Journal: Briefings in Bioinformatics

Volume 13, Issue 6

645 -- 0Gabriel Valiente, Graziano Pesole. Editorial
646 -- 655Johannes Dröge, Alice Carolyn McHardy. Taxonomic binning of metagenome samples generated by next-generation sequencing technologies
656 -- 668Weizhong Li, LiMin Fu, Beifang Niu, Sitao Wu, John C. Wooley. Ultrafast clustering algorithms for metagenomic sequence analysis
669 -- 681Sharmila S. Mande, Monzoorul Haque Mohammed, Tarini Shankar Ghosh. Classification of metagenomic sequences: methods and challenges
682 -- 695Monica Santamaria, Bruno Fosso, Arianna Consiglio, Giorgio De Caro, Giorgio Grillo, Flavio Licciulli, Sabino Liuni, Marinella Marzano, Daniel Alonso-Alemany, Gabriel Valiente, Graziano Pesole. Reference databases for taxonomic assignment in metagenomics
696 -- 710Carlotta De Filippo, Matteo Ramazzotti, Paolo Fontana, Duccio Cavalieri. Bioinformatic approaches for functional annotation and pathway inference in metagenomics data
711 -- 727Tulika Prakash, Todd D. Taylor. Functional assignment of metagenomic data: challenges and applications
728 -- 742Hanno Teeling, Frank Oliver Glöckner. Current opportunities and challenges in microbial metagenome analysis - a bioinformatic perspective
743 -- 746Chris I. Hunter, Alex Mitchell, Philip Jones, Craig McAnulla, Sebastien Pesseat, Maxim Scheremetjew, Sarah Hunter. Metagenomic analysis: the challenge of the data bonanza
747 -- 750Catherine Ngom-Bru, Caroline Barretto. Gut microbiota: methodological aspects to describe taxonomy and functionality
751 -- 768Matthew Collison, Robert P. Hirt, Anil Wipat, Sirintra Nakjang, Philippe Sanseau, James R. Brown. Data mining the human gut microbiota for therapeutic targets
769 -- 780Elhanan Borenstein. in silico modeling of the human microbiome

Volume 13, Issue 5

513 -- 523Tao Yu, Jialiang Li, Shuangge Ma. Adjusting confounders in ranking biomarkers: a model-based ROC approach
524 -- 535Age K. Smilde, Marieke E. Timmerman, Margriet M. W. B. Hendriks, Jeroen J. Jansen, Huub C. J. Hoefsloot. Generic framework for high-dimensional fixed-effects ANOVA
536 -- 546Matthew N. McCall, Anthony Almudevar. Affymetrix GeneChip microarray preprocessing for multivariate analyses
547 -- 554Jeffrey D. Allen, Siling Wang, Min Chen, Luc Girard, John D. Minna, Yang Xie, Guanghua Xiao. Probe mapping across multiple microarray platforms
555 -- 568Runqing Yang, Xin Wang, Yuehua Cui. Bayesian inference for genomic imprinting underlying developmental characteristics
569 -- 585Pietro Hiram Guzzi, Marco Mina, Concettina Guerra, Mario Cannataro. Semantic similarity analysis of protein data: assessment with biological features and issues
586 -- 614Ting Huang, Jingjing Wang, Weichuan Yu, Zengyou He. Protein inference: a review
615 -- 626Sarah A. Killcoyne, Jeremy Handcock, Thomas Robinson, Eric W. Deutsch, John Boyle. Interfaces to PeptideAtlas: a case study of standard data access systems
627 -- 644Martin Krzywinski, Inanç Birol, Steven J. M. Jones, Marco A. Marra. Hive plots - rational approach to visualizing networks

Volume 13, Issue 4

393 -- 394Russ B. Altman. Editorial: Current progress in Bioinformatics 2012
395 -- 405Samuel Flores, Julie Bernauer, Seokmin Shin, Ruhong Zhou, Xuhui Huang. Multiscale modeling of macromolecular biosystems
406 -- 419Jinlian Wang, Yuji Zhang, Catalin Marian, Habtom W. Ressom. Identification of aberrant pathways and network activities from high-throughput data
420 -- 429James A. Foster, John Bunge, Jack A. Gilbert, Jason H. Moore. Measuring the microbiome: perspectives on advances in DNA-based techniques for exploring microbial life
430 -- 445Chang F. Quo, Chanchala Kaddi, John H. Phan, Amin Zollanvari, Mingqing Xu, May D. Wang, Gil Alterovitz. Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities
446 -- 459Gürkan Bebek, Mehmet Koyutürk, Nathan D. Price, Mark R. Chance. Network biology methods integrating biological data for translational science
460 -- 494Udo Hahn, Kevin Bretonnel Cohen, Yael Garten, Nigam H. Shah. Mining the pharmacogenomics literature - a survey of the state of the art
495 -- 512Emidio Capriotti, Nathan L. Nehrt, Maricel G. Kann, Yana Bromberg. Bioinformatics for personal genome interpretation

