Motif-based analysis of large nucleotide data sets using MEME-ChIP
暂无分享,去创建一个
[1] Jie Zhang,et al. Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data , 2013, PLoS Comput. Biol..
[2] Yan Li,et al. A high-resolution map of three-dimensional chromatin interactome in human cells , 2013, Nature.
[3] Brendan J. Frey,et al. A compendium of RNA-binding motifs for decoding gene regulation , 2013, Nature.
[4] Graziano Pesole,et al. PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments , 2013, Nucleic Acids Res..
[5] Shyam Prabhakar,et al. TherMos: Estimating protein–DNA binding energies from in vivo binding profiles , 2013, Nucleic acids research.
[6] Juan M. Vaquerizas,et al. DNA-Binding Specificities of Human Transcription Factors , 2013, Cell.
[7] Yu-Cheng T. Yang,et al. Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae , 2013, Genome Biology.
[8] Data production leads,et al. An integrated encyclopedia of DNA elements in the human genome , 2012 .
[9] Marc D. Perry,et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia , 2012, Genome research.
[10] J. Helden,et al. A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs , 2012, Nature Protocols.
[11] Johannes Söding,et al. The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences , 2012, Nucleic Acids Res..
[12] T. Bailey,et al. Inferring direct DNA binding from ChIP-seq , 2012, Nucleic acids research.
[13] Martin Renqiang Min,et al. An integrated encyclopedia of DNA elements in the human genome , 2012 .
[14] B. Pugh,et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution , 2011, Cell.
[15] Uwe Ohler,et al. PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data , 2011, Genome Biology.
[16] M. Zavolan,et al. A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins , 2011, Nature Methods.
[17] R. Darnell,et al. Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data , 2011, Nature Biotechnology.
[18] Martin C. Frith,et al. Inferring transcription factor complexes from ChIP-seq data , 2011, Nucleic acids research.
[19] Timothy L. Bailey,et al. Gene expression Advance Access publication May 4, 2011 DREME: motif discovery in transcription factor ChIP-seq data , 2011 .
[20] Philip Machanick,et al. MEME-ChIP: motif analysis of large DNA datasets , 2011, Bioinform..
[21] Yongchao Liu,et al. CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments , 2010, Bioinform..
[22] Vsevolod J. Makeev,et al. Deep and wide digging for binding motifs in ChIP-Seq data , 2010, Bioinform..
[23] A. Nekrutenko,et al. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.
[24] Timothy L Bailey,et al. A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells. , 2010, Genome research.
[25] J. Ule,et al. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution , 2010, Nature Structural &Molecular Biology.
[26] Scott B. Dewell,et al. Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP , 2010, Cell.
[27] P. Park. ChIP–seq: advantages and challenges of a maturing technology , 2009, Nature Reviews Genetics.
[28] Victor X. Jin,et al. W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data , 2009, Bioinform..
[29] M. Kiebler,et al. Faculty Opinions recommendation of Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. , 2009 .
[30] A. Sharov,et al. Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder , 2009, DNA research : an international journal for rapid publication of reports on genes and genomes.
[31] Raymond K. Auerbach,et al. Mapping accessible chromatin regions using Sono-Seq , 2009, Proceedings of the National Academy of Sciences.
[32] A. Mele,et al. Ago HITS-CLIP decodes miRNA-mRNA interaction maps , 2009, Nature.
[33] Martha L. Bulyk,et al. UniPROBE: an online database of protein binding microarray data on protein–DNA interactions , 2008, Nucleic Acids Res..
[34] Matthew Mort,et al. Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. , 2009, Genome research.
[35] Tyson A. Clark,et al. HITS-CLIP yields genome-wide insights into brain alternative RNA processing , 2008, Nature.
[36] Daniel Herschlag,et al. Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System , 2008, PLoS biology.
[37] Clifford A. Meyer,et al. Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.
[38] B. Williams,et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.
[39] Claude Jacq,et al. Yeast Mitochondrial Biogenesis: A Role for the PUF RNA-Binding Protein Puf3p in mRNA Localization , 2008, PloS one.
[40] V. Iyer,et al. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. , 2007, Genome research.
[41] William Stafford Noble,et al. Quantifying similarity between motifs , 2007, Genome Biology.
[42] M. Daly,et al. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). , 2005, Genome research.
[43] P. Angel,et al. AP-1 subunits: quarrel and harmony among siblings , 2004, Journal of Cell Science.
[44] P. Brown,et al. Extensive Association of Functionally and Cytotopically Related mRNAs with Puf Family RNA-Binding Proteins in Yeast , 2004, PLoS biology.
[45] Wyeth W. Wasserman,et al. JASPAR: an open-access database for eukaryotic transcription factor binding profiles , 2004, Nucleic Acids Res..
[46] Tom H. Pringle,et al. The human genome browser at UCSC. , 2002, Genome research.
[47] S. Henikoff,et al. Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase , 2000, Nature Biotechnology.
[48] T. Rabbitts,et al. The LIM‐only protein Lmo2 is a bridging molecule assembling an erythroid, DNA‐binding complex which includes the TAL1, E47, GATA‐1 and Ldb1/NLI proteins , 1997, The EMBO journal.
[49] Charles Elkan,et al. Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer , 1994, ISMB.