Bioinformatics

ORIGINAL PAPERS:

SEQUENCE ANALYSIS:

Get checked abstract Matthew N. Davies, Andrew Secker, Alex A. Freitas, Miguel Mendao, Jon Timmis, and Darren R. Flower

On the hierarchical classification of G protein-coupled receptors
Bioinformatics Advance Access published on October 22, 2007
Bioinformatics 2007 23: 3113-3118; doi:10.1093/bioinformatics/btm506 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Get checked abstract Damien M. de Vienne, Tatiana Giraud, and Olivier C. Martin

A congruence index for testing topological similarity between trees
Bioinformatics Advance Access published on October 12, 2007
Bioinformatics 2007 23: 3119-3124; doi:10.1093/bioinformatics/btm500 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Mehdi Poursheikhali Asgary, Samad Jahandideh, Parviz Abdolmaleki, and Anoshirvan Kazemnejad

Analysis and identification of β-turn types using multinomial logistic regression and artificial neural network
Bioinformatics Advance Access published on June 28, 2007
Bioinformatics 2007 23: 3125-3130; doi:10.1093/bioinformatics/btm324 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Ingolf Sommer, Oliver Müller, Francisco S. Domingues, Oliver Sander, Joachim Weickert, and Thomas Lengauer

Moment invariants as shape recognition technique for comparing protein binding sites
Bioinformatics Advance Access published on October 31, 2007
Bioinformatics 2007 23: 3139-3146; doi:10.1093/bioinformatics/btm503 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Jiangning Song, Zheng Yuan, Hao Tan, Thomas Huber, and Kevin Burrage

Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure
Bioinformatics Advance Access published on October 17, 2007
Bioinformatics 2007 23: 3147-3154; doi:10.1093/bioinformatics/btm505 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Majid Masso and Iosif I. Vaisman

Accurate prediction of enzyme mutant activity based on a multibody statistical potential
Bioinformatics Advance Access published on October 31, 2007
Bioinformatics 2007 23: 3155-3161; doi:10.1093/bioinformatics/btm509 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Feng Tai and Wei Pan

Incorporating prior knowledge of gene functional groups into regularized discriminant analysis of microarray data
Bioinformatics Advance Access published on October 12, 2007
Bioinformatics 2007 23: 3170-3177; doi:10.1093/bioinformatics/btm488 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract K. Hao

Genome-wide selection of tag SNPs using multiple-marker correlation
Bioinformatics Advance Access published on November 15, 2007
Bioinformatics 2007 23: 3178-3184; doi:10.1093/bioinformatics/btm496 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract T. Fournier, J.P. Gabriel, C. Mazza, J. Pasquier, J.L. Galbete, and N. Mermod

Steady-state expression of self-regulated genes
Bioinformatics Advance Access published on October 12, 2007
Bioinformatics 2007 23: 3185-3192; doi:10.1093/bioinformatics/btm490 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Fangping Mu, Robert F. Williams, Clifford J. Unkefer, Pat J. Unkefer, James R. Faeder, and William S. Hlavacek

Carbon-fate maps for metabolic reactions
Bioinformatics Advance Access published on October 12, 2007
Bioinformatics 2007 23: 3193-3199; doi:10.1093/bioinformatics/btm498 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Niels Grabe, Thora Pommerencke, Thorsten Steinberg, Hartmut Dickhaus, and Pascal Tomakidi

Reconstructing protein networks of epithelial differentiation from histological sections
Bioinformatics 2007 23: 3200-3208; doi:10.1093/bioinformatics/btm504 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Minh Quach, Nicolas Brunel, and Florence d'Alché-Buc

Estimating parameters and hidden variables in non-linear state-space models based on ODEs for biological networks inference
Bioinformatics 2007 23: 3209-3216; doi:10.1093/bioinformatics/btm510 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Hyunjung Shin, Andreas Martin Lisewski, and Olivier Lichtarge

Graph sharpening plus graph integration: a synergy that improves protein functional classification
Bioinformatics Advance Access published on October 31, 2007
Bioinformatics 2007 23: 3217-3224; doi:10.1093/bioinformatics/btm511 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Dougu Nam, Sung Ho Yoon, and Jihyun F. Kim

Ensemble learning of genetic networks from time-series expression data
Bioinformatics Advance Access published on October 31, 2007
Bioinformatics 2007 23: 3225-3231; doi:10.1093/bioinformatics/btm514 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Colleen E. Crangle, J. Michael Cherry, Eurie L. Hong, and Alex Zbyslaw

Mining experimental evidence of molecular function claims from the literature
Bioinformatics Advance Access published on October 17, 2007
Bioinformatics 2007 23: 3232-3240; doi:10.1093/bioinformatics/btm495 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTES:

SEQUENCE ANALYSIS:

Get checked abstract Lawrence J.K. Wee, Tin Wee Tan, and Shoba Ranganathan

CASVM: web server for SVM-based prediction of caspase substrates cleavage sites
Bioinformatics Advance Access published on June 28, 2007
Bioinformatics 2007 23: 3241-3243; doi:10.1093/bioinformatics/btm334 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Itay Mayrose, Osnat Penn, Elana Erez, Nimrod D. Rubinstein, Tomer Shlomi, Natalia Tarnovitski Freund, Erez M. Bublil, Eytan Ruppin, Roded Sharan, Jonathan M. Gershoni, Eric Martz, and Tal Pupko

Pepitope: epitope mapping from affinity-selected peptides
Bioinformatics Advance Access published on October 31, 2007
Bioinformatics 2007 23: 3244-3246; doi:10.1093/bioinformatics/btm493 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Sergei Spirin, Mikhail Titov, Anna Karyagina, and Andrei Alexeevski

NPIDB: a Database of Nucleic Acids–Protein Interactions
Bioinformatics Advance Access published on October 31, 2007
Bioinformatics 2007 23: 3247-3248; doi:10.1093/bioinformatics/btm519 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Aravind Subramanian, Heidi Kuehn, Joshua Gould, Pablo Tamayo, and Jill P. Mesirov

GSEA-P: a desktop application for Gene Set Enrichment Analysis
Bioinformatics Advance Access published on July 20, 2007
Bioinformatics 2007 23: 3251-3253; doi:10.1093/bioinformatics/btm369 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

DATABASES AND ONTOLOGIES:

Get checked abstract José Luis López-Pérez, Roberto Therón, Esther del Olmo, and David Díaz

NAPROC-13: a database for the dereplication of natural product mixtures in bioassay-guided protocols
Bioinformatics Advance Access published on October 22, 2007
Bioinformatics 2007 23: 3256-3257; doi:10.1093/bioinformatics/btm516 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

LETTER TO THE EDITOR:

PHYLOGENETICS:

Get checked abstract Robert K. Bradley and Ian Holmes

Transducers: an emerging probabilistic framework for modeling indels on trees
Bioinformatics Advance Access published on September 5, 2007
Bioinformatics 2007 23: 3258-3262; doi:10.1093/bioinformatics/btm402 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

PHYLOGENETICS:

Get checked abstract Ian Holmes

Phylocomposer and phylodirector: analysis and visualization of transducer indel models
Bioinformatics Advance Access published on September 5, 2007
Bioinformatics 2007 23: 3263-3264; doi:10.1093/bioinformatics/btm432 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

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