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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2008 Bartlett, PL, Mendelson, S, and Philips, P (2008).
Optimal sample-based estimates of the expectation of the empirical minimizer
ESAIM: Probability and Statistics (ESAIM: P&S), Accepted.

Behr, J (2008).
Improving Gene Finding Accuracy with Tiling Array and RNA-Seq Data
Diplom Thesis, Jonas Behr.

Ben-Hur, A, Ong, CS, Sonnenburg, S, Schölkopf, B, and Rätsch, G (2008).
Support Vector Machines and Kernels for Computational Biology
PLoS Computational Biology, 4(10):e1000173.
Online Access Printable file

Bohnert, R, Zeller, G, Clark, RM, Childs, KL, Ulat, V, Stokowski, R, Ballinger, D, Frazer, K, Cox, D, Bruskiewich, R, Buell, CR, Leach, J, Leung, H, McNally, KL, Weigel, D, and Rätsch, G (2008).
Revealing Sequence Variation Patterns in Rice with Machine Learning Methods
BMC Bioinformatics, 9(S10):O8.
Online Access Printable file

Coghlan, A, Fiedler, TJ, McKay, SJ, Flicek, P, Harris, TW, Blasiar, D, nGASP Consortium, LD, and Stein (2008).
nGASP – the nematode genome annotation assessment project
BMC Bioinformatics.
Online Access Printable file

De Bona, F, Ossowski, S, Schneeberger, K, and Rätsch, G (2008).
QPALMA: Optimal Spliced Alignments of Short Sequence Reads
In: Bioinformatics/Proc. ECCB'08, Oxford University Press.
Online Access Printable file

De Bona, F, Ossowski, S, Schneeberger, K, and Rätsch, G (2008).
QPALMA:: Optimal Spliced Alignments of Short Sequence Reads
In: BMC Bioinformatics, vol. 9((Suppl 10)), pp. O7, BioMed Central Ltd.
Online Access Printable file

Graf, A, Bousquet, O, Rätsch, G, and Schölkopf, B (2008).
Prototype Classification: Insights from Machine Learning
Neural Computation.
Printable file

Laubinger, S, Sachsenberg, T, Zeller, G, Busch, W, Lohmann, J, Rätsch, G, and Weigel, D (2008).
Dual roles of the nuclear cap binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana
PNAS, 105(25):8795-8800.
Printable file

Laubinger, S, Zeller, G, Henz, S, Sachsenberger, T, Widmer, C, Naouar, N, Vuylsteke, M, Schölkopf, B, Rätsch, G, and Weigel, D (2008).
At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana
Genome Biology, 9:R112.
Online Access Printable file

Ong, CS and Zien, A (2008).
An Automated Combination of Kernels for Predicting Protein Subcellular Localization
In: Proceedings of the 8th Workshop on Algorithms in Bioinformatics (WABI), pp. 186-179, Springer. Lecture Notes in Bioinformatics.
Online Access Printable file

Schultheiss, SJ, Busch, W, Lohmann, JU, Kohlbacher, O, and Rätsch, G (2008).
KIRMES: Kernel-based Identification of Regulatory Modules in Euchromatic Sequences
In: German Conference on Bioinformatics, ed. by A. Beyer and M. Schroeder, pp. 158-167, GI, Heidelberg, Springer Verlag. Lecture notes in Informatics.
Online Access Printable file

Schweikert, G, Widmer, C, Schölkopf, B, and Rätsch, G (2008).
An empirical Analysis of Domain Adaptation Algorithms
In: Proc. NIPS 2008. Advances in Neural Information Processing Systems.
Online Access Printable file

Sonnenburg, S (2008).
Machine Learning for Genomic Sequence Analysis
PhD thesis, Berlin Institute of Technology.
Printable file

Sonnenburg, S, Zien, A, Philips, P, and Rätsch, G (2008).
POIMs: Positional Oligomer Importance Matrices - Understanding Support Vector Machine Based Signal Detectors
In: Bioinformatics/Proc. ISMB 2008, vol. 24(13), pp. i6, Oxford University Press.
Online Access Printable file

Warmuth, MK, Glocer, K, and Rätsch, G (2008).
Boosting Algorithms for Maximizing the Soft Margin
In: Advances in Neural Information Processing Systems (NIPS'08), MIT Press.
Printable file

Widmer, C (2008).
Domain Adaptation in Sequence Analysis
Diplomarbeit, University of Tübingen.
Printable file

Zeller, G, Clark, R, Schneeberger, K, Bohlen, A, Weigel, D, and Rätsch, G (2008).
Detecting Polymorphic Regions in Arabidopsis thaliana with Resequencing Microarrays
Genome Research, 18(6):918-929.
Online Access Printable file

Zeller, G, Henz, S, Laubinger, S, Weigel, D, and Rätsch, G (2008).
Transcript Normalization and Segmentation of Tiling Array Data
In: Pacific Symposium on Biocomputing, vol. 13, pp. 527-538, Stanford, World Scientific.
Online Access Printable file

2007 Bohnert, R (2007).
Polymorphism Detection in Rice
Diplom thesis, Friedrich Miescher Laboratory of the Max Planck Society and Eberhard Karls Universität Tübingen.
Printable file

Clark, R, Schweikert, G, Toomajian, C, Ossowski, S, Zeller, G, Shinn, P, Warthmann, N, Hu, T, Fu, G, Hinds, D, Chen, H, Frazer, K, Huson, D, Schölkopf, B, Nordborg, M, Rätsch, G, Ecker, J, and Weigel, D (2007).
Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana
Science, 317(5836):338 - 342.
Printable file

Georgii, E, Dietmann, S, Uno, T, Pagel, P, and Tsuda, K (2007).
Mining expression-dependent modules in the human interaction network
BMC Bioinformatics, 8(Suppl. 8):S4.
Printable file

Rätsch, G and Sonnenburg, S (2007).
Large Scale Hidden Semi-Markov SVMs
In: Advances in Neural Information Processing Systems (NIPS'06), ed. by B. Schölkopf and J. Platt and T. Hoffman, vol. 19, pp. 1161-1168, Cambridge, MA, MIT Press.
Online Access Printable file

Rätsch, G, Sonnenburg, S, Srinivasan, J, Witte, H, Müller, KR, Sommer, R, and Schölkopf, B (2007).
Improving the C. elegans genome annotation using machine learning
PLoS Computational Biology, 3(2):e20.
Online Access Printable file

Schultheiss, SJ (2007).
Inferring Regulatory Networks
Diplom thesis, University of Tübingen, Tübingen, Germany.
Printable file

 
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