Bioinformatics

DISCOVERY NOTE:

SEQUENCE ANALYSIS:

Get checked abstract Shuji Fujita and Hideo Iba

Putative promoter regions of miRNA genes involved in evolutionarily conserved regulatory systems among vertebrates
Bioinformatics Advance Access published on November 30, 2007
Bioinformatics 2008 24: 303-308; doi:10.1093/bioinformatics/btm589 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Get checked abstract Roger Pique-Regi, Jordi Monso-Varona, Antonio Ortega, Robert C. Seeger, Timothy J. Triche, and Shahab Asgharzadeh

Sparse representation and Bayesian detection of genome copy number alterations from microarray data
Bioinformatics Advance Access published on January 18, 2008
Bioinformatics 2008 24: 309-318; doi:10.1093/bioinformatics/btm601 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract Gabriel Moreno-Hagelsieb and Kristen Latimer

Choosing BLAST options for better detection of orthologs as reciprocal best hits
Bioinformatics Advance Access published on November 26, 2007
Bioinformatics 2008 24: 319-324; doi:10.1093/bioinformatics/btm585 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Xiaowei Wang and Issam M. El Naqa

Prediction of both conserved and nonconserved microRNA targets in animals
Bioinformatics Advance Access published on November 29, 2007
Bioinformatics 2008 24: 325-332; doi:10.1093/bioinformatics/btm595 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract S.D. Dunn, L.M. Wahl, and G.B. Gloor

Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction
Bioinformatics Advance Access published on December 5, 2007
Bioinformatics 2008 24: 333-340; doi:10.1093/bioinformatics/btm604 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Tak-Ming Chan, Kwong-Sak Leung, and Kin-Hong Lee

TFBS identification based on genetic algorithm with combined representations and adaptive post-processing
Bioinformatics Advance Access published on December 6, 2007
Bioinformatics 2008 24: 341-349; doi:10.1093/bioinformatics/btm606 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Laurent Jacob and Jean-Philippe Vert

Efficient peptide–MHC-I binding prediction for alleles with few known binders
Bioinformatics Advance Access published on December 14, 2007
Bioinformatics 2008 24: 358-366; doi:10.1093/bioinformatics/btm611 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Hisanori Kiryu, Taishin Kin, and Kiyoshi Asai

Rfold: an exact algorithm for computing local base pairing probabilities
Bioinformatics Advance Access published on December 4, 2007
Bioinformatics 2008 24: 367-373; doi:10.1093/bioinformatics/btm591 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Fangxin Hong and Rainer Breitling

A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments
Bioinformatics Advance Access published on January 18, 2008
Bioinformatics 2008 24: 374-382; doi:10.1093/bioinformatics/btm620 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract F.F. Vale, P. Encarnação, and J. M. B. Vítor

A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case
Bioinformatics Advance Access published on December 16, 2007
Bioinformatics 2008 24: 383-388; doi:10.1093/bioinformatics/btm621 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Anatoly L. Mayburd, Inna Golovchikova, and James L. Mulshine

Successful anti-cancer drug targets able to pass FDA review demonstrate the identifiable signature distinct from the signatures of random genes and initially proposed targets
Bioinformatics Advance Access published on October 8, 2007
Bioinformatics 2008 24: 389-395; doi:10.1093/bioinformatics/btm447 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract David J. Reiss, Marc T. Facciotti, and Nitin S. Baliga

Model-based deconvolution of genome-wide DNA binding
Bioinformatics Advance Access published on December 1, 2007
Bioinformatics 2008 24: 396-403; doi:10.1093/bioinformatics/btm592 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Peng Wei and Wei Pan

Incorporating gene networks into statistical tests for genomic data via a spatially correlated mixture model
Bioinformatics Advance Access published on December 14, 2007
Bioinformatics 2008 24: 404-411; doi:10.1093/bioinformatics/btm612 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Li Wang, Ji Zhu, and Hui Zou

