Call For Papers, Abstracts and Demonstrations

Pacific Symposium on Biocomputing

Big Island of Hawaii January 3-7, 2018

The paper submission deadline has passed; paper decision notification has been sent. The list of accepted papers has been selected by our referees. The proceedings are available online at http://www.worldscientific.com/worldscibooks/10.1142/10864; it will be available on the PSB website soon.

The twenty-third Pacific Symposium on Biocomputing (PSB), will be held January 3-7, 2018 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.

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's publisher, World Scientific Publishing, will initiate submission to PubMed Central (PMC) for accepted papers that must comply with the NIH Public Access Policy. Authors are responsible for ensuring that the manuscript is deposited into the NIHMS upon acceptance for publication. The author must complete all remaining steps in the NIHMS in order for the submission to be accepted.

Authors may post the preprint anywhere at any time, provided it is accompanied by the following applicable acknowledgement ([Journal]=Pacific Symposium on Biocomputing):

  • Preprint of an article submitted for consideration in [Journal] © [Year] [copyright World Scientific Publishing Company] [Journal URL]
  • Preprint of an article published in [Journal, Volume, Issue, Year, Pages] [Article DOI] © [copyright World Scientific Publishing Company] [Journal URL]

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, 2017 11:59PM PT
Notification of paper acceptance: September 15, 2017
Final paper deadline: October 2, 2017 11:59PM PT
Abstract deadline: November 13, 2017 11:59PM PT
Meeting: January 3-7, 2018

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. The bibliography is included in the 12 page limit. Please format your paper according to instructions found at http://psb.stanford.edu/psb-online/psb-submit/. If figures cannot 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. Supplemental material may be referenced by URL (PSB will not host supplemental material).

Papers must be submitted to the PSB 2018 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 2018 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.

Applications of Genetics, Genomics and Bioinformatics in Drug Discovery

Co-chairs: Richard Bourgon, Rick Dewey, Zhengyan Kan, and Dan Li

Genetics and genomics play an increasingly important role in enabling drug discovery. The topic in this session focuses on applying genetic, genomics and bioinformatics in various areas of drug discovery, including target identification and validation, biomarker development and understanding mechanisms for drug efficacy, toxicity and resistance, develop personalized therapeutic strategies including combination therapies, select disease relevant experimental models, and develop novel tools and methods for integrative data analysis.

  • Deadline extended for this session: Tuesday, August 8 12pm PT
  • Contact: Dan Li
  • Email: shuyudan.li at mssm.edu

Challenges of Pattern Recognition in Biomedical Data

Co-chairs: Anurag Verma, Anna Basile, Marta Byrska-Bishop, Christian Darabos, and Shefali Setia Verma

The analysis of big biomedical data is often presented with various challenges associated with the heterogeneity, multidimensionality, noisiness and incompleteness of the data itself, but also related to the computational resources required to complete the analysis. The data-intensive nature of computational genetics problem sets in the biomedical informatics field warrants the development and use of massive computer infrastructure and advanced software tools and platforms, including but not limited to the use of cloud computing. In this session, we will address innovative ways to identify and overcome challenges associated with the quality of various types of biomedical data, including Electronic Health Records, medical imaging etc. Additionally, we will focus on issues related to the optimization of tool development for large-scale datasets (keeping in mind issues like computing time and storage, the need for parallelization), as well as challenges associated with the cost in both time and resources of pattern recognition computational methods. Lastly, we will also address the challenges arising from trying to integrate biomedical data from various sources (including, but not limited to, one or across more species, use of raw data, or summary level statistics) to identify patterns in these multi-omic datasets.

  • Deadline extended for this session: Tuesday, August 8 12pm PT
  • Contact: Shefali Setia Verma
  • Email: ssetia at geisinger.edu

Democratizing Health Data for Translational Research

Co-chairs: Philip Payne, Nigam Shah, Jessie Tenenbaum, and Lara Mangravite

There is an expanding and intensive focus on the accessibility, reproducibility, and rigor of basic, clinical, and translational research. This focus complements the need to identify sustainable ways to generate actionable research results that improve human health. The principles and practices of open science offer a promising path to address both issues by facilitating: 1) increased transparency of data and methods which promotes research reproducibility and rigor; and 2) cumulative efficiencies wherein research tools and the output of research are combined to accelerate the delivery of new knowledge in proximal domains resulting in greater productivity and a reduction in redundant research investments. While great strides have been in made in terms of enabling the open science paradigm in the biological science domain, progress in sharing of patient-derived health data has not been as notable. This lack of widespread access to common and well characterized health data is a substantial impediment to the timely, efficient, and multi-disciplinary conduct of translational research, particularly in those instances where hypotheses spanning multiple scales (from molecular to patient to populations) are being developed and tested.

  • Contact: Philip Payne
  • Email: prpayne at gmail.com

Imaging Genomics

Co-chairs: Heng Huang, Junzhou Huang, Kun Huang, Li Shen, Paul M. Thompson, and Lin Yang

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 for this session: Tuesday, August 15 12pm PT
  • Contact: Heng Huang
  • Email: heng.huang at pitt.edu

Precision Medicine: from diplotypes to disparities towards improved health and therapies

Co-chairs: Bruce Aronow, Steven E. Brenner, Dana C. Crawford, Joshua C. Denny, and Alexander A. Morgan

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 for this session: Friday, August 4 12pm PT
  • Contact: Dana Crawford
  • Email: dcc64 at case dot edu

Reading Between the Genes: Computational Models to Discover Function and/or Clinical Utility from Noncoding DNA

Co-chairs: Yves Lussier, Maricel Kann, Jason Moore, Kenneth Ramos, Joanne Berghout, and Francesca Vitali

It remains difficult to assign functional mechanisms to variation in intergenic and/or noncoding DNA, even in cases where these can be confidently associated with variation of a biological trait. Altered regulatory activity is the most commonly considered candidate, but identifying the most relevant relationships or functions in the absence of an a priori biological hypothesis requires the intersection of big data, computing, and creativity.

  • Contact: Yves Lussier
  • Email: yves at email.arizona.edu

Text Mining and Visualization for Precision Medicine

Co-chairs: Graciela Gonzalez, Casey Greene, Hongfang Liu, and Abeed Sarker

According to the National Institutes of Health (NIH), precision medicine is “an emerging approach for disease treatment and prevention that takes into account individual variability in genes, environment, and lifestyle for each person.” Announced in 2015 by former President Obama in his State of the Union address, the Precision Medicine Initiative (PMI) seeks to promote research at the intersection of lifestyle, environment, and genetics to produce new knowledge for more effective ways to prolong health and treat disease. Although the text mining community had already explored this realm for some years, official endorsement and funding are beginning to bear fruit.

This session will attract researchers with a strong text mining and/or visualization background who are actively collaborating with bench scientists and clinicians for the deployment of integrative approaches in precision medicine that could impact scientific discovery.

  • Contact: Graciela Gonzalez
  • Email: gragon AT upenn DOT edu