Volume 13, Issue 3

269 -- 280Francesca Finotello, Enrico Lavezzo, Paolo Fontana, Denis Peruzzo, Alessandro Albiero, Luisa Barzon, Marco Falda, Barbara Di Camillo, Stefano Toppo. Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data
281 -- 291Jui-Hung Hung, Tun-Hsiang Yang, Zhenjun Hu, Zhiping Weng, Charles DeLisi. Gene set enrichment analysis: performance evaluation and usage guidelines
292 -- 304Anne-Laure Boulesteix, Andreas Bender, Justo Lorenzo Bermejo, Carolin Strobl. Random forest Gini importance favours SNPs with large minor allele frequency: impact, sources and recommendations
305 -- 316Norman Huang, Parantu K. Shah, Cheng Li. Lessons from a decade of integrating cancer copy number alterations with gene expression profiles
317 -- 328Xiyang Zhao, Chunfa Tong, Xiaoming Pang, Zhong Wang, Yunqian Guo, Fang Du, Rongling Wu. Functional mapping of ontogeny in flowering plants
329 -- 336Alfonso Benítez-Páez, Sonia Cárdenas-Brito, Andrés J. Gutiérrez. A practical guide for the computational selection of residues to be experimentally characterized in protein families
337 -- 349David duVerle, Hiroshi Mamitsuka. A review of statistical methods for prediction of proteolytic cleavage
350 -- 364Lianming Zhang, Keiko Udaka, Hiroshi Mamitsuka, Shanfeng Zhu. Toward more accurate pan-specific MHC-peptide binding prediction: a review of current methods and tools
365 -- 376Rebekka Schlatter, Nicole Philippi, Gaby Wangorsch, Robert Pick, Oliver Sawodny, Christoph Borner, Jens Timmer, Michael Ederer, Thomas Dandekar. Integration of Boolean models exemplified on hepatocyte signal transduction
377 -- 382Juan Wang, Zhi-xin Li, Chengxiang Qiu, Dong Wang, Qinghua Cui. The relationship between rational drug design and drug side effects
383 -- 389Maria Victoria Schneider, Peter Walter, Marie-Claude Blatter, James Watson, Michelle D. Brazas, Kristian Rother, Aidan Budd, Allegra Via, Celia W. G. van Gelder, Joachim Jacob, Pedro L. Fernandes, Tommi H. Nyrönen, Javier De Las Rivas, Thomas Blicher, Rafael C. Jimenez, Jane Loveland, Jennifer McDowall, Philip Jones, Brendan W. Vaughan, Rodrigo Lopez, Teresa K. Attwood, Catherine Brooksbank. Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers
390 -- 392Li Shen. Principles of Computational Modeling in NeuroscienceDavid Sterratt, Bruce Graham, Andrew Gillies and David Willshaw

Volume 13, Issue 2

135 -- 142Caroline Durrant, Morris A. Swertz, Rudi Alberts, Danny Arends, Steffen Möller, Richard Mott, Pjotr Prins, K. Joeri van der Velde, Ritsert C. Jansen, Klaus Schughart. Bioinformatics tools and database resources for systems genetics analysis in mice - a short review and an evaluation of future needs
143 -- 149Andrew Shelenkov, Eugene V. Korotkov. LEPSCAN - a web server for searching latent periodicity in DNA sequences
150 -- 161Ming Wu, Christina Chan. Learning transcriptional regulation on a genome scale: a theoretical analysis based on gene expression data
162 -- 174Yakun Wang, Meng Xu, Zhong Wang, Ming Tao, Junjia Zhu, Li Wang 0021, Runze Li, Scott A. Berceli, Rongling Wu. How to cluster gene expression dynamics in response to environmental signals
175 -- 186Xia Li, Wei Jiang, Wei Li, Baofeng Lian, Shuyuan Wang, Mingzhi Liao, Xiaowen Chen, Yanqiu Wang, Yingli Lv, Shiyuan Wang, Lei Yang. Dissection of human MiRNA regulatory influence to subpathway
187 -- 201Vladimir B. Teif, Karsten Rippe. Calculating transcription factor binding maps for chromatin
202 -- 215Elisabeth Wong, Brittany Baur, Saad Quader, Chun-Hsi Huang. Biological network motif detection: principles and practice
216 -- 227Jing Wang 0004, Xianxiao Zhou, Jing Zhu, Yunyan Gu, Wenyuan Zhao, Jinfeng Zou, Zheng Guo. GO-function: deriving biologically relevant functions from statistically significant functions
228 -- 243Julien Dutheil. Detecting coevolving positions in a molecule: why and how to account for phylogeny
244 -- 257Kristian Rother, Wojciech Potrzebowski, Tomasz Puton, Magdalena Rother, Ewa Wywial, Janusz M. Bujnicki. A toolbox for developing bioinformatics software
258 -- 268Shin Kawano, Hiromasa Ono, Toshihisa Takagi, Hidemasa Bono. Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV

Volume 13, Issue 1

1 -- 19Kristel Van Steen. Travelling the world of gene-gene interactions
20 -- 33Raphaël Mourad, Christine Sinoquet, Philippe Leray. Probabilistic graphical models for genetic association studies
34 -- 45Chenguang Wang, Zhong Wang, Daniel R. Prows, Rongling Wu. A computational framework for the inheritance pattern of genomic imprinting for complex traits
46 -- 60André Koschmieder, Karin Zimmermann, Silke Trißl, Thomas Stoltmann, Ulf Leser. Tools for managing and analyzing microarray data
61 -- 82Alberto Faro, Daniela Giordano, Concetto Spampinato. Combining literature text mining with microarray data: advances for system biology modeling
83 -- 97Daniel P. Berrar, Peter Flach. Caveats and pitfalls of ROC analysis in clinical microarray research (and how to avoid them)
98 -- 106Marc-Alexandre Nolin, Michel Dumontier, François Belleau, Jacques Corbeil. Building an HIV data mashup using Bio2RDF
107 -- 121Yijun Sun, Yunpeng Cai, Susan M. Huse, Rob Knight, William G. Farmerie, Xiaoyu Wang, Volker Mai. A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis
122 -- 134Ahmed Ragab Nabhan, Indra Neil Sarkar. The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy