Sequencing data analysis and interpretation 20110316 by CHI

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Cambridge Healthtech Institute's Second Annual

Sequencing Data Anaylsis & Interpretation
Turning Data into Knowledge

March 16-18, 2011 | Hilton San Diego Resort

(Part of X-Gen Congress & Expo)



To Register, please click here  


To View Final Agenda, please click here

For Sponsorship Information, please click here

Java and Jive Breakfast Breakout Discussion Groups

Join focused groups designed for conference attendees to discuss important and interesting topics related
to sequencing and genomic tools. These are moderated discussions with brainstorming and interactive
problem solving, allowing conference participants from diverse areas to exchange ideas, experiences, and
develop future collaborations around a focused topic. Complimentary coffee is included.


Java & Jive Topics Include:

- SNP Detection and Discovery -- Best Practices and Difficult Cases
- Mastering the Real Biology in NGS Data with Applied Statistics - What is Needed?
- Current Advances in Epigenetics Techniques: Applicability of LC/MS and the qPCR
- The Different Genome Browsers and Analyzers
- Tools for Single Molecule Analyses
- Provenance and Metadata for NGS

- Challenges in Next Generation Sequencing Informatics
- Solving the Library Preparation Bottleneck
- NGS Data Analysis in Medical Research -- Challenges
- Taking the Dive: Transitioning to Next-Generation Sequencing in the Setting of a Small Academic Lab

Please click here for more information on the Breakout Discussion Groups.

Plenary Keynote Session: The Personal Impact of Sequencing from Patient to Population

It Takes a Village
Hugh Rienhoff, M.D., Director,

Data-Driven Personalized Medicine
Atul Butte, M.D., Ph.D., Assistant Professor, Pediatrics, Medicine, Computer Science, Stanford
, Lucille Packard Children's Hospital

Clinical Significance of Indigenous Genome Sequencing
Vanessa Hayes, Ph.D., Professor, Human Genomics, J. Craig Venter Institute

Luncheon Presentation: Understanding Glaucoma through Genome-Wide      Sponsored by:  Agilent Technologies
Targeted Exome Re-Sequencing  
Terry Gaasterland, Ph.D., Professor, University of San Diego, California

Luncheon Presentation: Partnering for Multi-omics Excellence  Sponsored by: BGI
Joyce Peng, Ph.D., Marketing Director, BGI Americas

Thursday, March 17

Mapping and Assembly

ChIP-PaM: An Algorithm for Identifying Transcription Factor Targets through ChIP-Seq Data
Song Wu, Ph.D., Assistant Member, Biostatistics, St. Jude Children's Research Hospital

An Integrated Pipeline for Analyzing ChIP-Seq Transcription Factor Datasets
Gordon Robertson, Ph.D., Staff Scientist, Canada's Michael Smith Genome Sciences Centre, British Columbia
Cancer Agency

BiNGS!SL-Seq: Computational Analytical Pipeline to Analyze and Interpret Genome-Wide Synthetic
Lethal Screen
Aik Choon Tan, Ph.D., Assistant Professor, Bioinformatics, Medical Oncology, University of Colorado Denver School
of Medicine

RNA Binding Networks Determined by CLIP-Seq
Gene Yeo, Ph.D., Assistant Professor, Cellular and Molecular Medicine, Institute for Genomic Medicine, University of
California, San Diego

Analysis of High-Resolution and Genome-Scale DNA Methylation Data
Elena Harris, Ph.D., Research Associate, Molecular and Computational Biology, University of Southern California


Mapping Naturally Occurring Genetic, Epigenetic and Transcriptional Variation in Arabidopsis

Bob Schmitz, Ph.D., Postdoctoral Research Associate, Plant Biology and Genomics Analysis Laboratories,
Salk Institute for Biological Studies

Soybean QTL Introgression Mapping and Comparative Genomics Using Next-Generation
Sequencing Approaches
Robert Stupar, Ph.D., Assistant Professor, Agronomy and Plant Genetics, University of Minnesota

