List of Publications
| 2013 |
| Journal Articles (5) |
| Steijger T, Abril JF, Engström PG, Kokocinski F, The RGASP Consortium [including Zeller G], Hubbard TJ, Guigo R, Harrow J and Bertone P.
Assessment of transcript reconstruction methods for RNA-seq. Nat Methods, 10(12):1177-84, 2013. DOI: 10.1038/nmeth.2714 PMID: 24185837 [ abstract | bibtex | pdf ] |
| Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, The RGASP Consortium [including Zeller G], Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigo R and Bertone P.
Systematic evaluation of spliced alignment programs for RNA-seq data. Nat Methods, 10(12):1185-91, 2013. DOI: 10.1038/nmeth.2722 PMID: 24185836 [ abstract | bibtex | pdf ] |
| 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, Dore J, Ehrlich SD, Stamatakis A and Bork P.
Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods, 10(12):1196-9, 2013. DOI: 10.1038/nmeth.2693 PMID: 24141494 [ abstract | bibtex | pdf ] |
| Mende DR, Sunagawa S, Zeller G and Bork P.
Accurate and universal delineation of prokaryotic species. Nat Methods, 10(9):881-4, 2013. DOI: 10.1038/nmeth.2575 PMID: 23892899 [ abstract | bibtex | pdf ] |
| Iskar M, Zeller G, Blattmann P, Campillos M, Kuhn M, Kaminska KH, Runz H, Gavin AC, Pepperkok R, van Noort V and Bork P.
Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding. Mol Syst Biol, 9:662, 2013. DOI: 10.1038/msb.2013.20 PMID: 23632384 [ abstract | bibtex | pdf ] |
| 2012 |
| Invited Reviews (1) |
| Iskar M☯, Zeller G☯, Zhao XM, van Noort V and Bork P.
Drug discovery in the age of systems biology: the rise of computational approaches for data integration. Curr Opin Biotechnol, 23(4):609-16, 2012. DOI: 10.1016/j.copbio.2011.11.010 PMID: 22153034 [ abstract | bibtex | pdf ] |
| 2011 |
| Journal Articles (6) |
| Shao XM, Iskar M, Zeller G, Kuhn M, van Noort V, Bork P.
Prediction of drug combinations by integrating molecular and pharmacological data. PLoS Comput Biol, 7(12):e1002323, 2011. DOI: 10.1371/journal.pcbi.1002323 PMID: 22219721 [ abstract | bibtex | pdf ] |
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 et al. [70 add. authors including Zeller G].
Enterotypes of the human gut microbiome. Nature, 473(7346):174-80, 2011. DOI: 10.1038/nature09944 PMID: 21508958 [ abstract | bibtex | pdf ] |
| Eichner J, Zeller G, Laubinger S and Rätsch G.
Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays. BMC Bioinformatics, 12:55, 2011. DOI: 10.1186/1471-2105-12-55 PMID: 21324185 [ abstract | bibtex | pdf ] |
| 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 and Miller III DM.
A spatial and temporal map of C. elegans gene expression. Genome Res, 21(2):325-41, 2011. DOI: 10.1101/gr.114595.110 PMID: 21177967 [ abstract | bibtex | pdf ] |
| Hallem EA, Spencer WC, McWhirter RD, Zeller G, Henz SR, Rätsch G, Miller DM 3rd, Horvitz HR, Sternberg PW and Ringstad N.
Receptor-type guanylate cyclase is required for carbon dioxide sensation by Caenorhabditis elegans. Proc Natl Acad Sci U S A, 108(1):254-9, 2011. DOI: 10.1073/pnas.1017354108 PMID: 21173231 [ abstract | bibtex | pdf ] |
| Brouwers L, Iskar M, Zeller G, van Noort V and Bork P.
Network neighbors of drug targets contribute to drug side-effect similarity. PLoS One, 6(7):e22187, 2011. DOI: 10.1371/journal.pone.0022187 PMID: 21765950 [ abstract | bibtex | pdf ] |
| Conference Proceedings (1) |
| Görnitz N☯, Widmer CK☯, Zeller G, Kahles A, Sonnenburg S, Rätsch G.
Hierarchical multitask structured output learning for large-scale sequence segmentation. Advances in Neural Information Processing Systems (NIPS), 24:2690-2698, 2011. link to NIPS proceedings [ abstract | bibtex | pdf ] |
Other Invited Publications (1) |
| Zeller G.
Maschinelle Lernmethoden zur Analyse von Tiling-Array-Daten. [summary of my PhD Thesis in German] GI-Edition - Lecture Notes in Informatics, D-11 (Ausgezeichnete Informatikdissertationen 2010), pp. 371-380, 2011. link to GI-Edition - LNI, D-11 [ abstract | pdf ] |
| 2010 |
| Journal Articles (3) |
| 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☯ et al. [117 add. authors including Zeller G].
