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Program Information

Information about the Cancer Biomarker Bioinformatics Workshop. Please note that the Program Committee is currently working on an update to the agenda. Check back soon for updates.

All times listed are in the pacific time zone.

Day 1 — Monday, April 29

Time Topic Speakers
8.00 Registration, light refreshments
8.30 Welcome

Dan Crichton
Jet Propulsion Laboratory

8.45 Overview and Goals

Bioinformatics Tailored to Meet Cancer Biomarker Research Needs
Sudhir Srivastava
National Cancer Institute

9.15 Keynote
SPEAKER

Blueprint or Parts List?  The value of biomarkers for 21st century discovery science and for cancer prevention, diagnosis and treatment
Dan Masys
University of Washington School of Medicine

10.00 Break
10.15

Session 1: Informatics in Biomarker Discovery

The application of multiple biotechnologies to the development of cancer biomarkers is inextricably linked to the development of algorithms to support the analysis of complex data sets. This session will combine contributions from researchers who have identified key needs for support of experimental methodologies and from researchers who have developed needed algorithms for biomarker data capture, integration, and analysis.

ORGANIZER

Christos Patriotis
National Cancer Institute

SPEAKERS

Developing curated databases for cancer biomarkers
Akhilesh Pandey
Johns Hopkins School of Medicine

My Cancer Genome: Knowledge Resource to Support Genetically Informed Cancer Medicine
Christine Micheel
Vanderbilt University

A comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer
Markus Riester
Dana-Farber Cancer Institute

Panel Discussion

12.15

Lunch (on your own)

13.45

Session 2: Informatics in Biomarker Validation

As new biomarkers are discovered in journals each week, the need to test and validate candidate biomarkers has become critical for this field. This session will combine case studies from researchers engaged in biomarker assessment that highlight the need for informatics improvements and from researchers who have developed new algorithms to assist in biomarker data evaluation.

 

ORGANIZERS

Marc Lenburg
Boston University School of Medicine
David Elashoff
University of California, Los Angeles

SPEAKERS

Development and Validation of a Blood-Based Gene Expression Diagnostic for Coronary Disease
Michael Elashoff
Celmatix

Data preprocessing and integration strategies for reproducible multi-omic biomarker discovery and validation
Evan Johnson
Boston University School of Medicine

Lessons Learned from the FDA-led MAQC-II Project on the Development and Validation of Microarray-based Predictive Models
Leming Shi
School of Pharmacy, Fudan University, Shanghai, China and National Center for Toxicological Research, US Food and Drug

Biomarker Discovery for Heterogeneous Diseases
Garrick Wallstrom
Arizona State University

Panel Discussion

16.45 Poster Session
ORGANIZERS

Mervi Heiskanen
National Cancer Institute
Heather Kincaid
Jet Propulsion Laboratory

Day 2 — Tuesday, April 30

Time Topic Speakers
8.00 Light refreshments
8.30 Keynote
SPEAKER

Gaddy Getz
Broad Institute

9.15 Break
9.30

Session 3: Quality by Design in Biomarker Research

The use of quality-by-design methodologies can make biomarker discovery and validation more rigorous, increasing the reproducibility of significant biomarker findings. This session will feature case studies, documentation tools, standards for minimum data to annotate, and algorithms in support of variability assessment for experimental methodology, the characterization of performance over time for methods, and the confidence associated with experimental results. By assisting in the introduction of quality-by-design concepts for biomarker research, this session will aid researchers in validating their platforms for reliable biomarker research.

ORGANIZERS

Mark Thornquist
Fred Hutchinson Cancer Research Center
Zhen Zhang
Johns Hopkins Medicine

SPEAKERS

Selecting Clinical Specimens for Biomarker Evaluation
Margaret Pepe
Fred Hutchinson Cancer Research Center

When is Reproducibility an Ethical Issue? Forensic Bioinformatics in High-Throughput Biology
Keith Baggerly
MD Anderson Cancer Center

Design of Clinical Proteomic Studies – Bridge the Gap from Discovery to Clinical Applications
Zhen Zhang

Johns Hopkins Medicine

QuaMeter: Assessing longitudinal variability in LC-MS/MS proteomics
Dave Tabb
Vanderbilt University

Panel Discussion

12.15 Lunch (on your own)
13.45

Session 4: Data Integration and Biological Networks

The use of multiple biotechnologies introduces the challenge of integrating across multiple data types. Frequently, the incorporation of existing knowledge in the interpretation of an experiment implies organizing and evaluating results in accordance with existing biological network data. This session will include case studies and algorithmic developments for these two challenges, seeking to identify areas of research that are most likely to pay dividends in cancer biomarker research.

ORGANIZERS

Dave Tabb
Vanderbilt University
Chris Kinsinger
National Cancer Institute

SPEAKERS

Biomarkers as networks, not individual genes and proteins
Trey Ideker
UC San Diego School of Medicine

Discovering Cancer Driver Mutations in Cell Signaling Networks
Jüri Reimand
University of Toronto

Using personalized genome information in proteomics analyses
Sam Payne, Ph.D.
Pacific Northwest National Laboratory

Analysis and curation of short-read data from CGHub/TCGA using HIVE-XLD: Evaluation of non-synonymous variation in cancer cases and controls

Raja Mazumder
George Washington University

Panel Discussion



Day 3 — Wednesday, May 1

Time Topic Speakers
8.00 Light refreshments
8.30 Keynote
SPEAKER

Virtual Observatory, Astroinformatics, and Data-Rich Astronomy in the 21st Century
George Djorgovski
Caltech

9.15 Break
9.30

Session 5: Biomarker Informatics Infrastructure

This session will focus on supporting large-scale informatics systems for cancer research and other efforts. Examples will include large-scale data management, sharing, and discovery systems that support researchers for biomarker discovery, analysis and validation. It will include the development of data and metadata standards to enable data capture, sharing and analysis. This session will attempt to point the way forward for cancer biomarker repositories and shared analysis architecture.

ORGANIZERS
Dan Crichton
JPL
Mervi Heiskanen
National Cancer Institute
SPEAKERS

Informatics Support for Precision Medicine
George Komatsoulis

National Cancer Institute

The EDRN Knowledge System: A Big Data Infrastructure for Cancer Biomarker Research
Dan Crichton
JPL

Fast and Efficient Streaming Variant Calling in Resequencing Data
C. Titus Brown
Michigan State University

Intelligent Assistance to Disseminate Best Practices and Accelerate Discoveries in Cancer Omics
Shannon McWeeney
OHSU Knight Cancer Institute

Panel Discussion

12.15 Recommendations and Other Needs
MODERATOR
Mervi Heiskanen
National Cancer Institute



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Contact Information
EDRN Informatics Center
Jet Propulsion Laboratory
4800 Oak Grove Drive M/S 301-320
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edrn-ic@jpl.nasa.gov