EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
Biography
PhD 2010, Max Planck Institutes & University of Tübingen.
Postdoctoral research at EMBL Heidelberg.
Team leader at EMBL since 2015.
Publications
Total: 57 publication(s)
2021
Moreno-Indias I, Lahti L, Nedyalkova M, Elbere I, Roshchupkin G, Adilovic M, Aydemir O, Bakir-Gungor B, Santa Pau EC, D'Elia D, Desai MS, Falquet L, Gundogdu A, Hron K, Klammsteiner T, Lopes MB, Marcos-Zambrano LJ, Marques C, Mason M, May P, Pašić L, Pio G, Pongor S, Promponas VJ, Przymus P, Saez-Rodriguez J, Sampri A, Shigdel R, Stres B, Suharoschi R, Truu J, Truică CO, Vilne B, Vlachakis D, Yilmaz E, Zeller G, Zomer AL, Gómez-Cabrero D, Claesson MJ. (2021)
Statistical and machine learning techniques in human microbiome studies: contemporary challenges and solutions.
Front Microbiol 12 doi: 10.3389/fmicb.2021.635781
Europe PMC | doi
Wirbel J, Zych K, Essex M, Karcher N, Kartal E, Salazar G, Bork P, Sunagawa S, Zeller G. (2021)
Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox.
Genome Biol 22(1) doi: 10.1186/s13059-021-02306-1
Europe PMC | doi
Blasche S, Kim Y, Mars RAT, Machado D, Maansson M, Kafkia E, Milanese A, Zeller G, Teusink B, Nielsen J, Benes V, Neves R, Sauer U, Patil KR. (2021)
Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community.
Nat Microbiol 6(2):196-208. doi: 10.1038/s41564-020-00816-5
Europe PMC | doi
2020
Garza DR, Taddese R, Wirbel J, Zeller G, Boleij A, Huynen MA, Dutilh BE. (2020)
Metabolic models predict bacterial passengers in colorectal cancer.
Cancer Metab 8(1) doi: 10.1186/s40170-020-0208-9
Europe PMC | doi
Baghai Arassi M, Zeller G, Karcher N, Zimmermann M, Toenshoff B. (2020)
The gut microbiome in solid organ transplantation.
Pediatr Transplant 24(7) doi: 10.1111/petr.13866
Europe PMC | doi
Karcher N, Pasolli E, Asnicar F, Huang KD, Tett A, Manara S, Armanini F, Bain D, Duncan SH, Louis P, Zolfo M, Manghi P, Valles-Colomer M, Raffaetà R, Rota-Stabelli O, Zeller G, Collado MC, Maixner F, Falush D, Huttenhower C, Walker AW, Segata N. (2020)
Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations.
Genome Biol 21(1) doi: 10.1186/s13059-020-02042-y
Europe PMC | doi
Sowah SA, Hirche F, Milanese A, Johnson TS, Grafetstätter M, Schübel R, Kirsten R, Ulrich CM, Kaaks R, Zeller G, Kühn T, Stangl GI. (2020)
Changes in plasma short-chain fatty acid levels after dietary weight loss among overweight and obese adults over 50 weeks.
Nutrients 12(2) doi: 10.3390/nu12020452
Europe PMC | doi
Maier L, Goemans CV, Pruteanu M, Wirbel J, Kuhn M, Cacace E, Banerjee T, Anderson EE, Milanese A, Löber U, Forslund SK, Patil KP, Zeller G, Bork P, Typas A. (2020)
Dissecting the collateral damage of antibiotics on gut microbes.
bioRxivorg doi: 10.1101/2020.01.09.893560
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
2019
Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh HJ, Cuenca M, Field CM, Coelho LP, Cruaud C, Engelen S, Gregory AC, Labadie K, Marec C, Pelletier E, Royo-Llonch M, 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
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
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
2018
Tramontano M, Andrejev S, Pruteanu M, Klünemann M, Kuhn M, Galardini M, Jouhten P, Zelezniak A, Zeller G, Bork P, Typas A, Patil KR. (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
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
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
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
2016
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
2015
Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, 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
2014
Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, 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
2013
Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, 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
2012
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
2011
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
Europe PMC | doi
2010
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
2009
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
2008
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
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Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana
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