Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data

[1] Farnham PJ(2009)Insights from genomic profiling of transcription factors Nat Rev Genet 10 605-616

[2] Kolchanov NA(2011)A user's guide to the encyclopedia of DNA elements (ENCODE) PLoS Biol 9 e1001046-274

[3] Merkulova TI(2007)Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes Brief Bioinform 8 266-23

[4] Ignatieva EV(2010)Efficient double fragmentation ChIP-Seq provides nucleotide resolution protein-DNA binding profiles PLoS One 5 e15092-1464

[5] Ananko EA(2000)DNA binding sites: representation and discovery Bioinformatics 16 16-D110

[6] Oshchepkov DY(2006)Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques Genome Res 16 1455-D110

[7] Levitsky VG(2006)TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes Nucl Acids Res 34 D108-D202

[8] Vasiliev GV(2010)JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles Nucleic Acids Res 38 D105-2301

[9] Klimova NV(2013)HOCOMOCO: a comprehensive collection of human transcription factor binding sites models Nucl Acids Res 41 D195-15

[10] Merkulov VM(2005)Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites Nucl Acids Res 33 2290-941

[1] Farnham PJ(2009)Insights from genomic profiling of transcription factors Nat Rev Genet 10 605-616

[2] Kolchanov NA(2011)A user's guide to the encyclopedia of DNA elements (ENCODE) PLoS Biol 9 e1001046-274

[3] Merkulova TI(2007)Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes Brief Bioinform 8 266-23

[4] Ignatieva EV(2010)Efficient double fragmentation ChIP-Seq provides nucleotide resolution protein-DNA binding profiles PLoS One 5 e15092-1464

[5] Ananko EA(2000)DNA binding sites: representation and discovery Bioinformatics 16 16-D110

[6] Oshchepkov DY(2006)Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques Genome Res 16 1455-D110

[7] Levitsky VG(2006)TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes Nucl Acids Res 34 D108-D202

[8] Vasiliev GV(2010)JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles Nucleic Acids Res 38 D105-2301

[9] Klimova NV(2013)HOCOMOCO: a comprehensive collection of human transcription factor binding sites models Nucl Acids Res 41 D195-15

[10] Merkulov VM(2005)Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites Nucl Acids Res 33 2290-941