High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints
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[1] Wyeth W. Wasserman,et al. JASPAR: an open-access database for eukaryotic transcription factor binding profiles , 2004, Nucleic Acids Res..
[2] J. N. Mark Glover,et al. Crystal structure of the heterodimeric bZIP transcription factor c-Fos–c-Jun bound to DNA , 1995, Nature.
[3] Graziano Pesole,et al. An algorithm for finding signals of unknown length in DNA sequences , 2001, ISMB.
[4] Alexander J. Hartemink,et al. Informative priors based on transcription factor structural class improve de novo motif discovery , 2006, ISMB.
[5] Michael Q. Zhang,et al. A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information , 2011, Nucleic acids research.
[6] Sayaka Sekiya,et al. Direct conversion of mouse fibroblasts to hepatocyte-like cells by defined factors , 2011, Nature.
[7] P. Park. ChIP–seq: advantages and challenges of a maturing technology , 2009, Nature Reviews Genetics.
[8] D. Rubin,et al. Maximum likelihood from incomplete data via the EM - algorithm plus discussions on the paper , 1977 .
[9] R. Young,et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state , 2010, Proceedings of the National Academy of Sciences.
[10] Nir Friedman,et al. A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites , 2001, WABI.
[11] Cole Trapnell,et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.
[12] A. Visel,et al. ChIP-seq accurately predicts tissue-specific activity of enhancers , 2009, Nature.
[13] Raja Jothi,et al. Genome-wide identification of in vivo protein–DNA binding sites from ChIP-Seq data , 2008, Nucleic acids research.
[14] Clifford A. Meyer,et al. Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.
[15] D. Tenen,et al. Functional characterization of the promoter for the gene encoding human eosinophil peroxidase. , 1994, The Journal of biological chemistry.
[16] Alexander E. Kel,et al. TRANSFAC®: transcriptional regulation, from patterns to profiles , 2003, Nucleic Acids Res..
[17] C. Wolberger,et al. Multiprotein-DNA complexes in transcriptional regulation. , 1999, Annual review of biophysics and biomolecular structure.
[18] A. Philippakis,et al. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities , 2006, Nature Biotechnology.
[19] Alfred V. Aho,et al. Efficient string matching , 1975, Commun. ACM.
[20] Xi Chen,et al. Reciprocal Transcriptional Regulation of Pou5f1 and Sox2 via the Oct4/Sox2 Complex in Embryonic Stem Cells , 2005, Molecular and Cellular Biology.
[21] Emmanuel Barillot,et al. De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis , 2010, Nucleic acids research.
[22] Charles Elkan,et al. Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer , 1994, ISMB.
[23] Markella Ponticos,et al. Regulation of Collagen Type I in Vascular Smooth Muscle Cells by Competition between Nkx2.5 and δEF1/ZEB1 , 2004, Molecular and Cellular Biology.
[24] Hiroyoshi Ariga,et al. Cross-family interaction between the bHLHZip USF and bZip Fra1 proteins results in down-regulation of AP1 activity , 1997, Oncogene.
[25] R. Eisenman,et al. Max: a helix-loop-helix zipper protein that forms a sequence-specific DNA-binding complex with Myc. , 1991, Science.
[26] Martin C. Frith,et al. Inferring transcription factor complexes from ChIP-seq data , 2011, Nucleic acids research.
[27] P. Farnham. Insights from genomic profiling of transcription factors , 2009, Nature Reviews Genetics.
[28] Ernest Fraenkel,et al. Practical Strategies for Discovering Regulatory DNA Sequence Motifs , 2006, PLoS Comput. Biol..
[29] Jeannie T. Lee,et al. Identification of a Ctcf cofactor, Yy1, for the X chromosome binary switch. , 2007, Molecular cell.
[30] Anil K. Jain,et al. Unsupervised Learning of Finite Mixture Models , 2002, IEEE Trans. Pattern Anal. Mach. Intell..
[31] Zhaohui S. Qin,et al. On the detection and refinement of transcription factor binding sites using ChIP-Seq data , 2010, Nucleic acids research.
[32] William Stafford Noble,et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.
[33] Yuriy L Orlov,et al. The nuclear receptor Nr5a2 can replace Oct4 in the reprogramming of murine somatic cells to pluripotent cells. , 2010, Cell stem cell.
[34] B. Pugh,et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution , 2011, Cell.
[35] Jan Komorowski,et al. Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing , 2009, Nucleic acids research.
[36] Robert Grossman,et al. PeakRanger: A cloud-enabled peak caller for ChIP-seq data , 2011, BMC Bioinformatics.
[37] Kenneth M. Murphy,et al. Batf controls the global regulators of class switch recombination in both B and T cells , 2011, Nature Immunology.
[38] Cheng Cheng,et al. ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-Seq data , 2010, Theoretical Biology and Medical Modelling.
[39] Vsevolod J. Makeev,et al. Deep and wide digging for binding motifs in ChIP-Seq data , 2010, Bioinform..
[40] Panayiotis V. Benos,et al. DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies , 2007, PLoS Comput. Biol..
[41] Ernest Fraenkel,et al. High-resolution computational models of genome binding events , 2006, Nature Biotechnology.
[42] G. Church,et al. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. , 2000, Journal of molecular biology.
[43] N. D. Clarke,et al. Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells , 2008, Cell.
[44] A. Visel,et al. Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. , 2010, Genome research.
[45] E. Liu,et al. Evolution of the mammalian transcription factor binding repertoire via transposable elements. , 2008, Genome research.
[46] Y. Benjamini,et al. Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .
[47] Barbara Hoffman,et al. The proto-oncogene c-myc in hematopoietic development and leukemogenesis , 2002, Oncogene.
[48] G. Bourque,et al. Transposable elements have rewired the core regulatory network of human embryonic stem cells , 2010, Nature Genetics.
[49] Jun S. Liu,et al. An algorithm for finding protein–DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments , 2002, Nature Biotechnology.
[50] S. Batzoglou,et al. Genome-Wide Analysis of Transcription Factor Binding Sites Based on ChIP-Seq Data , 2008, Nature Methods.
[51] Yuchun Guo,et al. Discovering homotypic binding events at high spatial resolution , 2010, Bioinform..