This volume contains the papers accepted for presentation at the Fifteenth Conference on Intelligent Systems for Molecular Biology, which was held jointly with the Sixth European Conference on Computational Biology (ISMB/ECCB 2007; http://www.iscb.org/ismbeccb2007/). The conference was held from 21–25 July 2007 at the Austria Center in Vienna, Austria. The conference united the annual meetings of the International Society for Computational Biology (ISCB) and of the European Computational Biology Community. The papers presented here are noteworthy for several reasons. First, for the second time, papers are open access and freely available to the worldwide community ahead of the conference and subsequently form an online only part of a regular issue of the journal Bioinformatics. Second, the review process was conducted even more rigorously than in previous years, as we describe below. We believe the scientific content to be outstanding. At the time of print, we expect the conference to become the largest scientific event in Computational Biology worldwide in the year 2007. This attests to the role of the conference and its organizing societies in furthering science in Computational Biology and fostering interdisciplinary scientific dialog on an international scale.

The call for papers resulted in 417 submissions in 11 different categories (Table 1). Area Chairs were recruited for each category and they in turn assigned reviewers for each paper. The Program Committee comprised over 300 reviewers who were assisted by a sizeable number of subreviewers. Aside from a few editorial rejects, all papers received at least two reviews; most were reviewed by three experts. During a 10-day period of internet discussion, the referees exchanged their views on controversial papers, based on the original reviews. After that period the area chairs decided on 51 ‘definite accepts’ and handed 40 more papers over to an inter-area discussion involving all area chairs and the program chair. That discussion was carried out over the internet and took two intensive phone conferences, lasted for 10 more days and yielded 15 more papers that were accepted for the conference. In total 66 papers have been included corresponding to an acceptance rate of 15.8%. The ratio is less than for typical submission to Bioinformatics, for three reasons. First, papers submitted to ISMB/ECCB 2007 had to have the quality of a regular submission to Bioinformatics. In addition, they had to make for interesting talks and, finally, they had to be acceptable without major revision, because the timing of the paper selection process for the conference did not allow for a second round of reviewing.

Table 1.

ISMB/ECCB 2007 Program Areas, Area Chairs and Paper Distribution

Area Area Chairs Papers Received/Accepted 
Sequence Analysis and Alignment Des Higgins, Anders Gorm Pedersen 54/9 
Evolution and Phylogeny Manolo Gouy, Tandy Warnow 20/4 
Comparative Genomics Michal Linial, Manolis Kellis 20/3 
Gene Regulation and Transcriptomics Olga Troyanskaya, Zhaolei Zhang 58/12 
Protein Structure Nir Ben-Tal 47/6 
Protein Function Erik Sonnhammer 22/4 
Protein Interactions and Molecular Networks Joel Bader, Alfonso Valencia 43/7 
Databases and Ontologies Helen Parkinson, Robert Stevens 35/3 
Text Mining Christian Blaschke, Dietrich Rebholz-Schuhmann 29/3 
Bioinformatics of Disease Yanay Ofran, Predrag Radivojac 49/12 
Other Janice Glasgow, Rick Lathrop 40/3 
Area Area Chairs Papers Received/Accepted 
Sequence Analysis and Alignment Des Higgins, Anders Gorm Pedersen 54/9 
Evolution and Phylogeny Manolo Gouy, Tandy Warnow 20/4 
Comparative Genomics Michal Linial, Manolis Kellis 20/3 
Gene Regulation and Transcriptomics Olga Troyanskaya, Zhaolei Zhang 58/12 
Protein Structure Nir Ben-Tal 47/6 
Protein Function Erik Sonnhammer 22/4 
Protein Interactions and Molecular Networks Joel Bader, Alfonso Valencia 43/7 
Databases and Ontologies Helen Parkinson, Robert Stevens 35/3 
Text Mining Christian Blaschke, Dietrich Rebholz-Schuhmann 29/3 
Bioinformatics of Disease Yanay Ofran, Predrag Radivojac 49/12 
Other Janice Glasgow, Rick Lathrop 40/3 

Corresponding authors of submitted papers came from 42 countries, 194 papers were from North America, 140 from Europe and Israel, 69 from Asia, 5 from South America, 7 from Australia and 2 from Africa.

