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Better estimation of protein-DNA interaction parameters improve prediction of functional sites

By Vijayalakshmi H Nagaraj, Ruadhan A O'Flanagan and Anirvan M Sengupta
Topics: Methodology Article
Publisher: BioMed Central
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Provided by: PubMed Central

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  1. (2006). A genomic code for nucleosome positioning. Nature
  2. (2005). AM: Non-additivity in protein-DNA binding. Bioinformatics
  3. (2002). An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol
  4. (2004). Analyzing protein-DNA recognition mechanisms. Structure (Camb)
  5. (2007). Callan CG Jr: Precise physical models of protein-DNA interaction from high-throughput data. Proc Natl Acad Sci USA
  6. (1984). Computer methods to locate signals in nucleic acid sequences.
  7. (2000). Developmental biology.
  8. (2000). eds.: DNA-protein interactions: a practical approach.
  9. (2002). Egan SM: Ni+-affinity purification of untagged cAMP receptor protein. Biotechniques
  10. (2004). Evolutionary comparisons suggest many novel cAMP response protein binding sites in Escherichia coli.
  11. (2000). F: TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res
  12. (2004). Fraenkel E, Young RA: Transcriptional regulatory code of a eukaryotic genome. Nature
  13. (1998). free energy and information content in protein-DNA interactions. Trends Biochem Sci
  14. (1995). GD: MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices.
  15. (1996). Gene transcription: DNA binding proteins.
  16. (2000). Genome-wide location and function of DNA binding proteins. Science
  17. (2001). Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature
  18. (1998). GM: A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome.
  19. (2004). GM: Advanced sequencing technologies: methods and goals. Nat Rev Genet
  20. (2001). GM: Exploring the DNAbinding specificities of zinc fingers with DNA microarrays.
  21. (1999). GM: Quantifying DNAprotein interactions by double-stranded DNA arrays. Nat Biotechnol
  22. (1989). Hartzell GW 3rd: Identifying protein-binding sites from unaligned DNA fragments.
  23. (2002). High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. Nat Biotechnol
  24. (1995). Kinzler KW: Serial analysis of gene expression. Science
  25. (2002). Mining genome databases to identify and understand new gene regulatory systems.
  26. (1996). Organization and function of transcription regulatory elements.
  27. (1987). Practical methods of optimization. 2nd edition.
  28. (1986). Quantitative analysis of the relationship between nucleotide sequence and functional activity. Nucleic Acids Res
  29. (2002). RA: Transcriptional regulatory networks in Saccharomyces cerevisiae. Science
  30. (2001). RC: Estimating the support of a high-dimensional distribution. Neural Comput
  31. (1999). RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli. Nucleic Acids Res
  32. (2001). RH: Site-specific incorporation of fluorescent probes into protein: hexahistidine-tagmediated fluorescent labeling with (Ni(2+):nitrilotriacetic Acid (n)-fluorochrome conjugates.
  33. (2006). Sengupta AM: Quantitative modeling and data analysis of SELEX experiments. Phys Biol
  34. (2003). Shraiman BI: A biophysical approach to transcription factor binding site discovery. Genome Res
  35. Siggia E: Stubb: a program for discovery and analysis of cis-regulatory modules.
  36. (2005). SJ: Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome. Proc Natl Acad Sci USA
  37. (2002). Specificity and robustness in transcription control networks.
  38. (2005). Stormo GD: Combining SELEX with quantitative assays to rapidly obtain accurate models of protein-DNA interactions.
  39. (1990). Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science
  40. (2000). Transcription regulation in prokaryotes. N e w York:
  41. (1987). von Hippel PH: Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters.
  42. (2000). WW: Discovery and modeling of transcriptional regulatory regions. Curr Opin Biotechnol
  43. (1999). Zhang MQ: SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics

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