Discriminative motif analysis of high-throughput dataset
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Robert Gentleman | Walter L. Ruzzo | Zizhen Yao | Kyle L. MacQuarrie | Abraham P. Fong | Stephen J. Tapscott | W. L. Ruzzo | R. Gentleman | Zizhen Yao | S. Tapscott | K. MacQuarrie
[1] J. van Helden,et al. RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets , 2011, Nucleic acids research.
[2] Martha L Bulyk,et al. Precise temporal control of the eye regulatory gene Pax6 via enhancer-binding site affinity. , 2010, Genes & development.
[3] Saurabh Sinha,et al. On counting position weight matrix matches in a sequence, with application to discriminative motif finding , 2006, ISMB.
[4] M. Berger,et al. Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors , 2009, Nature Protocols.
[5] Abraham P. Fong,et al. Genetic and epigenetic determinants of neurogenesis and myogenesis. , 2012, Developmental cell.
[6] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[7] H. Bussemaker,et al. Regulatory element detection using correlation with expression , 2001, Nature Genetics.
[8] Timothy L. Bailey,et al. Gene expression Advance Access publication May 4, 2011 DREME: motif discovery in transcription factor ChIP-seq data , 2011 .
[9] T. Bailey,et al. Inferring direct DNA binding from ChIP-seq , 2012, Nucleic acids research.
[10] Xiaoyu Chen,et al. RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors , 2007, ISMB/ECCB.
[11] W. L. Ruzzo,et al. Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming. , 2010, Developmental cell.
[12] Ole Winther,et al. JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update , 2007, Nucleic Acids Res..
[13] William Stafford Noble,et al. Improved similarity scores for comparing motifs , 2011, Bioinform..
[14] Jean YH Yang,et al. Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.
[15] Gary D. Stormo,et al. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences , 1999, Bioinform..
[16] D. S. Fields,et al. Specificity, free energy and information content in protein-DNA interactions. , 1998, Trends in biochemical sciences.
[17] Christopher D. Brown,et al. Receiver operating characteristics curves and related decision measures: A tutorial , 2006 .
[18] J. Stamatoyannopoulos,et al. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns , 2011, Nature Genetics.
[19] William Stafford Noble,et al. Assessing computational tools for the discovery of transcription factor binding sites , 2005, Nature Biotechnology.
[20] Michael Q. Zhang,et al. DNA motifs in human and mouse proximal promoters predict tissue-specific expression. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[21] Timothy L. Bailey,et al. Discriminative motif discovery in DNA and protein sequences using the DEME algorithm , 2007, BMC Bioinformatics.
[22] Stephan Sauer,et al. Cohesins Functionally Associate with CTCF on Mammalian Chromosome Arms , 2008, Cell.
[23] I. Davydov,et al. The role of NF-Y and IRF-2 in the regulation of human IL-4 gene expression. , 1994, Journal of immunology.
[24] Tomoki Chiba,et al. Interplay of transcription factors in T‐cell differentiation and function: the role of Runx , 2011, Immunology.
[25] Shane J. Neph,et al. An expansive human regulatory lexicon encoded in transcription factor footprints , 2012, Nature.
[26] Charles Elkan,et al. The Value of Prior Knowledge in Discovering Motifs with MEME , 1995, ISMB.
[27] Hirokazu Chiba,et al. PeakRegressor Identifies Composite Sequence Motifs Responsible for STAT1 Binding Sites and Their Potential rSNPs , 2010, PloS one.
[28] Martha L. Bulyk,et al. UniPROBE: an online database of protein binding microarray data on protein–DNA interactions , 2008, Nucleic Acids Res..