A High-Resolution Variation Map in the Maize: Signatures of Recombination, Selection and
Jer-Ming Chia, Ph.D., Scientific Informatics Analyst, Genomics, Cold Spring Harbor Laboratories

Luncheon Technology Workshop: Elucidation of Transcription Regulatory          Sponsored by: Genomatix
Networks Governing Homeostasis of Retinal Photoreceptors by ChIP-Seq
Hong Hao, Ph.D., Research Fellow, Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute,
National Institutes of Health 


FEATURED SPEAKER: Statistical Methods and Software for High-Throughput Gene Expression
Experiments Using mRNA-Seq
Sandrine Dudoit, Ph.D., Professor, Biostatistics and Statistics, University of California, Berkeley

Software Drive Presentation Using Transcriptomics to Identify the Algal       Sponsored by:  DNASTAR
Lipid Trigger
Christopher Yohn, Ph.D., Section Leader, Sapphire Energy

Statistical Methods for the Analysis of RNA-Seq Data
Wei Li, Ph.D., Assistant Professor, Biostatistics, Molecular and Cellular Biology, Baylor College of Medicine

Unveiling Transcriptome Structure by Accurate Mapping of RNA-Seq Reads
Jinze Liu, Ph.D., Assistant Professor, Computer Science, University of Kentucky

Friday, March 18

Breakfast Presentation: Insights into Prostate Cancer Mechanisms  
    Sponsored by:  Ingenuity Systems
via Integrated In Silico RNA-Seq Analysis of NGS Patient Data
Antoaneta Vladimirova, Ph.D., Scientific Manager, Ingenuity Systems, Inc.



Plenary Session: Sequencing Selects 
X-Gen Congress and Expo is proud to launch Sequencing Selects. Matching the NGS platform or service
provider for your research project is a balancing act of cost-quality-quantity. The best qualified people
to help answer these questions are customers. Hear real-world experiences from selected users hosted
by NGS platform and service providers. Compare, contrast, and come away with concrete conclusions.

Making Sense of Rare Human DNA Sequence Variations                                      Sponsored by: Complete Genomics
Nicholas J. Schork, Ph.D., Director, Biostatistics and Bioinformatics, The Scripps Translational
Science Institute & Professor, Molecular and Experimental Medicine, The Scripps Research Institute

Partnering Next Generation Sequencing for Precision Medicine in Pharmaceutical       Sponsored by:
Research and Development
Brian Dougherty, Ph.D., Associate Director, Molecular Medicine, Pfizer Worldwide Research and Development

Panel Discussion with NGS Leaders                    Sponsored by: 

Poster Awards                                                Sponsored by: 
Oxford Nanopore Technologies

Luncheon Presentation: Large-Scale, Complete Human Genome        Sponsored by: Complete Genomics
Sequencing for Advanced Disease Studies

Recognition Tunneling for DNA Sequencing
Stuart Lindsay, Ph.D., Professor, Physics and Chemistry Director, Center for Single Molecular Biophysics,
Arizona State University

Low-Cost Diagnostic DNA Sequencer
Stephen J. Gordon, Ph.D., President & CEO, Intelligent Bio-Systems, Inc.

Moving Polony Sequencing into the Third Generation
Jeremy S. Edwards, Ph.D., Co-Director, Mathematical Modeling, New Mexico Spatiotemporal Modeling Center

Rapid Single Molecule Level Genomic Analysis Using Disposable Nanochannel Arrays
Gary Zweiger, Ph.D., Vice President, Business Development, BioNanomatrix, Inc.

Nanopore DNA Sequencing with MspA
Jens Gundlach, Ph.D., Professor, Biological Physics, University of Washington




Monday, March 14
9:00 am - 12:00 pm

SC1: Exploring the Epigenetic Toolbox                                       
SC2: Sequencing-Based Molecular Diagnostics                 

Dinner Short Courses -- Tuesday, March 15                                  
6:00 pm - 9:00 pm

SC3: Start-to-Finish RNA-Seq Data Analysis                                      
SC4: The Key to Quality: Sample Preparation

For full programming details, please
click here.

*Separate registration required
Next-Next Generation Sequencing 


Wednesday, March 16
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