Bioinformatics

DISCOVERY NOTE:

SEQUENCE ANALYSIS:

Get checked abstract Isabelle Callebaut and Jean-Paul Mornon

OCRE: a novel domain made of imperfect, aromatic-rich octamer repeats
Bioinformatics Advance Access published on October 14, 2004
Bioinformatics 2005 21: 699-702; doi:10.1093/bioinformatics/bti065 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Get checked abstract Xiangqun H. Zheng, Fu Lu, Zhen-Yuan Wang, Fei Zhong, Jeffrey Hoover, and Richard Mural

Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs
Bioinformatics Advance Access published on September 30, 2004
Bioinformatics 2005 21: 703-710; doi:10.1093/bioinformatics/bti045 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Alejandro Panjkovich and Francisco Melo

Comparison of different melting temperature calculation methods for short DNA sequences
Bioinformatics Advance Access published on October 22, 2004
Bioinformatics 2005 21: 711-722; doi:10.1093/bioinformatics/bti066 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract David J. Bakewell and Ernst Wit

Weighted analysis of microarray gene expression using maximum-likelihood
Bioinformatics Advance Access published on September 28, 2004
Bioinformatics 2005 21: 723-729; doi:10.1093/bioinformatics/bti051 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Y.-h. Taguchi and Y. Oono

Relational patterns of gene expression via non-metric multidimensional scaling analysis
Bioinformatics Advance Access published on October 27, 2004
Bioinformatics 2005 21: 730-740; doi:10.1093/bioinformatics/bti067 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Peter J. Woolf, Wendy Prudhomme, Laurence Daheron, George Q. Daley, and Douglas A. Lauffenburger

Bayesian analysis of signaling networks governing embryonic stem cell fate decisions
Bioinformatics Advance Access published on October 12, 2004
Bioinformatics 2005 21: 741-753; doi:10.1093/bioinformatics/bti056 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Juliane Schäfer and Korbinian Strimmer

An empirical Bayes approach to inferring large-scale gene association networks
Bioinformatics Advance Access published on October 12, 2004
Bioinformatics 2005 21: 754-764; doi:10.1093/bioinformatics/bti062 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract John Jeremy Rice, Yuhai Tu, and Gustavo Stolovitzky

Reconstructing biological networks using conditional correlation analysis
Bioinformatics Advance Access published on October 14, 2004
Bioinformatics 2005 21: 765-773; doi:10.1093/bioinformatics/bti064 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Chin-Rang Yang, Bruce E. Shapiro, Eric D. Mjolsness, and G. Wesley Hatfield

An enzyme mechanism language for the mathematical modeling of metabolic pathways
Bioinformatics Advance Access published on October 27, 2004
Bioinformatics 2005 21: 774-780; doi:10.1093/bioinformatics/bti068 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract D. Y. Lin

An efficient Monte Carlo approach to assessing statistical significance in genomic studies
Bioinformatics Advance Access published on September 28, 2004
Bioinformatics 2005 21: 781-787; doi:10.1093/bioinformatics/bti053 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Dilip Rajagopalan and Pankaj Agarwal

Inferring pathways from gene lists using a literature-derived network of biological relationships
Bioinformatics Advance Access published on October 27, 2004
Bioinformatics 2005 21: 788-793; doi:10.1093/bioinformatics/bti069 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Get checked abstract Yong-Meng Teo, Xianbing Wang, and Yew-Kwong Ng

GLAD: a system for developing and deploying large-scale bioinformatics grid
Bioinformatics Advance Access published on September 23, 2004
Bioinformatics 2005 21: 794-802; doi:10.1093/bioinformatics/bti034 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Steve W. Cole, Weihong Yan, Zoran Galic, Jesusa Arevalo, and Jerome A. Zack

Expression-based monitoring of transcription factor activity: the TELiS database
Bioinformatics Advance Access published on September 16, 2004
Bioinformatics 2005 21: 803-810; doi:10.1093/bioinformatics/bti038 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract T. Boby, A.-M. Patch, and S. J. Aves

TRbase: a database relating tandem repeats to disease genes for the human genome
Bioinformatics Advance Access published on October 12, 2004
Bioinformatics 2005 21: 811-816; doi:10.1093/bioinformatics/bti059 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

GENOME ANALYSIS:

Get checked abstract I. Miklós, P. Ittzés, and J. Hein

ParIS Genome Rearrangement server
Bioinformatics Advance Access published on October 12, 2004
Bioinformatics 2005 21: 817-820; doi:10.1093/bioinformatics/bti060 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Ole Christian Lingjærde, Lars O. Baumbusch, Knut Liestøl, Ingrid K. Glad, and Anne-Lise Børresen-Dale

CGH-Explorer: a program for analysis of array-CGH data
Bioinformatics Advance Access published on November 5, 2004
Bioinformatics 2005 21: 821-822; doi:10.1093/bioinformatics/bti113 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Cameron Wellock, Vijay Chickarmane, and Herbert M. Sauro

The SBW–MATLAB interface
Bioinformatics Advance Access published on November 5, 2004
Bioinformatics 2005 21: 823-824; doi:10.1093/bioinformatics/bti110 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Get checked abstract Stuart Aitken, Roman Korf, Bonnie Webber, and Jonathan Bard

COBrA: a bio-ontology editor
Bioinformatics Advance Access published on October 28, 2004
Bioinformatics 2005 21: 825-826; doi:10.1093/bioinformatics/bti097 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Thijs Beuming, Lucy Skrabanek, Masha Y. Niv, Piali Mukherjee, and Harel Weinstein

PDZBase: a protein–protein interaction database for PDZ-domains
Bioinformatics Advance Access published on October 28, 2004
Bioinformatics 2005 21: 827-828; doi:10.1093/bioinformatics/bti098 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Yu Rang Park, Chan Hee Park, and Ju Han Kim

GOChase: correcting errors from Gene Ontology-based annotations for gene products
Bioinformatics Advance Access published on October 28, 2004
Bioinformatics 2005 21: 829-831; doi:10.1093/bioinformatics/bti106 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Philipp Pagel, Stefan Kovac, Matthias Oesterheld, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Goar Frishman, Corinna Montrone, Pekka Mark, Volker Stümpflen, Hans-Werner Mewes, Andreas Ruepp, and Dmitrij Frishman

The MIPS mammalian protein–protein interaction database
Bioinformatics Advance Access published on November 5, 2004
Bioinformatics 2005 21: 832-834; doi:10.1093/bioinformatics/bti115 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Saranyan K. Palaniswamy, Victor X. Jin, Hao Sun, and Ramana V. Davuluri

OMGProm: a database of orthologous mammalian gene promoters
Bioinformatics Advance Access published on November 5, 2004
Bioinformatics 2005 21: 835-836; doi:10.1093/bioinformatics/bti119 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

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