Event schedule

February 9

Day 1
Continental Breakfast

Public note taking at this google doc: http://bit.ly/genevariation3d

Welcome and Introductions
  • Eric Deutsch Institute for Systems Biology

  • Andeas Prlić RCSB PDB, UCSD

Session 1: Protein Structures

Chair: Andreas Prlić

Using the Protein Data Bank to Understand Cancer-related Point Mutations in 3D
  • Stephen K. Burley RCSB Protein Data Bank Rutgers University/UC San Diego

Adventures in structure-based variant annotation: SNPs3D, CAGI, and IPES
  • John Moult Institute for Bioscience and Biotechnology Research

Constrained and not Constrained: What can human variation tell us about protein structure?
  • Geoff Barton University of Dundee


Session 2: Genetic Variations

Chair: Eric Deutsch

Genome variation databases
  • Gustavo Glusman Institute for Systems Biology - Kaviar database

Representing the diversity of human proteins: from sequence to structure annotation.
  • Lydie Lane Swiss Institute of Bioinformatics

Mining the 1000 Bull genomes, to link gene variants to protein function.
  • Emøke Bendixen Aarhus University

Fast and comprehensive detection of variant peptides using MSFragger
  • Andy Kong University of Michigan

Getting the entire message: Full-length RNA isoforms in human brain and cells
  • Hagen Tilgner Weill Cornell Medical College, Cornell University

Lunch & Poster Session

Session 3: Mapping Variations to Structures - Part 1

Chair: Gustavo Glusman

Mapping cancer mutations to Kinome interactions
  • Marija Buljan ETH Zurich

Toward predicting the effect of mutations on membrane protein structure
  • Julia Koehler Leman Simons Center for Data Analysis

Modeling at the intersection of structural biology and systems biology
  • Elizabeth Brunk UCSD

3D cluster analysis of cancer variants identifies rare driver events
  • Jianjiong Gao Memorial Sloan Kettering Cancer Center, cBioPortal


Session 4: Applications

Chair: Eric Deutsch

Differential Expression of Splice Isoforms of Transcripts and Proteins in Cancers: Potential Diagnostic Biomarkers and More Specific Targets for Therapy
  • Gil Omenn University of Michigan

3D variant interpretation using whole genome sequencing data
  • Michael Hicks Human Longevity

Comparing mutations in tumour supressors and oncogenes
  • Frances Pearl University of Sussex

Open Discussion Day 1

February 10

Day 2
Continental Breakfast

Getting started in the morning.

Session 5: Mapping Variations to Structures - Part 2

Chair: Andreas Prlić

Mapping sequence annotation to structure by automated protein structure homology modeling
  • Torsten Schwede University of Basel, Biozentrum

MuPIT - the mutation position imaging toolkit
  • Rachel Karchin Johns Hopkins University

Mapping variant-specific cystic fibrosis-related endophenotypes to CFTR structure
  • David Masica Johns Hopkins University

Analysis of cancer mutations in the context of 3D protein structures
  • Adam Godzik Sanford Burnham Prebys Medical Discovery Institute


Session 6: Big Data Technologies

Chair: Peter Rose

A 3D structural view of the human genome; data, technologies, challenges.
  • Andeas Prlić RCSB PDB, UCSD

Tools and practices for open and reproducible data-driven discovery
  • Ariel Rokem University of Washington eScience Institute

Big Data Genomics: Data-intensive science using scalable analytics systems
  • Michael Heuer Amplab, U.C. Berkeley

ISB-CGC: The ISB Cancer Genomics Cloud
  • Sheila Reynolds Institute for Systems Biology

Lunch & Poster Session

Session 7: Breakout Sessions

Chair: Eric Deutsch

Breakout organizers: Eric Deutsch, Andreas Prlić, Gustavo Glusman, Gil Omenn

Session 8: Future

Chair: Andreas Prlić

Reports back from breakout groups
Open Discussion Day 2
Closing Remarks
  • Eric Deutsch Institute for Systems Biology