Talks & Lectures

Below is an incomplete list of talks, lectures and tutorials given by group members.

2011

Talk on "Simultaneous RNA-seq-based Transcript Inference and Quantification Using Mixed Integer Programming" by Jonas Behr at the NIPS Machine Learning in Comp Bio Workshop in Sierra Nevada, Spain, on December 17, 2011.
Invited talk on "A spatial and temporal map of C. elegans gene expression" by Gunnar Rätsch at the Memorial Sloan-Kettering Cancer Center in New York City, USA, on August 30, 2011.
Invited talk on "Towards Empirical Models of the Central Dogma" by Gunnar Rätsch at the Institute of Science and Technology in Vienna, Austria, on July 25, 2011.

Talk on "oqtans -- A Galaxy-integrated workflow for quantitative transcriptome analysis from NGS data" by Geraldine Jean and Sebastian J Schultheiss at the Technology Track of ISMB/ECCB 2011 in Vienna, Austria, on July 19, 2011.

Presentation of "Oqtans - A Galaxy-integrated workflow for quantitative transcriptome analysis from NGS data" by Sebastian J Schultheiss at the 7th Student Council Symposium in Vienna, Austria on July 15, 2011. Winner of the 2nd place Best Oral Presentation Award.

Talk on "Quantitatively Deconvolving Alternative RNA Secondary Structures" by Regina Bohnert at the Short-SIG of ISMB/ECCB 2011 in Vienna, Austria, on July 15, 2011.

Invited talk on "Transfer Learning in Computational Biology" at the Workshop on Unsupervised and Transfer Learning by Gunnar Rätsch in Bellevue, WA, on July 2, 2011.

Invited talk on "Towards Empirical Models of the Central Dogma of Molecular Biology" at the Frankfurt Institute for Advanced Studies in Frankfurt, Germany, on May 26, 2011.

Conference talk entitled "Efficient Tool Deployment to the Galaxy Cloud An RNA-Seq Workflow Case Study" at the Galaxy Community Conference 2011 by Sebastian J Schultheiss on May 25, 2011. Watch the video.

Invited talk on "Machine Learning for Understanding Transcriptome Complexity and Plasticity" at the Max Planck Institute for Molecular Cell Biology and Genetics in Dresden, Germany, on May 16, 2011.

Talks on "Computational Challenges in RNA-seq-based Transcriptome Reconstruction" and "Towards the Understanding of Transcriptome Variation" by Gunnar Rätsch at the Symposium at the Max Delbrück Center in Berlin, Germany, on April 18 & 19, 2011.
Talk on "Accurate RNA-seq alignments with Palmapper" by Gunnar Rätsch at the RGASP.3 Workshop in Barcelona, Spain, on April 6, 2011.

Talk on "Evaluation of RGASP.2 Read Alignment Submissions" by Gunnar Rätsch at the RGASP.3 Workshop in Barcelona, Spain, on April 6, 2011.

Talk on "mTiM - margin-based transcript mapping from RNA-seq" by Nico Görnitz at the RECOMB Satellite Workshop on Massively Parallel Sequencing 2011 in Vancouver, Canada, on March 26, 2011.

2010

Talk on "Multitask Multiple Kernel Learning" by Christian Widmer at the NIPS workshop on New Directions in Multiple Kernel Learning, Whister, B.C., on December 11, 2010.

Invited talk on "Methods for Quantitative RNA-seq-based Genome Analyses" by Gunnar Rätsch at the Memorial Sloan-Kettering Cancer Center in New York City, USA, on December 6, 2010.
Invited talk on "Fully Automated Genome Annotation with Deep RNA Sequencing" by Gunnar Rätsch at the 2nd Bio-IT World Europe in Hannover, Germany, on October 5, 2010.
Short Course on "Kernel Methods for Fusing Diverse Biomedical Data" by Gunnar Rätsch at the 2nd Bio-IT World Europe in Hannover, Germany, on October 4, 2010.
Talk on "Novel Machine Learning Methods for MHC Class I Binding Prediction" by Christian Widmer at the Pattern Recognition in Bioinformatics (PRIB 2010), Nijmegen, The Netherlands, on September 23, 2010.

