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    Journal: Briefings in Bioinformatics

    Volume 14, Issue 6

    671 -- 683Marie-Agnès Dillies, Andrea Rau, Julie Aubert, Christelle Hennequet-Antier, Marine Jeanmougin, Nicolas Servant, Céline Keime, Guillemette Marot, David Castel, Jordi Estelle, Gregory Guernec, Bernd Jagla, Luc Jouneau, Denis Laloë, Caroline Le Gall, Brigitte Schaeffer, Stéphane Le Crom, Mickaël Guedj, Florence Jaffrézic. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
    684 -- 695Stefano Castellana, Marta Romani, Enza Maria Valente, Tommaso Mazza. A solid quality-control analysis of AB SOLiD short-read sequencing data
    696 -- 712Robert Hoehndorf, Michel Dumontier, Georgios V. Gkoutos. Evaluation of research in biomedical ontologies
    713 -- 723Sheng Zhu, Zhong Wang, Jianxin Wang, Yaqun Wang, Ningtao Wang, Zuoheng Wang, Meng Xu, Xiaohua Su, Mingxiu Wang, Shougong Zhang, Minren Huang, Rongling Wu. A quantitative model of transcriptional differentiation driving host-pathogen interactions
    724 -- 736Mehdi Maadooliat, Xin Gao, Jianhua Z. Huang. Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles
    737 -- 744Monica Chagoyen, Florencio Pazos. Tools for the functional interpretation of metabolomic experiments
    745 -- 752Georgios A. Dalkas, Dimitrios Vlachakis, Dimosthenis Tsagkrasoulis, Anastasia N. Kastania, Sophia Kossida. State-of-the-art technology in modern computer-aided drug design
    753 -- 774Stephen J. Goodswen, Paul J. Kennedy, John T. Ellis. in silico vaccine discovery for eukaryotic pathogens
    775 -- 783Heather M. Vincent, Christopher Page. Developing an online programme in computational biology

    Volume 14, Issue 5

    527 -- 0Maria Victoria Schneider, John R. Jungck. Editorial: International, interdisciplinary, multi-level bioinformatics training and education
    528 -- 537Allegra Via, Thomas Blicher, Erik Bongcam-Rudloff, Michelle D. Brazas, Catherine Brooksbank, Aidan Budd, Javier De Las Rivas, Jacqueline Dreyer, Pedro L. Fernandes, Celia W. G. van Gelder, Joachim Jacob, Rafael C. Jimenez, Jane Loveland, Federico Moran, Nicola J. Mulder, Tommi H. Nyrönen, Kristian Rother, Maria Victoria Schneider, Teresa K. Attwood. Best practices in bioinformatics training for life scientists
    538 -- 547Benilton S. Carvalho, Gabriella Rustici. The challenges of delivering bioinformatics training in the analysis of high-throughput data
    548 -- 555Jing-Woei Li, Dan M. Bolser, Magnus Manske, Federico Manuel Giorgi, Nikolay Vyahhi, Björn Usadel, Bernardo J. Clavijo, Ting-Fung Chan, Nathalie Wong, Daniel Zerbino, Maria Victoria Schneider. The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability
    556 -- 562Michelle D. Brazas, B. F. Francis Ouellette. Navigating the changing learning landscape: perspective from bioinformatics.ca
    563 -- 574Nathan S. Watson-Haigh, Catherine A. Shang, Matthias Haimel, Myrto Kostadima, Remco Loos, Nandan Deshpande, Konsta Duesing, Xi Li, Annette McGrath, Sean McWilliam, Simon Michnowicz, Paula Moolhuijzen, Steve Quenette, Jerico Nico De Leon Revote, Sonika Tyagi, Maria Victoria Schneider. Next-generation sequencing: a challenge to meet the increasing demand for training workshops in Australia
    575 -- 588Jing Wang, Patricia A. McLenachan, Patrick J. Biggs, Linton H. Winder, Barbara I. K. Schoenfeld, Vinay V. Narayan, Bernard J. Phiri, Peter J. Lockhart. Environmental bio-monitoring with high-throughput sequencing
    589 -- 598Sanne Abeln, Douwe Molenaar, K. Anton Feenstra, Huub C. J. Hoefsloot, Bas Teusink, Jaap Heringa. Bioinformatics and Systems Biology: bridging the gap between heterogeneous student backgrounds
    599 -- 609John R. Jungck, Anton E. Weisstein. Mathematics and evolutionary biology make bioinformatics education comprehensible
    610 -- 617Ran Libeskind-Hadas, Eliot Bush. A first course in computing with applications to biology
    618 -- 632Tamás Korcsmáros, Zsuzsanna A. Dunai, Tibor Vellai, Peter Csermely. Teaching the bioinformatics of signaling networks: an integrated approach to facilitate multi-disciplinary learning
    633 -- 647Dick de Ridder, Jeroen de Ridder, Marcel J. T. Reinders. Pattern recognition in bioinformatics
    648 -- 660Yossy Machluf, Anat Yarden. Integrating bioinformatics into senior high school: design principles and implications
    661 -- 670Allan Orozco, Jessica Morera, Sergio Jiménez, Ricardo Boza. A review of Bioinformatics training applied to research in Molecular Medicine, Agriculture and Biodiversity in Costa Rica and Central America

