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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
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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
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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

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
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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

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

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
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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

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

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
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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

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

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

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

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

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

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

Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans coordinators, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P. (2015)

Ocean plankton. Structure and function of the global ocean microbiome.

Science 348(6237) doi: 10.1126/science.1261359
Europe PMC | doi

Voigt AY, Costea PI, Kultima JR, Li SS, Zeller G, Sunagawa S, Bork P. (2015)

Temporal and technical variability of human gut metagenomes.

Genome Biol. 16(1) doi: 10.1186/s13059-015-0639-8
Europe PMC | doi

Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P. (2014)

Potential of fecal microbiota for early-stage detection of colorectal cancer.

Mol. Syst. Biol. 10(11):766. doi: 10.15252/msb.20145645
Europe PMC | doi

van Noort VV, Schölch S, Iskar M, Zeller G, Ostertag K, Schweitzer C, Werner K, Weitz J, Koch M, Bork P. (2014)

Novel drug candidates for the treatment of metastatic colorectal cancer through global inverse gene expression profiling

Cancer Res. 74(20) doi: 10.1158/0008-5472.CAN-13-3540
Europe PMC | doi

Sreedharan VT, Schultheiss SJ, Jean G, Kahles A, Bohnert R, Drewe P, Mudrakarta P, Görnitz N, Zeller G, Rätsch G. (2014)

Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis

Bioinformatics 30(9):1300-1301. doi: 10.1093/bioinformatics/btt731
Europe PMC | doi

Costea PI, Zeller G, Sunagawa S, Bork P. (2014)

A fair comparison

Nat. Methods 11(4):359. doi: 10.1038/nmeth.2897
Europe PMC | doi

Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A, Bork P. (2013)

Metagenomic species profiling using universal phylogenetic marker genes

Nat. Methods 10(12):1196-1199. doi: 10.1038/nmeth.2693
Europe PMC | doi

Mende DR, Sunagawa S, Zeller G, Bork P. (2013)

Accurate and universal delineation of prokaryotic species

Nat. Methods 10(9):881-884. doi: 10.1038/nmeth.2575
Europe PMC | doi

Iskar M, Zeller G, Blattmann P, Campillos M, Kuhn M, Kaminska KH, Runz H, Gavin AC, Pepperkok R, van Noort V, Bork P. (2013)

Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding

Mol. Syst. Biol. 9:662. doi: 10.1038/msb.2013.20
Europe PMC | doi

Iskar M, Zeller G, Zhao XM, van Noort V, Bork P. (2012)

Drug discovery in the age of systems biology: the rise of computational approaches for data integration

Curr. Opin. Biotechnol. 23(4):609-616. doi: 10.1016/j.copbio.2011.11.010
Europe PMC | doi

Zhao XM, Iskar M, Zeller G, Kuhn M, van Noort V, Bork P. (2011)

Prediction of drug combinations by integrating molecular and pharmacological data

PLoS Comput. Biol. 7(12):e1002323. doi: 10.1371/journal.pcbi.1002323
Europe PMC | doi

Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J, MetaHIT Consortium, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Mérieux A, Melo Minardi R, M'rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P. (2011)

Enterotypes of the human gut microbiome

Nature 473(7346):174-180. doi: 10.1038/nature09944
Europe PMC | doi

Spencer WC, Zeller G, Watson JD, Henz SR, Watkins KL, McWhirter RD, Petersen S, Sreedharan VT, Widmer C, Jo J, Reinke V, Petrella L, Strome S, Von Stetina SE, Katz M, Shaham S, Rätsch G, Miller DM 3rd. (2011)

A spatial and temporal map of C. elegans gene expression

Genome Res. 21(2):325-341. doi: 10.1101/gr.114595.110
Europe PMC | doi

Brouwers L, Iskar M, Zeller G, van Noort V, Bork P. (2011)

Network neighbors of drug targets contribute to drug side-effect similarity

PLoS ONE 6(7):e22187. doi: 10.1371/journal.pone.0022187
Europe PMC | doi

Eichner J, Zeller G, Laubinger S, Rätsch G. (2011)

Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays

BMC Bioinformatics 12:55. doi: 10.1186/1471-2105-12-55
Europe PMC | doi

Hallem EA, Spencer WC, McWhirter RD, Zeller G, Henz SR, Rätsch G, Miller DM 3rd, Horvitz HR, Sternberg PW, Ringstad N. (2011)

Receptor-type guanylate cyclase is required for carbon dioxide sensation by Caenorhabditis elegans

