAG, Bartenschlager R. (2017)

Deciphering the Origin and Evolution of Hepatitis B Viruses by Means of a Family of Non-enveloped Fish Viruses.

Cell Host Microbe 22(3):387-399.e6. doi: 10.1016/j.chom.2017.07.019
Europe PMC | doi

Turoňová B, Schur FKM, Wan W, Briggs JAG. (2017)

Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å.

J. Struct. Biol. 199(3) doi: 10.1016/j.jsb.2017.07.007
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

Dodonova SO, Aderhold P, Kopp J, Ganeva I, Röhling S, Hagen WJH, Sinning I, Wieland F, Briggs JAG. (2017)

9Å structure of the COPI coat reveals that the Arf1 GTPase occupies two contrasting molecular environments.

Elife 6 doi: 10.7554/eLife.26691
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

Bharat TAM, Kureisaite-Ciziene D, Hardy GG, Yu EW, Devant JM, Hagen WJH, Brun YV, Briggs JAG, Löwe J. (2017)

Structure of the hexagonal surface layer on Caulobacter crescentus cells.

Nat Microbiol 2(7) doi: 10.1038/nmicrobiol.2017.59
Europe PMC | doi

Briggs JAG. (2017)

Determination of protein structure at 8.5A resolution using cryo-electron tomography and sub-tomogram averaging.

J STRUCT BIOL 198(1):3-4. doi: 10.1016/j.jsb.2017.02.011
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

Schorb M, Gaechter L, Avinoam O, Sieckmann F, Clarke M, Bebeacua C, Bykov YS, Sonnen AF, Lihl R, Briggs JA. (2017)

New hardware and workflows for semi-automated correlative cryo-fluoresence and cryo-electron microscopy/tomography.

J. Struct. Biol. 197(2):83-93. doi: 10.1016/j.jsb.2016.06.020
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

Mattei S, Glass B, Hagen WJ, Kräusslich HG, Briggs JA. (2016)

The structure and flexibility of conical HIV-1 capsids determined within intact virions

Science 354(6318):1434-1437. doi: 10.1126/science.aah4972
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

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

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

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

Schur FK, Obr M, Hagen WJ, Wan W, Jakobi AJ, Kirkpatrick JM, Sachse C, Kräusslich HG, Briggs JA. (2016)

An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation.

Science 353(6298):506-508. doi: 10.1126/science.aaf9620
Europe PMC | doi

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, Pöhö P, Hellgren LI, Arumugam M, Sunagawa S, Vieira-Silva S, Jørgensen T, Holm JB, Trošt K, Consortium M, Kristiansen K, Brix S, Raes J, Wang J, Hansen T, Bork P, Brunak S, Oresic M, Ehrlich SD, Pedersen O. (2016)

Human gut microbes impact host serum metabolome and insulin sensitivity.

Nature 535(535):376-381. doi: 10.1038/nature18646
Europe PMC | doi

Letunic I, Bork P. (2016)

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees.

Nucleic Acids Res. 44(W1):W242-W245. doi: 10.1093/nar/gkw290
Europe PMC | doi

Bertipaglia C, Schneider S, Jakobi AJ, Tarafder AK, Bykov YS, Picco A, Kukulski W, Kosinski J, Hagen WJ, Ravichandran AC, Wilmanns M, Kaksonen M, Briggs JA, Sachse C. (2016)

Higher-order assemblies of oligomeric cargo receptor complexes form the membrane scaffold of the Cvt vesicle.

EMBO Rep. 17(7):1044-1060. doi: 10.15252/embr.201541960
Europe PMC | doi

Kukulski W, Picco A, Specht T, Briggs JA, Kaksonen M. (2016)

Clathrin modulates vesicle scission, but not invagination shape, in yeast endocytosis.

Elife 5 doi: 10.7554/elife.16036
Europe PMC | doi

Hagen WJ, Wan W, Briggs JA. (2016)

Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging.

J. Struct. Biol. 197(16) doi: 10.1016/j.jsb.2016.06.007
Europe PMC | doi

Huerta-Cepas J, Serra F, Bork P. (2016)

ETE 3: Reconstruction, analysis and visualization of phylogenomic data.

Mol. Biol. Evol. 33(6):1635-1638. doi: 10.1093/molbev/msw046
Europe PMC | doi

Saliba AE, Vonkova I, Deghou S, Ceschia S, Tischer C, Kugler KG, Bork P, Ellenberg J, Gavin AC. (2016)

A protocol for the systematic and quantitative measurement of protein-lipid interactions using the liposome-microarray-based assay.

Nat Protoc 11(6):1021-1038. doi: 10.1038/nprot.2016.059
Europe PMC | doi

Vogtmann E, Hua X, Zeller G, Sunagawa S, Voigt AY, Hercog R, Goedert JJ, Shi J, Bork P, Sinha R. (2016)

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing.

PLoS ONE 11(5):e0155362. doi: 10.1371/journal.pone.0155362
Europe PMC | doi

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, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M, Quest for Orthologs consortium, Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C. (2016)

Standardized benchmarking in the quest for orthologs.

Nat. Methods 13(5):425-430. doi: 10.1038/nmeth.3830
Europe PMC | doi

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. (2016)

Durable coexistence of donor and recipient strains after fecal microbiota transplantation.

