The Rätsch laboratory advances computational methods for the analysis of big biomedical data. The group utilizes, develops, and integrates ideas from machine learning, operations research, sequence analysis, statistical genetics, text mining, and computer vision with the aim to discover relationships in complex biomedical data.

Publications

Selected Publications

Behr J, A Kahles, Y Zhong, VT Sreedharan, P Drewe, G Rätsch. MiTie: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples. Bioinformatics, 29(20):2529-38, 2013. [Pubmed], [PDF].

Drewe P, O Stegle, L Hartmann L, A Kahles, R Bohnert, A Wachter, K Borgwardt, G Rätsch. Accurate detection of differential RNA processing. Nucleic Acids Res., 41(10):5189-98, 2013. [Pubmed], [PDF].

Engström PG, T Steijger, B Sipos, GR Grant, A Kahles, RGASP Consortium, G Rätsch, N Goldman, TJ Hubbard, J Harrow, R Guigo, P Bertone. Systematic evaluation of spliced aligners for RNA-seq. Nature Methods, Epub November 4th, 2013. [Pubmed], [PDF].

Gan X, O Stegle O, J Behr, JG Steffen, P Drewe, KL Hildebrand, R Lyngsoe, SJ Schultheiss, EJ Osborne, VT Sreedharan, A Kahles, R Bohnert, G Jean, P Derwent, P Kersey, EJ Belfield, NP Harberd, E Kemen, C Toomajian, PX Kover, RM Clark, G Rätsch, R Mott. Multiple reference genomes and transcriptomes for A. thaliana. Nature, 477(7365):419-23, 2011. [Pubmed], [PDF].

Spencer WC, G Zeller, JD Watson, SR Henz, KL Watkins, RD McWhirter, S Petersen, VT Sreedharan, C, Widmer, J Jo, V Reinke, L Petrella, S Strome, SE Von Stetina, M Katz, S Shaham, G Rätsch, DM Miller, 3rd. A spatial and temporal map of C. elegans gene expression. Genome Res, Jan 2011. [Pubmed], [PDF].

Ben-Hur A, CS Ong, Sonnenburg S, Schölkopf B, G Rätsch. Support Vector Machines and Kernels for Computational Biology. PLoS Comput Biol 4(10): e1000173, 2008. [Pubmed], [PDF].

Clark RM, G Schweikert, C Toomajian, S Ossowski, G Zeller, P Shinn, N Warthmann, TT Hu, G Fu, D Hinds, H Chen, K Frazer, D Huson, B Schölkopf, M Nordborg, G Rätsch, J Ecker, D Weigel. Common sequence polymorphisms shaping genetic diversity in A. thaliana. Science, 317(5836):338-342, 2007. [Pubmed], [PDF].

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Office phone:
646-888-2802
Office fax:
646-888-3105
Selected Achievements

Suite of innovative analysis tools for deep RNA sequencing (RNA-Seq)

Algorithmic and theoretical contributions in machine learning

Large-scale algorithms for sequence classification and gene annotation

Olympus Award of the German Society of Pattern Recognition (2007)

Max Planck Young and Independent Investigator Award (2005-2011)