cBio@MSKCC

2014

• Conference Talk “Unsupervised Structure Detection in Biomedical Data” by Julia Vogt at the International Workshop on Data Mining in Bioinformatics, New York City, August, 2014.

2013

• Invited talk “Understanding and Modeling Transcriptome Variability” by Gunnar Rätsch at Max Planck Institute for Molecular Genetics, Berlin, August, 2013.
• Invited course “Introduction to RNA-seq Analysis” by Gunnar Rätsch at Max Planck Institute for Molecular Genetics, August, 2013.
• Keynote “Introduction to Machine Learning in Science and Engineering” by Gunnar Rätsch at the Shogun Developer Meeting, July, 2013.
• Graduate course modules “Introduction to Machine Learning” and “Introduction to Deep Sequencing and Analysis Methods” by Gunnar Rätsch at Weill-Cornell Medical College, March, 2013.
• Invited talk “Methods for Analyzing Multiple Genomes and Transcriptomes” by Gunnar Rätsch at University of Southern California, April, 2013.
• Invited talk “Transfer Learning and its Applications in Computational Biology” by Gunnar Rätsch at New York University, February, 2013.

2012

• Conference talk entitled "Easier Workflows & Tool Comparison with Oqtans+" at the Galaxy Community Conference 2012 by Vipin T Sreedharan on July 26, 2012.

• Talk on "Multiple Reference Genomes and Transcriptomes for Arabidopsis thaliana" by Gunnar Rätsch in the Highlights Track of ISMB 2012 in Long Beach, USA, on July 16, 2012.
• Talk on "Simultaneous RNA-seq-based Transcript Inference and Quantification in Multiple Samples" by Jonas Behr at the 5th Conference on High Throughput Sequencing in Long Beach, USA, on July 14th, 2012.
• Tutorial "Introduction to Kernel Methods for Classification, Regression and Structured Data" by Gunnar Rätsch at the Machine Learning Summer School in Santa Cruz, USA, on July 9 & 10, 2012.
• Talk on "oqtans — A Galaxy-integrated workflow for quantitative transcriptome analysis from NGS data" by Geraldine Jean and Sebastian J Schultheiss at the RNA-seq workshop in Halle, Germany, on June 21-22, 2012.
• Keynote on "Computational Methods for Accurate Transcriptome Reconstruction" by Gunnar Rätsch at the RNA-seq workshop in Halle, Germany, on June 21, 2012.
• Talk on "Towards Empirical Models of the Central Dogma of Molecular Biology" by Gunnar Rätsch at the PBSB Weill-Cornell Graduate School in New York, USA, on April 23, 2012.

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.

• Talk on "mGene—A Novel Discriminative Gene Finding System" by Gabriele Schweikert at the Worm Genomics and Systems Biology meeting in Cambridge, on July 24, 2008.

• Talk on "Methods for Discovering Common Sequence Variation in Arabidopsis thaliana" by Gunnar Rätsch at the Highlights Session of ISMB 2008 in Toronto, on July 22, 2008.

• Talk on "Positional Oligomer Importance Matrices (POIMs) – Understanding Support Vector Machine Based Signal Detectors" by Sören Sonnenburg at ISMB 2008 in Toronto, on July 21, 2008.
• Talk on "Optimal Spliced Alignments of Short Sequence Reads" by Fabio De Bona at the Short-SIG of ISMB 2008 in Toronto, on July 19, 2008.

• Talk on "Revealing Sequence Variation Patterns in Rice with Machine Learning Methods" by Regina Bohnert at the ISCB Student Council Symposium of ISMB 2008 in Toronto, on July 18, 2008.
• Talk on "Reannotating the Arabidopsis transcriptome with tiling microarrays" by Georg Zeller at the ISCB Student Council Symposium of ISMB 2008 in Toronto, on July 18, 2008.
• Talk on "QPalma – Optimal Spliced Alignments of Short Sequence Reads" by Fabio De Bona at the ISCB Student Council Symposium of ISMB 2008 in Toronto, on July 18, 2008.

• Talk on "Methods for Transcriptome Analysis with Tiling Arrays and mRNA-Seq" by Gunnar Rätsch at the University of Toronto, on July 17, 2008.
• Lecture on Semi-Supervised Learning at the Summer School on Neural Networks, July 7-11, by Alex Zien.
• Lecture on Multiple Kernel Learning at the Summer School on Neural Networks, July 7-11, by Alex Zien.
• Talk on "Discriminative Learning Methods for Gene Finding and Polymorphism Identification" by Gunnar Rätsch at University of Liège, Belgium, on May 21, 2008.
• Invited plenary talk on "Boosting, Margins and Beyond" by Gunnar Rätsch at Benelearn08 in Spa, Belgium, on May 20, 2008.