The contributed papers presented here comprise only one aspect of the scientific offerings of the conference, albeit a very important one. Ten invited keynotes were held by outstanding scientists in the field (Table 2), among them this year's ISCB Award Winners Eran Segal (Overton Prize) and Temple Smith (ISCB Senior Scientist Accomplishment Award). Furthermore, the conference offered a Highlight Papers Track organized by Burkhard Rost featuring 65 talks on previously published high-quality work in computational biology, a PLoS Abstracts Track organized by Barbara Bryant, Phil Bourne and Steven Brenner with well over 30 talks on so far unpublished biology-oriented work in computational biology, and six ‘Special Sessions’ on relevant up-to-date topics (Table 3). Over 950 posters were selected to be presented in a Poster Session organized by Marco Punta. Reinhard Schneider organized an Industry Track with scientific presentations from industry and Shoba Ranganathan organized a Software Demonstrations Track. Before the conference, one Satellite Meeting and seven Special Interest Groups Meetings (SIGs) were held that were selected by Hershel Safer, Jill Mesirov and David Gilbert (Table 4), and there was a day of tutorials, featuring 14 tutorials selected by Janet Kelso and Fran Lewitter (Table 5).

Table 2.

ISMB/ECCB 2007 Keynotes

Name Affiliation Title 
Søren Brunak Technical University of Denmark, Lyngby, Denmark Understanding interactomes by data integration 
 
Stephen K. Burley SGX Pharmaceuticals, Inc., San Diego, CA, USA Fragment-based discovery of BCR-ABL inhibitors for treatment of chronic myelogenous leukemia 
 
Michael Eisen University of California, Berkeley, CA, USA Understanding and exploiting the evolution of the sequences that control gene expression 
 
Anne-Claude Gavin European Molecular Biology Laboratory, Heidelberg, Germany Interaction networks probed by mass spectrometry 
John Mattick University of Queensland, Brisbane, Australia The majority of the genome of complex organisms is devoted to an RNA regulatory system that directs differentiation and development 
 
Erin K. O'Shea Harvard University, Cambridge, MA, USA Dissecting transcriptional network structure and function 
 
Renée Schroeder University of Vienna, Austria Genomic SELEX for the identification of novel non-coding RNAs independent of their expression level 
 
Eran Segal Computer Science and Applied Mathematics Department, Weizmann Institute of Sciences Quantitative models for chromatin and transcription regulation 
 
Temple F. Smith Boston University, College of Engineering, Department of Biomedical Engineering, BioMolecular Engineering Research Center Computational Biology: What is next? 
 
Terry Speed Department of Statistics, University of California at Berkeley, Bioinformatics Division, Walter & Eliza Hall Institute of Medical Research Genome-wide genotyping: the great classification challenge 
Name Affiliation Title 
Søren Brunak Technical University of Denmark, Lyngby, Denmark Understanding interactomes by data integration 
 
Stephen K. Burley SGX Pharmaceuticals, Inc., San Diego, CA, USA Fragment-based discovery of BCR-ABL inhibitors for treatment of chronic myelogenous leukemia 
 
Michael Eisen University of California, Berkeley, CA, USA Understanding and exploiting the evolution of the sequences that control gene expression 
 
Anne-Claude Gavin European Molecular Biology Laboratory, Heidelberg, Germany Interaction networks probed by mass spectrometry 
John Mattick University of Queensland, Brisbane, Australia The majority of the genome of complex organisms is devoted to an RNA regulatory system that directs differentiation and development 
 
Erin K. O'Shea Harvard University, Cambridge, MA, USA Dissecting transcriptional network structure and function 
 
Renée Schroeder University of Vienna, Austria Genomic SELEX for the identification of novel non-coding RNAs independent of their expression level 
 
Eran Segal Computer Science and Applied Mathematics Department, Weizmann Institute of Sciences Quantitative models for chromatin and transcription regulation 
 
Temple F. Smith Boston University, College of Engineering, Department of Biomedical Engineering, BioMolecular Engineering Research Center Computational Biology: What is next? 
 
