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Previous Next 		Contents: Volume 23, Number 14, 15 July 2007   [Index by Author] 
       REVIEW
                SEQUENCE ANALYSIS
       ORIGINAL PAPERS
                SEQUENCE ANALYSIS
                PHYLOGENETICS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                GENETICS AND POPULATION ANALYSIS
                DATABASES AND ONTOLOGIES
       APPLICATIONS NOTES
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                GENETICS AND POPULATION ANALYSIS
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
                DATABASES AND ONTOLOGIES
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REVIEW:

SEQUENCE ANALYSIS:

Sudhir Kumar and Joel Dudley
Bioinformatics software for biologists in the genomics era
Bioinformatics Advance Access published on May 7, 2007
Bioinformatics 2007 23: 1713-1717; doi:10.1093/bioinformatics/btm239 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

SEQUENCE ANALYSIS:

Lee A. Newberg, William A. Thompson, Sean Conlan, Thomas M. Smith, Lee Ann McCue, and Charles E. Lawrence
A phylogenetic Gibbs sampler that yields centroid solutions for cis-regulatory site prediction
Bioinformatics Advance Access published on May 8, 2007
Bioinformatics 2007 23: 1718-1727; doi:10.1093/bioinformatics/btm241 [Abstract] [FREE Full Text] [Print PDF] [Supplementary data]   OPEN ACCESS ARTICLE  

Sepp Hochreiter, Martin Heusel, and Klaus Obermayer
Fast model-based protein homology detection without alignment
Bioinformatics Advance Access published on May 8, 2007
Bioinformatics 2007 23: 1728-1736; doi:10.1093/bioinformatics/btm247 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Libi Hertzberg, Shai Izraeli, and Eytan Domany
STOP: searching for transcription factor motifs using gene expression
Bioinformatics Advance Access published on May 8, 2007
Bioinformatics 2007 23: 1737-1743; doi:10.1093/bioinformatics/btm249 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Xiaomeng Wu, Zhipeng Cai, Xiu-Feng Wan, Tin Hoang, Randy Goebel, and Guohui Lin
Nucleotide composition string selection in HIV-1 subtyping using whole genomes
Bioinformatics Advance Access published on May 11, 2007
Bioinformatics 2007 23: 1744-1752; doi:10.1093/bioinformatics/btm248 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

STRUCTURAL BIOINFORMATICS:

Peter M. Kasson, Afra Zomorodian, Sanghyun Park, Nina Singhal, Leonidas J. Guibas, and Vijay S. Pande
Persistent voids: a new structural metric for membrane fusion
Bioinformatics Advance Access published on May 8, 2007
Bioinformatics 2007 23: 1753-1759; doi:10.1093/bioinformatics/btm250 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Ganesh Bagler and Somdatta Sinha
Assortative mixing in Protein Contact Networks and protein folding kinetics
Bioinformatics Advance Access published on May 22, 2007
Bioinformatics 2007 23: 1760-1767; doi:10.1093/bioinformatics/btm257 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

GENE EXPRESSION:

Martin Schumacher, Harald Binder, and Thomas Gerds
Assessment of survival prediction models based on microarray data
Bioinformatics Advance Access published on May 7, 2007
Bioinformatics 2007 23: 1768-1774; doi:10.1093/bioinformatics/btm232 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Feng Tai and Wei Pan
Incorporating prior knowledge of predictors into penalized classifiers with multiple penalty terms
Bioinformatics Advance Access published on May 5, 2007
Bioinformatics 2007 23: 1775-1782; doi:10.1093/bioinformatics/btm234 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Mark P. Brynildsen, Tung-Yun Wu, Shi-Shang Jang, and James C. Liao
Biological network mapping and source signal deduction
Bioinformatics Advance Access published on May 11, 2007
Bioinformatics 2007 23: 1783-1791; doi:10.1093/bioinformatics/btm246 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

María José Nueda, Ana Conesa, Johan A. Westerhuis, Huub C. J. Hoefsloot, Age K. Smilde, Manuel Talón, and Alberto Ferrer
Discovering gene expression patterns in time course microarray experiments by ANOVA–SCA
Bioinformatics Advance Access published on May 22, 2007
Bioinformatics 2007 23: 1792-1800; doi:10.1093/bioinformatics/btm251 [Abstract] [FREE Full Text] [Print PDF] [Supplementary data]   OPEN ACCESS ARTICLE  

GENETICS AND POPULATION ANALYSIS:

Mattias Jakobsson and Noah A. Rosenberg
CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure
Bioinformatics Advance Access published on May 7, 2007
Bioinformatics 2007 23: 1801-1806; doi:10.1093/bioinformatics/btm233 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Donna M. Toleno, Peter L. Morrell, and Michael T. Clegg
Error detection in SNP data by considering the likelihood of recombinational history implied by three-site combinations
Bioinformatics Advance Access published on May 17, 2007
Bioinformatics 2007 23: 1807-1814; doi:10.1093/bioinformatics/btm260 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Ashwini Bhasi, Ram Vinay Pandey, Suriya Prabha Utharasamy, and Periannan Senapathy
EuSplice: a unified resource for the analysis of splice signals and alternative splicing in eukaryotic genes
Bioinformatics Advance Access published on March 7, 2007
Bioinformatics 2007 23: 1815-1823; doi:10.1093/bioinformatics/btm084 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Roman A. Laskowski
Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature
Bioinformatics Advance Access published on March 24, 2007
Bioinformatics 2007 23: 1824-1827; doi:10.1093/bioinformatics/btm085 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTES:

