Associating cellular epigenetic models with human phenotypes

[1]  Warren A. Cheung,et al.  Correction to: Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome , 2017, Genome Biology.

[2]  Tom R. Gaunt,et al.  Epigenome-wide association study of body mass index, and the adverse outcomes of adiposity , 2016, Nature.

[3]  Guangliang Yin,et al.  Distinct epigenomes in CD4+ T cells of newborns, middle-ages and centenarians , 2016, Scientific Reports.

[4]  Matthew T. Maurano,et al.  Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells , 2016, Cell.

[5]  A. M. Arias,et al.  Transition states and cell fate decisions in epigenetic landscapes , 2016, Nature Reviews Genetics.

[6]  A. Hofman,et al.  Blood lipids influence DNA methylation in circulating cells , 2016, Genome Biology.

[7]  E. Birney,et al.  Epigenome-wide Association Studies and the Interpretation of Disease -Omics , 2016, PLoS genetics.

[8]  J. Matthews,et al.  Mechanisms of DNA-binding specificity and functional gene regulation by transcription factors. , 2016, Current opinion in structural biology.

[9]  Sui Huang,et al.  Conceptual Confusion: The case of Epigenetics , 2016, bioRxiv.

[10]  M. Mann,et al.  Molecular basis of PRC1 targeting to Polycomb response elements by PhoRC , 2016, Genes & development.

[11]  Tom R. Gaunt,et al.  DNA Methylation and BMI: Investigating Identified Methylation Sites at HIF3A in a Causal Framework , 2016, Diabetes.

[12]  C. Angelini,et al.  ZFP57 recognizes multiple and closely spaced sequence motif variants to maintain repressive epigenetic marks in mouse embryonic stem cells , 2015, Nucleic acids research.

[13]  Anaïs F. Bardet,et al.  Competition between DNA methylation and transcription factors determines binding of NRF1 , 2015, Nature.

[14]  I. Amit,et al.  Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors , 2015, Cell.

[15]  P. Hart,et al.  The effects of in utero vitamin D deficiency on airway smooth muscle mass and lung function. , 2015, American journal of respiratory cell and molecular biology.

[16]  Tuuli Lappalainen,et al.  Functional genomics bridges the gap between quantitative genetics and molecular biology , 2015, Genome research.

[17]  R. Klose,et al.  Targeting Polycomb systems to regulate gene expression: modifications to a complex story , 2015, Nature Reviews Molecular Cell Biology.

[18]  S. Krawetz,et al.  Environmental Susceptibility of the Sperm Epigenome During Windows of Male Germ Cell Development , 2015, Current Environmental Health Reports.

[19]  Brian S. Roberts,et al.  CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins , 2015, Genome research.

[20]  A. Regev,et al.  Spatial reconstruction of single-cell gene expression data , 2015 .

[21]  Ash A. Alizadeh,et al.  Robust enumeration of cell subsets from tissue expression profiles , 2015, Nature Methods.

[22]  L. Kruglyak,et al.  The role of regulatory variation in complex traits and disease , 2015, Nature Reviews Genetics.

[23]  A. Regev,et al.  Spatial reconstruction of single-cell gene expression , 2015, Nature Biotechnology.

[24]  D. Moazed,et al.  RNA-mediated epigenetic regulation of gene expression , 2015, Nature Reviews Genetics.

[25]  C. Marsit.  Influence of environmental exposure on human epigenetic regulation , 2015, Journal of Experimental Biology.

[26]  Jonathan K. Pritchard,et al.  The Genetic and Mechanistic Basis for Variation in Gene Regulation , 2015, PLoS genetics.

[27]  J. Greally,et al.  Genome-wide assays that identify and quantify modified cytosines in human disease studies , 2015, Epigenetics & Chromatin.

[28]  Z. Weng,et al.  Principles of regulatory information conservation between mouse and human , 2014, Nature.

[29]  E. Heard,et al.  Noncoding RNAs and epigenetic mechanisms during X-chromosome inactivation. , 2014, Annual review of cell and developmental biology.

[30]  Richard A. Olshen,et al.  Diversity and clonal selection in the human T-cell repertoire , 2014, Proceedings of the National Academy of Sciences.

[31]  J. Mar,et al.  The meta-epigenomic structure of purified human stem cell populations is defined at cis-regulatory sequences , 2014, Nature Communications.

[32]  O. Stegle,et al.  Single-Cell Genome-Wide Bisulfite Sequencing for Assessing Epigenetic Heterogeneity , 2014, Nature Methods.