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science, 330(6012):1775-87, 2010. DOI: 10.1126/science.1196914 PMID: 21177976 [ abstract | bibtex | pdf ] |
| Laubinger S☯, Zeller G☯, Henz SR, Buechel S, Sachsenberg T, Wang JW, Rätsch G and Weigel D.
Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome. Proc Natl Acad Sci U S A, 107(41):17466-73, 2010. DOI: 10.1073/pnas.1012891107 PMID: 20870966 [ abstract | bibtex | pdf ] |
| 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 and Hennig L.
AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling. Plant Physiol, 152(2):487-99, 2010. DOI: 10.1104/pp.109.150185 PMID: 20032078 [ abstract | bibtex | pdf ] |
| Thesis (1) |
| Zeller G.
Machine learning algorithms for the analysis of data from whole-genome tiling microarrays. PhD Thesis, University of Tübingen, 2010. link to electronic library [ abstract | bibtex | pdf ] |
| 2009 |
| Journal Articles (6) |
| 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 and Rätsch G.
mGene: accurate SVM-based gene finding with an application to nematode genomes. Genome Res, 19(11):2133-43, 2009. DOI: 10.1101/gr.090597.108 PMID: 19564452 [ abstract | bibtex | pdf ] |
| 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 and Leach JE.
Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci U S A, 106(30):12273-8, 2009. DOI: 10.1073/pnas.0900992106 PMID: 19597147 [ abstract | bibtex | pdf ] |
| Schweikert G, Behr J, Zien A, Zeller G, Ong CS, Sonnenburg S and Rätsch G.
mGene.web: a web service for accurate computational gene finding. Nucleic Acids Res, 37(Web Server issue):W312-6, 2009. DOI: 10.1093/nar/gkp479 PMID: 19494180 [ abstract | bibtex | pdf ] |
| Zeller G☯, Henz SR☯, Widmer CK, Sachsenberg T, Rätsch G, Weigel D and Laubinger S.
Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays. Plant J, 58(6):1068-82, 2009. DOI: 10.1111/j.1365-313X.2009.03835.x PMID: 19222804 [ abstract | bibtex | pdf ] |
| Plantegenet S, Weber J, Goldstein DR, Zeller G, Nussbaumer C, Thomas J, Weigel D, Harshman K and Hardtke CS.
Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance. Mol Syst Biol, 5:242, 2009. DOI: 10.1038/msb.2008.79 PMID: 19225455 [ abstract | bibtex | pdf ] |
| Naouar N, Vandepoele K, Lammens T, Casneuf T, Zeller G, van Hummelen P, Weigel D, Rätsch G, Inzé D, Kuiper M, De Veylder L and Vuylsteke M.
Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes. Plant J, 57(1):184-94, 2009. DOI: 10.1111/j.1365-313X.2008.03662.x PMID: 18764924 [ abstract | bibtex | pdf ] |
| 2008 |
| Journal Articles (3) |
| Laubinger S, Sachsenberg T, Zeller G, Busch W, Lohmann JU, Rätsch G and Weigel D.
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):8795-800, 2008. DOI: 10.1073/pnas.0802493105 PMID: 18550839 [ abstract | bibtex | pdf ] |
| Zeller G, Clark RM☯, Schneeberger K☯, Bohlen A, Weigel D and Rätsch G.
Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays. Genome Res, 18(6):918-29, 2008. DOI: 10.1101/gr.070169.107 PMID: 18323538 [ abstract | bibtex | pdf ] |
| Laubinger S, Zeller G, Henz SR, Sachsenberg T, Widmer CK, Naouar N, Vuylsteke M, Schölkopf B, Rätsch G and Weigel D.
At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana. Genome Biol, 9(7):R112, 2008. DOI: 10.1186/gb-2008-9-7-r112 PMID: 18613972 [ abstract | bibtex | pdf ] |
| Conference Proceedings (1) |
| Zeller G, Henz SR, Laubinger S, Weigel D and Rätsch G.
Transcript normalization and segmentation of tiling array data. Pac Symp Biocomput, :527-38, 2008. PMID: 18229713 [ abstract | bibtex | pdf ] |
| Before 2008 |
| Journal Articles (1) |
| 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 and Weigel D.
Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science, 317(5836):338-42, 2007. DOI: 10.1126/science.1138632 PMID: 17641193 [ abstract | bibtex | pdf ] |
| Thesis (1) |
| Zeller G.
Resequencing data of 20 Arabidopsis ecotypes. Diplom Thesis (Master's equivalent), University of Tübingen, 2005. [ abstract | bibtex | pdf ] |
☯ these authors contributed equally.
Updated on 15 December 2013