Call For Papers, Abstracts and Demonstrations

Pacific Symposium on Biocomputing

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

The twenty-first Pacific Symposium on Biocomputing (PSB), will be held January 4-8, 2016 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.

• Discovery of Molecularly Targeted Therapies
• Innovative Approaches to Combining Genotype, Phenotype, Epigenetic, and Exposure Data for Precision Diagnostics
• Methods to Enhance the Reproducibility of Precision Medicine
• Precision Medicine: Data and Discovery for Improved Health and Therapy
• Regulatory RNA
• Social Media Mining for Public Health Monitoring and Surveillance

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: July 27, 2015 midnight PT
Notification of paper acceptance: September 14, 2015
Final paper deadline: October 5, 2015 11:59PM PT
Abstract deadline: November 17, 2015 11:59PM PT
Meeting: January 4-8, 2016

Paper format

The accepted file formats are: postscript (*.ps) and Adobe Acrobat (*.pdf). Attached files should be named with the last name of the first author (e.g. altman.ps or 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 2016 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 2016 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.

• Discovery of Molecularly Targeted Therapies
• Innovative Approaches to Combining Genotype, Phenotype, Epigenetic, and Exposure Data for Precision Diagnostics
• Methods to Enhance the Reproducibility of Precision Medicine
• Precision Medicine: Data and Discovery for Improved Health and Therapy
• Regulatory RNA
• Social Media Mining for Public Health Monitoring and Surveillance

This session will specifically focus on the use of multi-modeling approaches for improving molecularly targeted therapies and precision medicine. We invite submissions which integrate multiple data types, including but not limited to: clinical trial, electronic health record, drug toxicity, genomic, pharmacogenomic, proteomic, metabolomic, microbiome, exposome and structural data.

• Contact: Philip Payne
• Email: Philip dot Payne at osumc dot edu

This session will explore problems in combining genotype and phenotype data to support rare disease and/or precision diagnostics. This includes the use of large-scale genomic and related data, such as SNPs, population frequency, structural variants, epigenetics, RNAseq and other expression data, interactome data, and a variety of pathogenicity measures. This would also include phenotypic analysis performed by EHR text mining, use of clinical terminologies such as SNOMED-CT and the Human Phenotype Ontology, patient self-phenotyping, rare disease registry data, lab tests, and chronological change. We particularly welcome submissions that span many types of these data. The focus will be on methods for determining causality and clinical actionability, evidence evaluation, and comparisons across approaches.

Contact: Melissa Haendel
Email: haendel at ohsu dot edu

Earlier this year, President Obama announced the Precision Medicine Initiative, strengthening communal efforts to integrate linked molecular, environmental, and clinical “big” data. Such efforts have already improved clinical care in areas such as non-small cell lung carcinoma, breast cancer, and cardiomyopathy. To maintain this track record, it is necessary to cultivate practices that ensure reproducibility as large shared heterogeneous datasets and databases proliferate. In this PSB 2016 session, we invite manuscripts that explore and propose solutions to the many challenges of reproducibility in the era of precision medicine.

Manuscripts might describe (1) methods for automated meta-analysis of clinical trials across diverse data sources, (2) new software and/or databases to help coordinate analyses across institutions, (3) proposals to implement “n of 1” clinical trials needed for therapeutic decision making, (4) methods to account for uncertainty and bias from associations derived from observational studies (e.g., associations from epidemiological studies), (5) new methods and extensions to visualization (e.g., StratomeX) and pipeline tools (e.g., knitr, IPython notebook, Galaxy) that promote reproducible use of heterogeneous individual-level and high-dimensional information, and (6) methods to combine information from multiple databases for clinical decision making, such as ClinVar, Human Gene Mutation Database, and PubMed.

• Contact: Arjun K. Manrai
• Email: manrai (at) post.harvard.edu

Rapid advances in sequencing, proteomics, biosensors, mobile health devices and apps are opening up new vistas of personalized biomedical data. Meanwhile, clinical genome editing, the ultimate personal genomics, is becoming tractable. To achieve the vaunted goals of precision medicine and go from measurement to clinical translation, substantial gains still need to be made in methods of data integration, analysis and interpretation. We welcome all submissions relevant to this exciting and growing area of research.

• Contact: Alexander Morgan
• Email: alexmo at stanford dot edu

Our session will bring together scientists studying RNA, RNA-protein complexes (RNPs) and RNA-protein interaction networks, with a focus on the regulatory roles of RNAs and RNPs. We encourage submissions on a wide range of computational and experimental research on the structure, functions and dynamics of RNAs, RNPs, and RNA-protein networks.

• Contact: Drena Dobbs
• Email: ddobbs at iastate dot edu

This session invites researchers who are interested in automatic methods for the collection, extraction, representation, analysis, and validation of social media data for public health surveillance and monitoring, including epidemiological and behavioral studies. It serves as a unique forum to discuss novel approaches to text and data mining methods that respond to the specific requirements of social media and that can prove invaluable for public health surveillance.

• Contact: Graciela Gonzalez
• Email: ggonzalez at asu dot edu