[33]  John D. Blischak,et al.  Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels , 2014, bioRxiv.

[34]  S. Henikoff,et al.  High-resolution mapping defines the cooperative architecture of Polycomb response elements , 2014, Genome research.

[35]  Martin J. Aryee,et al.  Epigenome-wide association studies without the need for cell-type composition , 2014, Nature Methods.

[36]  I. Amit,et al.  Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types , 2014, Science.

[37]  L. Quadro,et al.  Prenatal retinoid deficiency leads to airway hyperresponsiveness in adult mice. , 2014, The Journal of clinical investigation.

[38]  E. Andres Houseman,et al.  Reference-free cell mixture adjustments in analysis of DNA methylation data , 2014, Bioinform..

[39]  R. Irizarry,et al.  Accounting for cellular heterogeneity is critical in epigenome-wide association studies , 2014, Genome Biology.

[40]  F. Tang,et al.  Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing , 2013, Genome research.

[41]  Lukas Burger,et al.  Transcription Factor Occupancy Can Mediate Active Turnover of DNA Methylation at Regulatory Regions , 2013, PLoS genetics.

[42]  Mark I. McCarthy,et al.  Global analysis of DNA methylation variation in adipose tissue from twins reveals links to disease-associated variants in distal regulatory elements. , 2013, American journal of human genetics.

[43]  Robert A Holt,et al.  Sequence analysis of T-cell repertoires in health and disease , 2013, Genome Medicine.

[44]  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.

[45]  K. Helin,et al.  Transcriptional regulation by Polycomb group proteins , 2013, Nature Structural &Molecular Biology.

[46]  Alexandra M. Binder,et al.  Recommendations for the design and analysis of epigenome-wide association studies , 2013, Nature Methods.

[47]  J. Greally,et al.  In vitro and in vivo testing methods of epigenomic endpoints for evaluating endocrine disruptors. , 2013, ALTEX.

[48]  E. Dermitzakis,et al.  Passive and active DNA methylation and the interplay with genetic variation in gene regulation , 2013, eLife.

[49]  S. Eddy,et al.  Transcription Factors That Convert Adult Cell Identity Are Differentially Polycomb Repressed , 2013, PloS one.

[50]  Hao Sun,et al.  YY1TargetDB: an integral information resource for Yin Yang 1 target loci , 2013, Database J. Biol. Databases Curation.

[51]  R. Weksberg,et al.  Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray , 2013, Epigenetics.

[52]  R. Mann,et al.  Disentangling the many layers of eukaryotic transcriptional regulation. , 2012, Annual review of genetics.

[53]  Vilmundur Gudnason,et al.  Heterogeneity in White Blood Cells Has Potential to Confound DNA Methylation Measurements , 2012, PloS one.

[54]  Devin C. Koestler,et al.  DNA methylation arrays as surrogate measures of cell mixture distribution , 2012, BMC Bioinformatics.

[55]  Robin M. Murray,et al.  Epigenome-Wide Scans Identify Differentially Methylated Regions for Age and Age-Related Phenotypes in a Healthy Ageing Population , 2012, PLoS genetics.

[56]  Waddington Ch,et al.  The epigenotype. 1942. , 2012 .

[57]  G. Davey Smith,et al.  Two-step epigenetic Mendelian randomization: a strategy for establishing the causal role of epigenetic processes in pathways to disease. , 2012, International journal of epidemiology.

[58]  D. Haig.  Commentary: The epidemiology of epigenetics. , 2012, International journal of epidemiology.

[59]  J. Mill,et al.  Commentary: The seven plagues of epigenetic epidemiology , 2012, International journal of epidemiology.

[60]  Joseph K. Pickrell,et al.  DNaseI sensitivity QTLs are a major determinant of human expression variation , 2011, Nature.

[61]  Vijay K. Tiwari,et al.  DNA-binding factors shape the mouse methylome at distal regulatory regions , 2011, Nature.

[62]  Andrew J Sharp,et al.  DNA methylation profiles of human active and inactive X chromosomes. , 2011, Genome research.

[63]  Kevin M. Bowling,et al.  Analysis of DNA Methylation in a Three-Generation Family Reveals Widespread Genetic Influence on Epigenetic Regulation , 2011, PLoS genetics.

[64]  D. Balding,et al.  Epigenome-wide association studies for common human diseases , 2011, Nature Reviews Genetics.

[65]  Julie Herbstman,et al.  Prenatal environmental exposures, epigenetics, and disease. , 2011, Reproductive Toxicology.