Hybrid huberized support vector machines for microarray classification and gene selection
Bioinformatics Advance Access published on January 5, 2008
Bioinformatics 2008 24: 412-419; doi:10.1093/bioinformatics/btm579 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTES:

GENOME ANALYSIS:

Get checked abstract Tae-Min Kim, Yu-Chae Jung, Mun-Gan Rhyu, Myeong Ho Jung, and Yeun-Jun Chung

GEAR: genomic enrichment analysis of regional DNA copy number changes
Bioinformatics Advance Access published on November 23, 2007
Bioinformatics 2008 24: 420-421; doi:10.1093/bioinformatics/btm582 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Jacques Oberto

BAGET: a web server for the effortless retrieval of prokaryotic gene context and sequence
Bioinformatics Advance Access published on December 1, 2007
Bioinformatics 2008 24: 424-425; doi:10.1093/bioinformatics/btm600 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

GENE EXPRESSION:

Get checked abstract Daniele Masotti, Christine Nardini, Simona Rossi, Elena Bonora, Giovanni Romeo, Stefano Volinia, and Luca Benini

TOM: enhancement and extension of a tool suite for in silico approaches to multigenic hereditary disorders
Bioinformatics Advance Access published on November 29, 2007
Bioinformatics 2008 24: 428-429; doi:10.1093/bioinformatics/btm588 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Paolo Magni, Fulvia Ferrazzi, Lucia Sacchi, and Riccardo Bellazzi

TimeClust: a clustering tool for gene expression time series
Bioinformatics Advance Access published on December 6, 2007
Bioinformatics 2008 24: 430-432; doi:10.1093/bioinformatics/btm605 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Rudi Alberts, Gonzalo Vera, and Ritsert C. Jansen

affyGG: computational protocols for genetical genomics with Affymetrix arrays
Bioinformatics Advance Access published on December 16, 2007
Bioinformatics 2008 24: 433-434; doi:10.1093/bioinformatics/btm614 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Xiaoquan Wen and Dan L. Nicolae

Association studies for untyped markers with TUNA
Bioinformatics Advance Access published on December 5, 2007
Bioinformatics 2008 24: 435-437; doi:10.1093/bioinformatics/btm603 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Tianming Liu, Jingxin Nie, Gang Li, Lei Guo, and Stephen T. C. Wong

ZFIQ: a software package for zebrafish biology
Bioinformatics Advance Access published on December 18, 2007
Bioinformatics 2008 24: 438-439; doi:10.1093/bioinformatics/btm615 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Get checked abstract Stuart Aitken, Yin Chen, and Jonathan Bard

OBO Explorer: an editor for open biomedical ontologies in OWL
Bioinformatics Advance Access published on December 1, 2007
Bioinformatics 2008 24: 443-444; doi:10.1093/bioinformatics/btm593 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Quentin Kaas, Jan-C. Westermann, Reena Halai, Conan K. L. Wang, and David J. Craik

ConoServer, a database for conopeptide sequences and structures
Bioinformatics Advance Access published on December 6, 2007
Bioinformatics 2008 24: 445-446; doi:10.1093/bioinformatics/btm596 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract David Salgado, Gregory Gimenez, François Coulier, and Christophe Marcelle

COMPARE, a multi-organism system for cross-species data comparison and transfer of information
Bioinformatics Advance Access published on December 1, 2007
Bioinformatics 2008 24: 447-449; doi:10.1093/bioinformatics/btm599 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Gil Alterovitz, Adnaan Jiwaji, and Marco F. Ramoni

Automated programming for bioinformatics algorithm deployment
Bioinformatics Advance Access published on January 3, 2008
Bioinformatics 2008 24: 450-451; doi:10.1093/bioinformatics/btm602 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

CORRIGENDUM:

Exploiting indirect neighbours and topological weight to predict protein function from protein–protein interactions
Bioinformatics 2008 24: 452; doi:10.1093/bioinformatics/btm609 [Extract] [Full Text] [Print PDF] [Request Permissions]  

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