Publications of G Rätsch

Dubin, M.; Zhang, P.; Meng, D.; Remigereau, M.-S.; Osborne, E.; Casale, F.; Drewe, P.; Kahles, A.; Jean, G.; Vilhjálmsson, B. et al.; Jagoda, J.; Irez, S.; Voronin, V.; Song, Q.; Long, Q.; Rätsch, G.; Stegle, O.; Clark, R.; Nordborg, M.: DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation. eLife 4, e05255 (2015)

Chae, E.; Bomblies, K.; Kim, S.-T.; Karelina, D.; Zaidem, M.; Ossowski, S.; Martín-Pizarro, C.; Laitinen, R.; Rowan, B.; Tenenboim, H. et al.; Lechner, S.; Demar, M.; Habring-Müller, A.; Lanz, C.; Rätsch, G.; Weigel, D.: Species-wide Genetic Incompatibility Analysis Identifies Immune Genes as Hot Spots of Deleterious Epistasis. Cell 159 (6), pp. 1341 - 1351 (2014)

Sreedharan, V.; Schultheiss, S.; Jean, G.; Kahles, A.; Bohnert, R.; Drewe, P.; Mudrakarta, P.; Görnitz, N.; Zeller, G.; Rätsch, G.: Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis. Bioinformatics 30 (9), pp. 1300 - 1301 (2014)

Engström, P.; Steijger, T.; Sipos, B.; Grant, G.; Kahles, A.; Rätsch, G.; Goldman, N.; Hubbard, T.; Harrow, J.; Guigó, R. et al.; Bertone, P.; RGASP Consortium: Systematic evaluation of spliced alignment programs for RNA-seq data. Nature Methods 10 (12), pp. 1185 - 1191 (2013)

Steijger, T.; Abril, J.; Engström, P.; Kokocinski, F.; Akerman, M.; Alioto, T.; Ambrosini, G.; Antonarakis, S.; Behr, J.; Bohnert, R. et al.; Bucher, P.; Cloonan, N.; Derrien, T.; Djebali, S.; Du, J.; Dudoit, S.; Gerstein, M.; Gingeras, T.; Gonzalez, D.; Grimmond, S.; Habegger, L.; Iseli, C.; Jean, G.; Kahles, A.; Kokocinski, F.; Lagarde, J.; Leng, J.; Lefebvre, G.; Lewis, S.; Mortazavi, A.; Niermann, P.; Rätsch, G.; Reymond, A.; Ribeca, P.; Richard, H.; Rougemont, J.; Rozowsky, J.; Sammeth, M.; Sboner, A.; Schulz, M.; Searle, S.; Solorzano, N.; Solovyev, V.; Stanke, M.; Steijger, T.; Stevenson, B.; Stockinger, H.; Valsesia, A.; Weese, D.; White, S.; Wold, B.; Wu, J.; Wu, T.; Zeller, G.; Zerbino, D.; Zhang, M.; Hubbard, T.; Guigó, R.; Harrow, J.; Bertone, P.: Assessment of Transcript Reconstruction Methods for RNA-seq. Nature Methods 10 (12), pp. 1177 - 1184 (2013)

Behr, J.; Kahles, A.; Zhong, Y.; Sreedharan, V.; Drewe, P.; Rätsch, G.: MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples. Bioinformatics 29 (20), pp. 2529 - 2538 (2013)

Drewe, P.; Stegle, O.; Hartmann, L.; Kahles, A.; Bohnert, R.; Wachter, A.; Borgwardt, K.; Rätsch, G.: Accurate detection of differential RNA processing. Nucleic Acids Research 41 (10), pp. 5189 - 5198 (2013)

Kulemzina, I.; Schumacher, M.; Verma, V.; Reiter, J.; Metzler, J.; Failla, A.; Lanz, C.; Sreedharan, V.; Rätsch, G.; Ivanov, D.: Cohesin rings devoid of Scc3 and Pds5 maintain their stable association with the DNA. PLoS Genetics 8 (8), e1002856 (2012)

Preussner, M.; Schreiner, S.; Hung, L.-H.; Porstner, M.; Jäck, H.-M.; Benes, V.; Rätsch, G.; Bindereif, A.: HnRNP L and L-like cooperate in multiple-exon regulation of CD45 alternative splicing. Nucleic Acids Research (London) 40 (12), pp. 5666 - 5678 (2012)

Smith, L.; Hartmann, L.; Drewe, P.; Bohnert, R.; Kahles, A.; Lanz, C.; Rätsch, G.: Multiple insert size paired-end sequencing for deconvolution of complex transcriptomes. RNA Biology 9 (5), pp. 596 - 609 (2012)

Gan, X.; Stegle, O.; Behr, J.; Steffen, J.; Drewe, P.; Hildebrand, K.; Lyngsoe , R.; Schultheiss, S.; Osborne, E.; Sreedharan, V. et al.; Kahles, A.; Bohnert, R.; Jean, G.; Derwent, P.; Kersey, P.; Belfield, E.; Harberd, N.; Kemen, F.; Toomajian, C.; Kover , P.; Clark, R.; Rätsch, G.; Mott, R.: Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477 (7365), pp. 419 - 423 (2011)

