This special issue hosts the proceedings of the joint 21st annual meeting of Intelligent Systems for Molecular Biology (ISMB) and 12th European Conference on Computational Biology (ECCB), which will take place in Berlin, Germany, between July 21 and 23, 2013 (http://www.iscb.org/ismbeccb2013). This official conference of the International Society for Computational Biology (http://www.iscb.org/), preceded by 11 Special Interest Group (SIG) meetings of 1 or 2 days, two satellite meetings, a Student Council Symposium, Junior Principal Investigators Symposium and two half-day tutorials during July 19–20, 2013, is likely to be the largest annual gathering in the field.

The 40 articles in this volume were selected from 233 submissions divided into 13 research areas, led by 26 area chairs. The chairs selected their area’s program committee and oversaw the reviewing process. The chairs included a blend of individuals with experience from previous years and newcomers. Twelve submissions for which area chairs were in conflict were reviewed within ‘Applied Bioinformatics’ headed jointly by the two area chairs and the proceedings chair; four were accepted. Areas, co-chairs and acceptance data are listed in Table 1.

Table 1.

Areas, co-chairs and acceptance data

Topic area Chairs Submissions Accepted to round two Submitted to round two Accepted to proceedings Granted the opportunity to redirect to Bioinformatics 
Applied bioinformatics and conflicts management Nir Ben-Tal, Thomas Lengauer and Ora Schueler-Furman 18 11 10 
Bioimaging and data visualization Sean O’Donoghue and Carolina Wählby 11 
Databases and ontologies and text mining Alex Bateman and Hagit Shatkay 13 
Disease models and epidemiology Simon Kasif 12 
Evolution and comparative genomics Tal Pupko and Tandy Warnow 13 
Gene regulation and transcriptomics Alexander Hartemink and Zohar Yakhini 42 14 11 
Mass spectrometry and proteomics Rob Russell and Olga Vitek 
Metabolic networks Bonnie Berger and Jason Papin 
Population genomics Eleazar Eskin and Russell Schwartz 
Protein interactions and molecular networks Roded Sharan and Mona Singh 32 
Protein structure and function Lenore Cowen and Jie Liang 30 10 10 
RNA bioinformatics Ivo Hofacker and Hanah Margalit 
Sequence analysis Serafim Batzoglou and Cenk Sahinalp 32 12 12 
Total 26 233 89 85 40 11 
Topic area Chairs Submissions Accepted to round two Submitted to round two Accepted to proceedings Granted the opportunity to redirect to Bioinformatics 
Applied bioinformatics and conflicts management Nir Ben-Tal, Thomas Lengauer and Ora Schueler-Furman 18 11 10 
Bioimaging and data visualization Sean O’Donoghue and Carolina Wählby 11 
Databases and ontologies and text mining Alex Bateman and Hagit Shatkay 13 
Disease models and epidemiology Simon Kasif 12 
Evolution and comparative genomics Tal Pupko and Tandy Warnow 13 
Gene regulation and transcriptomics Alexander Hartemink and Zohar Yakhini 42 14 11 
Mass spectrometry and proteomics Rob Russell and Olga Vitek 
Metabolic networks Bonnie Berger and Jason Papin 
Population genomics Eleazar Eskin and Russell Schwartz 
Protein interactions and molecular networks Roded Sharan and Mona Singh 32 
Protein structure and function Lenore Cowen and Jie Liang 30 10 10 
RNA bioinformatics Ivo Hofacker and Hanah Margalit 
Sequence analysis Serafim Batzoglou and Cenk Sahinalp 32 12 12 
Total 26 233 89 85 40 11 

A two-tire review procedure was used, which is different from previous years. Of the total submissions, 89 were accepted to round two, including some with conflicting opinions. Of these, 85 were submitted to the second round. The final decision was made based on the revised submissions, taking into consideration the authors response to the reviewer reports, as well as reviewer reports on the revisions. Only 40 articles could be accommodated in the proceedings, forcing us to turn down 35, many of which were of high quality. I was hoping that the authors of most of these would be granted the opportunity to submit revised manuscripts to Bioinformatics, where they could be evaluated while their review history is considered. Unfortunately this opportunity was granted only to 11 manuscripts; I hope that if submitted, these will be readily accepted. More importantly, I would like to extend my apology to the authors of the remaining 24 who went through highly demanding and painful review process. I am hopeful that the authors of these manuscripts found the reviewer comments helpful.

The division into areas was somewhat different this year. Two new areas were defined: ‘Metabolic Networks’ and ‘RNA Bioinformatics’ and chairs and reviewers with suitable expertise recruited. ‘Databases and Ontologies’ and ‘Text Mining’ were merged into a single area.

All in all 368 members of the bioinformatics community provided reviews. Most articles were assigned to three reviewers and some to four or more. There was significant discussion of the merits of the articles first between referees and the area chairs, and then between area chairs and the proceedings chair. The review also included two conference calls with the area chairs. I am hopeful that the revised review process, which resembles that of journal articles, helped us to correctly choose the most suitable articles for the proceedings, but there is no guarantee.

I thank the area chairs and reviewers for their hard work in maintaining a professional review process; it has been harder and longer this year. I thank Steven Leard’s team for extensive technical support with the EasyChair submission and reviewing system; the team at Oxford University Press for type-setting the articles; Conference Chairs Burkhard Rost, Anna Tramontano and Martin Vingron, as well as the ISMB 2013 Steering Committee, for their valuable input; and Steven Leard for helping us oversee the process. Special thanks to Mona Singh for her valuable notes from 2010 and to Bonnie Berger for many good advices at critical moments.

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