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BMCBI
2010
131views more  BMCBI 2010»
13 years 11 months ago
Prediction of epigenetically regulated genes in breast cancer cell lines
Background: Methylation of CpG islands within the DNA promoter regions is one mechanism that leads to aberrant gene expression in cancer. In particular, the abnormal methylation o...
Leandro A. Loss, Anguraj Sadanandam, Steffen Durin...
BMCBI
2010
118views more  BMCBI 2010»
13 years 11 months ago
svdPPCS: an effective singular value decomposition-based method for conserved and divergent co-expression gene module identifica
Background: Comparative analysis of gene expression profiling of multiple biological categories, such as different species of organisms or different kinds of tissue, promises to e...
Wensheng Zhang, Andrea Edwards, Wei Fan, Dongxiao ...
BMCBI
2010
208views more  BMCBI 2010»
13 years 11 months ago
Using machine learning to speed up manual image annotation: application to a 3D imaging protocol for measuring single cell gene
Background: Image analysis is an essential component in many biological experiments that study gene expression, cell cycle progression, and protein localization. A protocol for tr...
Zafer Aydin, John I. Murray, Robert H. Waterston, ...
BMCBI
2010
92views more  BMCBI 2010»
13 years 11 months ago
Integrating gene expression and GO classification for PCA by preclustering
Background: Gene expression data can be analyzed by summarizing groups of individual gene expression profiles based on GO annotation information. The mean expression profile per g...
Jorn R. de Haan, Ester Piek, René C. van Sc...
BMCBI
2010
120views more  BMCBI 2010»
13 years 11 months ago
Modeling expression quantitative trait loci in data combining ethnic populations
Background: Combining data from different ethnic populations in a study can increase efficacy of methods designed to identify expression quantitative trait loci (eQTL) compared to...
Ching-Lin Hsiao, Ie-Bin Lian, Ai-Ru Hsieh, Cathy S...
BMCBI
2010
97views more  BMCBI 2010»
13 years 11 months ago
Biomarker discovery in heterogeneous tissue samples -taking the in-silico deconfounding approach
Background: For heterogeneous tissues, such as blood, measurements of gene expression are confounded by relative proportions of cell types involved. Conclusions have to rely on es...
Dirk Repsilber, Sabine Kern, Anna Telaar, Gerhard ...
BIOINFORMATICS
2008
106views more  BIOINFORMATICS 2008»
13 years 11 months ago
Small RNA gene identification and mRNA target predictions in bacteria
Motivation: Bacterial small ribonucleic acids (sRNAs) that are not ribosomal and transfer or messenger RNAs were initially identified in the sixties whereas their molecular functi...
Christophe Pichon, Brice Felden
BMCBI
2010
165views more  BMCBI 2010»
13 years 11 months ago
Bayesian integrated modeling of expression data: a case study on RhoG
Background: DNA microarrays provide an efficient method for measuring activity of genes in parallel and even covering all the known transcripts of an organism on a single array. T...
Rashi Gupta, Dario Greco, Petri Auvinen, Elja Arja...
BMCBI
2010
147views more  BMCBI 2010»
13 years 11 months ago
Indirect two-sided relative ranking: a robust similarity measure for gene expression data
Background: There is a large amount of gene expression data that exists in the public domain. This data has been generated under a variety of experimental conditions. Unfortunatel...
Louis Licamele, Lise Getoor
BMCBI
2010
161views more  BMCBI 2010»
13 years 11 months ago
GeneMesh: a web-based microarray analysis tool for relating differentially expressed genes to MeSH terms
Background: An important objective of DNA microarray-based gene expression experimentation is determining interrelationships that exist between differentially expressed genes and ...
Saurin D. Jani, Gary L. Argraves, Jeremy L. Barth,...