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Previous Next 		Contents: Volume 23, Number 17, 1 September 2007   [Index by Author] 
       REVIEW
                STRUCTURAL BIOINFORMATICS
       ORIGINAL PAPERS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
       APPLICATIONS NOTES
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATABASES AND ONTOLOGIES
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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.

REVIEW:

STRUCTURAL BIOINFORMATICS:

Huan-Xiang Zhou and Sanbo Qin
Interaction-site prediction for protein complexes: a critical assessment
Bioinformatics Advance Access published on June 22, 2007
Bioinformatics 2007 23: 2203-2209; doi:10.1093/bioinformatics/btm323 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

SEQUENCE ANALYSIS:

Jian Feng, Daniel Q. Naiman, and Bret Cooper
Probability-based pattern recognition and statistical framework for randomization: modeling tandem mass spectrum/peptide sequence false match frequencies
Bioinformatics Advance Access published on May 17, 2007
Bioinformatics 2007 23: 2210-2217; doi:10.1093/bioinformatics/btm267 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Zhuqing Zhang, Hao Chen, and Luhua Lai
Identification of amyloid fibril-forming segments based on structure and residue-based statistical potential
Bioinformatics Advance Access published on June 28, 2007
Bioinformatics 2007 23: 2218-2225; doi:10.1093/bioinformatics/btm325 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Christina Kiel and Luis Serrano
Prediction of Ras-effector interactions using position energy matrices
Bioinformatics Advance Access published on June 28, 2007
Bioinformatics 2007 23: 2226-2230; doi:10.1093/bioinformatics/btm336 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Anna V. Glyakina, Sergiy O. Garbuzynskiy, Michail Yu. Lobanov, and Oxana V. Galzitskaya
Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms
Bioinformatics Advance Access published on June 28, 2007
Bioinformatics 2007 23: 2231-2238; doi:10.1093/bioinformatics/btm345 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

GENE EXPRESSION:

Anat Reiner-Benaim, Daniel Yekutieli, Noah E. Letwin, Gregory I. Elmer, Norman H. Lee, Neri Kafkafi, and Yoav Benjamini
Associating quantitative behavioral traits with gene expression in the brain: searching for diamonds in the hay
Bioinformatics Advance Access published on September 7, 2007
Bioinformatics 2007 23: 2239-2246; doi:10.1093/bioinformatics/btm300 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

George C. Tseng
Penalized and weighted K-means for clustering with scattered objects and prior information in high-throughput biological data
Bioinformatics Advance Access published on June 27, 2007
Bioinformatics 2007 23: 2247-2255; doi:10.1093/bioinformatics/btm320 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Claudio Lottaz, Joern Toedling, and Rainer Spang
Annotation-based distance measures for patient subgroup discovery in clinical microarray studies
Bioinformatics Advance Access published on June 22, 2007
Bioinformatics 2007 23: 2256-2264; doi:10.1093/bioinformatics/btm322 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Antonis Daskalakis, Dionisis Cavouras, Panagiotis Bougioukos, Spiros Kostopoulos, Dimitris Glotsos, Ioannis Kalatzis, George C. Kagadis, Christos Argyropoulos, and George Nikiforidis
Improving gene quantification by adjustable spot-image restoration
Bioinformatics Advance Access published on June 28, 2007
Bioinformatics 2007 23: 2265-2272; doi:10.1093/bioinformatics/btm337 [Abstract] [FREE Full Text] [Print PDF] [Supplementary data]   OPEN ACCESS ARTICLE  

Andreas Buness, Ruprecht Kuner, Markus Ruschhaupt, Annemarie Poustka, Holger Sültmann, and Achim Tresch
Identification of aberrant chromosomal regions from gene expression microarray studies applied to human breast cancer
Bioinformatics Advance Access published on June 28, 2007
Bioinformatics 2007 23: 2273-2280; doi:10.1093/bioinformatics/btm340 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

SYSTEMS BIOLOGY:

Julio Vera, Raul Curto, Marta Cascante, and Néstor V. Torres
Detection of potential enzyme targets by metabolic modelling and optimization: Application to a simple enzymopathy
Bioinformatics Advance Access published on June 22, 2007
Bioinformatics 2007 23: 2281-2289; doi:10.1093/bioinformatics/btm326 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Wei Sun, Tianwei Yu, and Ker-Chau Li
Detection of eQTL modules mediated by activity levels of transcription factors
Bioinformatics Advance Access published on June 28, 2007
Bioinformatics 2007 23: 2290-2297; doi:10.1093/bioinformatics/btm327 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Dongxiao Zhu, Youjuan Li, and Hua Li
Multivariate correlation estimator for inferring functional relationships from replicated genome-wide data
Bioinformatics Advance Access published on June 22, 2007
Bioinformatics 2007 23: 2298-2305; doi:10.1093/bioinformatics/btm328 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

E. Yang, P.T. Foteinou, K.R. King, M.L. Yarmush, and I.P. Androulakis
A novel non-overlapping bi-clustering algorithm for network generation using living cell array data
Bioinformatics Advance Access published on September 7, 2007
Bioinformatics 2007 23: 2306-2313; doi:10.1093/bioinformatics/btm335 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Pao-Yang Chen, Charlotte M. Deane, and Gesine Reinert
A statistical approach using network structure in the prediction of protein characteristics
Bioinformatics Advance Access published on June 28, 2007
Bioinformatics 2007 23: 2314-2321; doi:10.1093/bioinformatics/btm342 [Abstract] [FREE Full Text] [Print PDF] [Supplementary data]   OPEN ACCESS ARTICLE  

DATA AND TEXT MINING:

Chad L. Myers and Olga G. Troyanskaya
Context-sensitive data integration and prediction of biological networks
Bioinformatics Advance Access published on June 28, 2007
Bioinformatics 2007 23: 2322-2330; doi:10.1093/bioinformatics/btm332 [Abstract] [FREE Full Text] [Print PDF] [Supplementary data]   OPEN ACCESS ARTICLE  

APPLICATIONS NOTES:

GENOME ANALYSIS:

Namshin Kim and Christopher Lee
QPRIMER: a quick web-based application for designing conserved PCR primers from multigenome alignments
Bioinformatics Advance Access published on June 28, 2007
Bioinformatics 2007 23: 2331-2333; doi:10.1093/bioinformatics/btm343 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Wenjie Deng, David C. Nickle, Gerald H. Learn, Brandon Maust, and James I. Mullins
ViroBLAST: a stand-alone BLAST web server for flexible queries of multiple databases and user's datasets
Bioinformatics Advance Access published on June 22, 2007
Bioinformatics 2007 23: 2334-2336; doi:10.1093/bioinformatics/btm331 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Kana Shimizu, Shuichi Hirose, and Tamotsu Noguchi
POODLE-S: web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix
Bioinformatics Advance Access published on June 28, 2007
Bioinformatics 2007 23: 2337-2338; doi:10.1093/bioinformatics/btm330 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Laetitia Marisa, Jean-Laurent Ichanté, Nancie Reymond, Lawrence Aggerbeck, Hervé Delacroix, and Marie-Hélène Mucchielli-Giorgi
MAnGO: an interactive R-based tool for two-colour microarray analysis
Bioinformatics Advance Access published on June 22, 2007
Bioinformatics 2007 23: 2339-2341; doi:10.1093/bioinformatics/btm321 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

K.O. Cheng, N.F. Law, W.C. Siu, and T.H. Lau
BiVisu: software tool for bicluster detection and visualization
Bioinformatics Advance Access published on June 22, 2007
Bioinformatics 2007 23: 2342-2344; doi:10.1093/bioinformatics/btm338 [Abstract] [FREE Full Text] [Print PDF] [Supplementary data]   OPEN ACCESS ARTICLE  

SYSTEMS BIOLOGY:

John H. Morris, Conrad C. Huang, Patricia C. Babbitt, and Thomas E. Ferrin
structureViz: linking Cytoscape and UCSF Chimera
Bioinformatics Advance Access published on July 10, 2007
Bioinformatics 2007 23: 2345-2347; doi:10.1093/bioinformatics/btm329 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Jonathan H. Chen, Erik Linstead, S. Joshua Swamidass, Dennis Wang, and Pierre Baldi
ChemDB update—full-text search and virtual chemical space
Bioinformatics Advance Access published on June 28, 2007
Bioinformatics 2007 23: 2348-2351; doi:10.1093/bioinformatics/btm341 [Abstract] [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.