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Group web servers and resources
We have updated and consolidated the web servers and resources provided/maintained by the group.
Simple Alignment Filtering Tool (SAFT) released
We released the first version of the Simple Alignment Filtering Tool SAFT
Another successful HiTSeq this year
We coorganized the 5th Conference on High-throughput Sequencing in Long Beach, California (http://hitseq.org).
Postdoc Positions in Computational Biology available
We are looking for enthusiastic candidates for postdoctoral positions interested in applying/developing data analysis techniques for deep sequencing, systems biology and statistical genetics aiming to advance a) the systemic understanding of molecular and disease phenotypes and b) personalized medicine and treatment.
Elisabeth Georgii's defense on Dec 15, 2010
Elisabeth Georgii will defend her doctoral thesis on Dec 15, 2010 at the Eberhard-Karls-Universität Tübingen.
Georg Zeller received his doctoral degree
Georg Zeller received his doctoral degree (Dr. rer. nat.) with summa cum laude from the Eberhard-Karls-Universität Tübingen.
Paper on Transfer Learning and Sequence Segmentation accepted at NIPS'11
A paper "Hierarchical Multitask Structured Output Learning for Large-scale Sequence Segmentation" by Nico Görnitz, Christian Widmer, Georg Zeller, Sören Sonnenburg, and Gunnar Rätsch was accepted at NIPS 2011.
Machine Learning in Systems Biology meeting
We are co-organizing the Machine Learning in Systems Biology meeting in September 2012 in Basel (http://mlsb.cc).
The group will join the Sloan-Kettering Institute in New York City in January 2012
Most members of the group will join the cBio department at the Sloan-Kettering Institute in New York City in January 2012.
Paper about a faster way to train sequence classifiers has been accepted for presentation at ICML 2010.
The paper "COFFIN : A Computational Framework for Linear SVMs" by Sören Sonnenburg and Vojtech Franc has been accepted for publication at ICML'2010.
Paper on Genome-wide SNP variation analysis in rice published in PNAS.
A paper "Genome-wide SNP variation reveals relationships among landraces and modern varieties of rice" by Kenneth L. McNally, Kevin L. Childs, Regina Bohnert, Rebecca M. Davidson, Keyan Zhao, Victor J. Ulat, Georg Zeller, Richard M. Clark, Douglas R. Hoen, Thomas E. Bureau, Renee Stokowski, Dennis G. Ballinger, Kelly A. Frazer, David R. Cox, Badri Padhukasahasram, Carlos D. Bustamante, Detlef Weigel, David J. Mackill, Richard M. Bruskiewich, Gunnar Rätsch, C. Robin Buell, Hei Leung, and Jan E. Leach has been published in PNAS.
New release of the spliced-alignment tool QPALMA
QPalma is an alignment tool targeted to align spliced reads produced by Next Generation sequencing platforms such as Illumina Solexa or 454. We have released QPALMA version 0.9.9, which is considerably easier to install and use.
Paper on a novel Support Vector Machine-based Gene Finding System has been accepted for publication in Genome Research
A paper "mGene: Accurate SVM-Based Gene Finding with an Application to Nematode Genomes" by Gabriele Schweikert, Alexander Zien, Georg Zeller, Jonas Behr, Christoph Dieterich, Cheng Soon Ong, Petra Philips, Fabio De Bona, Lisa Hartmann, Anja Bohlen, Nina Krüger, Sören Sonnenburg, Gunnar Rätsch has been accepted for publication in Genome Research.
Paper on Arabidopsis genome tiling array resource published in Genome Biology
A paper "At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana" by Sascha Laubinger, Georg Zeller, Stefan Henz, Timo Sachsenberg, Christian Widmer, Naira Naouar, Marnik Vuylsteke, Bernhard Schölkopf, Gunnar Rätsch and Detlef Weigel has been published in Genome Biology.
Paper on Domain Adaptation accepted at NIPS'08
A paper "An empirical Analysis of Domain Adaptation Algorithms " by Gabriele Schweikert, Christian Widmer, Bernhard Schölkopf, and Gunnar Rätsch was accepted at NIPS 2008.
Paper on Optimized Cutting Plane Algorithm accepted by Journal of Machine Learning Research
A paper "Optimized Cutting Plane Algorithm for Large-Scale Risk Minimization" by Vojtech Franc and Sören Sonnenburg was accepted for publication in Journal of Machine Learning Research.
