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Briefings 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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