    Volume 14, Issue 4

    391 -- 401Yunda Huang, Raphael Gottardo. Comparability and reproducibility of biomedical data
    402 -- 410Kaye E. Basford, Geoffrey J. McLachlan, Suren I. Rathnayake. On the classification of microarray gene-expression data
    411 -- 422Santo Motta, Francesco Pappalardo. Mathematical modeling of biological systems
    423 -- 436Roman Sloutsky, Nicolas Jimenez, S. Joshua Swamidass, Kristen M. Naegle. Accounting for noise when clustering biological data
    437 -- 447Abu Z. Dayem Ullah, Nicholas R. Lemoine, Claude Chelala. A practical guide for the functional annotation of genetic variations using SNPnexus
    448 -- 459Stefano Castellana, Tommaso Mazza. Congruency in the prediction of pathogenic missense mutations: state-of-the-art web-based tools
    460 -- 468Yafei Lv, Xiaoxia Yang, Chunfa Tong, Xin Li, Sisi Feng, Zhong Wang, Xiaoming Pang, Yaqun Wang, Ningtao Wang, Christian M. Tobias, Rongling Wu. A multivalent three-point linkage analysis model of autotetraploids
    469 -- 490Cosmin Lazar, Stijn Meganck, Jonatan Taminau, David Steenhoff, Alain Coletta, Colin Molter, David Y. Weiss Solís, Robin Duque, Hugues Bersini, Ann Nowé. Batch effect removal methods for microarray gene expression data integration: a survey
    491 -- 505Elaine L. Leung, Zhi Wei Cao, Zhi-Hong Jiang, Hua Zhou, Liang Liu. Network-based drug discovery by integrating systems biology and computational technologies
    506 -- 519Qingguo Wang, Junfeng Xia, Peilin Jia, William Pao, Zhongming Zhao. Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives
    520 -- 526Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Jennifer R. Smith, Timothy Lowry, Rajni Nigam, Victoria Petri, Jeff de Pons, Melinda R. Dwinell, Mary Shimoyama, Diane H. Munzenmaier, Elizabeth A. Worthey, Howard J. Jacob. The Rat Genome Database 2013 - data, tools and users

    Volume 14, Issue 3

    261 -- 262Jingchu Luo, Harm Nijveen, Teresa K. Attwood, David Phillip Judge, Sándor Pongor, David Landsman, Martin Bishop. Obituary: In memory of Jack Leunissen
    263 -- 278Ander Muniategui, Jon Pey, Francisco J. Planes, Angel Rubio. Joint analysis of miRNA and mRNA expression data
    279 -- 292Kemal Eren, Mehmet Deveci, Onur Küçüktunç, Ümit V. Çatalyürek. A comparative analysis of biclustering algorithms for gene expression data
    293 -- 301Chaogang Shao, Ming Chen 0005, Yijun Meng. A reversed framework for the identification of microRNA-target pairs in plants
    302 -- 314Xiaoming Pang, Zhong Wang, John S. Yap, Jianxin Wang, Junjia Zhu, Wenhao Bo, Yafei Lv, Fang Xu, Tao Zhou, Shaofeng Peng, Dengfeng Shen, Rongling Wu. A statistical procedure to map high-order epistasis for complex traits
    315 -- 326Wouter G. Touw, Jumamurat R. Bayjanov, Lex Overmars, Lennart Backus, Jos Boekhorst, Michiel Wels, Sacha A. F. T. van Hijum. Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle?
    327 -- 343Yi Sun, Ruixin Zhu, Hao Ye, Kailin Tang, Jing Zhao, Yujia Chen, Qi Liu, Zhiwei Cao. Towards a bioinformatics analysis of anti-Alzheimer's herbal medicines from a target network perspective
    344 -- 360Zexian Liu, Jian Ren, Jun Cao, Jiang He, Xuebiao Yao, Changjiang Jin, Yu Xue. Systematic analysis of the Plk-mediated phosphoregulation in eukaryotes
    361 -- 374David C. Dallas, William F. Martin, Serenus Hua, J. Bruce German. Automated glycopeptide analysis - review of current state and future directions
    375 -- 390Jürgen Hartler, Ravi Tharakan, Harald C. Köfeler, David R. Graham, Gerhard G. Thallinger. Bioinformatics tools and challenges in structural analysis of lipidomics MS/MS data

