Workshops

Spring 2016

Algorithmic Challenges in Genomics Reunion

Jun. 27 – Jun. 30, 2017

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Tuesday, June 27th, 2017
9:00 am – 9:30 am		Coffee and Check-In
9:30 am – 9:40 am		Opening Remarks
9:40 am – 10:20 am		Advances in Computational Approaches to Understand Post-Transcriptional Gene Regulation Uwe Ohler, MDC Berlin
10:20 am – 10:50 am		Break
10:50 am – 11:30 am		Most Transcription Factors Recognize DNA Shape Independent of Sequence Katherine Pollard, UCSF
11:30 am – 12:10 pm		Structural Analysis of the Compendium of RNA-Binding Proteins Yaron Orenstein, MIT
12:10 pm – 2:00 pm		Lunch
2:00 pm – 2:40 pm		A Network-based Approach to Elucidate Disease Mechanisms Roded Sharan, Tel Aviv University
2:40 pm – 3:20 pm		Protein Mover’s Distance: A Geometric Approach for Global Alignment of PPI Networks Hu Ding, Michigan State University
3:20 pm – 3:50 pm		Break
3:50 pm – 5:00 pm		Panel/Discussion

Wednesday, June 28th, 2017
8:30 am – 9:00 am		Coffee and Check-In
9:00 am – 9:40 am		Data-Parallel De Bruijn Graph Construction For De Novo Short Read Micro-Assembly on the GPU Victoria Popic, Stanford University
9:40 am – 10:20 am		Enhancer Bioengineering and Therapeutic Sciences Nadav Ahituv, UCSF
10:20 am – 10:50 am		Break
10:50 am – 11:30 am		Optimality Results on Compressed Representations for High Throughput Sequence Data Cenk Şahinalp, Indiana University
11:30 am – 12:10 pm		Reverse Engineering of Networks Under Non-Linear Relationships Martin Vingron, Max Planck Institute for Molecular Genetics
12:10 pm – 2:00 pm		Lunch
2:00 pm – 5:00 pm		Special Session Celebrating Mike Waterman's 75th Birthday
2:00 pm – 2:40 pm		TBA Bonnie Berger, MIT
2:40 pm – 3:20 pm		De Bruijn Graphs and Drug Discovery Pavel Pevzner, UC San Diego
3:20 pm – 3:50 pm		Break
3:50 pm – 4:30 pm		TBA Lior Pachter, UC Berkeley
4:30 pm – 5:00 pm		TBA Michael Waterman, University of Southern California

Thursday, June 29th, 2017
8:30 am – 9:00 am		Coffee and Check-In
9:00 am – 9:40 am		Extracting Replicable Associations Across Multiple Studies: Empirical Bayes Algorithms for Controlling the False Discovery Rate David Amar, Stanford University
9:40 am – 10:20 am		Periodicity in Streams Funda Ergün, Indiana University
10:20 am – 10:50 am		Break
10:50 am – 11:30 am		ZINB-WaVE: A General and Flexible Method for Signal Extraction from Single-cell RNA-seq Data Jean-Philippe Vert, Mines Paristech
11:30 am – 12:10 pm		Experiments with Integer Linear Programming in Computational Biology Dan Gusfield, UC Davis
12:10 pm – 2:00 pm		Lunch
2:00 pm – 2:40 pm		Genomic Characterization and Applications of Read-cloud Sequencing Technologies Iman Hajirasouliha, Cornell University
2:40 pm – 3:20 pm		Universal Hitting Sets and Minimizers Ron Shamir, Tel Aviv University
3:20 pm – 3:50 pm		Break
3:50 pm – 4:30 pm		The Soil and Other Problems of Precision Oncology Colin Collins, University of British Columbia
4:30 pm – 5:30 pm		Panel/Discussion

Friday, June 30th, 2017
8:45 am – 9:15 am		Coffee and Check-In
9:15 am – 9:40 am		MethylMarker: The Predictive DNA Methylation Marker Selection Algorithm for Liquid Biopsy Hayan Lee, Stanford University
9:40 am – 10:20 am		Algorithms for Inferring Evolution and Migration of Tumors Benjamin Raphael, Princeton University
10:20 am – 10:50 am		Break
10:50 am – 11:30 am		Learning Tumor Phylogenies from Single-Cell Data Niko Beerenwinkel, ETH Zurich
11:30 am – 12:10 pm		BeWith: A Between-Within Method to Discover Relationships between Cancer Modules via Integrated Analysis of Mutual Exclusivity, Co-occurrence and Functional Interactions Teresa Przytycka, National Center for Biotechnology Information