Call For Papers, Abstracts and Demonstrations

Pacific Symposium on Biocomputing

Big Island of Hawaii January 3-7, 2017

The twenty-second Pacific Symposium on Biocomputing (PSB), will be held January 3-7, 2017 at the Fairmont Orchid on the Big Island of Hawaii. PSB will bring together top researchers from North America, the Asian Pacific nations, Europe and around the world to exchange research results and address open issues in all aspects of computational biology. PSB will provide a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology. PSB intends to attract a balanced combination of computer scientists and biologists, presenting significant original research, demonstrating computer systems, and facilitating formal and informal discussions on topics of importance to computational biology.

To provide focus for the very broad area of biological computing, PSB is organized into a series of specific sessions. Each session will involve both formal research presentations and open discussion groups.

• Computational approaches to understanding the evolution of molecular function
• Imaging Genomics
• Methods to Ensure the Reproducibility of Biomedical Research
• Patterns in Biomedical Data - How do we find them?
• Precision medicine: from genotypes and molecular phenotypes towards improved health and therapies
• Single-cell analysis and modelling of cell population heterogeneity

Papers and posters

The core of the conference consists of rigorously peer-reviewed full-length papers reporting on original work. All accepted papers will be published electronically and indexed in PubMed, and the best of these will be presented orally to the entire conference. PSB will also initiate submission to PubMed Central (PMC); however, PMC indexing applies only to papers that comply with the NIH Public Access Policy.

Researchers wishing to present their research without official publication are encouraged to submit a one page abstract by the abstract deadline listed below to present their work in the poster sessions.

Important dates

Paper submissions due: August 1, 2016 11:59PM PT August 7, 2016 11:59PM PT
Notification of paper acceptance: September 12, 2016
Final paper deadline: October 3, 2016 11:59PM PT
Abstract deadline: November 14, 2016 11:59PM PT
Meeting: January 3-7, 2017

Paper format

The accepted file format is PDF (Adobe Acrobat preferred). Attached files should be named with the last name of the first author (e.g. altman.pdf). Hardcopy submissions or unprocessed TEX or LATEX files or electronic submissions not submitted through the paper management system will be rejected without review.

Each paper must be accompanied by a cover letter. The cover letter should be the first page of your paper submission. The cover letter must state the following:

• The email address of the corresponding author.
• The specific PSB session that should review the paper or abstract.
• The submitted paper contains original, unpublished results, and is not currently under consideration elsewhere.
• All co-authors concur with the contents of the paper.

Submitted papers are limited to twelve (12) pages (not including the cover letter) in our publication format. Please format your paper according to instructions found at http://psb.stanford.edu/psb-online/psb-submit/. If figures can not be easily resized and placed precisely in the text, then it should be clear that with appropriate modifications, the total manuscript length would be within the page limit. Color images are accepted for publication at no additional charge.

Papers must be submitted to the PSB 2017 paper management system.

Contact PSB (psb.hawaii @ gmail.com) for additional information about paper submission requirements.

Travel support

We have been able to offer partial travel support to many PSB attendees in the past. However, please note that no one is guaranteed travel support. The online travel support application form will open in August.

PSB 2017 Sessions:

Each session 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 for each session.

• Computational approaches to understanding the evolution of molecular function
• Imaging Genomics
• Methods to Ensure the Reproducibility of Biomedical Research
• Patterns in Biomedical Data - How do we find them?
• Precision medicine: from genotypes and molecular phenotypes towards improved health and therapies
• Single-cell analysis and modelling of cell population heterogeneity

Our session is primarily intended to bring together researchers from the evolutionary biology and protein function communities, but we also expect other disciplines to participate. The following lists some of the areas we are interested in including in our session:

• Deadline extended: August 7, 2016
• Contact: Predrag Radivojac
• Email: predrag at indiana dot edu

Imaging genomics is an emerging research field, where integrative analysis of imaging and omics data is performed to provide new insights into the phenotypic characteristics and genetic mechanisms of normal and/or disordered biological structures and functions, and to impact the development of new diagnostic, therapeutic and preventive approaches. This session aims to encourage discussion on fundamental concepts, new methods and innovative applications in this young and rapidly evolving field.

• Deadline extended: August 7, 2016
• Contact: Li Shen
• Email: shenli at iu dot edu

A few weeks ago, Vice President Joe Biden, in announcing his new research funding initiatives, criticized the current state of scientific research, which is “trapped in silos, preventing faster progress and greater reach to patients.” To make matters worse, the New England Journal of Medicine published a commentary calling scientists who repurpose data “research parasites” who may use data generated by others to demonstrate alternative hypotheses. We, the organizers of this session, believe this is absolutely unacceptable and that the concept of data hoarding not only runs contrary to the spirit of, but also actively damages scientific research. Scientific research is meant to seek objective truth, rather than promote a personal agenda, and we believe the only way to do so is through transparency and reproducibility.

• Deadline extended: August 7, 2016
• Contact: Konrad Karczewski
• Email: konradk (at) broadinstitute.org

Given the exponential growth of biomedical data, researchers are faced with numerous challenges in extracting and interpreting information from theses large, high-dimensional, and often noisy and incomplete data. To facilitate addressing this growing concern, this PSB 2017 session is devoted to exploring pattern recognition using data-driven approaches for biomedical and precision medicine applications. We invite manuscripts that focus on novel pattern recognition approaches, applications of established methods to heterogeneous data, and those which address the present challenges in data-driven approaches.

• Deadline extended: August 7, 2016
• Contact: Anna Okula Basile
• Email: azo121 at psu dot edu

This session will explore new and open problems pertaining to various genome-wide and other large scale data, including rare and common SNPs, structural variants, epigenetic scans, multi-omic data, intermediate phenotypes, clinical variables from electronic medical records, disease and quantified-self sensor-based data.

• Deadline extended: August 7, 2016
• Contact: Dana Crawford
• Email: dcc64 at case dot edu

The ability to quantify molecular events with single cell resolution is intrinsically linked to analytical advances. Until recently, many of those variations could not be systematically studied because traditional molecular biology methods, such as PCR, Western Blotting, IP, genome sequencing, microarrays and RNA-seq, lacked single cell resolution. As an exception, the field of immunology has enormously benefitted from early adoption of the single-cell analysis by flow cytometry and FACS. Flow cytometry has been pivotal to detailed characterization of various immunological processes, such as blood cell development and activating and has enabled systematic mapping of the roles of various immune cell populations in health in disease states. Cytometry has always emphasized multiparametric analysis, distinguishing various cell populations by complex combinations of multiple markers on cells. A plethora of excellent computational methods aimed at flow data has been created over the last decades.

• Deadline extended: August 7, 2016
• Contact: Nikolay Samusik
• Email: samusik at stanford dot edu