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ORCIDBriefings in Bioinformatics, Volume 10
Volume 10, Number 1, January 2009
- Zhang Zhang
, Kei-Hoi Cheung, Jeffrey P. Townsend:
Bringing Web 2.0 to bioinformatics. 1-10 - Mohamed 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. 11-23 - Irina Dinu, John D. Potter, Thomas F. Mueller, Qi Liu, Adeniyi J. Adewale, Gian S. Jhangri, Gunilla Einecke, Konrad S. Famulski, Philip Halloran, Yutaka Yasui:
Gene-set analysis and reduction. 24-34 - Rachel Karchin:
Next generation tools for the annotation of human SNPs. 35-52 - Jürgen Pahle:
Biochemical simulations: stochastic, approximate stochastic and hybrid approaches. 53-64 - Dong-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. 65-74 - Jan Baumbach, Andreas Tauch, Sven Rahmann:
Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks. 75-83 - Yuseob Kim, Thomas Wiehe:
Simulation of DNA sequence evolution under models of recent directional selection. 84-96 - Wayne Delport, Konrad Scheffler, Cathal Seoighe:
Models of coding sequence evolution. 97-109
Volume 10, Number 2, March 2009
- Kei-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. 111-113
- Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson:
Moby and Moby 2: Creatures of the Deep (Web). 114-128 - Sudeshna Das, Lisa Girard, Tom Green, Louis Weitzman, Alister Lewis-Bowen, Tim Clark:
Building biomedical web communities using a semantically aware content management system. 129-138 - Jun Zhao, Alistair Miles, Graham Klyne, David M. Shotton:
Linked data and provenance in biological data webs. 139-152 - Michel Dumontier, Natalia Villanueva-Rosales:
Towards pharmacogenomics knowledge discovery with the semantic web. 153-163 - Maurice Manning, Amit Aggarwal, Kevin Gao, Greg Tucker-Kellogg:
Scaling the walls of discovery: using semantic metadata for integrative problem solving. 164-176 - Huajun Chen, Li Ding, Zhaohui Wu, Tong Yu, Lavanya Dhanapalan, Jake Yue Chen:
Semantic web for integrated network analysis in biomedicine. 177-192 - Alan Ruttenberg, Jonathan Rees, Matthias Samwald, M. Scott Marshall:
Life sciences on the Semantic Web: the Neurocommons and beyond. 193-204
Volume 10, Number 3, May 2009
- Malay Kumar Basu, Eugenia Poliakov, Igor B. Rogozin:
Domain mobility in proteins: functional and evolutionary implications. 205-216 - Nurcan 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. 217-232 - Iakes Ezkurdia, Lisa Bartoli, Piero Fariselli, Rita Casadio, Alfonso Valencia, Michael L. Tress:
Progress and challenges in predicting protein-protein interaction sites. 233-246 - Peng Zhou, Zhicai Shang:
2D molecular graphics: a flattened world of chemistry and biology. 247-258 - William B. Langdon, Graham J. G. Upton, Andrew P. Harrison:
Probes containing runs of guanines provide insights into the biophysics and bioinformatics of Affymetrix GeneChips. 259-277 - Paolo Ballarini, Rosita Guido, Tommaso Mazza, Davide Prandi:
Taming the complexity of biological pathways through parallel computing. 278-288 - Robert M. Flight, Peter D. Wentzell:
Potential Bias in GO: : TermFinder. 289-294 - Masanori Arita:
A pitfall of wiki solution for biological databases. 295-296 - Bill Andreopoulos, Aijun An, Xiaogang Wang, Michael Schroeder:
A roadmap of clustering algorithms: finding a match for a biomedical application. 297-314 - Lee 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. 315-329 - Francesco Pappalardo, Mark D. Halling-Brown, Nicolas Rapin, Ping Zhang, Davide Alemani, Andrew P. J. 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. 330-340
- Nadav Ahituv:
Introduction to Computational Genomics: A Case Studies Approach Nello Cristianini and Matthew W. Hahn. 341
