16th Annual
International Conference
Intelligent Systems
for Molecular Biology

Metro Toronto Convention Centre (South Building)
Toronto, Canada


Satellite Meetings and SIGs

ISMB 2008 will hold a number of one-day and two-day specialized meetings in computational biology. These meetings will be held on Friday, July 18 and Saturday, July 19, and new for 2008 there will be two, one-day SIG meetings held in parallel with the main conference, one on Sunday, July 20, and one on Monday, July 21. All meetings will be held at the Metro Toronto Convention Centre (South Building). Program information and registration details are noted below.

To inquire about the possibility of forming a new SIG for ISMB/ECCB 2009 or beyond, please address your inquiry to

Registrants are not required to register as delegates for the ISMB 2008 conference to attend a Satellite Meeting. You may select "Satellite only" to register just for the 3Dsig Satellite Meeting. Please note Satellite Meeting registration does not allow access to the SIG Meetings.

The registration fee for the Satellite Meeting includes daily lunches and the 3Dsig Evening Session and Dinner. Each Satellite Meeting participant will receive a booklet that includes meeting notes.

Two-Day Satellite Meeting - Friday, July 18 and Saturday, July 19, 2008

3Dsig: Structural Bioinformatics & Computational Biophysics Satellite Meeting.

SIG Registrants are not required to register as delegates for the ISMB 2008 conference to attend a SIG meeting. You may select "SIG only" to register just for a SIG.

Registering for a SIG allows you to move freely between all SIGs that take place on the same day as the meeting for which you are registered, to the extent that the room capacities can accommodate. SIG registration does not allow access to the Satellite Meeting.

Each SIG participant will receive a booklet that includes handouts from all SIGs and daily lunches are included.

Please register for the SIG in which you are most interested so that we can assign SIGs to larger and smaller rooms as appropriate.

NOTE: One-Day SIG registrants are able to participate in SIG meetings only on the day for which they have registered unless registering for two one-day SIG meetings.

One-Day SIG (Pre-conference) - Friday, July 18, 2008
One-Day SIG (Pre-conference) - Saturday, July 19, 2008
Next Generation Sequencing
One-Day SIG (Parallel with ISMB conference) - Sunday, July 20, 2008
One-Day SIG (Parallel with ISMB conference) - Monday, July 21, 2008
Genome-scale Pattern Analysis in the Post-ENCODE Era
Two-Day SIGs - Friday, July 18 and Saturday, July 19, 2008
Alternative Splicing AS-SIG
Bioinformatics Open Source Conference (BOSC)
Joint AFP-Biosapiens SIG



3Dsig: Structural Bioinformatics & Computational Biophysics Satellite Meeting

Date: Friday, July 18 and Saturday, July 19, 2008
Start time: 8:30 a.m. - End time: 6:30 p.m.
Room Location: 701A
*Friday July 18 - 3Dsig Dinner and Evening Presentation
7:00 p.m. Reception (Cash bar)
7:30 p.m. Dinner

We are happy to announce the fourth 3Dsig meeting consisting of two full days with a balance of invited talks, short oral presentations, two laptop / poster sessions, and critical, topic-focused discussions. 3Dsig is a unique event bringing together the structural computational biology community.

Relevant topics include:
  • Structure representation, structure prediction, structural genomics
  • Structural databases and 3D data mining
  • Structure-based function prediction
  • Evolution studied through structure
  • Protein-protein, protein-ligand, and protein-RNA/DNA interactions (docking, analysis & prediction)
  • Prediction and analysis of domains
  • Membrane protein structure prediction and analysis
  • The role of geometry and energetics in protein and RNA structure and function
  • Protein and RNA dynamics and simulation: folding, stability, interactions, conformational gating
  • Computer-aided protein and RNA design
  • Structure-based drug design and pharmacophore analysis

3Dsig 2008 is continuing the tradition successfully established. The program will be built around talks from accepted abstracts and invited speakers. The scientific committee is looking for fresh, effective voices with new, high impact ideas. Further, accepted abstracts will be presented as regular posters, a laptop presentation, or a combination thereof. The aim of the poster/laptop session is to facilitate in-depth interactions between the presenter and the viewers.

