Bioinformatics

ORIGINAL PAPERS

GENOME ANALYSIS

Get checked abstract Pan Du, Warren A. Kibbe, and Simon M. Lin

Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching
Bioinformatics Advance Access published on July 4, 2006
Bioinformatics 2006 22: 2059-2065; doi:10.1093/bioinformatics/btl355 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Philippe La Rosa, Eric Viara, Philippe Hupé, Gaëlle Pierron, Stéphane Liva, Pierre Neuvial, Isabel Brito, Séverine Lair, Nicolas Servant, Nicolas Robine, Elodie Manié, Caroline Brennetot, Isabelle Janoueix-Lerosey, Virginie Raynal, Nadège Gruel, Céline Rouveirol, Nicolas Stransky, Marc-Henri Stern, Olivier Delattre, Alain Aurias, François Radvanyi, and Emmanuel Barillot

VAMP: Visualization and analysis of array-CGH, transcriptome and other molecular profiles
Bioinformatics Advance Access published on July 4, 2006
Bioinformatics 2006 22: 2066-2073; doi:10.1093/bioinformatics/btl359 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract P. Thébault, S. de Givry, T. Schiex, and C. Gaspin

Searching RNA motifs and their intermolecular contacts with constraint networks
Bioinformatics Advance Access published on July 4, 2006
Bioinformatics 2006 22: 2074-2080; doi:10.1093/bioinformatics/btl354 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS

STRUCTURAL BIOINFORMATICS

Get checked abstract Yu Chen and Gordon M. Crippen

An iterative refinement algorithm for consistency based multiple structural alignment methods
Bioinformatics Advance Access published on June 29, 2006
Bioinformatics 2006 22: 2087-2093; doi:10.1093/bioinformatics/btl351 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Sjoerd J. de Vries and Alexandre M. J. J. Bonvin

Intramolecular surface contacts contain information about protein–protein interface regions
Bioinformatics Advance Access published on June 9, 2006
Bioinformatics 2006 22: 2094-2098; doi:10.1093/bioinformatics/btl275 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Mingyue Zheng, Zhiguo Liu, Chunxia Xue, Weiliang Zhu, Kaixian Chen, Xiaomin Luo, and Hualiang Jiang

Mutagenic probability estimation of chemical compounds by a novel molecular electrophilicity vector and support vector machine
Bioinformatics Advance Access published on July 12, 2006
Bioinformatics 2006 22: 2099-2106; doi:10.1093/bioinformatics/btl352 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION

Get checked abstract Xuejun Liu, Marta Milo, Neil D Lawrence, and Magnus Rattray

Probe-level measurement error improves accuracy in detecting differential gene expression
Bioinformatics Advance Access published on July 4, 2006
Bioinformatics 2006 22: 2107-2113; doi:10.1093/bioinformatics/btl361 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Andrea Malossini, Enrico Blanzieri, and Raymond T. Ng

Detecting potential labeling errors in microarrays by data perturbation
Bioinformatics Advance Access published on July 4, 2006
Bioinformatics 2006 22: 2114-2121; doi:10.1093/bioinformatics/btl346 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS

SYSTEMS BIOLOGY

Get checked abstract Wentao Zhao, Erchin Serpedin, and Edward R. Dougherty

Inferring gene regulatory networks from time series data using the minimum description length principle
Bioinformatics Advance Access published on July 15, 2006
Bioinformatics 2006 22: 2129-2135; doi:10.1093/bioinformatics/btl364 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING

Get checked abstract Shao Li, Lijiang Wu, and Zhongqi Zhang

Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach
Bioinformatics Advance Access published on July 4, 2006
Bioinformatics 2006 22: 2143-2150; doi:10.1093/bioinformatics/btl363 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Rainer Malik, Lude Franke, and Arno Siebes

Combination of text-mining algorithms increases the performance
Bioinformatics Advance Access published on June 9, 2006
Bioinformatics 2006 22: 2151-2157; doi:10.1093/bioinformatics/btl281 [Abstract] [Full Text] [Print PDF] [Supplement] [Request Permissions]  

APPLICATIONS NOTE

SEQUENCE ANALYSIS

Get checked abstract Gill Bejerano

Branch and bound computation of exact p-values
Bioinformatics Advance Access published on August 7, 2006
Bioinformatics 2006 22: 2158-2159; doi:10.1093/bioinformatics/btl357 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Simon N. Jarman

Cleaver: software for identifying taxon specific restriction endonuclease recognition sites
Bioinformatics Advance Access published on June 20, 2006
Bioinformatics 2006 22: 2160-2161; doi:10.1093/bioinformatics/btl330 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS

Get checked abstract Joshua W. K. Ho, Cameron E. Adams, Jie Bin Lew, Timothy J. Matthews, Chiu Chin Ng, Arash Shahabi-Sirjani, Leng Hong Tan, Yu Zhao, Simon Easteal, Susan R Wilson, and Lars S Jermiin

SeqVis: Visualization of compositional heterogeneity in large alignments of nucleotides
Bioinformatics Advance Access published on June 9, 2006
Bioinformatics 2006 22: 2162-2163; doi:10.1093/bioinformatics/btl283 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS

Get checked abstract Rachel Kolodny and Barry Honig

VISTAL—a new 2D visualization tool of protein 3D structural alignments
Bioinformatics Advance Access published on July 12, 2006
Bioinformatics 2006 22: 2166-2167; doi:10.1093/bioinformatics/btl353 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Douglas L. Theobald and Deborah S. Wuttke

THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures
Bioinformatics Advance Access published on June 15, 2006
Bioinformatics 2006 22: 2171-2172; doi:10.1093/bioinformatics/btl332 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS

Get checked abstract William S. Bush, Scott M. Dudek, and Marylyn D. Ritchie

Parallel multifactor dimensionality reduction: a tool for the large-scale analysis of gene–gene interactions
Bioinformatics Advance Access published on June 29, 2006
Bioinformatics 2006 22: 2173-2174; doi:10.1093/bioinformatics/btl347 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY

Get checked abstract Zhi Liang, Meng Xu, Maikun Teng, and Liwen Niu

NetAlign: a web-based tool for comparison of protein interaction networks
Bioinformatics Advance Access published on June 9, 2006
Bioinformatics 2006 22: 2175-2177; doi:10.1093/bioinformatics/btl287 [Abstract] [Full Text] [Print PDF] [supplementary] [Request Permissions]  

Get checked abstract James Vlasblom, Samuel Wu, Shuye Pu, Mark Superina, Gina Liu, Chris Orsi, and Shoshana J. Wodak

GenePro: a cytoscape plug-in for advanced visualization and analysis of interaction networks
Bioinformatics 2006 22: 2178-2179; doi:10.1093/bioinformatics/btl356 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES

Get checked abstract Yun-Ching Chen, Chung-Der Hsiao, Wen-Dar Lin, Chung-Ming Hu, Pung-Pung Hwang, and Jan-Ming Ho

ZooDDD: a cross-species database for digital differential display analysis
Bioinformatics Advance Access published on July 4, 2006
Bioinformatics 2006 22: 2180-2182; doi:10.1093/bioinformatics/btl358 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

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