Volume 10, Number 4, July 2009
- Werner Dubitzky:
Editorial. 343-344
- Kei-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. 345-353 - Mihai Pop:
Genome assembly reborn: recent computational challenges. 354-366 - Francisco Azuaje, Yvan Devaux, Daniel R. Wagner:
Computational biology for cardiovascular biomarker discovery. 367-377 - Jeffrey Skolnick, Michal Brylinski:
FINDSITE: a combined evolution/structure-based approach to protein function prediction. 378-391 - Erick Antezana, Martin Kuiper, Vladimir Mironov:
Biological knowledge management: the emerging role of the Semantic Web technologies. 392-407 - Wei-Po Lee, Wen-Shyong Tzou:
Computational methods for discovering gene networks from expression data. 408-423 - Attila Csikász-Nagy:
Computational systems biology of the cell cycle. 424-434 - Karthik Raman, Nagasuma R. Chandra:
Flux balance analysis of biological systems: applications and challenges. 435-449 - Dawn C. Walker, Jennifer Southgate:
The virtual cell - a candidate co-ordinator for 'middle-out' modelling of biological systems. 450-461 - Niall M. Palfreyman:
Exploring autonomy through computational biomodelling. 462-474
Volume 10, Number 5, September 2009
- Giulia 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. 475-489 - Chad Creighton, Jeffrey G. Reid, Preethi H. Gunaratne:
Expression profiling of microRNAs by deep sequencing. 490-497 - Jia Zeng, Shanfeng Zhu, Hong Yan:
Towards accurate human promoter recognition: a review of currently used sequence features and classification methods. 498-508 - Peter Van Loo, Peter Marynen:
Computational methods for the detection of cis-regulatory modules. 509-524 - Jan Mrázek:
Finding sequence motifs in prokaryotic genomes - a brief practical guide for a microbiologist. 525-536 - Songjoon Baek, Chen-An Tsai, James J. Chen:
Development of biomarker classifiers from high-dimensional data. 537-546 - Laura 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. 547-555 - Anne-Laure Boulesteix, Martin Slawski:
Stability and aggregation of ranked gene lists. 556-568 - Jan A. Hiss, Gisbert Schneider:
Architecture, function and prediction of long signal peptides. 569-578 - Chun Meng Song, Shen Jean Lim, Joo Chuan Tong:
Recent advances in computer-aided drug design. 579-591
Volume 10, Number 6, November 2009
- Jo L. Dicks:
Editorial. 593-594 - Jitender Cheema, Jo L. Dicks:
Computational approaches and software tools for genetic linkage map estimation in plants. 595-608 - Michael Imelfort, David Edwards:
De novo sequencing of plant genomes using second-generation technologies. 609-618 - Jérôme Salse, Michael Abrouk, Florent Murat, Umar Masood Quraishi, Catherine Feuillet:
Improved criteria and comparative genomics tool provide new insights into grass paleogenomics. 619-630 - Matthew D. Wilkerson, Yuanbin Ru, Volker Brendel:
Common introns within orthologous genes: software and application to plants. 631-644 - Ian Armstead, Lin Huang, Adriana Ravagnani, Paul Robson, Helen Ougham:
Bioinformatics in the orphan crops. 645-653 - Carol Soderlund:
Computational techniques for elucidating plant-pathogen interactions from large-scale experiments on fungi and oomycetes. 654-663 - Zhiwu Zhang, Edward S. Buckler, Terry M. Casstevens, Peter J. Bradbury:
Software engineering the mixed model for genome-wide association studies on large samples. 664-675 - Artem Lysenko, Matthew Morritt Hindle, Jan Taubert, Mansoor A. S. Saqi, Christopher J. Rawlings:
Data integration for plant genomics - exemplars from the integration of Arabidopsis thaliana databases. 676-693
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