Key Dates:

  • March 5 - Abstract Submissions Open
  • June 4, 2008 - Deadline for submitting an abstract to 3Dsig laptop session AND/OR oral presentation.
  • June 15, 2008 - Announcement of the abstracts selected for oral presentation and laptop/poster session (full program and online abstracts will be posted soon afterwards).

3DSig Scientific Committee:
John Moult, University of Maryland Biotechnology Institute

3DSig Organizing Committee:
John Moult, University of Maryland Biotechnology Institute
Melissa Landon, Boston University
Rafael Najmanovich, European Bioinformatics Institute
Ilan Samish, University of Pennsylvania

Contact: Rafael Najmanovich, European Bioinformatics Institute, UK,



Date: Friday, July 18 and Saturday, July 19, 2008
Start time: 8:30 a.m. - End time: 6:30 p.m.
Room Location: 714A

Towards elucidating the splicing code

The processing of precursors to mature mRNAs constitutes a critical mode for the regulation of gene expression. The choice of splice-sites is conspicuously often not constitutive but variable, as splice sites are often differentially selected, giving rise to multiple mRNA products and protein isoforms with different biochemical and/or physical properties. Splicing is a highly regulated mechanism and produces isoforms enriched to different cell or tissue types, as well as to different stages of cell differentiation or development, and integrates with other components of RNA processing and quality control pathways; variations in either cis-acting elements or trans-acting factors can lead to aberrant splicing and cause disease.

RNA splicing is now positioned at the interplay of genomes, regulatory networks and evolution, and it has emerged as a ubiquitous and dynamic mechanism of gene regulation. This is supported by a stream of novel insights and discoveries derived from genomics, bioinformatics and molecular biology, as well as new approaches toward more parallel measurements of expressed isoforms. Identifying, quantifying, analyzing and understanding the regulation, function and evolution of splicing is constitutes a challenge to eventually arrive at a regulatory "RNA map" of splicing in model organisms.

The AS-SIG meeting is evolving as a permanent forum at ISMB for splicing regulatory biologists, as well as for biologists in related fields, to discuss collaboratively, by addressing the latest findings and open questions in this exciting field, and bringing together bioinformatics and biology on a systems level. The AS-SIG meeting will include studies of AS of both humans and model organisms, reflecting the added biological value of comparative genomics.

The meeting will have three main session topics:

Post-transcriptional regulation of gene expression
Model systems: from yeast to human; mRNA isofoms: conservation and divergence; expression and regulation of tissue - and developmental stage-specific genes; RNA processing (including 5' and 3' ends, decay, editing, and antisense); evolution: splicing/alternative splicing, exon shuffling, intron gain and loss; RNA regulatory maps: determination of cis-functional elements active in splice site choice; high-throughput: sequencing and microarrays; platforms: annotation, storage, and data exchange formats

Protein structure, functional impact, and interactions
Interaction: splicing factors and their interaction with cis-regulatory functional elements; function: impact of isoforms on protein structure and function; RNA quality control: scope and action of NMD; chemogenomics and small-molecules-protein interactions

Splicing and RNA pathogenesis
Identification: classification and characterization of cryptic splice variants linked to disease in human and model systems; disease: tools and strategies to detect pathogenic splice variations and to restore authentic and/or suppress disease-associated variants

Benjamin Blencowe, University of Toronto,
Dirk Holste, Institute of Molecular Pathology, Austria,
Eduardo Eyras, Pompeu Fabra University, Spain,
Graziano Pesole, University of Bari,


Date: Friday, July 18 and Saturday, July 19, 2008
Start time: 8:30 a.m. - End time: 6:30 p.m.
Room Location: 715A

The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form.