Talk on "De novo RNA-seq-based Genome Annotation" by Gunnar Rätsch at the Genome Informatics Meeting in Hinxton, UK, on September 19, 2010.
Tutorials on "Introduction to Genomics and Predictive Sequence Analysis" and "Functional Genomics by Deep Sequencing" by Gunnar Rätsch at the Bioinformatics Summer School in Erice, Italy, on September 13-14, 2010.
Invited talk on "Regularization Methods for Sequence Analysis" by Gunnar Rätsch at the Workshop "Regularized Estimation for modeling of molecular data" (GMDS 2010) in Mannheim, on September 6, 2010.
Talk on "Leveraging Sequence Classification by Taxonomy-based Multitask Learning" by Christian Widmer at the Conference on Research in Computational Molecular Biology 2010 (RECOMB 2010) in Lisbon, Portugal, on August 15, 2010.
Talk on "SHOGUN - A Large Scale Machine Learning Toolbox (R interface)" by Christian Widmer at The R User Conference 2010 (useR! 2010) in Gaithersburg, Maryland, U.S.A., on July 22, 2010.
Tutorial "Functional Genomics with Deep Sequencing" by Gunnar Rätsch and Ali Mortazavi at ISMB 2010 in Boston, USA, on July 10, 2010.

Talk on "RGASP Evaluation of RNA-Seq Read Alignment Algorithms" by Gunnar Rätsch at the Conference on High Throughput Sequencing (Hitseq 2010) in Boston, U.S.A., on July 10, 2010.
Talk on "Long-term Availability of Bioinformatics Web Services" by Sebastian J Schultheiss at the 2010 ISMB SIG Bioinformatics Open Source Conference (BOSC) in Boston, USA, on July 10, 2010.

Talk on "Next Generation Genome Annotation with mGene.ngs" by Jonas Behr at ISCB Student Council Symposium in Boston, USA, on July 9, 2010.

Talk on "Online Quantitative Transcriptome Analysis" by Gunnar Rätsch at the Conference on High Throughput Sequencing (Hitseq 2010) in Boston, U.S.A., on July 9, 2010.
Talk on "SHOGUN - A Large Scale Machine Learning Toolbox (python interface)" by Christian Widmer at the Python for Scientific Computing Conference 2010 (SciPy 2010) in Austin, TX, U.S.A., on June 30, 2010.
Invited talk on "Computational Challenges in RNA-seq-based Transcriptome Reconstruction" by Gunnar Rätsch at the StatSeq meeting in Ghent, Belgium, on May 20/21, 2010.
Invited talk on the Transcriptome Analysis with Galaxy by Gunnar Rätsch at the Galaxy Developer Meeting at CSHL on May 16, 2010.
Invited talk on "Machine Learning Methods for RNA-seq-based Transcriptome Reconstruction" by Gunnar Rätsch at the NGS Bioinformatics meeting in Paris, France, on March 24, 2010.
Tutorial "An Introductions to Modern Methods for Transcriptome Analysis" by Gunnar Rätsch at the 10th Spring School on Bioinformatics and Systems Biology in Hohenkammer, Germany, on March 16, 2010.

2009

Talk on "Transfer Learning Methods and Applications in Computational Biology" by Gunnar Rätsch at the NIPS workshop on Transfer Learning for Structured Data, Whister, B.C., on December 12, 2009. Supplementary Website

Talk on "Scalable Hierarchical Multitask Learning in Sequence Biology" by Christian Widmer at the NIPS workshop on Machine Learning in Computational Biology, Whister, B.C., on December 11, 2009.

Talk on "Next Generation Genome Annotation" by Gunnar Rätsch at the RGASP Workshop on The Wellcome Trust Genome Campus, Hinxton, on November 10, 2009.

Talk on "Large Scale Sequence Analysis and Applications to Genomics" by Gunnar Rätsch at the Centrum Wiskunde and Informatica, Amsterdam, on October 23, 2009.

Talk on "Methods for Computational Transcriptome Analysis" by Gunnar Rätsch at the Berlin late Summer Meeting, in Berlin, Germany, on October 8, 2009.

Talk on "Towards Understanding of Transcriptome Complexity and Plasticity" by Gunnar Rätsch at the Symposium "Future of Computational Biology" in Berlin/Potsdam, Germany, on September 22, 2009.

Keynote on "Novel Inference Methods for Computational Transcriptome Analysis" by Gunnar Rätsch at the Pattern Recognition in Bioinformatics conference, in Sheffield, UK, on September 7, 2009.

