BIB's first impact factor is 24.37

We are delighted to announce that Briefings in Bioinformaticshas just received its first impact factor—of 24.37! This is a fantastic achievement for the journal, and surelya reflection of     

The growth of bioinformatics

Briefings in Bioinformatics, or BiB for short, will celebrateits 7th anniversary this year. The journal's mission has remainedunchanged throughout this period: we are committed to disseminatingknowledge on databases and computational tools for life sciencesthrough review articles. During its history, some 250 articleshave been published and they have been cited more than 2700times, making BiB the premier bioinformatics journal using theper-article citation impact measure. The common theme for thisissue is the cross-disciplinary nature of bioinformatics     

The Bioinformatics Open Access option

We are pleased to report that July 2005 saw the launch of ournew Open Access option, part of the Oxford Open initiative (http://www.oxfordjournals.org/oxfordopen/).Bioinformatics authors can now choose to publish their work‘open access’ in an established, high-impact journal,under what we believe is a sustainable publication model. WHAT THIS MEANS FOR AUTHORS SUBMITTING TO BIOINFORMATICS The decision of whether to pay for open access is made by thecorresponding author upon acceptance (importantly this decisionis kept completely separate from the editorial review process).If a Bioinformatics author chooses to pay for the Open Accessoption, his or her paper will be made freely available onlineimmediately; if an author does not choose the option his orher     

Annual Progress in Bioinformatics 2006

In this issue, Briefings in Bioinformatics is happy to presentthe next installment of our special annual issue devoted toreviews of very active subdisciplines within our field. Theeditors surveyed recent publications in order to identify fieldsthat are moving rapidly and would be good targets for summaryand review. We asked authors to provide brief introductionsto their field, and then to concentrate on contributions inthe last 12–24 months of particular interest. In somecases, they also provided annotated bibliographies in whichthey highlighted papers of particularly high interest. The resultis seven outstanding reviews. The influence of high-throughputgenomic experimental techniques and the increasing intereston synthesis of information comes through strongly in this year'sselections. We     

Current progress in bioinformatics 2007

Briefings in Bioinformatics is pleased to present our thirdannual ‘Current Progress in Bioinformatics’ specialissue. As in previous years, we have attempted to identify excitingor emerging fields of bioinformatics, and have asked leadersin these fields to present a brief summary of progress overthe last 18–24 months and an annotated biography drawingattention to papers of particular significance. Each year, we have a logistical task of setting the order ofthe articles to appear in this volume. Typically, we organizethem based on the linear logic of biology's central dogma: fromDNA to RNA to protein to function and phenotype. The centraldogma has undergone a transformation in the     

ProtBuD: a database of biological unit structures of protein families and superfamilies

Bioinformatics (2006)      

Systems biology * Metabolic systems cost-benefit analysis for interpreting network structure and regulation

Bioinformatics (2007) 23(10),     

Modular organization of protein interaction networks

Bioinformatics (2007) 23(2),     

'ANOVA-simultaneous component analysis (ASCA): a new tool for analyzing designed metabolomics data'

Smilde et al. Bioinformatics (2005), 21(13); 3043–3048 The above paper by Smilde et al. inappropriately quotes results     

The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks

Bioinformatics (2006) 22(23), 2968–2970 The authors would like     

A simple shape characteristic of protein protein recognition

Bioinformatics (2007) 23(7), 789–792 The authors wish to apologize for the omission     

Editorial note

It has come to the attention of the Executive Editors of Bioinformaticsthat there is significant overlap between the following publications: Rodin A, Mosley TH Jr, Clark AG, Sing     

INCREASING THE IMPACT OF BIOINFORMATICS

The year 2004 has been very successful for Bioinformatics. Thejournal's latest impact factor from the Institute for ScientificInformation has increased from 4.615 to 6.701. This is quitean exceptional increase reflecting the increasing standard ofwork in the journal as well as the increasing stature of thefield. Early in 2004, we implemented     

A multivariate test of association

Summary: Although genetic association studies often test multiple,related phenotypes, few formal multivariate tests of associationare available. We describe a test of association that can beefficiently applied to large population-based designs. Availability: A C++ implementation can be obtained from theauthors. Contact: manuel.ferreira{at}qimr.edu.au Supplementary information: Supplementary figures are availableat Bioinformatics online. Associate Editor: Alex Bateman     