Science 352(6285):586-589. doi: 10.1126/science.aad8852
Europe PMC | doi

Chen WH, Lu G, Bork P, Hu S, Lercher MJ. (2016)

Energy efficiency trade-offs drive nucleotide usage in transcribed regions.

Nat Commun 7 doi: 10.1038/ncomms11334
Europe PMC | doi

Kosinski J, Mosalaganti S, von Appen A, Teimer R, DiGuilio AL, Wan W, Bui KH, Hagen WJ, Briggs JA, Glavy JS, Hurt E, Beck M. (2016)

Molecular architecture of the inner ring scaffold of the human nuclear pore complex.

Science 352(6283):363-365. doi: 10.1126/science.aaf0643
Europe PMC | doi

Frauenfeld J, Löving R, Armache JP, Sonnen AF, Guettou F, Moberg P, Zhu L, Jegerschöld C, Flayhan A, Briggs JA, Garoff H, Löw C, Cheng Y, Nordlund P. (2016)

A saposin-lipoprotein nanoparticle system for membrane proteins.

Nat. Methods 13(4):345-351. doi: 10.1038/nmeth.3801
Europe PMC | doi

Bykov YS, Cortese M, Briggs JA, Bartenschlager R. (2016)

Correlative light and electron microscopy methods for the study of virus-cell interactions.

FEBS Lett. 590(13) doi: 10.1002/1873-3468.12153
Europe PMC | doi

Cornejo-Castillo FM, Cabello AM, Salazar G, Sanchez-Baracaldo P, Lima-Mendez G, Hingamp P, Alberti A, Sunagawa S, Bork P, de Vargas C, Raes J, Bowler C, Wincker P, Zehr JP, Gasol JM, Massana R, Acinas SG. (2016)

Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton.

NAT COMMUN 7 doi: 10.1038/ncomms11071
Europe PMC | doi

Mattei S, Schur FK, Briggs JA. (2016)

Retrovirus maturation-an extraordinary structural transformation.

Curr Opin Virol 18:27-35. doi: 10.1016/j.coviro.2016.02.008
Europe PMC | doi

Ori A, Iskar M, Buczak K, Kastritis P, Parca L, Andrés-Pons A, Singer S, Bork P, Beck M. (2016)

Spatiotemporal variation of mammalian protein complex stoichiometries.

Genome Biol. 17(1) doi: 10.1186/s13059-016-0912-5
Europe PMC | doi

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, Estany C, Herrero C, Saz J, Sirera G, Torrela A, Navarro J, Crespo M, Brander C, Negredo E, Blanco J, Guarner F, Calle ML, Bork P, Sönnerborg A, Clotet B, Paredes R. (2016)

Gut Microbiota Linked to Sexual Preference and HIV Infection.

EBioMedicine 5:135-146. doi: 10.1016/j.ebiom.2016.01.032
Europe PMC | doi

Lloréns-Rico V, Cano J, Kamminga T, Gil R, Latorre A, Chen WH, Bork P, Glass JI, Serrano L, Lluch-Senar M. (2016)

Bacterial antisense RNAs are mainly the product of transcriptional noise.

Sci Adv 2(3) doi: 10.1126/sciadv.1501363
Europe PMC | doi

Wan W, Briggs JA. (2016)

Cryo-Electron Tomography and Subtomogram Averaging.

Meth. Enzymol. 579:329-367. doi: 10.1016/bs.mie.2016.04.014
Europe PMC | doi

Füzik T, Píchalová R, Schur FK, Strohalmová K, Křížová I, Hadravová R, Rumlová M, Briggs JA, Ulbrich P, Ruml T. (2016)

Nucleic Acid Binding by Mason-Pfizer Monkey Virus CA Promotes Virus Assembly and Genome Packaging.

J. Virol. 90(9) doi: 10.1128/JVI.03197-15
Europe PMC | doi

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, Kandels-Lewis S, Picheral M, Poulain J, Searson S, Tara Oceans Consortium Coordinators, Stemmann L, Not F, Hingamp P, Speich S, Follows M, Karp-Boss L, Boss E, Ogata H, Pesant S, Weissenbach J, Wincker P, Acinas SG, Bork P, de Vargas C, Iudicone D, Sullivan MB, Raes J, Karsenti E, Bowler C, Gorsky G. (2016)

Plankton networks driving carbon export in the oligotrophic ocean.

Nature 532(7600) doi: 10.1038/nature16942
Europe PMC | doi

Zhang XD, Song J, Bork P, Zhao XM. (2016)

The exploration of network motifs as potential drug targets from post-translational regulatory networks.

Sci Rep 6 doi: 10.1038/srep20558
Europe PMC | doi

Korpela K, Salonen A, Virta LJ, Kekkonen RA, Forslund K, Bork P, de Vos WM. (2016)

Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children.

Nat Commun 7 doi: 10.1038/ncomms10410
Europe PMC | doi

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. (2016)

Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances.

Nucleic Acids Res. 44(3) doi: 10.1093/nar/gkw004
Europe PMC | doi

Silva-Martin N, Daudén MI, Glatt S, Hoffmann NA, Kastritis P, Bork P, Beck M, Müller CW. (2016)

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(1) doi: 10.1371/journal.pone.0146457
Europe PMC | doi