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EDITORIAL NEWS ISSUE 7 • 2014 01001010001100001010000101000100001111100 10100010010010001001000101101001111101010Welcome to the 2014 Bioinformatics Editorial Newsletter Bioinformatics continues to go from strength to strength thanks to our authors, 10001010101001010100001010100101010100100reviews, board members and editors. We would like to take this opportunity to thank everyone who has supported the journal this year. Submissions have increased again to nearly 2300 in 2014, and we appreciate the support from reviewers to help us 10101010010101001001000100000010111101001process these papers. More authors are choosing to publish their papers under an open access licence, with uptake reaching 27% in 2014. 00010100100010101001010100100101000110000As always we very much welcome your suggestions for new developments, review or editorial topics, and feedback on any aspect of the journal. 10100001010001000011111001010001001001000Best regards The Bioinformatics Editor team, [email protected] 10010001011010011111010100010101010010101 Editorial Office and Reviews Update 00001010100101010100100101010010101001010Production Update Reviews published this year have covered topics including: 100100100010000001011110100100010100100012014 f Toward better understanding of artifacts in variant calling from high-coverage samples (http://bioinformatics.oxfordjournals.org/ 01010010101010010100101Submissions 2295 content/30/20/2843.abstract) f Challenges in RNA virus bioinformatics (http://bioinformatics.oxfordjournals.org/ Acceptance rate 33% 1011 content/30/13/1793.abstract) Algorithms and tools for protein–protein Time from submission to first f 37 days interaction networks clustering, with decision (average) 101 a special focus on population-based stochastic methods (http://bioinformatics. Advance Access online publication 5 days oxfordjournals.org/content/30/10/1343. 10 time (average) abstract) 1 Issue publication time (average) 49 days Optional open access uptake 27% 0100101000110000101000010100010000111110 0101000100100100010010001011010011111010 Here are the top 10 cited articles published in 2014: 1010001010101001010100001010100101010100Title Authors Issue Pages Citations RAxML version 8: a tool for 1001010101001010100100100010000001011110phylogenetic analysis and post- Stamatakis, Alexandros 9 1312 87 analysis of large phylogenies 1001000101001000101010010101001001010001Trimmomatic: a flexible trimmer for Bolger, Anthony M.; Lohse, Marc; 15 2114 38 Illumina sequence data Usadel, Bjoern 1000010100001010001000011111001010001001 Combining evolutionary information extracted from frequency profiles Liu, Bin; Zhang, Deyuan; Xu, 4 472 32 with sequence-based kernels for Ruifeng; et al. 0010001001000101101001111101010001010101protein remote homology detection iNuc-PseKNC: a sequence-based 0010101000010101001010101001001010100101predictor for predicting nucleosome Guo, Shou-Hui; Deng, En-Ze; Xu, 11 1522 25 positioning in genomes with pseudo Li-Qin; et al. 0100101010010010001000000101111010010001k-tuple nucleotide composition Causal analysis approaches in Kraemer, Andreas; Green, Jeff; 4 523 25 01001000101010010101010010100101Ingenuity Pathway Analysis Pollard, Jack, Jr.; et al. InterProScan 5: genome-scale pro- Jones, Philip; Binns, David; 9 1236 19 1011tein function classification Chang, Hsin-Yu; et al. DIYABC v2.0: a software to make approximate Bayesian computation inferences about population Cornuet, Jean-Marie; Pudlo, 8 1187 19 history using single nucleotide Pierre; Veyssier, Julien; et al. polymorphism, DNA sequence and microsatellite data featureCounts: an efficient general Liao, Yang; Smyth, Gordon K.; purpose program for assigning 7 923 16 Shi, Wei sequence reads to genomic features Protter: interactive protein feature Omasits, Ulrich; Ahrens, Chris- visualization and integration with 6 884 16 tian H.; Mueller, Sebastian; et al. experimental proteomic data Prokka: rapid prokaryotic genome Seemann, Torsten 14 2068 14 annotation 0100101000110000101000010100010000111110010100010010010 0010010001011010011111010101000101010100101010000101010 0101010100100101010100101010010010001000000101111010010 0100101000110000101000010100010000111110 0101000100100100010010001011010011111010 1010001010101001010100001010100101010100Conferences Bioinformatics has been represented at a number 1001010101001010100100100010000001011110of conferences this year, including of course ISMB 2014 in Boston, where the HiTSeq SIG was held as usual. Selected papers from HiTSeq can be found here: http://bioinformatics.oxfordjournals.org/ 1001000101001000101010010101001001010001content/30/24.toc#HITSEQPAPERS. 1000010100001010001000011111001010001001 IMPROVER Challenge special issue 0010001001000101101001111101010001010101Bioinformatics also published selected papers from the sbv IMPROVER Challenge, which can be found here: 0010101000010101001010101001001010100101http://bioinformatics.oxfordjournals.org/content/31/4 . 0100101010010010001000000101111010010001 New Impact Factor 01001000101010010101010010100101The Bioinformatics impact factor for 2014 was 4.621. The journal is ranked fourth in the Mathematical and Computational Biology category. 1011 4.621 ISCB articles Bioinformatics is an official journal of ISCB, and we have collected together the ISCB articles published in the journal over the past year (http://www. oxfordjournals.org/our_journals/bioinformatics/iscb_ articles.html). 0100101000110000101000010100010000111110010100010010010 0010010001011010011111010101000101010100101010000101010 0101010100100101010100101010010010001000000101111010010 0100101000110000101000010100010000111110 0101000100100100010010001011010011111010 1010001010101001010100001010100101010100Executive Editors John Hancock, UK Honorary Editors Janet Kelso, Germany Igor Jurisica, Canada Alex Bateman, UK Ivo Hofacker, Austria 1001010101001010100100100010000001011110Alfonso Valencia, Spain Martin Bishop, UK David Posada, Spain Cristos Ouzounis, Greece Associate Editors Burkhard Rost, USA Chris Sander, USA 1001000101001000101010010101001001010001Ziv Bar-Joseph, USA Anna Tramontano, Italy Gary Stormo, USA Inanc Birol, Canada Jonathan Wren, USA 1000010100001010001000011111001010001001Michael Brudno, Canada Robert Murphy, USA 0010001001000101101001111101010001010101 Editorial Board C Hodgman, UK P Park, USA 0010101000010101001010101001001010100101V Bafna, USA L Holm, Finland H Peng, USA S Brunak, Denmark W Huber, UK P Radivojac, USA 0100101010010010001000000101111010010001K A Crandall, USA T Ideker, USA C Sahinalp, Canada J Dopazo, Spain L Jensen, Germany C Seoighe, Irelend 01001000101010010101010010100101D Frishman, Germany A Navarro, Spain M Vingron, Germany D Higgins, Ireland C Ouzounis, UK 1011 How editorial board members can support Bioinformatics You can help us in a number of ways by: f acting as reviewers and identifying colleagues who might review manuscripts for the journal; f evaluating manuscripts in difficult cases where we need an extra solid opinion; f writing editorials and reviews, or suggesting review topics and authors; f contributing advice and ideas on the future development of the journal; f helping to raise awareness of the journal. We also see the Editorial Board as a good source of future Associate Editors, so if you would be interested in taking on such a role, let us know. 0100101000110000101000010100010000111110010100010010010 0010010001011010011111010101000101010100101010000101010 0101010100100101010100101010010010001000000101111010010.
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