Observation of multiple folding pathways of beta-hairpin trpzip2 from independent continuous folding trajectories

Motivation: After 10-year investigations, the folding mechanismsof β-hairpins are still under debate. Experiments stronglysupport zip-out pathway, while most simulations prefer the hydrophobiccollapse model (including middle-out and zip-in pathways). Inthis article, we show that all pathways can occur during thefolding of β-hairpins but with different probabilities.The zip-out pathway is the most probable one. This is in agreementwith the experimental results. We came to our conclusions by38 100-ns room-temperature all-atom molecular dynamics simulationsof the β-hairpin trpzip2. Our results may help to clarifythe inconsistencies in the current pictures of β-hairpinfolding mechanisms. Contact: yxiao{at}mail.hust.edu.cn Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Anna Tramontano     

Editorial

This issue of Briefings in Functional Genomics and Proteomicsbrings together another collection of topical reviews that spanan ever-broadening field. The application of high-throughputapproaches in functional genomics and proteomics permits theexploration of systems biology, where diverse data are modelledto attempt to simulate a system as a whole, whether it be atthe molecular, cellular, organ, organismal or ecosystem level. In the first review, John Nolan and Loretta Yang review ‘theflow of cytometry into systems biology’. Flow cytometryhas the potential to contribute greatly to the advancement ofcellular systems     

Maximum likelihood of phylogenetic networks

Bioinformatics (2006) 22(21), 2604–2611 The authors would like to apologize for errors of graph misplacementin Figures 4–6, and an     

Model-based deconvolution of genome-wide DNA binding

Motivation: Chromatin immunoprecipitation followed by hybridizationto a genomic tiling microarray (ChIP-chip) is a routinely usedprotocol for localizing the genomic targets of DNA-binding proteins.The resolution to which binding sites in this assay can be identifiedis commonly considered to be limited by two factors: (1) theresolution at which the genomic targets are tiled in the microarrayand (2) the large and variable lengths of the immunoprecipitatedDNA fragments. Results: We have developed a generative model of binding sitesin ChIP-chip data and an approach, MeDiChI, for efficientlyand robustly learning that model from diverse data sets. Wehave evaluated MeDiChI's performance using simulated data, aswell as on several diverse ChIP-chip data sets collected onwidely different tiling array platforms for two different organisms(Saccharomyces cerevisiae and Halobacterium salinarium NRC-1).We find that MeDiChI accurately predicts binding locations toa resolution greater than that of the probe spacing, even foroverlapping peaks, and can increase the effective resolutionof tiling array data by a factor of 5x or better. Moreover,the method's performance on simulated data provides insightsinto effectively optimizing the experimental design for increasedbinding site localization accuracy and efficacy. Availability: MeDiChI is available as an open-source R package,including all data, from http://baliga.systemsbiology.net/medichi. Contact: dreiss{at}systemsbiology.org Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Martin Bishop     

Combining multiple positive training sets to generate confidence scores for protein-protein interactions

Motivation: High-throughput experimental and computational methodsare generating a wealth of protein–protein interactiondata for a variety of organisms. However, data produced by currentstate-of-the-art methods include many false positives, whichcan hinder the analyses needed to derive biological insights.One way to address this problem is to assign confidence scoresthat reflect the reliability and biological significance ofeach interaction. Most previously described scoring methodsuse a set of likely true positives to train a model to scoreall interactions in a dataset. A single positive training set,however, may be biased and not representative of true interactionspace. Results: We demonstrate a method to score protein interactionsby utilizing multiple independent sets of training positivesto reduce the potential bias inherent in using a single trainingset. We used a set of benchmark yeast protein interactions toshow that our approach outperforms other scoring methods. Ourapproach can also score interactions across data types, whichmakes it more widely applicable than many previously proposedmethods. We applied the method to protein interaction data fromboth Drosophila melanogaster and Homo sapiens. Independent evaluationsshow that the resulting confidence scores accurately reflectthe biological significance of the interactions. Contact: rfinley{at}wayne.edu Supplementary information: Supplementary data are availableat Bioinformatics Online. Associate Editor: Burkhard Rost