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» Gene Expression Data Management: A Case Study
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BMCBI
2010
109views more  BMCBI 2010»
14 years 9 months ago
Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression
Background: In the last decade, biochemical studies have revealed that epigenetic modifications including histone modifications, histone variants and DNA methylation form a comple...
Xiaojiang Xu, Stephen Hoang, Marty W. Mayo, Stefan...
BMCBI
2010
183views more  BMCBI 2010»
14 years 7 months ago
The complexity of gene expression dynamics revealed by permutation entropy
Background: High complexity is considered a hallmark of living systems. Here we investigate the complexity of temporal gene expression patterns using the concept of Permutation En...
Xiaoliang Sun, Yong Zou, Victoria J. Nikiforova, J...
BMCBI
2007
130views more  BMCBI 2007»
14 years 9 months ago
A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression da
Background: Proteins are the primary regulatory agents of transcription even though mRNA expression data alone, from systems like DNA microarrays, are widely used. In addition, th...
Reuben Thomas, Carlos J. Paredes, Sanjay Mehrotra,...
BMCBI
2006
153views more  BMCBI 2006»
14 years 9 months ago
Discovery of time-delayed gene regulatory networks based on temporal gene expression profiling
Background: It is one of the ultimate goals for modern biological research to fully elucidate the intricate interplays and the regulations of the molecular determinants that prope...
Xia Li, Shaoqi Rao, Wei Jiang, Chuanxing Li, Yun X...
RECOMB
2002
Springer
15 years 10 months ago
Discovering local structure in gene expression data: the order-preserving submatrix problem
This paper concerns the discovery of patterns in gene expression matrices, in which each element gives the expression level of a given gene in a given experiment. Most existing me...
Amir Ben-Dor, Benny Chor, Richard M. Karp, Zohar Y...