Many Open Source bioinformatics packages are widely used by the research community across many application areas and form a cornerstone in enabling research in the genomic and post-genomic era. Open source bioinformatics software has facilitated rapid innovation and dissemination of new computational methods as well as informatics infrastructure. Since the work of the Open Source Bioinformatics Community represents some of the most cutting edge of Bioinformatics in general, the overall themes for the conference this year are emerging technologies and hard problems in bioinformatics. Topics under this umbrella include infrastructure and data modeling, web 2.0 technologies, workflows, visualization, and best practices of software design and engineering. We will also have a series of update talks about the main Open Source Bioinformatics Software suites.

One of the hallmarks of BOSC is the coming together of the open source developer community in one location. A face-to-face meeting of this community creates synergy where participants can work together to create use cases, prototype working code, or run bootcamps for developers from other projects as short, informal, and hands-on tutorials in new software packages and emerging technologies. In short, BOSC is not just a conference for presentations of completed work, but is a dynamic meeting where collaborative work gets done.

Darin London, Duke University,
Kam D. Dahlquist, Loyola Marymount University,


BioLINK SIG: Linking Literature, Information and Knowledge for Biology

Date: Friday, July 18, 2008
Start time: 8:30 a.m. - End time: 6:30 p.m.
Room Location: 716B

The Annual Meeting of The ISMB BioLINK Special Interest Group on Text Data Mining

With the increasing availability of textual information related to biology including Medline abstracts and full-text journal articles, the field of biomedical text mining has been rapidly maturing. It is concerned with using techniques from natural language processing, information extraction and information retrieval to automate knowledge discovery from biomedical text.

The BioLINK SIG meeting has been regularly held in association with the ISMB conference since 2001. The SIG focuses on the development and application of resources and tools for biomedical text mining. It is interdisciplinary in nature, and brings together researchers applying natural language processing, text mining, information extraction and retrieval in the biomedical domain, with scientists from bioinformatics and biology.

The meeting includes invited talks, presentations of peer-reviewed contributed papers, as well as a poster session. This year's SIG will focus on the theme of automated linkage of the literature to biological resources in support of applications such as: automated indexing of the biomedical literature, generation of structured digital abstracts and the use of text-mined data in biology and bioinformatics pipelines. To stimulate discussion, we will invite a set of "end users" to present their applications and text mining needs, with a specific goal of encouraging partnerships among the end users and the developers of text mining tools.

The SIG solicits papers that discuss current biological text-related needs, the challenges of meeting them, and the tools that may help address them. Topics may include development and application of text-tools for biomedical research and for biological database curation, inter-relations between database curation and text mining, as well as new tools, new applications and future directions in biomedical text mining.

We anticipate a fruitful workshop that will facilitate discussion and exchange of ideas, by bringing researchers applying natural language processing, ontologies, text mining, information extraction and retrieval in the biomedical domain, together with scientists from bioinformatics and biology.

Information about last year's meeting is available at the BioLINK07 web site

Christian Blaschke, Bioalma, Spain,
Hagit Shatkay, Queen's University, Canada,


Date: Sunday, July 20, 2008
Start time: 8:30 a.m. - End time: 6:30 p.m.
Room Location: 715

Program Schedule Now Available here:

Bio-Ontologies has existed as a SIG at ISMB for more than a decade, making it one of the longest running. For this time, Bio-Ontologies has provided a forum for discussion on the latest and most cutting edge research on ontologies.

