ARCHIVE Snapshot of the Rätsch lab website (Tübingen, then New York) as of February 2016: preserved, not maintained. The group today: bmi.inf.ethz.ch
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Bibliography

References to publications, sorted by year and author.
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2012 Kulemzina, I, Schumacher, M, Verma, V, Reiter, J, Metzler, J, Failla, A, Sreedharan, V, Rätsch, G, and Ivanov, D (2012).
Cohesin rings devoid of Scc3 and Pds5 maintain their stable association with the DNA.
PLoS Genetics.

Preußner, M, Schreiner, S, Hung, L, Porstner, M, Jäck, H, Benes, V, Rätsch, G, and Bindereif, A (2012).
HnRNP L and L-like cooperate in multiple-exon regulation of CD45 alternative splicing
Nucleic Acids Res.
Online Access Printable file

Smith, L, Hartmann, L, Drewe, P, Bohnert, R, Kahles, A, Lanz, C, and Rätsch, G (2012).
Multiple insert size paired-end sequencing for deconvolution of complex transcriptomes
RNA Biology, 9(5).
Online Access Supplementary website

Widmer, C and Rätsch, G (2012).
Multitask Learning in Computational Biology
In: ICML 2011 Unsupervised and Transfer Learning Workshop, ed. by Isabelle Guyon and Danny Silver, vol. 27, pp. 207-216, JMLR W&CP.
Printable file

Widmer, C, Kloft, M, Görnitz, N, and Rätsch, G (2012).
Efficient Training of Graph-Regularized Multitask SVMs
In: Proceedings of ECML 2012, Springer. Lecture Notes in Computer Science.
Printable file

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).
Online Access

Gan, X, Stegle, O, Behr, J, Steffen, JG, Drewe, P, Hildebrand, KL, Lyngsoe, R, Schultheiss, SJ, Osborne, EJ, Sreedharan, V, 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, 477:419–423.
Online Access Supplementary website Printable file

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.
Printable file

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.

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.
Online Access

Bohnert, R and Rätsch, G (2010).
rQuant.web: a tool for RNA-Seq-based transcript quantitation
Nucleic Acids Research, 38(Suppl 2):W348-51.
Online Access Supplementary website Printable file

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.
Supplementary website Printable file

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.
Online Access Printable file

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.
Supplementary website Printable file

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.
Online Access Printable file

Rätsch, G and Bohnert, R (2010).
Modern Methods for Transcriptome Reconstruction
In: Jahresbericht der Max-Planck-Gesellschaft, Max-Planck-Gesellschaft, München.
Online Access Printable file

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.
Supplementary website Printable file

 
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