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» GPX: Interactive Mining of Gene Expression Data
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BMCBI
2010
100views more  BMCBI 2010»
13 years 7 months ago
Trimming of mammalian transcriptional networks using network component analysis
Background: Network Component Analysis (NCA) has been used to deduce the activities of transcription factors (TFs) from gene expression data and the TF-gene binding relationship. ...
Linh M. Tran, Daniel R. Hyduke, James C. Liao
BMCBI
2008
162views more  BMCBI 2008»
13 years 7 months ago
Background correction using dinucleotide affinities improves the performance of GCRMA
Background: High-density short oligonucleotide microarrays are a primary research tool for assessing global gene expression. Background noise on microarrays comprises a significan...
Raad Z. Gharaibeh, Anthony Fodor, Cynthia Gibas
BIBM
2008
IEEE
125views Bioinformatics» more  BIBM 2008»
13 years 7 months ago
Systems Biology via Redescription and Ontologies (III): Protein Classification Using Malaria Parasite's Temporal Transcriptomic
This paper addresses the protein classification problem, and explores how its accuracy can be improved by using information from time-course gene expression data. The methods are ...
Antonina Mitrofanova, Samantha Kleinberg, Jane Car...
BMCBI
2004
149views more  BMCBI 2004»
13 years 7 months ago
MiCoViTo: a tool for gene-centric comparison and visualization of yeast transcriptome states
Background: Information obtained by DNA microarray technology gives a rough snapshot of the transcriptome state, i.e., the expression level of all the genes expressed in a cell po...
Gaëlle Lelandais, Philippe Marc, Pierre Vince...
ALMOB
2007
111views more  ALMOB 2007»
13 years 7 months ago
Transcriptional regulatory network discovery via multiple method integration: application to e. coli K12
Motivation: Transcriptional regulatory network (TRN) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack ...
Jingjun Sun, Kagan Tuncay, Alaa Abi Haidar, Lisa E...