Paper on taxonomy-based transfer learning for Sequence classification of has been accepted for RECOMB 2010
A paper "Leveraging Sequence Classification by Taxonomy-based Multitask Learning" by Christian Widmer, Jose Leiva, Yasemin Altun, and Gunnar Rätsch has been accepted for RECOMB 2010
Paper on the SHOGUN Machine Learning Toolbox published in Journal of Machine Learning Research
A paper entitled "The SHOGUN Machine Learning Toolbo" by Sören Sonnenburg, Gunnar Rätsch, Sebastian Henschel, Christian Widmer, Jonas Behr, Alexander Zien, Fabio de Bona, Alexander Binder, Christian Gehl, and Vojtech Franc was accepted for publication in the MLOSS section of Journal of Machine Learning Research.
Presentations about Shogun have been accepted at SciPy, EuroPython and useR!
Oral presentations about the shogun machine learning toolbox have bee accepted for publications at several conferences.
Regina Bohnert was selected for an Anita Borg EMENA 2009 Scholarship
Regina Bohnert was selected for The Google Anita Borg Memorial Scholarship (Europe, the Middle East and North Africa).
Results of the nGASP competition with mGene predictions were published in BMC Bioinformatics
The paper "nGASP - the nematode genome annotation assessment project" by Avril Coghlan, Tristan J Fiedler, Sheldon J McKay, Paul Flicek, Todd W Harris, Darin Blasiar, The nGASP Consortium and Lincoln D Stein has been published in BMC Bioinformatics.
RNA-seq read alignment program PALMapper source code release
We have released the source code of PALMapper, a fusion of GenomeMapper and QPalma for RNA-seq read alignments.
Sören Sonnenburg received the Best Student Paper Award at ISMB
Sören Sonnenburg's paper "POIMs: Positional Oligomer Importance Matrices - Understanding Support Vector Machine Based Signal Detectors" was selected for the Best Student Paper Award at this years ISMB conference in Toronto.
The Scientists writes about QPALMA in the current issue
The scientist features an article "Benching Bases" which also writes about using QPALMA for mapping reads from RNA-Seq experiments.
Tutorial on Support Vector Machines and Kernels for Computational Biology accepted for PLoS Computational Biology
A paper "Support Vector Machines and Kernels for Computational Biology" by Asa Ben-Hur, Cheng Soon Ong, Sören Sonnenburg and Bernhard Schölkopf, and Gunnar Rätsch Weigel has been accepted for publication in PLoS Computational Biology.
Web-based Gene finding system mGene.web available and published in Nucleic Acids Research
mGene.web is a web service for the genome-wide prediction of protein coding genes from eukaryotic DNA sequences. Currently it is the only web-based gene finding system for eukaryotic genomes that can be adapted to new genomes. It has been described in a paper "mGene.web: a web service for accurate computational gene finding" by Gabriele Schweikert, Jonas Behr, Alexander Zien, Georg Zeller, Cheng Soon Ong, Sören Sonnenburg, and Gunnar Rätsch that recently been published in Nucleic Acids Research.
Gabriele Schweikert received her doctoral degree
Gabriele Schweikert received her doctoral degree (Dr. rer. nat.) with summa cum laude from the Technische Universität Berlin.
RNA-seq quantitation program rQuant source code release
We released the source code of rQuant, a tool for transcript quantitation from RNA-seq experiments.
Tutorial paper about how to use PALMapper was published in Current Protocols in Bioinformatics
A tutorial paper "RNA-Seq Read Alignments with PALMapper" by Geraldine Jean, Andre Kahles, Vipin T. Sreedharan, Fabio De Bona and Gunnar Raetsch was published in Current Protocols in Bioinformatics.
Best Oral Presentation Award Runner Up presented to Sebastian J. Schultheiss at SCS7
Sebastian J. Schultheiss received the 2nd place Oral Presentation Award at the 7th Student Council Symposium in Vienna, Austria.
Best paper award for paper on transfer learning
Christian Widmer and Gunnar Rätsch received the best paper award for their paper "Transfer Learning in Computational Biology".
PLoS ONE accepts publication on Persistence and Availability of Web Services in Computational Biology
A publication on the Persistence and Availability of Web Services in Computational Biology by Sebastian J. Schultheiss, Marc-Christian Münch, Gergana D. Andreeva and Gunnar Rätsch has been accepted by PLoS ONE.
Paper on the Analysis of 19 Genomes and Transcriptomes of Arabidopsis thaliana has been published in Nature
The paper "Multiple reference genomes and transcriptomes for Arabidopsis thaliana" by Xiangchao Gan, Oliver Stegle, Jonas Behr, Joshua G. Steffen, Philipp Drewe, Katie L. Hildebrand, Rune Lyngsoe, Sebastian J. Schultheiss, Edward J. Osborne, Vipin T. Sreedharan, André Kahles, Regina Bohnert, Géraldine Jean, Paul Derwent, Paul Kersey, Eric J. Belfield, Nicholas P. Harberd, Eric Kemen, Christopher Toomajian, Paula X. Kover, Richard M. Clark, Gunnar Rätsch & Richard Mott has been published in Nature.
