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Publications

References to publications, sorted by year and author.
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2012 Lisa Smith, Lisa Hartmann, Philipp Drewe, Regina Bohnert, André Kahles, Christa Lanz and Gunnar Rätsch (2012).
Multiple insert size paired-end sequencing for deconvolution of complex transcriptomes.
RNA biology Volume 9, Issue 5 May 2012.
Supplementary material
Preußner M, Schreiner S, Hung LH, Porstner M, Jäck HM, Benes V, Rätsch G, Bindereif A (2012).
HnRNP L and L-like cooperate in multiple-exon regulation of CD45 alternative splicing.
Nucleic Acids Res. 2012 Mar 8.
Supplementary material
2011 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).
Supplementary material
Gan, X, Stegle, O, Behr, J, Steffen, JG, Drewe, P, Hildebrand, KL, Lyngsoe, R, Schultheiss, SJ, Osborne, EJ, Sreedharan, VT, Kahles, A, Bohnert, R, Jean, G, Derwent, P, Kersey, P, Belfield, EJ, Harberd, NP, Kemen, E, Toomajian, C, Kover, PX, Clark, RM, Ratsch, G, and Mott, R (2011).
Multiple reference genomes and transcriptomes for Arabidopsis thaliana.
Nature.
Printable file Supplementary website
Georgii, E, Tsuda, K, and Schölkopf, B (2011).
Multi-way set enumeration in weight tensors
Machine Learning, 82(2):123-155.
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.
Rösel, T, Hung, L, Medenbach, J, Donde, K, Benes, V, Rätsch, G, and Bindereif, A (2011).
RNA-Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation
EMBO Journal, 30:1965 - 1976.
Schultheiss, SJ (2011).
Ten Simple Rules for Providing a Scientific Web Resource
PLoS Computational Biology, 7(5):e1001126.
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.
Schultheiss, SJ, Münch, M, Andreeva, GD, and Rätsch, G (2011).
Persistence and Availability of Web Services in Computational Biology
PLoS ONE, 6(9):e24914.
Widmer, C and Rätsch, G (2011).
Transfer Learning in Computational Biology
In: Proceedings on the Workshop on Unsupervised and Transfer Learning, ed. by Isabelle Guyon and Danny Silver, JMLR.
2010 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.
Supplementary material
Bohnert, R and Rätsch, G (2010).
rQuant.web: a tool for RNA-Seq-based transcript quantitation
Nucleic Acids Research, 38(Suppl 2):W348-51.
Printable file Supplementary material Supplementary website
Busch, W, Miotk, A, Ariel, F, Forner, J, Daum, G, Suzaki, T, Schuster, C, Schultheiss, SJ, Leibfried, A, Haubeiß, S, Ha, N, Chan, R, and Lohmann, J (2010).
Transcriptional Control of a Plant Stem Cell Niche
Developmental Cell, 18(5):849-861.
Printable file Supplementary website
De Bona, F, Hall, K, Riezler, S, Ciaramita, M, Herdagdelen, A, and Holmqvist, M (2010).
Learning Dense Models of Query Similarity from User Click Logs
In: NAACL 2010.
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
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.
Printable file Supplementary material
Jean, G, Kahles, A, Sreedharan, VT, De Bona, F, and Rätsch, G (2010).
RNA-Seq Read Alignments with PALMapper
Curr. Protoc. Bioinform., 32:11.6.1- 11.6.37.
Printable file Supplementary website
Kloft, M, Brefeld, U, Sonnenburg, S, and Zien, A (2010).
Non-Sparse Regularization and Efficient Training with Multiple Kernels
University of California, Berkeley.
Printable file
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.
Printable file Supplementary material
Rätsch, G and Bohnert, R (2010).
Modern Methods for Transcriptome Reconstruction
In: Jahresbericht der Max-Planck-Gesellschaft, Max-Planck-Gesellschaft, München.
Printable file Supplementary material
Schultheiss, SJ (2010).
Kernel-based identification of regulatory modules
In: Computational Biology of Transcription Factor Binding, ed. by Istvan Ladunga. Springer, Heidelberg, chap. 13, pp. 213-224.
Sonnenburg, S and Franc, V (2010).
COFFIN : A Computational Framework for Linear SVMs
In: Proc. ICML 2010.
Printable file Supplementary website
Sonnenburg, S, Rätsch, G, Henschel, S, Widmer, C, Behr, J, Zien, A, de Bona, F, Binder, A, Gehl, C, and Franc, V (2010).
The SHOGUN Machine Learning Toolbox
Journal of Machine Learning Research, 11:1799-1802.
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.
Printable file Supplementary website
Stegle, O, Drewe, P, Bohnert, R, Borgwardt, K, and Rätsch, G (2010).
Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts
Preprint.
Printable file Supplementary material Supplementary website
Toussaint, NC, Widmer, C, Kohlbacher, O, and Rätsch, G (2010).
Exploiting Physico-Chemical Properties in String Kernels
BMC Bioinformatics, 11(Suppl. 8):S7.
Printable file Supplementary material
 
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