Impact of cytosine methylation on DNA binding specificities of human transcription factors
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Title
Impact of cytosine methylation on DNA binding specificities of human transcription factors
Authors
Keywords
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Journal
SCIENCE
Volume 356, Issue 6337, Pages eaaj2239
Publisher
American Association for the Advancement of Science (AAAS)
Online
2017-05-05
DOI
10.1126/science.aaj2239
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Note: Only part of the references are listed.- Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape
- (2016) Ronan C. O’Malley et al. CELL
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- (2016) Syed Khund-Sayeed et al. Integrative Biology
- deepTools2: a next generation web server for deep-sequencing data analysis
- (2016) Fidel Ramírez et al. NUCLEIC ACIDS RESEARCH
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- (2016) Huaiyu Mi et al. NUCLEIC ACIDS RESEARCH
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- (2015) Yiping Wang et al. MOLECULAR CELL
- Function and information content of DNA methylation
- (2015) Dirk Schübeler NATURE
- Competition between DNA methylation and transcription factors determines binding of NRF1
- (2015) Silvia Domcke et al. NATURE
- DNA-dependent formation of transcription factor pairs alters their binding specificity
- (2015) Arttu Jolma et al. NATURE
- The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis
- (2015) Mark M Pomerantz et al. NATURE GENETICS
- CTCF/cohesin-binding sites are frequently mutated in cancer
- (2015) Riku Katainen et al. NATURE GENETICS
- Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates
- (2015) Hao Wu et al. NUCLEIC ACIDS RESEARCH
- Suboptimization of developmental enhancers
- (2015) E. K. Farley et al. SCIENCE
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- (2015) Kazuhiro R Nitta et al. eLife
- Unusual Characteristics of the DNA Binding Domain of Epigenetic Regulatory Protein MeCP2 Determine Its Binding Specificity
- (2014) Sergei Khrapunov et al. BIOCHEMISTRY
- Spec-seq: determining protein-DNA-binding specificity by sequencing
- (2014) G. D. Stormo et al. Briefings in Functional Genomics
- Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes
- (2014) Jason T. Huff et al. CELL
- Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity
- (2014) Matthew T. Weirauch et al. CELL
- Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence
- (2014) Hideharu Hashimoto et al. GENES & DEVELOPMENT
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- (2014) Kyle Kai-How Farh et al. NATURE
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- (2014) Qilai Huang et al. NATURE GENETICS
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- (2014) Yaron Orenstein et al. NUCLEIC ACIDS RESEARCH
- UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions
- (2014) Maxwell A. Hume et al. NUCLEIC ACIDS RESEARCH
- Structural basis for Klf4 recognition of methylated DNA
- (2014) Y. Liu et al. NUCLEIC ACIDS RESEARCH
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- (2014) J. Vierstra et al. SCIENCE
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- (2014) Raghunath Chatterjee et al. Epigenetics & Chromatin
- One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering
- (2013) Haoyi Wang et al. CELL
- Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites
- (2013) Jian Yan et al. CELL
- DNA-Binding Specificities of Human Transcription Factors
- (2013) Arttu Jolma et al. CELL
- Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives
- (2013) Cornelia G. Spruijt et al. CELL
- Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells
- (2013) T. J. Looney et al. GENOME RESEARCH
- CG methylated microarrays identify a novel methylated sequence bound by the CEBPB ATF4 heterodimer that is active in vivo
- (2013) I. K. Mann et al. GENOME RESEARCH
- The PR/SET Domain Zinc Finger Protein Prdm4 Regulates Gene Expression in Embryonic Stem Cells but Plays a Nonessential Role in the Developing Mouse Embryo
- (2013) D. Bogani et al. MOLECULAR AND CELLULAR BIOLOGY
- Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues
- (2013) Gary C Hon et al. NATURE GENETICS
- Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
- (2013) Jason D Buenrostro et al. NATURE METHODS
- DNA methylation presents distinct binding sites for human transcription factors
- (2013) Shaohui Hu et al. eLife
- Towards automated crystallographic structure refinement withphenix.refine
- (2012) Pavel V. Afonine et al. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
- Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome
- (2012) Miao Yu et al. CELL
- A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells
- (2012) Jose M. Polo et al. CELL
- Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules
- (2012) T. K. Kelly et al. GENOME RESEARCH
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- Overview of theCCP4 suite and current developments
- (2011) Martyn D. Winn et al. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
- Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
- (2011) Felix Krueger et al. BIOINFORMATICS
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- (2011) Ho Sung Rhee et al. CELL
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- (2011) Biswajyoti Sahu et al. EMBO JOURNAL
- In Embryonic Stem Cells, ZFP57/KAP1 Recognize a Methylated Hexanucleotide to Affect Chromatin and DNA Methylation of Imprinting Control Regions
- (2011) Simon Quenneville et al. MOLECULAR CELL
- DNA-binding factors shape the mouse methylome at distal regulatory regions
- (2011) Michael B. Stadler et al. NATURE
- A computational pipeline for comparative ChIP-seq analyses
- (2011) Anaïs F Bardet et al. Nature Protocols
- Structural Basis for Sequence Specific DNA Binding and Protein Dimerization of HOXA13
- (2011) Yonghong Zhang et al. PLoS One
- XDS
- (2010) Wolfgang Kabsch ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
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- PHENIX: a comprehensive Python-based system for macromolecular structure solution
- (2010) Paul D. Adams et al. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
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- (2010) Gong-Hong Wei et al. EMBO JOURNAL
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- High-throughput production of human proteins for crystallization: The SGC experience
- (2010) Pavel Savitsky et al. JOURNAL OF STRUCTURAL BIOLOGY
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- (2010) V. Rishi et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- MOODS: fast search for position weight matrix matches in DNA sequences
- (2009) J. Korhonen et al. BIOINFORMATICS
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- Natural similarity measures between position frequency matrices with an application to clustering
- (2008) Utz J. Pape et al. BIOINFORMATICS
- Model-based Analysis of ChIP-Seq (MACS)
- (2008) Yong Zhang et al. GENOME BIOLOGY
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