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BMCBI
2008
88views more  BMCBI 2008»
8 years 9 months ago
Microarray-based gene set analysis: a comparison of current methods
Background: The analysis of gene sets has become a popular topic in recent times, with researchers attempting to improve the interpretability and reproducibility of their microarr...
Sarah Song, Michael A. Black
BMCBI
2008
129views more  BMCBI 2008»
8 years 9 months ago
Mining phenotypes for gene function prediction
Background: Health and disease of organisms are reflected in their phenotypes. Often, a genetic component to a disease is discovered only after clearly defining its phenotype. In ...
Philip Groth, Bertram Weiss, Hans-Dieter Pohlenz, ...
BMCBI
2008
105views more  BMCBI 2008»
8 years 9 months ago
SIGMA2: A system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes
Background: High throughput microarray technologies have afforded the investigation of genomes, epigenomes, and transcriptomes at unprecedented resolution. However, software packa...
Raj Chari, Bradley P. Coe, Craig Wedseltoft, Marie...
BMCBI
2008
98views more  BMCBI 2008»
8 years 9 months ago
The strength of co-authorship in gene name disambiguation
Background: A biomedical entity mention in articles and other free texts is often ambiguous. For example, 13% of the gene names (aliases) might refer to more than one gene. The ta...
Richárd Farkas
BMCBI
2008
201views more  BMCBI 2008»
8 years 9 months ago
A copula method for modeling directional dependence of genes
Background: Genes interact with each other as basic building blocks of life, forming a complicated network. The relationship between groups of genes with different functions can b...
Jong-Min Kim, Yoon-Sung Jung, Engin A. Sungur, Kap...
BMCBI
2007
138views more  BMCBI 2007»
8 years 9 months ago
A full Bayesian hierarchical mixture model for the variance of gene differential expression
Background: In many laboratory-based high throughput microarray experiments, there are very few replicates of gene expression levels. Thus, estimates of gene variances are inaccur...
Samuel O. M. Manda, Rebecca E. Walls, Mark S. Gilt...
BMCBI
2008
187views more  BMCBI 2008»
8 years 9 months ago
PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes
Background: The conservation of gene order among prokaryotic genomes can provide valuable insight into gene function, protein interactions, or events by which genomes have evolved...
Christine Fong, Laurence Rohmer, Matthew Radey, Mi...
BMCBI
2008
113views more  BMCBI 2008»
8 years 9 months ago
SynBlast: Assisting the analysis of conserved synteny information
Motivation: In the last years more than 20 vertebrate genomes have been sequenced, and the rate at which genomic DNA information becomes available is rapidly accelerating. Gene du...
Jörg Lehmann, Peter F. Stadler, Sonja J. Proh...
BMCBI
2008
173views more  BMCBI 2008»
8 years 9 months ago
Gene Vector Analysis (Geneva): A unified method to detect differentially-regulated gene sets and similar microarray experiments
Background: Microarray experiments measure changes in the expression of thousands of genes. The resulting lists of genes with changes in expression are then searched for biologica...
Stephen W. Tanner, Pankaj Agarwal
BMCBI
2008
101views more  BMCBI 2008»
8 years 9 months ago
Reranking candidate gene models with cross-species comparison for improved gene prediction
Background: Most gene finders score candidate gene models with state-based methods, typically HMMs, by combining local properties (coding potential, splice donor and acceptor patt...
Qian Liu, Koby Crammer, Fernando C. N. Pereira, Da...
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