ABRF 2013: Genomics Track
SCIENTIFIC SESSIONS AND TUTORIALS
High Performance Computing and the Life Sciences: Trends From the Trenches
Chris Dagdigian, BioTeam
Mendelian Genomics
Recent Advances in Mendelian Genomics at the Yale Center for Genome Analysis
Shrikant Mane, W.M. Keck Foundation Biotechnology Resource Laboratory, Yale University
Whole Exome Sequencing in Nervous System Disorders
Kaya Bilguvar, Yale University
An Integrated Approach for Prioritizing Causal Variants in Whole Exome and Whole Genome Sequencing
Martin Kircher, University of Washington
Community Resource Solutions to Analyzing Large Genomic Data Sets
Analysis of Shotgun Metagenomes with MG-RAST
Folker Meyer, Argonne National Laboratory
Galaxy for Core Facilities
Dave Clements, Emory University
CloVR: An Automated Genomic Analysis Tool Using Virtual Machine and Cloud Computing
Mahesh Vangala, Norwich University
Advances in Targeted Gene Modifications
Starting a TALEN Core Facility Service
Kym Delventhal, Stowers Institute
University of Wisconsin-Madison TALEN Facility
Fang Wan, University of Wisconsin
Using TALEN Technology as a Core Facility Resource
Timothy Dahlem, University of Utah
Epigenomics
Rob Mitra, Washington University School of Medicine
Peter Jones, USC Epigenome Center
John Stamatoyannopoulos, University of Washington
Advances in Single Cell Genomics and Transcriptomics
20 Years of Single Cell Transcriptomics (Publications)
Herbert Auer, Institute for Research in Biomedicine
Analysis of Human Colon Tissue Cell Composition Using Single-Cell Gene-Expression PCR
Piero Dalerba, Stanford University
Microarray Comparative Genomic Hybridization and Comprehensive Chromosomal Screening in Reproductive Medicine: In Vitro Fertilization Applications to Reduce Multiple Gestation and Preterm Birth Rate
Scott Sills, Pacific Reproductive Center
The Challenges and Successes of Establishing CLIA Certification for Modern Genomics Technologies
Don’t Jump Off the Building! Considerations to Ensure Your Core Lab to CLIA-Certified Lab Transition is Only Moderately Painful
Lisa White, Baylor College of Medicine
The Good, the Bad and the Ugly: Getting CLIA-Certification for a Basic Research Lab
Nicholas P. Ambulos, University of Maryland School of Medicine
Exome Sequencing: Applications from the Lab Bench to the Clinic
Donna M. Muzny, Baylor College of Medicine
RESEARCH GROUP STUDIES
ABRF Next-Generation Sequencing Study (ABRF-NGS)
Don Baldwin, University of Pennsylvania
Scott Tighe, University of Vermont
Chris Mason, Weill Cornell Medical College
George Grills, Cornell University
Nucleic Acids Research Group (NARG)
Role of DNA Extraction in Metagenomic Sample Identification
Jennifer Holbrook, AI Dupont Hospital for Children
Russ Carmical, The University of Texas Medical Branch at Galveston
Genomics Research Group (GRG)
Evaluation of Technologies for miRNA Analysis Using Synthetic miRNA Standards
Nalini Raghavachari, Genetics and Development Biology Center, NHLBI
Oyster Transcriptome Analysis by Next Gen Sequencing
Natalia Reyero, The Interdisciplinary Center for Nanotoxicity
Research Activities of the Genomics Research Group
Sridar Chittur, State University of New York at Albany
DNA Sequencing Research Group (DSRG)
Update on DSRG Projects
Deb Grove, Penn State University
Evaluation of Commercially Available RNA Amplification Kits at Sub-Nanogram Input Amounts of Total RNA for RNA-Seq: Study Design and Workflow
Savita Shankar, University of Florida
Evaluation of Commercially Available RNA Amplification Kits at Sub-Nanogram Input Amounts of Total RNA for RNA-Seq: Analysis
Charles Nicolet, University of Southern California
Genomic Bioinformatics Research Group (GBIRG)
Background and Overview
Nadereh Jafari, Northwestern University
The Cross-Platform ABRF-NGS Study Leads to Improved Genome and Transcriptome Standards
Chris Mason, Weill Cornell Medical College of Cornell University
RNA-Seq Algorithms and Evaluation with Simulated Datasets
Yuan Gao, Johns Hopkins University
SATELLITE WORKSHOP: Application of Next Generation Sequencing Technologies for Whole Transcriptome and Genome Analysis
Please note that Satellite Workshops are in addition to the ABRF conference and require an additional registration fee.
http://conf.abrf.org/index.cfm/page/satellite_workshops/SW1.htm
Welcome and Introduction
Nalini Raghavachari, Genetics and Development Biology Center, NHLBI
Overview of NGS Technology/Platforms
Mike Metzker, Baylor College of Medicine
Next Generation Sequence Analyses of the COmplex Dual Genome Mitochondrial Disorders: Technical Approach
Lee Jun Wong, Baylor College of Medicine
Integrated NGS Sample Preparation Solutions For Limiting Amounts of RNA and DNA
Targeted Sequencing: Removing Sample Prep Bottlenecks Using Access Arrays
Uma Dandrekar, University of California, Los Angeles
Panel Discussion
Breakout Session 1 - Biological Applications / Sample Preparation
Application of NGS in HIV/Forensics
Mike Metzker, Baylor College of Medicine
Dynamics of Open Chromatin Accessibility During Myeloid Differentiation
Ali Mortazavi, University of California, Irvine
Challenges and Solutions For Sequencing DNA and RNA From Clinical Samples
John Langmore, Rubicon Genomics
Next Generation Sequence Analyses of the Complex Dual Genome Mitochondrial Disorders: Actual Clinical Application
Lee Jun Wong, Baylor College of Medicine
Breakout Session 2 – Bioinformatics
Breaking the Data Analysis Bottleneck: Solutions That Work For RNA and Exome Sequencing
Rebecca Laborde, Mayo Clinic
Accessible, Transparent and Reproducible Analysis With Galaxy
Dave Clements, Emory University
An In-Depth Look at Metagenome Analysis With MG-RAST
Folker Meyer, Argonne National Laboratory
Panel discussion