Terry Speed Department of Statistics, University of California at Berkeley, Bioinformatics Division, Walter & Eliza Hall Institute of Medical Research Genome-wide genotyping: the great classification challenge 
Table 3.

Special Sessions

Title Organizer Affiliation 
Private fears in public places? Ethical and regulatory concerns regarding human genomics databases David Gurwitz Tel-Aviv University, Israel 
 
 Barbara Praisack University of Vienna, Austria 
Cheminformatics Matthias Rarey University of Hamburg, Germany 
 
Genetic networks: Inferring pathways by combinatorial perturbation Frederick “Fritz” Roth Harvard Medical School, Cambridge, MA, USA 
 
Computational epigenetics and chromatin regulation Michael Q. Zhang Cold Spring Harbor Laboratory, NY, USA 
 
Computational Approaches to the Modern RNA World Ivo Hofacker University of Vienna, Austria 
 
Dry work in a wet world: Improving methodology and access of computational methods in Systems Biology Ewan Birney European Bioinformatics Institute, Hinxton, UK 
Title Organizer Affiliation 
Private fears in public places? Ethical and regulatory concerns regarding human genomics databases David Gurwitz Tel-Aviv University, Israel 
 
 Barbara Praisack University of Vienna, Austria 
Cheminformatics Matthias Rarey University of Hamburg, Germany 
 
Genetic networks: Inferring pathways by combinatorial perturbation Frederick “Fritz” Roth Harvard Medical School, Cambridge, MA, USA 
 
Computational epigenetics and chromatin regulation Michael Q. Zhang Cold Spring Harbor Laboratory, NY, USA 
 
Computational Approaches to the Modern RNA World Ivo Hofacker University of Vienna, Austria 
 
Dry work in a wet world: Improving methodology and access of computational methods in Systems Biology Ewan Birney European Bioinformatics Institute, Hinxton, UK 
Table 4.

ISMB/ECCB 2007 SIGs and Satellite Meetings

Title Organizer Affiliation 
Alternative Splicing AS-SIG Shoba Ranganathan Macquarie University, Sydney, Australia 
 Dirk Holste University of Vienna, Austria 
 Eduardo Eyras Pompeu Fabra University, Barcelona, Spain 
 Andrea Barta University of Vienna, Austria 
 
Bioinformatics Open Source Conference (BOSC) Darin London Duke University, Durham, NC, USA 
 
Bioinformatics Open Source Conference David London Duke University 
 
BioLINK SIG Christian Blaschke Bioalma, Madrid, Spain 
 Lynette Hirschman MITRE Corp., Bedford, MA, USA 
 Hagit Shatkay Queen's University, Kingston, Ontario, Canada 
 Alfonso Valencia Spanish National Cancer Research Center, Madrid, Spain 
 
Bio-Ontologies SIG Phillip Lord Newcastle University, UK 
 Robert Stevens University of Manchester, UK 
 Robin McEntire GlaxoSmithKline, Uxbridge, UK 
 Susanna-Assunta Sansone European Bioinformatics Institute, Hinxton, UK 
 
BioPathways Vincent Danos University Paris-Diderot, France 
 Joanne Luciano Harvard Medical School, Boston, MA, USA 
 Eric Neumann Teranode Corp., Boston, MA, USA 
 Aviv Regev The Broad Institute, Cambridge, MA, USA 
 Vincent Schachter Genoscope, Evry, France 
 
Joint AFP-Biosapiens SIG Iddo Friedberg University of California, San Diego, CA, USA 
 Christine Orengo University College London, UK 
 Adam Godzik University of California, San Diego, CA, USA 
 
Microbe-SIG: Comparative Genomics, Evolution and Regulation in Microbes Adam Arkin Lawrence Berkeley Laboratory, CA, USA 
 Eric Alm Massachusetts Institute of Technology, Cambridge, MA, USA 
 Inna Dubchak Lawrence Berkeley Laboratory, CA, USA 
 
