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Previous Next 		Contents: Volume 22, Number 13, 1 July 2006   [Index by Author] 
       EDITORIALS
       DISCOVERY NOTE
                SEQUENCE ANALYSIS
       ORIGINAL PAPERS
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
       APPLICATIONS NOTE
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                DATA AND TEXT MINING
       CORRIGENDUM
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EDITORIALS:

Jonathan D. Wren
Theory and reality for software patents: good in concept, not so good in practice
Bioinformatics 2006 22: 1543-1545; doi:10.1093/bioinformatics/btl168 [Extract] [Full Text] [Print PDF] [Request Permissions]  

DISCOVERY NOTE:

SEQUENCE ANALYSIS:

Elhanan Magidovich, Sarel J. Fleishman, and Ofer Yifrach
Intrinsically disordered C-terminal segments of voltage-activated potassium channels: a possible fishing rod-like mechanism for channel binding to scaffold proteins
Bioinformatics Advance Access published on April 6, 2006
Bioinformatics 2006 22: 1546-1550; doi:10.1093/bioinformatics/btl137 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Christina Toft and Mario A. Fares
GRAST: a new way of genome reduction analysis using comparative genomics
Bioinformatics Advance Access published on April 6, 2006
Bioinformatics 2006 22: 1551-1561; doi:10.1093/bioinformatics/btl139 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Burkhard Heil, Jost Ludwig, Hella Lichtenberg-Fraté, and Thomas Lengauer
Computational recognition of potassium channel sequences
Bioinformatics Advance Access published on April 4, 2006
Bioinformatics 2006 22: 1562-1568; doi:10.1093/bioinformatics/btl132 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Kavitha Bhasi, Li Zhang, Daniel Brazeau, Aidong Zhang, and Murali Ramanathan
VizStruct for visualization of genome-wide SNP analyses
Bioinformatics Advance Access published on April 13, 2006
Bioinformatics 2006 22: 1569-1576; doi:10.1093/bioinformatics/btl144 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Zhi Wei and Shane T. Jensen
GAME: detecting cis-regulatory elements using a genetic algorithm
Bioinformatics Advance Access published on April 21, 2006
Bioinformatics 2006 22: 1577-1584; doi:10.1093/bioinformatics/btl147 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Orhan Çamoglu, Tolga Can, and Ambuj K. Singh
Integrating multi-attribute similarity networks for robust representation of the protein space
Bioinformatics Advance Access published on April 4, 2006
Bioinformatics 2006 22: 1585-1592; doi:10.1093/bioinformatics/btl130 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Deniz Dalli, Andreas Wilm, Indra Mainz, and Gerhard Steger
STRAL: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time
Bioinformatics Advance Access published on April 13, 2006
Bioinformatics 2006 22: 1593-1599; doi:10.1093/bioinformatics/btl142 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Adrian Alexa, Jörg Rahnenführer, and Thomas Lengauer
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
Bioinformatics Advance Access published on April 10, 2006
Bioinformatics 2006 22: 1600-1607; doi:10.1093/bioinformatics/btl140 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

G.J. McLachlan, R.W. Bean, and L. Ben-Tovim Jones
A simple implementation of a normal mixture approach to differential gene expression in multiclass microarrays
Bioinformatics Advance Access published on April 21, 2006
Bioinformatics 2006 22: 1608-1615; doi:10.1093/bioinformatics/btl148 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Golan Yona, William Dirks, Shafquat Rahman, and David M. Lin
Effective similarity measures for expression profiles
Bioinformatics Advance Access published on April 4, 2006
Bioinformatics 2006 22: 1616-1622; doi:10.1093/bioinformatics/btl127 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY:

Hon Nian Chua, Wing-Kin Sung, and Limsoon Wong
Exploiting indirect neighbours and topological weight to predict protein function from protein–protein interactions
Bioinformatics Advance Access published on April 21, 2006
Bioinformatics 2006 22: 1623-1630; doi:10.1093/bioinformatics/btl145 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Dong-Yeon Cho, Kwang-Hyun Cho, and Byoung-Tak Zhang
Identification of biochemical networks by S-tree based genetic programming
Bioinformatics Advance Access published on April 3, 2006
Bioinformatics 2006 22: 1631-1640; doi:10.1093/bioinformatics/btl122 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Lei Nie, Gang Wu, Fred J. Brockman, and Weiwen Zhang
Integrated analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: zero-inflated Poisson regression models to predict abundance of undetected proteins
Bioinformatics Advance Access published on May 4, 2006
Bioinformatics 2006 22: 1641-1647; doi:10.1093/bioinformatics/btl134 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Shanfeng Zhu, Keiko Udaka, John Sidney, Alessandro Sette, Kiyoko F. Aoki-Kinoshita, and Hiroshi Mamitsuka
Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules
Bioinformatics Advance Access published on April 13, 2006
Bioinformatics 2006 22: 1648-1655; doi:10.1093/bioinformatics/btl141 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

SEQUENCE ANALYSIS:

I. Mihalek, I. Res, and O. Lichtarge
Evolutionary trace report_maker: a new type of service for comparative analysis of proteins
Bioinformatics Advance Access published on April 27, 2006
Bioinformatics 2006 22: 1656-1657; doi:10.1093/bioinformatics/btl157 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Weizhong Li and Adam Godzik
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Bioinformatics Advance Access published on May 26, 2006
Bioinformatics 2006 22: 1658-1659; doi:10.1093/bioinformatics/btl158 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

STRUCTURAL BIOINFORMATICS:

Olga Kirillova and Wladek Minor
Map2mod—a server for evaluation of crystallographic models and their agreement with electron density maps
Bioinformatics Advance Access published on April 27, 2006
Bioinformatics 2006 22: 1660-1661; doi:10.1093/bioinformatics/btl152 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Hiro Takahashi and Hiroyuki Honda
Modified signal-to-noise: a new simple and practical gene filtering approach based on the concept of projective adaptive resonance theory (PART) filtering method
Bioinformatics Advance Access published on April 21, 2006
Bioinformatics 2006 22: 1662-1664; doi:10.1093/bioinformatics/btl156 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Fei Pan, Kiran Kamath, Kangyu Zhang, Sudip Pulapura, Avinash Achar, Juan Nunez-Iglesias, Yu Huang, Xifeng Yan, Jiawei Han, Haiyan Hu, Min Xu, Jianjun Hu, and Xianghong Jasmine Zhou
Integrative Array Analyzer: a software package for analysis of cross-platform and cross-species microarray data
Bioinformatics Advance Access published on May 3, 2006
Bioinformatics 2006 22: 1665-1667; doi:10.1093/bioinformatics/btl163 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

DATA AND TEXT MINING:

X. Yuan, Z. Z. Hu, H. T. Wu, M. Torii, M. Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker, and C. H. Wu
An online literature mining tool for protein phosphorylation
Bioinformatics Advance Access published on April 27, 2006
Bioinformatics 2006 22: 1668-1669; doi:10.1093/bioinformatics/btl159 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Justin Klekota, Frederick P. Roth, and Stuart L. Schreiber
Query Chem: a Google-powered web search combining text and chemical structures
Bioinformatics Advance Access published on May 3, 2006
Bioinformatics 2006 22: 1670-1673; doi:10.1093/bioinformatics/btl155 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

CORRIGENDUM:

A. Clare, A. Karwath, H. Ougham, and R. D. King
Functional bioinformatics for Arabidopsis thaliana
Bioinformatics 2006 22: 1674; doi:10.1093/bioinformatics/btl169 [Extract] [Full Text] [Print PDF] [Request Permissions]  

To see an article, click its [Full Text] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.