Genome-wide Detection of DNase I Hypersensitive Sites in Single Cells and FFPE Samples

[1]  Howard Y. Chang,et al.  Single-cell chromatin accessibility reveals principles of regulatory variation , 2015, Nature.

[2]  Andrew C. Adey,et al.  Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing , 2015, Science.

[3]  Shan Xu,et al.  TXNL1 induces apoptosis in cisplatin resistant human gastric cancer cell lines. , 2015, Current cancer drug targets.

[4]  Rona S. Gertner,et al.  Single cell RNA Seq reveals dynamic paracrine control of cellular variation , 2014, Nature.

[5]  John M. Asara,et al.  Depletion of a Putatively Druggable Class of Phosphatidylinositol Kinases Inhibits Growth of p53-Null Tumors , 2013, Cell.

[6]  R. Young,et al.  Super-Enhancers in the Control of Cell Identity and Disease , 2013, Cell.

[7]  K. Zhao,et al.  Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3 , 2013, Genome Biology.

[8]  David A. Orlando,et al.  Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes , 2013, Cell.

[9]  Boris Lenhard,et al.  Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions , 2013, Genome research.

[10]  Kairong Cui,et al.  H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation. , 2013, Cell stem cell.

[11]  Alexander S. Garruss,et al.  The RNA Pol II Elongation Factor Ell3 Marks Enhancers in ES Cells and Primes Future Gene Activation , 2013, Cell.

[12]  H. Ueda,et al.  Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity , 2013, Genome Biology.

[13]  Nathan C. Sheffield,et al.  The accessible chromatin landscape of the human genome , 2012, Nature.

[14]  Philip Cayting,et al.  An encyclopedia of mouse DNA elements (Mouse ENCODE) , 2012, Genome Biology.

[15]  Peter A. Jones,et al.  Cancer genetics and epigenetics: two sides of the same coin? , 2012, Cancer cell.

[16]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[17]  Ryan A. Flynn,et al.  A unique chromatin signature uncovers early developmental enhancers in humans , 2011, Nature.

[18]  A. Ziegler,et al.  HDAC2 and TXNL1 distinguish aneuploid from diploid colorectal cancers , 2011, Cellular and Molecular Life Sciences.

[19]  J. Stamatoyannopoulos,et al.  Chromatin accessibility pre-determines glucocorticoid receptor binding patterns , 2011, Nature Genetics.

[20]  R. Young,et al.  Histone H3K27ac separates active from poised enhancers and predicts developmental state , 2010, Proceedings of the National Academy of Sciences.

[21]  Cory Y. McLean,et al.  GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.

[22]  G. Crawford,et al.  DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. , 2010, Cold Spring Harbor protocols.

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

[24]  Chen Zeng,et al.  A clustering approach for identification of enriched domains from histone modification ChIP-Seq data , 2009, Bioinform..

[25]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[26]  R. Hartmann-Petersen,et al.  Thioredoxin Txnl1/TRP32 Is a Redox-active Cofactor of the 26 S Proteasome* , 2009, Journal of Biological Chemistry.

[27]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[28]  Michael Q. Zhang,et al.  Combinatorial patterns of histone acetylations and methylations in the human genome , 2008, Nature Genetics.

[29]  G. Botti,et al.  HMGA2 mRNA expression correlates with the malignant phenotype in human thyroid neoplasias. , 2008, European journal of cancer.

[30]  Z. Weng,et al.  High-Resolution Mapping and Characterization of Open Chromatin across the Genome , 2008, Cell.

[31]  J. Bullerdiek,et al.  Upregulation of HMGA2 in thyroid carcinomas: A novel molecular marker to distinguish between benign and malignant follicular neoplasias , 2008, Genes, chromosomes & cancer.

[32]  Nathaniel D. Heintzman,et al.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome , 2007, Nature Genetics.

[33]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[34]  Keji Zhao,et al.  Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. , 2005, Genes & development.

[35]  Doron Lancet,et al.  Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification , 2005, Bioinform..

[36]  T. Dwight,et al.  Expression profiling reveals a distinct transcription signature in follicular thyroid carcinomas with a PAX8-PPARγ fusion oncogene , 2005, Oncogene.

[37]  C. Allis,et al.  Correlation Between Histone Lysine Methylation and Developmental Changes at the Chicken β-Globin Locus , 2001, Science.

[38]  John G. Collard,et al.  Identification of an invasion-inducing gene, Tiam-1, that encodes a protein with homology to GDP-GTP exchangers for Rho-like proteins , 1994, Cell.