    Volume 14, Issue 2

    129 -- 130Scott Markel, Richard Carter. Editorial
    131 -- 143Jun Wang, Lei Kong, Ge Gao, Jingchu Luo. A brief introduction to web-based genome browsers
    144 -- 161Robert M. Kuhn, David Haussler, W. James Kent. The UCSC genome browser and associated tools
    162 -- 171Lincoln D. Stein. Using GBrowse 2.0 to visualize and share next-generation sequence data
    172 -- 177Oscar Westesson, Mitchell Skinner, Ian Holmes. Visualizing next-generation sequencing data with JBrowse
    178 -- 192Helga Thorvaldsdóttir, James T. Robinson, Jill P. Mesirov. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
    193 -- 202Iain Milne, Gordon Stephen, Micha Bayer, Peter J. A. Cock, Leighton Pritchard, Linda Cardle, Paul D. Shaw, David Marshall. Using Tablet for visual exploration of second-generation sequencing data
    203 -- 212Tim Carver, Simon R. Harris, Thomas D. Otto, Matthew Berriman, Julian Parkhill, Jacqueline A. McQuillan. BamView: visualizing and interpretation of next-generation sequencing read alignments
    213 -- 224Michael C. Schatz, Adam M. Phillippy, Daniel D. Sommer, Arthur L. Delcher, Daniela Puiu, Giuseppe Narzisi, Steven L. Salzberg, Mihai Pop. Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies
    225 -- 237Federico Zambelli, Graziano Pesole, Giulio Pavesi. Motif discovery and transcription factor binding sites before and after the next-generation sequencing era
    238 -- 250Vivekanand Sharma, Indra Neil Sarkar. Bioinformatics opportunities for identification and study of medicinal plants
    251 -- 260Rosanna Upstill-Goddard, Diana Eccles, Jörg Fliege, Andrew Collins. Machine learning approaches for the discovery of gene-gene interactions in disease data

    Volume 14, Issue 1

    1 -- 12Emily J. Richardson, Mick Watson. The automatic annotation of bacterial genomes
    13 -- 26Wei-Jiun Lin, James J. Chen. Class-imbalanced classifiers for high-dimensional data
    27 -- 35Leo Lahti, Martin Schäfer, Hans-Ulrich Klein, Silvio Bicciato, Martin Dugas. Cancer gene prioritization by integrative analysis of mRNA expression and DNA copy number data: a comparative review
    36 -- 45Vernell Williamson, Albert Kim, Bin Xie 0004, G. Omari McMichael, Yuan Gao, Vladimir Vladimirov. Detecting miRNAs in deep-sequencing data: a software performance comparison and evaluation
    46 -- 55Joseph A. Neuman, Ofer Isakov, Noam Shomron. Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection
    56 -- 66Xiao Yang, Sriram P. Chockalingam, Srinivas Aluru. A survey of error-correction methods for next-generation sequencing
    67 -- 81Kian Guan Lim, Chee Keong Kwoh, Li Yang Hsu, Adrianto Wirawan. Review of tandem repeat search tools: a systematic approach to evaluating algorithmic performance
    82 -- 95Zhong Wang, Xiaoming Pang, Yafei Lv, Fang Xu, Tao Zhou, Xin Li, Sisi Feng, Jiahan Li, Zhikang Li, Rongling Wu. A dynamic framework for quantifying the genetic architecture of phenotypic plasticity
    96 -- 108Xiaoxia Yang, Yafei Lv, Xiaoming Pang, Chunfa Tong, Zhong Wang, Xin Li, Sisi Feng, Christian M. Tobias, Rongling Wu. A unifying framework for bivalent multilocus linkage analysis of allotetraploids
    109 -- 125Huajun Chen, Tong Yu, Jake Y. Chen. Semantic Web meets Integrative Biology: a survey
    126 -- 127Artem Zykovich. Bioinformatics for Biologists. Edited by Pavel Pevzner and Ron Shamir
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