Call for Papers
Cancer Pathways:
Automatic Extraction, Representation, and Reasoning
in the Big Data Era
20th Anniversary of the Pacific Symposium on
Biocomputing
January 4-8, 2015
Fairmont
Orchid, Big Island
Hawaii,
U.S.A.
There has been great interest
and research initiatives in the biomedical community around harnessing "big data",
including data from the literature, high-throughput gene expression
experiments, array CGH and high-throughput siRNA and many other types of data
to generate novel hypothesis to address the most crucial biomedical questions
and aid in the discovery of more effective and improved therapeutic options for
the treatment of complex diseases. Given its ever increasing volume and
diversity, interest in taming "big data" through methods and systems to
extract, represent, and transform it to knowledge that can be used for
reasoning and question answering will only increase over time, enabling
scientists to effectively use it for discovery and validation..
This session will bring together researchers in text mining and knowledge representation and reasoning with bench scientists, geneticists and translational scientists. It serves as a unique forum to discuss novel approaches to the complex text extraction and knowledge representation and reasoning problems that come with dealing with big data. Given that computational approaches often draw upon disease-specific resources and expertise, we focus the session on disseminating approaches to extract, represent, or reason with knowledge derived from the literature, databases, or experimental data that respond to biological questions about the signaling pathways in cancer pathophysiology.
There have been increased efforts to develop such systems and approaches, but there is no single place to present them. This session will attract cross-discipline collaborators in areas such as text and data mining, computational methods, artificial intelligence, knowledge representation, computational biology, and others, with focused applications in cancer pathophysiology. Some examples of topics of interest to this session include novel approaches in one or more of the following areas:
- Extraction of protein interactions and signaling
pathways from biomedical literature
- Extraction and assembly of knowledge about signaling
pathways from heterogenous sources
- Knowledge representation platforms and approaches
- Use of curated databases or ontologies to perform
discovery-related tasks
- Detection of agreement and contradiction in
biomolecular mechanisms
- Gene prioritization
- Binding site prediction
- Gene/protein function prediction,
- Prediction of associations (protein-protein, gene-drug,
gene-disease, drug-drug, and others)
- Pathway generation or validation
- Pharmacogenomics, pharmacokinetics, and
pharmacodynamics
- Clinical pharmacokinetics for personalized medicine
- Personalized medicine
- Genome-phenome derivation and validation
- Gene function extraction and prediction
- Reasoning and question answering
applied to the study of cancer pathophysiology and its underlying signaling pathways. Submissions should emphasize the translational value of their contribution.
Session Organizers
Chair:
Graciela H. González
Arizona State University
Co-Chairs:
Chitta Baral
Arizona State University
Suengchan Kim
Translational Genomics Research
Institute
Jeff Kiefer
Translational Genomics Research
Institute
Jieping Ye
Arizona State University
Submission
Information
Please note that the submitted papers are reviewed and accepted on a competitive basis. At least three reviewers will be assigned to each submitted manuscript.
Important Dates
Paper submissions
due: July 31, 2014 August 4, 2014
Notification of paper
acceptance: September 9, 2014
Final paper deadline: October 1, 2014 at 11:59pm PT
Registration opens: August 1, 2014 at noon PT
Travel award applications
PSB
has been able to offer travel support to many attendees in the past. However, please
note that no one is guaranteed travel support.
Available: August 1, 2014 at noon PT
Deadline: October 6, 2014 at noon PT
Decisions
will be announced in mid-October.
For
details, please see http://psb.stanford.edu/keydates.html
Abstract Submissions
Poster
presenters will be provided with an easel and a poster board 32"W x
40"H (80x100cm). One poster from each paid participant is accepted.
Available: August 1, 2014 at noon PT
Deadline: November 17, 2014 at noon PT
Decisions
will be announced in mid-October.
Paper
Format
Please
see the PSB paper format template and instructions at http://psb.stanford.edu/psb-online/psb-submit.
The file formats we accept 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 will be
rejected without review.
Each paper must be accompanied by a cover
letter. 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 in our publication format. 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.