Journal: Briefings in Bioinformatics

Volume 10, Issue 6

593 -- 594Jo L. Dicks. Editorial
595 -- 608Jitender Cheema, Jo L. Dicks. Computational approaches and software tools for genetic linkage map estimation in plants
609 -- 618Michael Imelfort, David Edwards. De novo sequencing of plant genomes using second-generation technologies
619 -- 630Jerome Salse, Michael Abrouk, Florent Murat, Umar Masood Quraishi, Catherine Feuillet. Improved criteria and comparative genomics tool provide new insights into grass paleogenomics
631 -- 644Matthew D. Wilkerson, Yuanbin Ru, Volker Brendel. Common introns within orthologous genes: software and application to plants
645 -- 653Ian Armstead, Lin Huang, Adriana Ravagnani, Paul Robson, Helen Ougham. Bioinformatics in the orphan crops
654 -- 663Carol Soderlund. Computational techniques for elucidating plant-pathogen interactions from large-scale experiments on fungi and oomycetes
664 -- 675Zhiwu Zhang, Edward S. Buckler, Terry M. Casstevens, Peter J. Bradbury. Software engineering the mixed model for genome-wide association studies on large samples
676 -- 693Artem Lysenko, Matthew Morritt Hindle, Jan Taubert, Mansoor Saqi, Christopher J. Rawlings. Data integration for plant genomics - exemplars from the integration of ::::Arabidopsis thaliana:::: databases

Volume 10, Issue 5

475 -- 489Giulia Soldà, Igor V. Makunin, Osman Ugur Sezerman, Alberto Corradin, Giorgio Corti, Alessandro Guffanti. An Ariadne s thread to the identification and annotation of noncoding RNAs in eukaryotes
490 -- 497Chad Creighton, Jeffrey G. Reid, Preethi H. Gunaratne. Expression profiling of microRNAs by deep sequencing
498 -- 508Jia Zeng, Shanfeng Zhu, Hong Yan. Towards accurate human promoter recognition: a review of currently used sequence features and classification methods
509 -- 524Peter Van Loo, Peter Marynen. Computational methods for the detection of ::::cis::::-regulatory modules
525 -- 536Jan Mrázek. Finding sequence motifs in prokaryotic genomes - a brief practical guide for a microbiologist
537 -- 546Songjoon Baek, Chen-An Tsai, James J. Chen. Development of biomarker classifiers from high-dimensional data
547 -- 555Laura Elo, Jukka Hiissa, Jarno Tuimala, Aleksi Kallio, Eija Korpelainen, Tero Aittokallio. Optimized detection of differential expression in global profiling experiments: case studies in clinical transcriptomic and quantitative proteomic datasets
556 -- 568Anne-Laure Boulesteix, Martin Slawski. Stability and aggregation of ranked gene lists
569 -- 578Jan A. Hiss, Gisbert Schneider. Architecture, function and prediction of long signal peptides
579 -- 591Chun Meng Song, Shen Jean Lim, Joo Chuan Tong. Recent advances in computer-aided drug design

Volume 10, Issue 4

343 -- 344Werner Dubitzky. Editorial
345 -- 353Kei-Hoi Cheung, Ernest Lim, Matthias Samwald, Huajun Chen, Luis N. Marenco, Matthew Holford, Thomas M. Morse, Pradeep Mutalik, Gordon M. Shepherd, Perry L. Miller. Approaches to neuroscience data integration
354 -- 366Mihai Pop. Genome assembly reborn: recent computational challenges
367 -- 377Francisco Azuaje, Yvan Devaux, Daniel Wagner. Computational biology for cardiovascular biomarker discovery
378 -- 391Jeffrey Skolnick, Michal Brylinski. FINDSITE: a combined evolution/structure-based approach to protein function prediction
392 -- 407Erick Antezana, Martin Kuiper, Vladimir Mironov. Biological knowledge management: the emerging role of the Semantic Web technologies
408 -- 423Wei-Po Lee, Wen-Shyong Tzou. Computational methods for discovering gene networks from expression data
424 -- 434Attila Csikasz-Nagy. Computational systems biology of the cell cycle
435 -- 449Karthik Raman, Nagasuma Chandra. Flux balance analysis of biological systems: applications and challenges
450 -- 461Dawn C. Walker, Jennifer Southgate. The virtual cell - a candidate co-ordinator for middle-out modelling of biological systems
462 -- 474Niall M. Palfreyman. Exploring autonomy through computational biomodelling

