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Latest group news
Gabriele Schweikert received her doctoral degree
Gabriele Schweikert received her doctoral degree (Dr. rer. nat.) with summa cum laude from the Technische Universität Berlin.
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.
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 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.
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.
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.
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 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.
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.
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.
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.
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).
Meeting of the Regional Student Group Germany in Stockholm at ISMB
Prior to the 5th ISCB Student Council Symposium and the ISMB 2009 conference in Stockholm, the Regional Student Group Germany, represented by Regina Bohnert and Sebastian J. Schultheiss, invite you to join us for dinner on June 26th, 2009.
Paper on KIRMES and Regulatory Modules Kernel accepted by Bioinformatics
The article "KIRMES: Kernel-based identification of regulatory modules in euchromatic sequences" has been accepted.