3D-SIG: Structural Bioinformatics and Computational Biophysics Meeting (Satellite Meeting) John Moult University of Maryland, College Park, MD, USA 
 Rafael Najmanovich European Bioinformatics Institute, Hinxton, UK 
 Ilan Samish University of Pennsylvania, Philadelphia, PA, USA 
 Melissa Landon Boston University, MA, USA 
Title Organizer Affiliation 
Alternative Splicing AS-SIG Shoba Ranganathan Macquarie University, Sydney, Australia 
 Dirk Holste University of Vienna, Austria 
 Eduardo Eyras Pompeu Fabra University, Barcelona, Spain 
 Andrea Barta University of Vienna, Austria 
 
Bioinformatics Open Source Conference (BOSC) Darin London Duke University, Durham, NC, USA 
 
Bioinformatics Open Source Conference David London Duke University 
 
BioLINK SIG Christian Blaschke Bioalma, Madrid, Spain 
 Lynette Hirschman MITRE Corp., Bedford, MA, USA 
 Hagit Shatkay Queen's University, Kingston, Ontario, Canada 
 Alfonso Valencia Spanish National Cancer Research Center, Madrid, Spain 
 
Bio-Ontologies SIG Phillip Lord Newcastle University, UK 
 Robert Stevens University of Manchester, UK 
 Robin McEntire GlaxoSmithKline, Uxbridge, UK 
 Susanna-Assunta Sansone European Bioinformatics Institute, Hinxton, UK 
 
BioPathways Vincent Danos University Paris-Diderot, France 
 Joanne Luciano Harvard Medical School, Boston, MA, USA 
 Eric Neumann Teranode Corp., Boston, MA, USA 
 Aviv Regev The Broad Institute, Cambridge, MA, USA 
 Vincent Schachter Genoscope, Evry, France 
 
Joint AFP-Biosapiens SIG Iddo Friedberg University of California, San Diego, CA, USA 
 Christine Orengo University College London, UK 
 Adam Godzik University of California, San Diego, CA, USA 
 
Microbe-SIG: Comparative Genomics, Evolution and Regulation in Microbes Adam Arkin Lawrence Berkeley Laboratory, CA, USA 
 Eric Alm Massachusetts Institute of Technology, Cambridge, MA, USA 
 Inna Dubchak Lawrence Berkeley Laboratory, CA, USA 
 
3D-SIG: Structural Bioinformatics and Computational Biophysics Meeting (Satellite Meeting) John Moult University of Maryland, College Park, MD, USA 
 Rafael Najmanovich European Bioinformatics Institute, Hinxton, UK 
 Ilan Samish University of Pennsylvania, Philadelphia, PA, USA 
 Melissa Landon Boston University, MA, USA 
Table 5.

ISMB/ECCB 2007 Tutorials

Title Organizer Affiliation 
Comparative analysis of protein structures: Principles, tools, and applications for establishing evolutionary relationship and predicting function Raza Mazumder Georgetown University, Washington DC, USA 
 Sona Vasudevan  
 
Workflow Approaches to Transcriptomics Analysis Katy Wolstencroft University of Manchester, UK 
 Georgina Moulton  
 
Ontologies for Biomedicine – How to make and use them Barry Smith University at Buffalo, USA 
 Nigam Shah  
 
Exploring computational biology with a massively parallel high performance computing environment Kirk Jordan IBM T.J. Watson Research Center, Yorktown Heights, NY, USA 
 Srinivas Aluru Iowa State University, Ames, IA, USA 
 
Genomes, browsers and databases: Tools for integrative sequence and annotation data from multiple genomes Peter Schattner University of California, Santa Cruz, CA,USA 
 
Implementing phylogenetic workflows for comparative genomics using BioPerl Jason Stajich University of California, Berkeley, CA, USA 
 Albert Vilella European Bioinformatics Institute, Hinxton, UK 
 
Genomic data fusion for gene prioritization and function prediction Yves Moreau University of Leuven, Belgium 
 