Talk on "Methods for Understanding Transcriptome Complexity and Plasticity" by Gunnar Rätsch at the PhD Retreat, in Bad Saarow, Germany, on August 21, 2009.

Talk on "Mathematical Programming for Multiple Kernel Learning (MKL)" by Alex Zien at the Mathematical Programming Stream of the 23rd European Conference on Operational Research (EURO 2009) in Bonn on July 7, 2009.
Talk on "Machine Learning Challenges in Analysing Short Read Sequencing and Tiling Array Data" by Gunnar Rätsch at the Computational Statistics Workshop in London, UK, on July 6, 2009.

Talk on "Towards the Understanding of Transcriptome Complexity and Plasticity" by Gunnar Rätsch at the 40 year anniversary symposium of the Friedrich Miescher Laboratory in Tübingen, Germany, on July 3, 2009.

Talk on "Characterizing transcriptome plasticity using whole-genome tiling arrays and machine learning" by Georg Zeller at the ISMB/ECCB 2009 in Stockholm, Sweden, on July 2, 2009.
Talk on "Quantitative Detection of Alternative Transcripts with RNA-Seq Data" by Regina Bohnert at the Short-SIG of ISMB/ECCB 2009 in Stockholm, Sweden, on June 28, 2009.

Tutorial "Support Vector Machines and Kernels for Computational Biology" by Gunnar Rätsch and Sören Sonnenburg at ISMB/ECCB 2009 in Stockholm, Sweden, on June 28, 2009.

Talk on "KIRMES: Kernel-based identification of regulatory modules in euchromatic sequences" by Sebastian J. Schultheiss at the ISCB Student Council Symposium of ISMB/ECCB 2009 in Stockholm, Sweden, on June 27, 2009.

Lecture by Sebastian J. Schultheiss on "Automated Genome Annotation 2009" during the PhD Student Course of the FML and MPI for Developmental Biology, May 2009 in Tuebingen.

Talks by Georg Zeller, Sören Sonnenburg and Sebastian J. Schultheiss at the Tübingen Bioinformatics Day hosted by ZBIT on Friday, April 24, 2009.
Tutorial "Next Generation Sequencing, Tiling Arrays and Predictive Sequence Analysis for Transcriptome Analysis" by Gunnar Rätsch at the 9th course in Bioinformatics and Systems Biology for Molecular Biologists in Bertinoro, Italy, on March 24, 2009.

Talk on "Large Scale Sequence Analysis with Applications to Genomics" by Gunnar Rätsch at the Centre for Computational Statistics and Machine Learning, University College London, Great Britain, on March 18, 2009.

Keynote lecture on "Novel Methods for Computational Transcriptome Analyses" by Gunnar Rätsch at the NBIC Conference 2009, Lunteren, Netherlands, on March 17, 2009.

Lecture on "Advanced Methods for Sequence Analysis" by Daniel Huson, Gunnar Rätsch and Johannes Fischer at University of Tübingen, Germany, in October 2008-February 2009.

2008

Lecture by Sebastian J. Schultheiss and Alexander Zien on "Automated Genome Annotation" during the PhD Student Course of the FML and MPI for Developmental Biology, November 4-19, 2008 in Tuebingen.

Talk on "Novel Methods for Computational Transcriptome Analysis" by Gunnar Rätsch at the 1st Life Sciences Meeting in Tübingen, on November 6, 2008.

Talk on "QPalma-Optimal Spliced Alignments Of Short Sequence Reads" by Fabio De Bona at European Conference on Computational Biology in Cagliari, Italy on September 25, 2008.

Talk on "An Automated Combination of Kernels for Predicting Protein Subcellular Localization" by Alexander Zien at the 8th Workshop on Algorithms in Bioinformatics (WABI) in Karlsruhe on September 17, 2008.

Talk on "RNA-seq and tiling arrays for improved gene finding" by Gunnar Rätsch at the Genome Informatics meeting in Hinxton, on September 14, 2008.

Talk on "KIRMES: Kernel-based identification of regulatory modules in euchromatic sequences" by Sebastian J. Schultheiss at the German Conference on Bioinformatics 2008 in Dresden, Germany on September 10, 2008. The slides can be downloaded here.