Automated function prediction – call for papers for a special series

July 1, 2013

Editors: Mark Wass (University of Kent, UK), Iddo Friedberg (Miami University, Oxford, Ohio, USA), Predrag Radivojac (Indiana University, Bloomington, Indiana, USA)To tie in with the upcoming Automated Function Prediction Special Interest Group (AFP-SIG) at the ISMB/ECCB 2013 meeting in Berlin, GigaScience and the organisers are launching a call for submissions to a thematic series of research from the meeting and beyond highlighting (but not limited to) function prediction using sequence-based methods, function from genomic information,  molecular interactions, structure, use of combined methods, and phylogeny-based methods. The meeting will also kick off the second Critical Assessment of protein Function Annotation (CAFA) challenge, in which various function prediction algorithms will be tested for accuracy.The explosion in genomic data has unearthed an enormous number of genes of unknown function that are still awaiting biological and biochemical characterisation. The AFP-SIG brings together computational biologists who are dealing with the important problem of gene product function prediction, to share ideas and create collaborations. Being held at ISMB since 2005, this year’s meeting, held July 20^th, aligns well with key areas of GigaScience’s “large-scale data” scope, and we are pleased to be able to help promote and publish these efforts. The 2013 meeting will feature several great keynote speakers;  Patricia Babbitt (University of California, San Francisco), will be speaking on the topic of ‘Protein similarity networks: Identification of functional trends from the context of sequence similarity’; Alex Bateman (European Bioinformatics Institute), will be presenting work on ‘Using protein domains and families for functional prediction’; Keith Dunker (Indiana University School of Medicine), will give insight on ‘Functions of Intrinsically Disordered Proteins’; and a final keynote will be given by Anna Tramontano (Università degli Studi di Roma “La Sapienza”) who will be speaking about her experiences as an assessor of method performance at the Critical Assessment of Protein Structure Prediction or CASP.  Dr Tramontano will be the assessor for CAFA 2.GigaScience journal hopes that this series can be a forum of discussion that can help further the AFP-SIG’s mission, as well as revolutionise data dissemination, organisation, understanding, use and promote further collaboration amongst computational biologists crossing many different data domains. Edited by Mark Wass, Iddo Friedberg and Predrag Radivojac, and the GigaScience team, the series will remain open for submissions beyond this years meeting as the work on the important problem of gene and gene product function prediction continues.For more information about the GigaScience journal and for those attending the AFP-SIG meeting and ISMB/ECCB 2013, our Executive Editor, Scott Edmunds will be on hand. Scott is also the co-organiser of a workshop on July 22 that focuses on ‘What Bioinformaticians need to know about digital publishing beyond the PDF’. GigaScience’s co-publisher, BioMed Central, will also have a stand at booth 18 – so please come and talk to Scott and BMC team there.BGI is generously covering the open-access article-processing charges for the series, as well as all submissions until January 2014, so please contact us at editorial@gigasciencejournal.com if you have related work you would like to submit to this series or journal, or submit a manuscript here.Follow the AFP SIG and ISMB/ECCB conferences on Twitter at @gigascience and the #AFP13  and #ISMB13 hashtags. We’ll also be posting updates from GigaBlog and posting relevant slides from SlideShare.