Methods to Enhance the Reproducibility of
Precision Medicine

Pacific Symposium on Biocomputing
The Big Island of Hawaii
January 4-8, 2016

PAPER DEADLINE EXTENDED to AUGUST 13, 2015

Submit Paper

Motivation

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.




whitehouse.gov

Relevant challenges include:

  • The analysis challenges of using heterogeneous measurement platforms (genomic, clinical, quantified self [e.g., FitBit, Apple HealthKit enabled apps], and exposure data)
  • The tradeoff in making personalized decisions using more relevant but noisier subsets of data
  • The unprecedented scale of asynchronous observational and population-level inquiry (i.e. many investigators separately mining shared/publicly-available data)

Session Topics

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:

  • Methods for automated meta-analysis of clinical trials across diverse data sources
  • New software and/or databases to help coordinate analyses across institutions
  • Proposals to implement “n of 1” clinical trials needed for therapeutic decision making
  • Methods to account for uncertainty and bias from associations derived from observational studies (e.g., associations from epidemiological studies)
  • 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
  • Methods to combine information from multiple databases for clinical decision making, such as ClinVar, Human Gene Mutation Database, and PubMed

Session Organizers

Arjun K. Manrai
Harvard Medical School
manrai (at) post.harvard.edu

Chirag J. Patel
Harvard Medical School
chirag_patel (at) hms.harvard.edu

Nils Gehlenborg
Harvard Medical School
nils (at) hms.harvard.edu

Nicholas P. Tatonetti
Columbia University
nick.tatonetti (at) columbia.edu

John P.A. Ioannidis
Stanford University
jioannid (at) stanford.edu

Isaac S. Kohane
Harvard Medical School
isaac_kohane (at) hms.harvard.edu

Key Dates

Paper Submission Deadline: August 13, 2015
Notification of Acceptances: September 14, 2015
Revised Papers Due: October 5, 2015
Poster/Abstract Submission Deadline: November 17, 2015
PSB 2016: January 4-8, 2016

Submit

Papers must be submitted to the PSB paper management system

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 the instructions. 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.