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Staff at EMBL

Georg Zeller

Postdoctoral Fellow
Bork Group

EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

E-mail: send a mail

Publications

Total: 28 publication(s)

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. 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

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

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


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

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

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


2008

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, 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

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


2007

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