Volume 10, Issue 3

205 -- 216Malay Kumar Basu, Eugenia Poliakov, Igor B. Rogozin. Domain mobility in proteins: functional and evolutionary implications
217 -- 232Nurcan Tuncbag, Gozde Kar, Ozlem Keskin, Attila Gürsoy, Ruth Nussinov. A survey of available tools and web servers for analysis of protein-protein interactions and interfaces
233 -- 246Iakes Ezkurdia, Lisa Bartoli, Piero Fariselli, Rita Casadio, Alfonso Valencia, Michael L. Tress. Progress and challenges in predicting protein-protein interaction sites
247 -- 258Peng Zhou, Zhicai Shang. 2D molecular graphics: a flattened world of chemistry and biology
259 -- 277William B. Langdon, Graham J. G. Upton, Andrew P. Harrison. Probes containing runs of guanines provide insights into the biophysics and bioinformatics of Affymetrix GeneChips
278 -- 288Paolo Ballarini, Rosita Guido, Tommaso Mazza, Davide Prandi. Taming the complexity of biological pathways through parallel computing
289 -- 294Robert M. Flight, Peter D. Wentzell. Potential Bias in GO: : TermFinder
295 -- 296Masanori Arita. A pitfall of wiki solution for biological databases
297 -- 314Bill Andreopoulos, Aijun An, Xiaogang Wang, Michael Schroeder. A roadmap of clustering algorithms: finding a match for a biomedical application
315 -- 329Lee Lancashire, Christophe Lemetre, Graham R. Ball. An introduction to artificial neural networks in bioinformatics - application to complex microarray and mass spectrometry datasets in cancer studies
330 -- 340Francesco Pappalardo, Mark D. Halling-Brown, Nicolas Rapin, Ping Zhang, Davide Alemani, Andrew Emerson, Paola Paci, Patrice Duroux, Marzio Pennisi, Arianna Palladini, Olivo Miotto, Daniel Churchill, Elda Rossi, Adrian J. Shepherd, David S. Moss, Filippo Castiglione, Massimo Bernaschi, Marie-Paule Lefranc, Søren Brunak, Santo Motta, Pierluigi Lollini, Kaye E. Basford, Vladimir Brusic. ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization
341 -- 0Nadav Ahituv. Introduction to Computational Genomics: A Case Studies Approach Nello Cristianini and Matthew W. Hahn

Volume 10, Issue 2

111 -- 113Kei-Hoi Cheung, Eric Prud hommeaux, Yimin Wang, Susie Stephens. Semantic Web for Health Care and Life Sciences: a review of the state of the art
114 -- 128Ben P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson. Moby and Moby 2: Creatures of the Deep (Web)
129 -- 138Sudeshna Das, Lisa Girard, Tom Green, Louis Weitzman, Alister Lewis-Bowen, Tim Clark. Building biomedical web communities using a semantically aware content management system
139 -- 152Jun Zhao, Alistair Miles, Graham Klyne, David M. Shotton. Linked data and provenance in biological data webs
153 -- 163Michel Dumontier, Natalia Villanueva-Rosales. Towards pharmacogenomics knowledge discovery with the semantic web
164 -- 176Maurice Manning, Amit Aggarwal, Kevin Gao, Greg Tucker-Kellogg. Scaling the walls of discovery: using semantic metadata for integrative problem solving
177 -- 192Huajun Chen, Li Ding, Zhaohui Wu, Tong Yu, Lavanya Dhanapalan, Jake Yue Chen. Semantic web for integrated network analysis in biomedicine
193 -- 204Alan Ruttenberg, Jonathan Rees, Matthias Samwald, M. Scott Marshall. Life sciences on the Semantic Web: the Neurocommons and beyond

Volume 10, Issue 1

1 -- 10Zhang Zhang, Kei-Hoi Cheung, Jeffrey P. Townsend. Bringing Web 2.0 to bioinformatics
11 -- 23Mohamed Radhouene Aniba, Sophie Siguenza, Anne Friedrich, Frédéric Plewniak, Olivier Poch, Aron Marchler-Bauer, Julie Dawn Thompson. Knowledge-based expert systems and a proof-of-concept case study for multiple sequence alignment construction and analysis
24 -- 34Irina Dinu, John D. Potter, Thomas Mueller, Qi Liu, Adeniyi J. Adewale, Gian S. Jhangri, Gunilla Einecke, Konrad S. Famulski, Philip Halloran, Yutaka Yasui. Gene-set analysis and reduction
35 -- 52Rachel Karchin. Next generation tools for the annotation of human SNPs
53 -- 64Jürgen Pahle. Biochemical simulations: stochastic, approximate stochastic and hybrid approaches
65 -- 74Dong-Yup Lee, Rajib Saha, Faraaz Noor Khan Yusufi, Wonjun Park, Iftekhar A. Karimi. Web-based applications for building, managing and analysing kinetic models of biological systems
75 -- 83Jan Baumbach, Andreas Tauch, Sven Rahmann. Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks
84 -- 96Yuseob Kim, Thomas Wiehe. Simulation of DNA sequence evolution under models of recent directional selection
97 -- 109Wayne Delport, Konrad Scheffler, Cathal Seoighe. Models of coding sequence evolution