Publications of VT Sreedharan

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)

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)

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)

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)

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)

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)

Sreedharan, V.; Schultheiss, S.; Jean, G.; Kahles, A.; Bohnert, R.; Drewe, P.; Mudrakarta, P.; Görnitz, N.; Zeller, G.; Rätsch, G.: Oqtans: a multifunctional workbench for RNA-seq data analysis. In BMC Bioinformatics, 15 (Supplement 13), A7. Ninth International Society for Computational Biology (ISCB) Student Council Symposium 2013, Berlin, Germany, July 19, 2013. BioMed Central (2014)

Schultheiss, S.; Jean, G.; Sreedharan, V.; Kahles, A.; Bohnert, R.; Drewe, P.; Mudrakarta, P.; Görnitz, N.; Zeller, G.; Rätsch, G.: Easier Workflows & Tool Comparison with Oqtans+. In Galaxy Community Conference 2012 (GCC 2012). Galaxy Community Conference 2012 (GCC 2012), Chacago, IL, USA, July 25, 2012 - July 27, 2012. (2012)

Schultheiss, S.; Jean, G.; Behr, J.; Bohnert, R.; Drewe, P.; Görnitz, N.; Kahles, A.; Mudrakarta, P.; Sreedharan, V.; Zeller, G. et al.; Rätsch, G.: Oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS Data. In BMC Bioinformatics, 12 (Supplement 11), A7. Seventh International Society for Computational Biology (ISCB) Student Council Symposium 2011 at ISMB/ECCB 2011, Wien, Austria, July 15, 2011. BioMed Central (2011)

Behr, J.; Clark, J.; Drewe, P.; Hildebrand, K.; Kover, P.; Lyngsoe, R.; Mott, E.; Osborne, R.; Rätsch, G.; Schultheiss, S. et al.; Sreedharan, V.; Steffen, J.; Stegle, O.; Toomajian, C.; Xiangchao, G.: Multiple reference genomes and transcriptomes for Arabidopsis thaliana. In HiTSeq 2011: Conference on High Throughput Sequencing Analysis and Algorithms, p. 22. HiTSeq 2011: Conference on High Throughput Sequencing Analysis and Algorithms, Wien, Austria, July 15, 2011 - July 16, 2011. (2011)

Sreedharan, V.: Reproducible Quantitative Transcriptome Analysis with oqtans. 14th Bioinformatics Open Source Conference, Berlin, Germany (2013)

Sreedharan, V.; Schultheiss, S.; Jean, G.; Kahles, A.; Bohnert, R.; Drewe, P.; Mudrakarta, P.; Görnitz, N.; Zeller, G.; Rätsch, G.: Oqtans: a multifunctional workbench for RNA-seq data analysis. 14th Annual Bioinformatics Open Source Conference (BOSC 2013), Berlin, Germany (2013)

Rätsch, G.; Gan, X.; Stegle, O.; Behr, J.; Drewe, P.; Drewe, P.; Steffen, J.; Clark, R.; Osborne, E.; Schultheiss, S. et al.; Sreedharan, V.; Kahles, A.; Bohnert, R.; Jean, G.; Hildebrand, K.; Toomajian, C.; Lyngsoe, R.; Derwent, P.; Kersey, P.; Belfield, E.; Harberd, N.; Kemen, E.; Kover, P.: Multiple reference genomes and transcriptomes for Arabidopsis thaliana. 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2012), Long Beach, CA, USA (2012)