• Lecture slides on "Halbüberwachtes Lernen" ("Semi-Supervised Learning"; slides in English) by Alexander Zien in the series "Maschinelles Lernen – Theorie und Anwendung" at Technical University Berlin, Germany, on April 22, 2008.
• Lecture on "Überwachtes und unüberwachtes Lernen" ("Supervised and Unsupervised Learning"; slides in English) by Alexander Zien in the series "Maschinelles Lernen – Theorie und Anwendung" at Technical University Berlin, Germany, on April 15, 2008.
• Talk on "Machine Learning Methods for Discovering Common Sequence Variation in Arabidopsis thaliana" by Gunnar Rätsch at the Institute for Software Technology and Theoretical Computer Science at the Technical University Berlin in Berlin, Germany, on March 31, 2008.
• Tutorial "Introduction to Machine Learning" by Gunnar Rätsch at the 8th course in Bioinformatics and Systems Biology for Molecular Biologists in Bertinoro, Italy, on March 19, 2008.
• Lecture on "Boosting Algorithms for Maximizing the Soft Margin" by Gunnar Rätsch in the 4th Workshop on Ensemble Methods at Technical University Berlin, Germany, in February 11, 2008.
• Lecture on "Advanced Methods for Sequence Analysis in Bioinformatics" by Cheng Soon Ong, Petra Philips and Gunnar Rätsch at University of Tübingen, Germany, in October 2007-February 2008.
• Talk on "mGene: A Novel Discriminative Gene Finding System" by Alex Zien at the Zeuner Symposium on Statistics in the Biosciences at January 10, 2008.

2007

• Talk on "Discovering Common Sequence Variation in Arabidopsis thaliana" by Gunnar Rätsch at Machine Learning in Systems Biology in Evry, France, on September 25, 2007. A video recording of this lecture is available at http://videolectures.net/mlsb07_ratsch_dcs.
• Talk on "Discovering Common Sequence Variation in Arabidopsis thaliana" by Gunnar Rätsch at the CAS-MPG Partner Institute for Computational Biology in Shanghai, China, on September 19, 2007.
• Talk on "Discovering Common Sequence Variation in Arabidopsis thaliana" by Gunnar Rätsch at the Bio Korea Conference in Seoul, Korea, on September 14, 2007.
• Talk on "Boosting, Margins and Beyond" by Gunnar Rätsch at the award ceremony of the Olympus prize of the DAGM 2007 in Heidelberg, Germany, on September 12, 2007.
• Tutorial on "Machine Learning in Bioinformatics" by Gunnar Rätsch at the 9th Machine Learning Summer School in Tübingen, Germany, on August 20-22, 2007. A video recording of this lecture is available at http://videolectures.net/mlss07_gunnar_intbio.
• Talk on "Bootstrapping the alternative splicing annotation of newly sequenced genomes" by Cheng Soon Ong at the Alternative Splicing Special Interest Group" in Vienna, Austria, on July 20, 2007.
• Talk on "mGene: A Novel Discriminative Gene Finding System" by Gunnar Rätsch at the Automated Function Prediction Meeting in Vienna, Austria, on July 20, 2007.
• Talk on "Multiclass Multiple Kernel Learning" by Cheng Soon Ong at the "International Conference for Machine Learning" in Corvallis, Oregon, on June 2007.
• Tutorial on "Machine Learning for Predictive Sequence Analysis" by Gunnar Rätsch at the 7th course in Bioinformatics for Molecular Biologists in Bertinoro, Italy, on March 21, 2007.

2006

• Lecture on "Advanced Methods in Sequence Analysis" by Cheng Soon Ong, Petra Philips and Gunnar Rätsch at University of Tübingen, Germany, in October 2006-February 2007.
• Invited plenary talk on "The Solution of Semi-Infinite Linear Programs using Boosting-like methods" by Gunnar Rätsch at the Conference for Algorithmic Learning Theory 2006 in Barcelona, Spain, on October 9, 2006.
• Invited talk on "Semi-Supervised Support Vector Machines and Application to Spam Filtering" by Alexander Zien at the ECML Discovery Challenge Workshop (September 22, 2006).
• Tutorial on "Kernel Methods for Predictive Sequence Analysis" by Cheng Soon Ong and Gunnar Rätsch at GCB 2006 in Tübingen, Germany, on September 19, 2006.
• Tutorial on "Boosting" by Gunnar Rätsch at the Machine Learning Summer School 2006 in Taipei, Taiwan, August 2-3, 2006. A video recording of this lecture is available at http://videolectures.net/mlss06tw_ratsch_ib.
• Lecture on "Improving the Caenorhabditis elegans Genome Annotation using Machine Learning" by Gunnar Rätsch at the Probabilistic Modeling and Machine Learning in Structural and Systems Biology meeting in Helsinki, June 2006. A video recording of this lecture is available at http://videolectures.net/pmsb06_ratsch_icega.