In this decade, the use of ontologies has become mature, moving from niche to mainstream usage within bioinformatics. Following on from last year's reflective look, this year we are broadening the scope of SIG; we are interested in any formal or informal approach to organising, presenting and disseminating knowledge in biology.
So, for example:
  • Semantic and/or Scientific wikis.
  • Multimedia blogs
  • Folksonomies
  • Tag Clouds
  • Collaborative Curation Platforms

Collaborative Ontology Authoring and Peer-Review Mechanisms are topics which will now be of relevance to the SIG, in additional to the more traditional bio-ontologies topics:

Biological Applications of Ontologies
Reports on Newly Developed or Existing Bio-Ontologies
Tools for Developing Ontologies
Use of Semantic Web technologies in Bioinformatics.
The implications of Bio-Ontologies or the Semantic Web for the drug discovery
Current Research In Ontology Languages and its implication for Bio-Ontologies

In addition to submitted papers, a keynote presentation will be given by Dr.
Philip Bourne, and a panel of 4 invited panelists.

Phillip Lord, Newcastle University,
Matt Cockerill, BioMedCentral,
Susanna-Assunta Sansone, European Bioinformatics Institute,
Nigam Shah, Stanford University,


Date: Friday, July 18 and Saturday, July 19, 2008
Start time: 8:30 a.m. - End time: 6:30 p.m.
Room Location: 714B

The 10th BioPathways meeting organized by the BioPathways Consortium (, an open forum aimed at fostering computational approaches to the modeling, reconstruction, analysis and simulation of biological processes.

The meeting will include 3-4 plenary sessions, presenting invited talks on various aspects of computational systems biology, including:
  • computational methods for synthetic biology
  • computational methods for metagenomics
  • modelling of interactions within bacterial communities
  • evolution of metabolic networks
  • evolution of regulatory networks
  • computational methods for metabolomics
  • computational network approaches for discovering disease associations
  • reconstructing network dynamics from experimental data

Each plenary session will include several long invited presentations (45'), followed by a panel discussion on the session theme. To encourage presentation of cutting-edge research and work-in-progress in computational approaches to molecular pathways, we will also include contributed talks as part of the meeting's session. A contributed talk consists of a short presentation of relevant method, tools and analyses. Particular emphasis will be made on works along the themes of the plenary sessions, as well as research in pathway visualization and reconstruction, all of which are subjects followed by the consortium's workgroups. If you wish to present a contributed talk at BioPathways 2008, please send a 200 word abstract describing your work. Authors are encouraged to add URLs of web-based tools, and selected tools will be featured on the BioPathways web site. Abstracts should arrive by May 1, 2008, and presenters will be notified no later than May 30, 2008. Submissions should be sent to:

We look forward to seeing you at BioPathways 2008. For the organizers: Vincent Danos, Joanne Luciano, Vitor Martins dos Santos, Eric Neumann Aviv Regev and Vincent Schachter

Vincent Danos,
Joanne Luciano,
Vitor Martins dos Santos,


Date: Friday, July 18 and Saturday, July 19, 2008
Start time: 8:30 a.m. - End time: 6:30 p.m.
Room Location: 716A

The Joint Automated Function Prediction (AFP) SIG and the Biosapiens European Network of Excellence for genome annotation are teaming up again to hold a two-day SIG meeting. The deluge of genomic information is challenging biologists to annotate this data, from locating genes in the raw data through to predicting the function from protein sequence and structure. AFP and Biosapiens share many common goals. Following the successful meeting in 2007 in Vienna, this year we have decided yet again to join forces for a SIG that will deal with a wide scope of gene, protein, and genomic annotations.

We are soliciting abstracts for talks, posters and mini-tutorials in the following topics:

Various aspects of gene and protein function prediction:
  • Function prediction using sequence based methods. This would include "classic" methods such as detection of functional motifs and inferring function from sequence similarity.
  • Function from genomic information: prediction by genomic location; locus comparison with other organisms; function gain and loss.
  • Phylogeny based methods
  • Function from molecular interactions
  • Function from structure
  • Function prediction using combined methods
  • "Meta-talks" discussing the limitations and horizons of computational function prediction.
  • Assessing function prediction programs
Genomic annotation
  • Gene finding
  • Genome visualization
  • Collaborative annotation
  • Cooperation between experimental and computational biologists
  • Environmental genomics and metagenomics issues
Confirmed speakers include:
  • Barry Honig, Columbia University and Howard Hughes Medical Institute, USA
  • Peer Bork, European Molecular Biology Laboratories, Germany
  • Andrew Emily, University of Toronto, Canada
  • Olga Troyanskaya, Princeton University, USA
  • Kimmen Sjolander, University of California Berkeley, USA

