PSB Workshops

Pacific Symposium on Biocomputing

Big Island of Hawaii -- January 4-8, 2016

PSB is offering four 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.

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.

Computational Approaches to Study Microbes and Microbiomes

Organizers: Casey Greene, James Foster, Bruce Stanton, Deborah Hogan, Yana Bromberg

For our workshop, we are inviting speakers who are leading microbiologists as well as computational scientists who are developing the state-of-the-art computational methods that will generate discoveries from data measuring microbial systems. We aim to bring together computational and wet bench scientists to discuss open questions, to foster discoveries through the discussion of new methods, and to build new collaborations between participants.

Casey Greene
Email: greenescientist at gmail dot com

Biomedical Applications of Topology and Abstract Algebras

Co-chairs: Eric Neumann, Svetlana Lockwood, David Spivak, Bala Krishnamoorthy

The application of algebraic topology (e.g., simplicial complexes, homological algebra, sheaves) and abstract algebras to solve genomic and complex data problems is becoming more common. The relevance of finding structures in rich data is underscored by the increasing efforts to combine clinical data with genomic analyses in initiatives such as Big Data. Here we will illustrate the recasting of mathematical and logical models in unique and powerful ways, rather than on merely speeding existing algorithms, in order to address data challenges in bioinformatics and biomedicine.

Eric K. Neumann
Email: eneumann at foundationmedicine dot com

Use of Genome Data in Newborns as a Starting Point for Life-Long Precision Medicine

Organizers: Steven E. Brenner and Sean D. Mooney

Given the high burden of treatable genetic diseases in children, there is considerable interest in using Whole Genome Sequencing (WGS) to screen, diagnose and treat genetic diseases of infancy, both as an extension of current newborn screening programs (NBS), and as a pioneering implementation of precision medicine for affected infants. In this workshop, we will present ongoing efforts to integrate WGS into NBS programs and we will discuss the technical, scientific and ethical challenges.

Steven E. Brenner
Email: brenner at compbio dot berkeley dot edu

Translational Bioinformatics 101

Presenters: Jessica D. Tenenbaum, Subha Madhavan, Robert Freimuth, Josh Denny, Lewis Frey

This workshop will provide context for how the various bioinformatics methods may be applied toward the enhancement of human health, enabling health care providers to deliver the right intervention for the right patient at the right time.

Jessica D. Tenenbaum
Email: jessie.tenenbaum at duke dot edu

Social Media Mining Shared Task Workshop

Presenters: Graciela Gonzalez, Abeed Sarker, and Azadeh Nikfarjam

This workshop is a platform for teams to exercise their best NLP techniques applied to Social Media data. Specifically, to detecting and extracting mentions of adverse reactions. The workshop complements the Social Media Mining for Public Health Monitoring and Surveillance session.

Teams or individuals can participate in one or more of the proposed tasks, each posing distinct challenges.

Abeed Sarker
Email: abeed.sarker at asu dot edu