GENOME ANALYSIS:

Timothy R. O’Connor and John J. Wyrick
ChromatinDB: a database of genome-wide histone modification patterns for Saccharomyces cerevisiae
Bioinformatics Advance Access published on May 7, 2007
Bioinformatics 2007 23: 1828-1830; doi:10.1093/bioinformatics/btm236 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Arnaud Kerhornou and Roderic Guigó
BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations
Bioinformatics Advance Access published on May 12, 2007
Bioinformatics 2007 23: 1831-1833; doi:10.1093/bioinformatics/btm252 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Francois Beaussart, January Weiner, 3rd, and Erich Bornberg-Bauer
Automated Improvement of Domain ANnotations using context analysis of domain arrangements (AIDAN)
Bioinformatics Advance Access published on May 5, 2007
Bioinformatics 2007 23: 1834-1836; doi:10.1093/bioinformatics/btm240 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Eran Eyal, Shmuel Pietrokovski, and Ivet Bahar
Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices
Bioinformatics Advance Access published on May 12, 2007
Bioinformatics 2007 23: 1837-1839; doi:10.1093/bioinformatics/btm256 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Dominik Gront and Andrzej Kolinski
T-Pile—a package for thermodynamic calculations for biomolecules
Bioinformatics Advance Access published on May 17, 2007
Bioinformatics 2007 23: 1840-1842; doi:10.1093/bioinformatics/btm259 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Zuoshuang Xiang, Zhaohui S. Qin, and Yongqun He
CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering
Bioinformatics Advance Access published on May 7, 2007
Bioinformatics 2007 23: 1843-1845; doi:10.1093/bioinformatics/btm238 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Sean Davis and Paul S. Meltzer
GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor
Bioinformatics Advance Access published on May 12, 2007
Bioinformatics 2007 23: 1846-1847; doi:10.1093/bioinformatics/btm254 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

T. Antao, A. Beja-Pereira, and G. Luikart
MODELER4SIMCOAL2: A user-friendly, extensible modeler of demography and linked loci for coalescent simulations
Bioinformatics Advance Access published on May 8, 2007
Bioinformatics 2007 23: 1848-1850; doi:10.1093/bioinformatics/btm243 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

August E. Woerner, Murray P. Cox, and Michael F. Hammer
Recombination-filtered genomic datasets by information maximization
Bioinformatics Advance Access published on May 22, 2007
Bioinformatics 2007 23: 1851-1853; doi:10.1093/bioinformatics/btm253 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Edward H. Trager, Ritu Khanna, Adrian Marrs, Lawrence Siden, Kari E.H. Branham, Anand Swaroop, and Julia E. Richards
Madeline 2.0 PDE: a new program for local and web-based pedigree drawing
Bioinformatics Advance Access published on May 8, 2007
Bioinformatics 2007 23: 1854-1856; doi:10.1093/bioinformatics/btm242 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

SYSTEMS BIOLOGY:

Guillermo Rodrigo, Javier Carrera, and Alfonso Jaramillo
Genetdes: automatic design of transcriptional networks
Bioinformatics Advance Access published on May 7, 2007
Bioinformatics 2007 23: 1857-1858; doi:10.1093/bioinformatics/btm237 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Ravishankar Rao Vallabhajosyula and Herbert M. Sauro
Stochastic simulation GUI for biochemical networks
Bioinformatics Advance Access published on June 22, 2007
Bioinformatics 2007 23: 1859-1861; doi:10.1093/bioinformatics/btm231 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

J. Gregory Caporaso, William A. Baumgartner, Jr, David A. Randolph, K. Bretonnel Cohen, and Lawrence Hunter
MutationFinder: a high-performance system for extracting point mutation mentions from text
Bioinformatics Advance Access published on May 11, 2007
Bioinformatics 2007 23: 1862-1865; doi:10.1093/bioinformatics/btm235 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

DATABASES AND ONTOLOGIES:

Feng Gao and Chun-Ting Zhang
DoriC: a database of oriC regions in bacterial genomes
Bioinformatics Advance Access published on May 12, 2007
Bioinformatics 2007 23: 1866-1867; doi:10.1093/bioinformatics/btm255 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Dilvan A. Moreira and Mark A. Musen
OBO to OWL: a protégé OWL tab to read/save OBO ontologies
Bioinformatics Advance Access published on May 12, 2007
Bioinformatics 2007 23: 1868-1870; doi:10.1093/bioinformatics/btm258 [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.