Abstract submission deadline: March 31, 2008

Contact: Iddo Friedberg


Next Generation Sequencing: Algorithms for Short Read Assembly, Alignment & Variation Analysis


Date: Saturday, July 19, 2008
Start time: 8:30 a.m. - End time: 6:30 p.m.
Room Location: 716B

Next generation, rapid, low-cost genome sequencing promises to address a broad range of genetic analysis applications. In order to increase throughput, new sequencing platforms that are appearing in the marketplace carry out many parallel reactions. This results in much shorter reads (down to 25-50 bp), but the overall throughput is enormous, with each run producing billions of base-pairs of sequence data.

While the promise of next generation sequencing (NGS) technologies has become a reality, computational methods for assembly, alignment, and variation detection using such short reads are still in their infancy. Programs and algorithms developed for Sanger-style reads must be scaled, or completely reinvented to match the characteristics of the NGS data. For example, SNP discovery from Sanger sequencing reads is reasonably well understood - however, the situation is very different in the case of NGS, where error rates are higher to those of Sanger and alignment of short reads to reference sequences is complicated by the length of the reads. NGS platforms present not only new challenges, but also new opportunities, not only due to the massive amount of short reads, but also due to the different sequencing methodologies (e.g. dibase sequencing) and different underlying error models that are critical to distinguishing false positives from real variations. Because it is possible to generate mated reads with some NGS technologies, it is possible to infer genome rearrangements, however this will require new approaches as many reads will map to multiple locations in the genome. Short reads can also potentially be used for inferring copy number variants, but the methods for copy number detection using sequence data have not been developed. The problem of short read assembly and co-assembly is equally important, as solving this problem promises to drastically lower the cost of sequencing a new genome.

This session will provide a forum for in-depth presentations of the methods and discussion among the scientists working in this field.

Contact: Michael Brudno,


Genome-scale Pattern Analysis in the Post-ENCODE Era

Date: July 21, 2008
Start time: 8:30 a.m. - End time: 6:30 p.m.
Room Location: 715

According to the recent findings of the ENCODE project, the meaning of most of the human genome remains a mystery! Startling outcomes of the ENCODE project include the following:

  • much functional information is not "conserved" across organisms;
  • epigenetic marks predict the presence and activity of functional regions;
  • remarkably, up to 93% of bases in the ENCODE regions are transcribed; and
  • regulatory binding sites (motifs) extend upstream and downstream of transcription start sites.

An important implication of these outcomes is that the existing models for computational genomics are insufficient to handle the shifting paradigms of biological interpretation. Thus, the SIG will focus on specific research challenges that must be addressed to utilize computational genomics approaches to assimilate ENCODE's findings into research and technology. The SIG will consist of a mix of presentations and discussions. The objectives are to engage participants in discussion, to raise awareness of computational approaches that are likely to benefit current research projects, and to foster a collaborative research environment. We are planning 4 technical sessions, each consisting of 1 plenary talk, 3 research presentations, and group discussion. Program highlights include the following:

SESSION 1 - The Post-ENCODE Paradigm, Plenary Speaker: Bill Noble, University of Washington
SESSION 2 - Identification of Novel Functional Elements, Plenary Speaker: Manolis Kellis, MIT
KEYNOTE SPEECH - Mark Gerstein,Yale University
SESSION 3 - Genome-scale Pattern Analysis, Plenary Speaker: Adam Siepel, Cornell University
SESSION 4 - Personalized Medicine, Plenary Speaker: Jim Mullikin, National Human Genome Research Institute

Laura Elnitski, National Human Genome Research Institute,
Lonnie Welch, Ohio University ,