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BMCBI
2005
148views more  BMCBI 2005»
13 years 7 months ago
NemaFootPrinter: a web based software for the identification of conserved non-coding genome sequence regions between C. elegans
Background: NemaFootPrinter (Nematode Transcription Factor Scan Through Philogenetic Footprinting) is a web-based software for interactive identification of conserved, non-exonic ...
Davide Rambaldi, Alessandro Guffanti, Paolo Morand...
BMCBI
2006
137views more  BMCBI 2006»
13 years 7 months ago
Bounded search for de novo identification of degenerate cis-regulatory elements
Background: The identification of statistically overrepresented sequences in the upstream regions of coregulated genes should theoretically permit the identification of potential ...
Jonathan M. Carlson, Arijit Chakravarty, Radhika S...
BIBE
2007
IEEE
129views Bioinformatics» more  BIBE 2007»
13 years 11 months ago
Statistial Analysis of nucleosome occupancy and histone modification data
Abstract-- In eukaryotic cells, genomic DNAs wrap around beadlike molecules, called nucleosomes, so as to pack more compactly in the nucleus of the cell. The nucleosome is made up ...
Guo-Cheng Yuan, Jun S. Liu
BMCBI
2008
108views more  BMCBI 2008»
13 years 7 months ago
Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks
Background: High throughput signature sequencing holds many promises, one of which is the ready identification of in vivo transcription factor binding sites, histone modifications...
David A. Nix, Samir J. Courdy, Kenneth M. Boucher
RECOMB
2008
Springer
14 years 7 months ago
BayCis: A Bayesian Hierarchical HMM for Cis-Regulatory Module Decoding in Metazoan Genomes
The transcriptional regulatory sequences in metazoan genomes often consist of multiple cis-regulatory modules (CRMs). Each CRM contains locally enriched occurrences of binding site...
Tien-ho Lin, Pradipta Ray, Geir Kjetil Sandve, Sel...