Call For Papers, Abstracts and Demonstrations

Pacific Symposium on Biocomputing

Big Island of Hawaii January 3-7, 2019

The paper submission deadline has passed; paper decision notification has been sent. The list of accepted papers has been selected by our referees.

PSB 2019 will not be affected by the volcanic activity on the Big Island. Please rest assured that there are no circumstances under which we would not accept paper submissions, review them and publish the accepted papers. Click here for more information about the volcanic activity on the Big Island.

The twenty-fourth Pacific Symposium on Biocomputing (PSB), will be held January 3-7, 2019 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 (absolute deadline): August 6, 2018 11:59PM PT
Notification of paper acceptance: September 14, 2018
Final paper deadline: October 1, 2018 11:59PM PT
Abstract deadline: November 12, 2018 11:59PM PT
Meeting: January 3-7, 2019

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 2019 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 2019 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.

Pattern Recognition in Biomedical Data: Challenges in putting big data to work

Co-chairs: Shefali S. Verma, Dokyoon Kim, Anurag Verma, Christian Darabos

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.

  • Contact: Anurag Verma
  • Email: anuragv at upenn dot edu

Precision Medicine: improving health through high-resolution analysis of personal data

Co-chairs: Steven Brenner, Martha Bulyk, Dana Crawford, Jill Mesirov, Alexander Morgan, Predrag Radivojac

  • Contact: Predrag Radivojac
  • Email: predrag at indiana dot edu

Single Cell Analysis- What is in the future?

Co-chairs: Lana Garmire, Rong Fan, Gene Yeo, Guo-cheng Yuan, John Quackenbush

Single-cell genomics technology is an exciting emerging area holding the promise to revolutionize our understanding of diseases and associated biological processes at an unprecedented resolution. Parallel to new experimental protocols for single-cell omics, multi-omics, imaging-omics, new computational methods, software and and data portals to analyze, integrate and interpret the complexity in single cell data are much needed. This scientific session welcome new research development in these exemplary areas, but are not limited to: (1) new computational methods to reveal bona fide patterns of gene expression, mutations, or DNA methylation among single cells. (2) Live imaging transcriptomic analysis that reveals the spatial-temporal relationships of single cells. (3) New tools and methods to integrate multi-omics single cell data. (4) New software packages and data portals to enable cloud/HPC deployment to both developers and non-informatics end-users.

  • Contact: Lana Garmire
  • Email: garmire at gmail dot com

When biology gets personal: Hidden challenges of Privacy and Ethics in Biological Big Data

Co-chairs: Gamze Gursoy, Erman Ayday, Steven E. Brenner, Arif O. Harmanci, Haixu Tang

Biological data acquisition technologies are advancing at an increasing pace. With decreasing cost of DNA sequencing technologies, the number and the size of the available genomic datasets have exponentially increased and become available to broader audiences. This session will explore the unique privacy and ethical challenges related to the storage, processing, and sharing of individuals’ biological data generated by multitude of technologies including but not limited to genomics, proteomics, metagenomics, bioimaging, biosensors, and personal health trackers. The mission is to bring together computational biologists, experimental biologists, computer scientists, ethicists, and policy and lawmakers to share ideas, discuss the challenges related to biological data and privacy and hopefully create collaborations.

  • Contact: Gamze Gursoy
  • Email: gamze dot gursoy at yale dot edu