Transient and Permanent Reconfiguration of Chromatin and Transcription Factor Occupancy Drive Reprogramming.

[1]  Mirana Ramialison,et al.  Cell Type of Origin Dictates the Route to Pluripotency. , 2017, Cell reports.

[2]  D. Schübeler,et al.  Impact of cytosine methylation on DNA binding specificities of human transcription factors , 2017, Science.

[3]  K. Hall Faculty Opinions recommendation of Chromosomes. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation. , 2017 .

[4]  J. Ernst,et al.  Cooperative Binding of Transcription Factors Orchestrates Reprogramming , 2017, Cell.

[5]  J. Polo,et al.  An improved reprogrammable mouse model harbouring the reverse tetracycline-controlled transcriptional transactivator 3. , 2016, Stem cell research.

[6]  Hong Wang,et al.  Hierarchical Oct4 Binding in Concert with Primed Epigenetic Rearrangements during Somatic Cell Reprogramming. , 2016, Cell reports.

[7]  David J. Arenillas,et al.  JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles , 2015, Nucleic Acids Res..

[8]  Jeannie T. Lee,et al.  Chromosomes. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation. , 2015, Science.

[9]  G. Pan,et al.  The oncogene c-Jun impedes somatic cell reprogramming , 2015, Nature Cell Biology.

[10]  M. Pellegrini,et al.  Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming , 2015, Cell.

[11]  Gavin Sherlock,et al.  Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions , 2015, bioRxiv.

[12]  Steven L Salzberg,et al.  HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.

[13]  Robert J. Schmitz,et al.  MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing , 2015, Nature Protocols.

[14]  Edwin Cuppen,et al.  Sambamba: fast processing of NGS alignment formats , 2015, Bioinform..

[15]  William Ritchie,et al.  Genome-wide characterization of the routes to pluripotency , 2014, Nature.

[16]  David L. A. Wood,et al.  An epigenomic roadmap to induced pluripotency reveals DNA methylation as a reprogramming modulator , 2014, Nature Communications.

[17]  J. Polo,et al.  Cell Surface Marker Mediated Purification of iPS Cell Intermediates from a Reprogrammable Mouse Model , 2014, Journal of visualized experiments : JoVE.

[18]  Fidel Ramírez,et al.  deepTools: a flexible platform for exploring deep-sequencing data , 2014, Nucleic Acids Res..

[19]  Brian Bushnell,et al.  BBMap: A Fast, Accurate, Splice-Aware Aligner , 2014 .

[20]  Charity W. Law,et al.  voom: precision weights unlock linear model analysis tools for RNA-seq read counts , 2014, Genome Biology.

[21]  Howard Y. Chang,et al.  Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position , 2013, Nature Methods.

[22]  S. Sinha,et al.  ΔNp63 regulates select routes of reprogramming via multiple mechanisms , 2013, Cell Death and Differentiation.

[23]  Robert Gentleman,et al.  Software for Computing and Annotating Genomic Ranges , 2013, PLoS Comput. Biol..

[24]  Bernadett Papp,et al.  Stage-specific regulation of reprogramming to induced pluripotent stem cells by Wnt signaling and T cell factor proteins. , 2013, Cell reports.

[25]  S. Linnarsson,et al.  High resolution analysis with novel cell-surface markers identifies routes to iPS cells , 2013, Nature.

[26]  S. Ramaswamy,et al.  A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells , 2012, Cell.

[27]  Greg Donahue,et al.  Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome , 2012, Cell.

[28]  Data production leads,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[29]  Yong Zhang,et al.  Identifying ChIP-seq enrichment using MACS , 2012, Nature Protocols.

[30]  T. Bailey,et al.  Inferring direct DNA binding from ChIP-seq , 2012, Nucleic acids research.

[31]  Martin Renqiang Min,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[32]  Zachary D. Smith,et al.  Reprogramming factor expression initiates widespread targeted chromatin remodeling. , 2011, Cell stem cell.

[33]  N. D. Clarke,et al.  A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity , 2010, Nature.

[34]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[35]  J. Rossant,et al.  Global Chromatin Architecture Reflects Pluripotency and Lineage Commitment in the Early Mouse Embryo , 2010, PloS one.

[36]  Colin N. Dewey,et al.  RNA-Seq gene expression estimation with read mapping uncertainty , 2009, Bioinform..

[37]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[38]  Pao-Yang Chen,et al.  BS Seeker: precise mapping for bisulfite sequencing , 2010, BMC Bioinformatics.

[39]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[40]  Daniel J. Hoeppner,et al.  Global transcription in pluripotent embryonic stem cells. , 2008, Cell stem cell.

[41]  T. Mikkelsen,et al.  Genome-wide maps of chromatin state in pluripotent and lineage-committed cells , 2007, Nature.

[42]  Lokesh Kumar,et al.  Mfuzz: A software package for soft clustering of microarray data , 2007, Bioinformation.

[43]  S. Yamanaka,et al.  Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors , 2006, Cell.

[44]  T. Misteli,et al.  Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells. , 2006, Developmental cell.

[45]  H. Schöler,et al.  Germline regulatory element of Oct-4 specific for the totipotent cycle of embryonal cells. , 1996, Development.