Article thumbnail
Location of Repository

Dinucleotide Weight Matrices for Predicting Transcription Factor Binding Sites: Generalizing the Position Weight Matrix

By Rahul Siddharthan
Topics: Research Article
Publisher: Public Library of Science
OAI identifier: oai:pubmedcentral.nih.gov:2842295
Provided by: PubMed Central

Suggested articles

Citations

  1. (2003). A biophysical approach to transcription factor binding site discovery.
  2. (2008). A feature-based approach to modeling protein-DNA interactions.
  3. (2006). A genomic code for nucleosome positioning.
  4. (2003). A non-parametric model for transcription factor binding sites.
  5. (1993). A role for the transcription factors
  6. (2008). A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system.
  7. (2007). A systems approach to measuring the binding energy landscapes of transcription factors.
  8. (1991). ACE2, an activator of yeast metallothionein expression which is homologous to SWI5. Molecular and Cellular
  9. (2002). Additivity in protein-DNA interactions: how good an approximation is it?
  10. (2006). An improved map of conserved regulatory sites for Saccharomyces cerevisiae.
  11. (1998). Biological Sequence Analysis Cambridge University Press. DWMs to Predict Binding
  12. (2005). Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster.
  13. (1990). Identification of consensus patterns in unaligned DNA sequences known to be functionally related.
  14. (1989). Identifying protein-binding sites from unaligned DNA fragments.
  15. (1992). Longrange correlations in nucleotide sequences.
  16. (2003). Modeling dependencies in Protein-DNA binding sites.
  17. (2004). Modeling within-motif dependence for transcription factor binding site predictions.
  18. (2007). Nearest-neighbor non-additivity versus long-range non-additivity in TATA-box structure and its implications for TBP-binding mechanism.
  19. (2005). Non-additivity in protein-DNA binding.
  20. (2001). Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay.
  21. (2002). Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors.
  22. (2008). PhyloGibbs-MP: module prediction and discriminative motif-finding by Gibbs sampling.
  23. (2005). PhyloGibbs: A Gibbs sampling motif finder that incorporates phylogeny.
  24. (2002). Probabilistic clustering of sequences: Inferring new bacterial regulons by comparative genomics.
  25. (2008). REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila.
  26. (1999). SCPD: a promoter database of the yeast Saccharomyces cerevisiae.
  27. (1987). Selection of DNA binding sites by regulatory proteins : Statistical-mechanical theory and application to operators and promoters.
  28. (2006). Stubb: a program for discovery and analysis of cis-regulatory modules.
  29. (2008). Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm.
  30. (2004). Transcriptional regulatory code of a eukaryotic genome.
  31. (2008). Use of an evolutionary model to provide evidence for a wide heterogeneity of required affinities between transcription factors and their binding sites in yeast. In: Pacific Symposium on Biocomputing,
  32. (2004). WebLogo: A Sequence Logo Generator.

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.