Proc. Natl. Acad. Sci. U.S.A. 108(1):254-259. doi: 10.1073/pnas.1017354108
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Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM 3rd, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X, modENCODE Consortium, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH. (2010)

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

Science 330(6012):1775-1787. doi: 10.1126/science.1196914
Europe PMC | doi

Laubinger S, Zeller G, Henz SR, Buechel S, Sachsenberg T, Wang JW, Rätsch G, Weigel D. (2010)

Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome

Proc. Natl. Acad. Sci. U.S.A. 107(41):17466-17473. doi: 10.1073/pnas.1012891107
Europe PMC | doi

Rehrauer H, Aquino C, Gruissem W, Henz SR, Hilson P, Laubinger S, Naouar N, Patrignani A, Rombauts S, Shu H, Van de Peer Y, Vuylsteke M, Weigel D, Zeller G, Hennig L. (2010)

AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling

Plant Physiol. 152(2):487-499. doi: 10.1104/pp.109.150185
Europe PMC | doi

Schweikert G, Zien A, Zeller G, Behr J, Dieterich C, Ong CS, Philips P, De Bona F, Hartmann L, Bohlen A, Krüger N, Sonnenburg S, Rätsch G. (2009)

mGene: accurate SVM-based gene finding with an application to nematode genomes

Genome Res. 19(11):2133-2143. doi: 10.1101/gr.090597.108
Europe PMC | doi

McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ, Zeller G, Clark RM, Hoen DR, Bureau TE, Stokowski R, Ballinger DG, Frazer KA, Cox DR, Padhukasahasram B, Bustamante CD, Weigel D, Mackill DJ, Bruskiewich RM, Rätsch G, Buell CR, Leung H, Leach JE. (2009)

Genomewide SNP variation reveals relationships among landraces and modern varieties of rice

Proc. Natl. Acad. Sci. U.S.A. 106(30):12273-12278. doi: 10.1073/pnas.0900992106
Europe PMC | doi

Schweikert G, Behr J, Zien A, Zeller G, Ong CS, Sonnenburg S, Rätsch G. (2009)

mGene.web: a web service for accurate computational gene finding

Nucleic Acids Res. 37(Web Server issue):W312-6. doi: 10.1093/nar/gkp479
Europe PMC | doi

Zeller G, Henz SR, Widmer CK, Sachsenberg T, Rätsch G, Weigel D, Laubinger S. (2009)

Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays

Plant J. 58(6):1068-1082. doi: 10.1111/j.1365-313x.2009.03835.x
Europe PMC | doi

Naouar N, Vandepoele K, Lammens T, Casneuf T, Zeller G, van Hummelen P, Weigel D, Rätsch G, Inzé D, Kuiper M, De Veylder L, Vuylsteke M. (2009)

Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes

Plant J. 57(1):184-194. doi: 10.1111/j.1365-313x.2008.03662.x
Europe PMC | doi

Plantegenet S, Weber J, Goldstein DR, Zeller G, Nussbaumer C, Thomas J, Weigel D, Harshman K, Hardtke CS. (2009)

Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance

Mol. Syst. Biol. 5:242. doi: 10.1038/msb.2008.79
Europe PMC | doi

Laubinger S, Sachsenberg T, Zeller G, Busch W, Lohmann JU, Rätsch G, Weigel D. (2008)

Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana

Proc. Natl. Acad. Sci. U.S.A. 105(25):8795-8800. doi: 10.1073/pnas.0802493105
Europe PMC | doi

Zeller G, Clark RM, Schneeberger K, Bohlen A, Weigel D, Rätsch G. (2008)

Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays

Genome Res. 18(6):918-929. doi: 10.1101/gr.070169.107
Europe PMC | doi

Laubinger S, Zeller G, Henz SR, Sachsenberg T, Widmer CK, Naouar N, Vuylsteke M, Schölkopf B, Rätsch G, Weigel D. (2008)

At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana

Genome Biol. 9(7):R112. doi: 10.1186/gb-2008-9-7-r112
Europe PMC | doi

Zeller G, Henz SR, Laubinger S, Weigel D, Rätsch G. (2008)

Transcript normalization and segmentation of tiling array data

Pac Symp Biocomput 527-538.
Europe PMC

Clark RM, Schweikert G, Toomajian C, Ossowski S, Zeller G, Shinn P, Warthmann N, Hu TT, Fu G, Hinds DA, Chen H, Frazer KA, Huson DH, Schölkopf B, Nordborg M, Rätsch G, Ecker JR, Weigel D. (2007)

Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana

Science 317(5836):338-342. doi: 10.1126/science.1138632
Europe PMC | doi