16th Annual
International Conference
Intelligent Systems
for Molecular Biology

Metro Toronto Convention Centre (South Building)
Toronto, Canada




















ISMB 2008 will bring together Bioinformaticians and Computational Biologists working in a wide range of disciplines, including molecular biology, biology, medicine, computer science, mathematics and statistics. Papers that demonstrate both the development of new computational techniques AND their application to Molecular and Systems Biology, with significant outcomes to biomedical, agricultural, and environmental questions are especially encouraged.

Submission Schedule
Monday, November 5, 2007 Call for Papers Opens
Wednesday, January 16, 2008
Paper Submission Deadline
Wednesday, March 19, 2008 Paper Acceptance Notification
Saturday, March 30, 2008 Accepted Paper (Final Version) Submission

We are soliciting high-quality original research papers in any aspect of computational biology, including the following areas:

Area Area Chairs
Sequence Analysis and Alignment Des Higgins
Serafim Batzoglu
Evolution and Phylogeny Tandy Warnow
Junhyong Kim
Comparative Genomics Roderic Guigo
David Sankoff
Gene Regulation and Transcriptomics Olga Troyanskaya
Zhaolei Zhang
Protein Structure & function Nir Ben-Tal
Ora Schueler-Furman
Protein Interactions and Molecular Networks Joel Bader
Ed Marcotte
Databases and Ontologies Robert Stevens
Helen Parkinson
Text Mining Hagit Shatkay
Mark Craven
Bioinformatics of Disease Igor Jurisica
Anna Tramontano
Other Rick Lathrop
Janice Glasgow

New techniques are especially encouraged. Existing relevant computational techniques include, but are not limited to: machine learning; data mining; text analysis; pattern recognition; knowledge representation; databases; data modeling; combinatorics; stochastic modeling; string and graph algorithms; linguistic methods; robotics; constraint satisfaction; data visualization; parallel computation; data integration; modelling and simulation.

Submission Guidelines
Papers will be assigned to an Area and three reviews sought. Accepted papers will be published as conference proceedings in an open access, online-only, section of a regular issue of the Bioinformatics journal with CDs distributed to conference delegates. Printed proceedings will be available for pre-order purchase during the online conference registration until June 4, 2008. The proceedings will be available online approximately one month prior to the conference opening.

Publication of the proceedings as an online part of the Bioinformatics journal will result in fully citable articles, indexed by Medline and ISI. See the conference proceedings of ISMB 2006 or ISMB/ECCB 2007 for an example of online-only publication by Oxford University Press.

Presenters of accepted papers will be given a 20-minute time slot (plus 5 minutes for questions) in the conference schedule to provide a summary and update to their work.

Papers can be submitted in either a template-free format or in the format following the template for author submission to the OUP journal bioinformatics. If the OUP template is used the paper length must not exceed nine pages. If the template-free format is used the length of the paper must not exceed 12 pages (single space, 12 point font), including abstract, figures, tables, and bibliography. In either case, the paper must contain an abstract whose length does not exceed 250 words.

After acceptance papers will have to be formatted according to the layout style required by the OUP bioinformatics journal and will be limited to 9 pages. Formatting requirements can be found at:

If absolutely necessary, submissions can be accompanied by supplementary material, similar to submissions to scientific journals. The supplementary material should be collected in separate files that are appropriately marked. However, we advise against adding supplementary material, in general. Supplementary material will be published on the proceedings site alongside the online version of the conference paper. We do not support supplementary material presented at any other than the publisher's site. Additionally, OUP does not edit or typeset supplementary data - it is uploaded online exactly as it is received, so authors must ensure its accuracy before submitting.

Papers should be submitted in their final form since the evaluation procedure does not allow for additional rounds of refinement / modification in response to referee criticisms. Poor quality submissions or insufficiently prepared papers are very often rejected.


Papers will be accepted electronically at the submission site in PDF format only.

Papers submitted for review should represent original, previously unpublished work. At the time the paper is submitted to ISMB 2008, and for the entire review period, the paper should not be under review by any other conference or scientific journal.

The deadline for ISMB 2008 paper submissions is Wednesday, January 16, 2008. (You have until 11.59 p.m. in the time zone of your choice. This means that the submission server will be closed at noon, 11:59 am GMT (UTC+0), January 17, 2008).

Notification of acceptance will be provided by e-mail no later than Wednesday, March 19, 2008. Final, corrected versions of accepted papers, which must conform to the formatting guidelines available when the paper is accepted, are due no later than March 30, 2008. Details of the submission process and format of accepted papers will be provided at the time of paper acceptance. Papers not accepted may be resubmitted as a "regular conference poster" until March 26, 2008 or as a "late conference poster" until May 21, 2008. Poster information is available here.

For questions concerning the scientific content of submissions, please contact