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WABI
2001
Springer
162views Bioinformatics» more  WABI 2001»
13 years 9 months ago
A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites
A central issue in molecular biology is understanding the regulatory mechanisms that control gene expression. The recent flood of genomic and postgenomic data opens the way for co...
Yoseph Barash, Gill Bejerano, Nir Friedman
CSB
2005
IEEE
125views Bioinformatics» more  CSB 2005»
13 years 11 months ago
Discriminative Discovery of Transcription Factor Binding Sites from Location Data
Motivation: The availability of genome-wide location analyses based on chromatin immunoprecipitation (ChIP) data gives a new insight for in silico analysis of transcriptional regu...
Yuji Kawada, Yasubumi Sakakibara
BMCBI
2005
169views more  BMCBI 2005»
13 years 5 months ago
MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes
Background: Cis-regulatory modules are combinations of regulatory elements occurring in close proximity to each other that control the spatial and temporal expression of genes. Th...
Voichita D. Marinescu, Isaac S. Kohane, Alberto Ri...
BMCBI
2010
167views more  BMCBI 2010»
13 years 5 months ago
Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies
Background: Knowledge of transcription factor-DNA binding patterns is crucial for understanding gene transcription. Numerous DNA-binding proteins are annotated as transcription fa...
Denitsa Alamanova, Philip Stegmaier, Alexander E. ...
RECOMB
2005
Springer
14 years 5 months ago
Predicting Transcription Factor Binding Sites Using Structural Knowledge
Abstract. Current approaches for identification and detection of transcription factor binding sites rely on an extensive set of known target genes. Here we describe a novel structu...
Tommy Kaplan, Nir Friedman, Hanah Margalit