PSB 2012

PSB Workshops

Pacific Symposium on Biocomputing

Big Island of Hawaii -- January 3-7, 2012

PSB is offering three three-hour workshops during the meeting (exact dates to be determined). These workshops were created to provide an opportunity for a gathering that will not be based on peer-reviewed papers included in the proceedings book. The workshops will consist of presentations by invited speakers. Abstract submissions for the workshops will be evaluated by the workshop co-chairs.

PSB 2012 Workshops:

Each workshop has a chair who is responsible for organizing submissions. Please contact the specific session chair relevant to your interests for further information. Links on each of the session titles below lead to more detailed calls for participation.

The structure and function of chromatin and chromosomes

Co-chairs: William Stafford Noble, C. Anthony Blau, Job Dekker, Zhi-jun Duan, Yi Mao

This workshop aims to bring together researchers who are developing computational methods for interpreting the expanding collection of genome and chromatin architecture data. The session will bridge several dichotomies: research groups working on genome-wide characterization versus analyzing specific loci in detail; researchers who build models along the one dimension of the chromosome and those who work with data that is explicitly three-dimensional. The session will include papers that describe methods for building computational models of physical phenomena as well as methods for relating genome structure and function.

Important Dates
Call for Participation/Abstract Deadline: September 14, 2011
Notification: September 21, 2011

Contact: Yi Mao
Email: maoyi0 at gmail dot com

Law, Bioethics and the Current Status of
Ownership, Privacy, Informed Consent in the Genomic Age

Chair: Greg Hampikian, Eric M. Meslin

The rise of biobanks including the related databases containing increasing amount of health information are now commonplace - found on every continent of the globe including Antarctica. Common though they may be, legal and ethical issues for collecting, storing and using the associated health/genetic information continue to perplex clinicians, researchers, law enforcement, and the lay public alike. For example, one's image or likeness is copyrightable, but not one's genome. Yet billions of dollars are being made from patented genes, patented species, private databases, and human tissues. Several health care systems now collect human DNA samples from patients through "opt-out" programs, and vast collections of DNA are being assembled without compensation to donors. Now that whole genome sequencing is becoming more affordable, the bioinformatics community is rightly asking about its enduring obligations and responsibilities vis a vis genetic ownership, residual rights, privacy, and informed consent. And that's just in the USA. Many issues are magnified when material or data are intended to cross national borders. This workshop is designed to unpack many of the issues in pragmatic detail - hopefully dispelling certain myths while offering cautionary reminders about legal and ethical obligations. The two co-chairs will lead in-depth discussion and facilitate small group exercises to emphasize these issues. A particular highlight will be a mock "House of Commons" debate where workshop participants will be asked to take positions, ask questions, and vote with their feet. In other words, this workshop is meant to be provocative, user friendly and skill enhancing.

Greg Hampikian is a professor of Biology, and Criminal Justice, at Boise State University. He is also director of the Idaho Innocence Project, and spends a lot of time in US and foreign courtrooms.

Eric M. Meslin is Director of the Indiana University Center for Bioethics, Associate Dean (Bioethics) IU School of Medicine, and Professor of Medicine; Medical & Molecular Genetics; Public Health and Philosophy. He needs a larger business card.

Email: Greghampikian at bosestate dot edu

Systems Pharmacogenomics -- Bridging the Gap

Marylyn Ritchie, The Pennsylvania State University
Nancy Cox, University of Chicago
Cheng Cheng, St. Jude Children's Research Hospital

PGRN Systems Biology Group
Scott Weiss, Channing Laboratory, Harvard Medical School

Teri Klein and Russ Altman, Stanford University

Biological systems are quintessentially complex. Normal function requires the constant orchestration of numerous pathways on widely varying spatial and temporal scales. To understand such a complex system, data has been collected on the molecular, cellular, organ, and population scales and across various -omes such as the genome, proteome, and metabolome. Unfortunately, it is often the case that each data set is analyzed in vacuo, without regard to information on other scales or -omes. Multi-scale integration of data types to answer fundamental and practical questions in biomedicine is a significant challenge to the experimental and computational biology communities. This is a topic that is being tackled in a significant way in Systems Pharmacogenomics - which is exploring systems biology approaches for drug treatment response.

Systems researchers in the academic sector are more biology driven. The focus tends to be on developing models and solutions to various questions that lead to new hypotheses to test and explore back at the bench. Whereas the pharma sector tend to be more data driven, where the goal is to find predictive models that can be used for drug treatment development or prediction, but may not be intuitive in terms of the underlying biology. It seems as though approaches and techniques developed by each sector would be enhanced by coming together to discuss the strengths and weakness of their respective approaches.

We will host the second Systems Pharmacogenomics - Birds of a Feather workshop at PSB 2012 with invited speakers from both academic and pharma sectors. This event will be sponsored by the PGRN Systems Biology Working Group, PharmGKB, and P-STAR (the PGRN Statistical Analysis Resource). We will have a series of talks following by a panel discussion aimed at bridging the gap between academic and pharma systems pharmacogenomics.


Brooke Fridley
Associate Professor, Mayo Clinic

Invited speakers:

Trey Ideker
Division Chief of Genetics & Professor, Departments of Medicine and Bioengineering, UC San Diego

Nicholas J. Schork
Director of Bioinformatics and Biostatistics, Scripps Translational Science Institute; Director of Research, Scripps Genomic Medicine; Professor, Department of Molecular and Experimental Medicine, The Scripps Research Institute; Professor of Psychiatry and Biostatistics (adjunct), UC San Diego

Pankaj Agarwal
Director, Computational Biology, Bioinformatics at GlaxoSmithKline
Talk title: Disease indications for medicines from side effects, gene expression, and genetics

Stephane Bourgeois
Wellcome Trust Sanger Institute, United Kingdom

Contact: Marylyn Ritchie
Email: marylyn.ritchie at psu dot edu

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