Gene and protein networks Debra Goldberg University of Colorado, Boulder, CO, USA 
 Todd Gibson University of Colorado, Aurora, CO, USA 
 
Automatic text analysis based on Web Services Dietrich Rebholz-Schuhmann European Bioinformatics Institute, Hinxton, UK 
 
Reverse engineering mammalian transcriptional regulatory circuits Pavel Sumazin Columbia University, New York, NY, USA 
 Andrea Califano  
 Andrei D. Smith Cold Spring Harbor Laboratory, NY, USA 
 Michael Q. Zhang  
 
Systems Biology of host-pathogen interactions and microbial communities Christian Forst Los Alamos National Labs, Santa Fe, NM, USA 
 
Comprehensive analysis of Affymetrix exon expression data using BioConductor Crispin Miller University of Manchester, UK 
 Michal Okoniewski  
 
Introduction to phylogenetic networks Daniel Huson University of Tübingen, Germany 
An introduction to bioinformatics for glycomics research Kiyoko Aoki-Kinoshita Claus-Wilhelm von der Lieth Soka University, Hachioji, JapanGerman Cancer Research Center, Heidelberg, Germany 
Title Organizer Affiliation 
Comparative analysis of protein structures: Principles, tools, and applications for establishing evolutionary relationship and predicting function Raza Mazumder Georgetown University, Washington DC, USA 
 Sona Vasudevan  
 
Workflow Approaches to Transcriptomics Analysis Katy Wolstencroft University of Manchester, UK 
 Georgina Moulton  
 
Ontologies for Biomedicine – How to make and use them Barry Smith University at Buffalo, USA 
 Nigam Shah  
 
Exploring computational biology with a massively parallel high performance computing environment Kirk Jordan IBM T.J. Watson Research Center, Yorktown Heights, NY, USA 
 Srinivas Aluru Iowa State University, Ames, IA, USA 
 
Genomes, browsers and databases: Tools for integrative sequence and annotation data from multiple genomes Peter Schattner University of California, Santa Cruz, CA,USA 
 
Implementing phylogenetic workflows for comparative genomics using BioPerl Jason Stajich University of California, Berkeley, CA, USA 
 Albert Vilella European Bioinformatics Institute, Hinxton, UK 
 
Genomic data fusion for gene prioritization and function prediction Yves Moreau University of Leuven, Belgium 
 
Gene and protein networks Debra Goldberg University of Colorado, Boulder, CO, USA 
 Todd Gibson University of Colorado, Aurora, CO, USA 
 
Automatic text analysis based on Web Services Dietrich Rebholz-Schuhmann European Bioinformatics Institute, Hinxton, UK 
 
Reverse engineering mammalian transcriptional regulatory circuits Pavel Sumazin Columbia University, New York, NY, USA 
 Andrea Califano  
 Andrei D. Smith Cold Spring Harbor Laboratory, NY, USA 
 Michael Q. Zhang  
 
Systems Biology of host-pathogen interactions and microbial communities Christian Forst Los Alamos National Labs, Santa Fe, NM, USA 
 
Comprehensive analysis of Affymetrix exon expression data using BioConductor Crispin Miller University of Manchester, UK 
 Michal Okoniewski  
 
Introduction to phylogenetic networks Daniel Huson University of Tübingen, Germany 
An introduction to bioinformatics for glycomics research Kiyoko Aoki-Kinoshita Claus-Wilhelm von der Lieth Soka University, Hachioji, JapanGerman Cancer Research Center, Heidelberg, Germany 

We would like to thank the Area Chairs and reviewers for the quality they have brought to the conference, to Mario Albrecht for managing the paper selection process and coordinating the voluminous dialog with authors and reviewers, Andrei Voronkov for technical support with the EasyChair system which was used for managing the selection process, the team at Oxford University Press for proof-setting the papers, and Steven Leard for helping in many ways to get the proceedings out on time.

Thomas Lengauer, Conference Chair, ISMB/ECCB 2007 Burkhard Rost, Peter Schuster, Conference Co-Chairs, ISMB/ECCB 2007.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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