Publications of Georg Zeller

2011

Schultheiss, SJ, Jean, G, Behr, J, Drewe, P, Görnitz, N, Kahles, A, Mudrakarta, P, Sreedharan, VT, Zeller, G, and Rätsch, G (2011). oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS data In: 7th ISCB Student Council Symposium, ed. by Priscilla Grynberg, vol. 12(Suppl 11), pp. A7, ISCBSC, Vienna, Austria, BMC Bioinformatics.

Eichner, J, Zeller, G, Laubinger, S, and Rätsch, G (2011). Detection of Alternative Splicing in Arabidopsis thaliana from Whole-Genome Tiling Arrays with Support Vector Machines BMC Bioinformatics, 12(55). Online access

Görnitz, N, Widmer, C, Zeller, G, Kahles, A, Sonnenburg, S, and Rätsch, G (2011). Hierarchical Multitask Structured Output Learning for Large-scale Sequence Segmentation In: Advances in Neural Information Processing Systems (NIPS'11), NIPS Foundation. Printable file

2010	Laubinger, S, Zeller, G, Henz, SR, Buechel, S, Sachsenberg, T, Wang, J, Rätsch, G, and Weigel, D (2010). Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome PNAS. Online access Printable file

Spencer, WC, Zeller, G, Watson, JD, Henz, SR, Watkins, KL, McWhirter, RD, Petersen, S, Sreedharan, VT, Widmer, C, Reinke, V, Petrella, L, Strome, S, Von Stetina, S, Katz, M, Rätsch, G, and Miller III, DM (2010). A Spatial and Temporal Map of C. elegans Gene Expression Genome Research. Supplementary website Printable file

Hallem, EA, Spencer, WC, McWhirter, RD, Zeller, G, Henz, SR, Rätsch, G, Miller III, DM, Horvitz, HR, Sternberg, PW, and Ringstad, N (2010). A receptor-type guanylate cyclase is required for carbon dioxide sensation by C. elegans PNAS. Online access Printable file

Gerstein, MB, et al.,, Henz, SR, et al.,, Rätsch, G, et al.,, Zeller, G, et al.,, and Waterston, RH (2010). Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project Science, 330(6012):1775-1787. Printable file

Behr, J, Bohnert, R, Zeller, G, Schweikert, G, Hartmann, L, and Rätsch, G (2010). Next generation genome annotation with mGene.ngs BMC Bioinformatics, 11(S10):O8. Online access

2009	Schweikert, G, Behr, J, Zien, A, Zeller, G, Ong, CS, Sonnenburg, S, and Rätsch, G (2009). mGene.web: a web service for accurate computational gene finding Nucleic Acids Research, 37(Web Server issue):W312–W316. Online access Printable file

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 (2009). mGene: Accurate SVM-Based Gene Finding with an Application to Nematode Genomes Genome Research, 19:2133-2143. Online access Supplementary website Printable file

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 (2009). Quantitative RNA expression analysis with Affymetrix Tiling 1.0R Arrays identifies new E2F target genes Plant Journal, 57(1):184-194. Printable file

Zeller, G, Henz, SR, Widmer, CK, Sachsenberg, T, Rätsch, G, Weigel, D, and Laubinger, S (2009). Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole genome tiling arrays Plant Journal, 58(6):1068-1082. Online access Printable file

Plantegenet, S, Weber, J, Goldstein, DR, Zeller, G, Nussbaumer, C, Thomas, J, Weigel, D, Harshmann, K, and Hardtke, CS (2009). Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance Molecular Systems Biology, 5:Article 242. Printable file

Zeller, G (2009). Machine Learning Algorithms for the Analysis of Data from Whole-Genome Tiling Microarrays PhD thesis, Universitaet Tuebingen. Online access Printable file

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 (2009). Genomewide SNP variation reveals relationships among landraces and modern varieties of rice Proceedings of the National Academy of Sciences, 106(30):12273-8. Online access Supplementary website Printable file

2008	Zeller, G, Henz, S, Laubinger, S, Weigel, D, and Rätsch, G (2008). Transcript Normalization and Segmentation of Tiling Array Data In: Pacific Symposium on Biocomputing, vol. 13, pp. 527-538, Stanford, World Scientific. Online access Printable file

Zeller, G, Clark, R, Schneeberger, K, Bohlen, A, Weigel, D, and Rätsch, G (2008). Detecting Polymorphic Regions in Arabidopsis thaliana with Resequencing Microarrays Genome Research, 18(6):918-929. Online access Printable file

Laubinger, S, Sachsenberg, T, Zeller, G, Busch, W, Lohmann, J, Rätsch, G, and Weigel, D (2008). Dual roles of the nuclear cap binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana PNAS, 105(25):8795-8800. Printable file

Laubinger, S, Zeller, G, Henz, S, Sachsenberger, T, Widmer, C, Naouar, N, Vuylsteke, M, Schölkopf, B, Rätsch, G, and Weigel, D (2008). At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana Genome Biology, 9:R112. Online access Printable file

Bohnert, R, Zeller, G, Clark, RM, Childs, KL, Ulat, V, Stokowski, R, Ballinger, D, Frazer, K, Cox, D, Bruskiewich, R, Buell, CR, Leach, J, Leung, H, McNally, KL, Weigel, D, and Rätsch, G (2008). Revealing Sequence Variation Patterns in Rice with Machine Learning Methods BMC Bioinformatics, 9(S10):O8. Online access Printable file

2007

Clark, R, Schweikert, G, Toomajian, C, Ossowski, S, Zeller, G, Shinn, P, Warthmann, N, Hu, T, Fu, G, Hinds, D, Chen, H, Frazer, K, Huson, D, Schölkopf, B, Nordborg, M, Rätsch, G, Ecker, J, and Weigel, D (2007). Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana Science, 317(5836):338 - 342. Printable file

2005	Zeller, G (2005). Resequencing Data of 20 Arabidopsis Ecotypes Diplomarbeit, Universität Tübingen. Printable file