Workshops

Spring 2016

Algorithmic Challenges in Genomics Boot Camp

Jan 19, 2016 to Jan 22, 2016

Return to event »

Click on the titles of individual talks for abstract, slides and archived video (available approximately one week after the conclusion of the workshop).

Tuesday, January 19th, 2016
9:00 am–9:20 am		Coffee and Check-In
9:20 am–9:30 am		Opening Remarks
9:30 am–10:30 am		Fundamentals of Stringology I: Recap on Exact Pattern Matching and Alignment Algorithms Dan Gusfield (UC Davis)
10:30 am–11:00 am		Break
11:00 am–12:00 pm		Fundamentals of Stringology II: Probability and Statistics for Sequence Alignment Mike Waterman (University of Southern California)
12:00 pm–1:30 pm		Lunch
1:30 pm–2:30 pm		Fundamentals of Stringology III: Suffix Tress and Suffix Arrays Dan Gusfield (UC Davis)
2:30 pm–3:00 pm		Break
3:00 pm–4:00 pm		Fundamentals of Stringology IV: The Burrows-Wheeler Transform Dan Gusfield (UC Davis)
4:00 pm–4:30 pm		Break
4:30 pm–5:30 pm		Fundamental Algorithms in Deep Sequencing I: Assembly Pavel Pevzner (UC San Diego)

Wednesday, January 20th, 2016
8:30 am–9:00 am		Coffee and Check-In
9:00 am–10:30 am		Fundamental Algorithms in Deep Sequencing II: Mapping/Alignment Lior Pachter (UC Berkeley)
10:30 am–11:00 am		Break
11:00 am–12:30 pm		Fundamental Algorithms in Deep Sequencing III: Genomic Compression: Storage, Transmission, and Analytics Noah M. Daniels (MIT)
12:30 pm–2:00 pm		Lunch
2:00 pm–3:30 pm		Introduction to Cancer Bioinformatics I: Inferring Genomic Variation from Tumor Sequencing Data Ben Raphael (Brown University) and Niko Beerenwinkel (ETH Zürich)
3:30 pm–4:00 pm		Break
4:00 pm–5:00 pm		Introduction to Cancer Bioinformatics II: Tumor Phylogeny Ben Raphael (Brown University) and Niko Beerenwinkel (ETH Zürich)

Thursday, January 21st, 2016
8:30 am–9:00 am		Coffee and Check-In
9:00 am–10:00 am		Introduction to Cancer Bioinformatics III: Cancer Progression Networks Niko Beerenwinkel (ETH Zürich)
10:00 am–10:30 am		Break
10:30 am–11:30 am		Introduction to Regulatory Genomics and Epigenomics I: Introduction to the Biology of Gene Regulation Nadav Ahituv (UCSF)
11:30 am–1:30 pm		Lunch
1:30 pm–3:00 pm		Introduction to Regulatory Genomics and Epigenomics II: Motif Finding Yaron Orenstein (MIT)
3:00 pm–3:30 pm		Break
3:30 pm–5:00 pm		Introduction to Regulatory Genomics and Epigenomics III: Hidden Markov Models in Gene Regulation Uwe Ohler (MDC Berlin)

Friday, January 22nd, 2016
8:30 am–9:00 am		Coffee and Check-In
9:00 am–10:00 am		Introduction to Biological Network Analysis I: Network Basics and Properties Donna Slonim (Tufts University)
10:00 am–10:30 am		Break
10:30 am–11:30 am		Introduction to Biological Network Analysis II: Protein-Protein Interaction Networks: From Graphs to Function Donna Slonim (Tufts University)
11:30 am–1:30 pm		Lunch
1:30 pm–2:30 pm		Introduction to Biological Network Analysis III: Identifying Network Modules Roded Sharan (Tel Aviv University)
2:30 pm–3:00 pm		Break
3:00 pm–4:00 pm		Introduction to Biological Network Analysis IV: Network Alignment and Querying Roded Sharan (Tel Aviv University)