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RECOMB
2002
Springer
14 years 9 months ago
From promoter sequence to expression: a probabilistic framework
We present a probabilistic framework that models the process by which transcriptional binding explains the mRNA expression of different genes. Our joint probabilistic model unifie...
Eran Segal, Yoseph Barash, Itamar Simon, Nir Fried...
BMCBI
2010
112views more  BMCBI 2010»
13 years 9 months ago
Computational identification of rare codons of Escherichia coli based on codon pairs preference
Background: Codon bias is believed to play an important role in the control of gene expression. In Escherichia coli, some rare codons, which can limit the expression level of exog...
Xianming Wu, Songfeng Wu, Dong Li, Jiyang Zhang, L...
BMCBI
2010
167views more  BMCBI 2010»
13 years 9 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. ...
BMCBI
2004
117views more  BMCBI 2004»
13 years 8 months ago
CisOrtho: A program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting
Background: All known genomes code for a large number of transcription factors. It is important to develop methods that will reveal how these transcription factors act on a genome...
Henry R. Bigelow, Adam S. Wenick, Allan Wong, Oliv...
RECOMB
2006
Springer
14 years 9 months ago
Assessing Significance of Connectivity and Conservation in Protein Interaction Networks
Computational and comparative analysis of protein-protein interaction (PPI) networks enable understanding of the modular organization of the cell through identification of functio...
Mehmet Koyutürk, Ananth Grama, Wojciech Szpan...