Schultheiss, S.; Münch, M.-C.; Andreeva, G.; Rätsch, G.: Persistence and availability of Web services in computational biology. PLoS One 6 (9), e24914 (2011)

Rösel, T.; Hung, L.-H.; Medenbach, J.; Donde, K.; Starke, S.; Benes, V.; Rätsch, G.; Bindereif, A.: RNA-Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation. EMBO Journal 30 (10), pp. 1965 - 1976 (2011)

Eichner, J.; Zeller, G.; Laubinger, S.; Rätsch, G.: Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays. BMC Bioinformatics 12, 55 (2011)

Spencer, W.; Zeller, G.; Watson, J.; Henz, S.; Watkins, K.; McWhirter, R.; Petersen, S.; Sreedharan, V.; Widmer, C.; Jo, J. et al.; Reinke, V.; Petrella, L.; Strohme, S.; Von Stetina, S.; Katz, M.; Shaham, S.; Rätsch, G.; Miller, D.: A spatial and temporal map of C. elegans gene expression. Genome Research 21 (2), pp. 325 - 341 (2011)

Hallem, E.; Spencer, W.; McWhirter, R.; Zeller, G.; Henz, S.; Rätsch, G.; Miller, D.; Horvitz, H.; Sternberg, P.; Ringstad, N.: Receptor-type guanylate cyclase is required for carbon dioxide sensation by Caenorhabditis elegans. Proceedings of the National Academy of Sciences of the United States of America 108 (1), pp. 254 - 259 (2011)

Gerstein, M.; Lu, Z.; Van Nostrand, E.; Cheng, C.; Arshinoff, B.; Liu, T.; Yip, K.; Robilotto, R.; Rechtsteiner, A.; Ikegami, K. et al.; Alves, P.; Chateigner, A.; Perry, M.; Morris, M.; Auerbach, R.; Feng, X.; Leng, J.; Vielle, A.; Niu, W.; Rhrissorrakrai, K.; Agarwal, A.; Alexander, R.; Barber, G.; Brdlik, C.; Brennan, J.; Brouillet, J.; Carr, A.; Cheung, M.-S.; Clawson, H.; Contrino, S.; Dannenberg, L.; Dernburg, A.; Desai, A.; Dick, L.; Dosé, A.; Du, J.; Egelhofer, T.; Ercan, S.; Euskirchen, G.; Ewing, B.; Feingold, E.; Gassmann, R.; Good, P.; Green, P.; Gullier, F.; Gutwein, M.; Guyer, M.; Habegger, L.; Han, T.; Henikoff, J.; Henz, S.; Hinrichs, A.; Holster, H.; Hyman, A.; Iniguez, A. L.; Janette, J.; Jensen, M.; Kato, M.; Kent, W. J.; Kephart, E.; Khivansara, V.; Khurana, E.; Kim, J. K.; Kolasinska-Zwierz, P.; Lai, E. C.; Latorre, I.; Leahey, A.; Lewis, S. E.; Lloyd, P.; Lochovsky, L.; Lowdon, R. F.; Lubling, Y.; Lyne, R.; MacCoss, M.; Mackowiak, S. D.; Mangone, M.; McKay, S.; Mecenas, D.; Merrihew, G.; Miller, D. M.; Muroyama, A.; Murray, J. I.; Ooi, S.-L.; Pham, H.; Phippen, T.; Preston, E. A.; Rajewski, N.; Rätsch, G.; Rosenbaum, H.; Rozowksy, J.; Rutherford, K.; Ruzanov, P.; Sarov, M.; Sasidharan, R.; Sboner, A.; Scheid, P.; Segal, E.; Shin, H.; Shou, C.; Slack, F. J.; Slightham, C.; Smith, R.; Spencer, W. C.; Stinson, E. O.; Taing, S.; Takasaki, T.; Vafeados, D.; Voronina, K.; Wang, G.; Washington, N. L.; Whittle, C. M.; Wu, B.; Yang, K.-K.; Zeller, G.; Zha, Z.; Zhong, M.; Zhou, X.; Ahringer, J.; Strome, S.; Gunsalus, K. C.; Micklem, G.; Liu, X. S.; Reinke, V.; Kim, S. K.; Hillier, L. W.; Henikoff, S.; Piano, F.; Snyder, M.; Stein, L.; Lieb, J. D.; Waterston, R. H.: Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 330 (6012), pp. 1775 - 1787 (2010)

Jean, G.; Kahles, A.; Sreedharan, V.; De Bona, F.; Rätsch, G.: RNA-Seq read alignments with PALMapper. Current Protocols in Bioinformatics Chapter 11 (Supplement 32), Unit 11.6 (2010)

Laubinger, S.; Zeller, G.; Henz, S.; Buechel, S.; Sachsenberg, T.; Wang, J.-W.; Rätsch, G.; Weigel, D.: Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome. Proceedings of the National Academy of Sciences of the United States of America 107 (41), pp. 17466 - 17573 (2010)

Bohnert, R.; Rätsch, G.: rQuant.web: a tool for RNA-Seq-based transcript quantitation. Nucleic Acids Research (London) 38, pp. W348 - W351 (2010)