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» Discriminative motif discovery in DNA and protein sequences ...
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BMCBI
2010
95views more  BMCBI 2010»
13 years 7 months ago
An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data
Background: ChIP-Seq, which combines chromatin immunoprecipitation (ChIP) with high-throughput massively parallel sequencing, is increasingly being used for identification of prot...
Congmao Wang, Jie Xu, Dasheng Zhang, Zoe A. Wilson...
GCB
2000
Springer
99views Biometrics» more  GCB 2000»
13 years 11 months ago
Structure Motif Discovery and Mining the PDB
We describe an algorithm for the automatic discovery of recurring patterns in protein structures. The patterns consist of individual residues having a defined order along the prote...
Inge Jonassen, Ingvar Eidhammer, Darrell Conklin, ...
IMSCCS
2006
IEEE
14 years 1 months ago
Combining Comparative Genomics with de novo Motif Discovery to Identify Human Transcription Factor DNA-Binding Motifs
Background: As more and more genomes are sequenced, comparative genomics approaches provide a methodology for identifying conserved regulatory elements that may be involved in gen...
Linyong Mao, W. Jim Zheng
BMCBI
2006
103views more  BMCBI 2006»
13 years 7 months ago
Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequili
Background: The discovery of cis-regulatory motifs still remains a challenging task even though the number of sequenced genomes is constantly growing. Computational analyses using...
Kenneth W. Berendzen, Kurt Stüber, Klaus Hart...
RECOMB
2007
Springer
14 years 7 months ago
A Feature-Based Approach to Modeling Protein-DNA Interactions
Transcription factor (TF) binding to its DNA target site is a fundamental regulatory interaction. The most common model used to represent TF binding specificities is a position spe...
Eilon Sharon, Eran Segal