[66]  Hiroyuki Sasaki,et al.  Genomic imprinting in mammals: its life cycle, molecular mechanisms and reprogramming , 2011, Cell Research.

[67]  Joseph K. Pickrell,et al.  DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines , 2011, Genome Biology.

[68]  Danny Reinberg,et al.  Molecular Signals of Epigenetic States , 2010, Science.

[69]  David M. Simcha,et al.  Tackling the widespread and critical impact of batch effects in high-throughput data , 2010, Nature Reviews Genetics.

[70]  Lijun Cheng,et al.  Genetic control of individual differences in gene-specific methylation in human brain. , 2010, American journal of human genetics.

[71]  B. Blumberg,et al.  Prenatal exposure to the environmental obesogen tributyltin predisposes multipotent stem cells to become adipocytes. , 2010, Molecular endocrinology.

[72]  Hong Ma,et al.  Evolution of the RNA-dependent RNA polymerase (RdRP) genes: duplications and possible losses before and after the divergence of major eukaryotic groups. , 2009, Gene.

[73]  Peter Kraft,et al.  Replication in genome-wide association studies. , 2009, Statistical science : a review journal of the Institute of Mathematical Statistics.

[74]  Madeleine P. Ball,et al.  Corrigendum: Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells , 2009, Nature Biotechnology.

[75]  M. D. Simon,et al.  Polycomb Proteins Remain Bound to Chromatin and DNA during DNA Replication In Vitro , 2009, Cell.

[76]  Madeleine P. Ball,et al.  Targeted and genome-scale methylomics reveals gene body signatures in human cell lines , 2009, Nature Biotechnology.

[77]  P. Leder,et al.  A maternal-zygotic effect gene, Zfp57, maintains both maternal and paternal imprints. , 2008, Developmental cell.

[78]  W. Bender,et al.  Replacement of a Drosophila Polycomb response element core, and in situ analysis of its DNA motifs , 2008, Molecular Genetics and Genomics.

[79]  W. Bender,et al.  In situ dissection of a Polycomb response element in Drosophila melanogaster , 2007, Proceedings of the National Academy of Sciences.

[80]  U. Alon.  Network motifs: theory and experimental approaches , 2007, Nature Reviews Genetics.

[81]  Peter Gluckman,et al.  Meeting Report on the 3rd International Congress on Developmental Origins of Health and Disease (DOHaD) , 2007, Pediatric Research.

[82]  Daniel Chourrout,et al.  Genome Regulation by Polycomb and Trithorax Proteins , 2007, Cell.

[83]  Jeannie T. Lee,et al.  Identification of a Ctcf cofactor, Yy1, for the X chromosome binary switch. , 2007, Molecular cell.

[84]  S. Henikoff,et al.  Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription , 2007, Nature Genetics.

[85]  Bruce Blumberg,et al.  Endocrine-disrupting organotin compounds are potent inducers of adipogenesis in vertebrates. , 2006, Molecular endocrinology.

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

[87]  N. Negre,et al.  From genetics to epigenetics: the tale of Polycomb group and trithorax group genes , 2006, Chromosome Research.

[88]  S. Hunt,et al.  Genome-Wide Associations of Gene Expression Variation in Humans , 2005, PLoS genetics.

[89]  C. Molony,et al.  Genetic analysis of genome-wide variation in human gene expression , 2004, Nature.

[90]  B. Horsthemke,et al.  Epigenetic changes may contribute to the formation and spontaneous regression of retinoblastoma , 1989, Human Genetics.

[91]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[92]  L. Kruglyak,et al.  Genetic Dissection of Transcriptional Regulation in Budding Yeast , 2002, Science.

[93]  A. Bird.  DNA methylation patterns and epigenetic memory. , 2002, Genes & development.

[94]  T. Magnuson,et al.  Imprinted X inactivation maintained by a mouse Polycomb group gene , 2001, Nature Genetics.

[95]  M. Zavortink,et al.  The MCP silencer of the Drosophila Abd-B gene requires both Pleiohomeotic and GAGA factor for the maintenance of repression. , 2001, Development.

[96]  J. Vilar,et al.  Mild vitamin A deficiency leads to inborn nephron deficit in the rat. , 1998, Kidney international.

[97]  Rudolf Jaenisch,et al.  Role for DNA methylation in genomic imprinting , 1993, Nature.

[98]  B. Migeon,et al.  DNA methylation stabilizes X chromosome inactivation in eutherians but not in marsupials: evidence for multistep maintenance of mammalian X dosage compensation. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[99]  M. Ehrlich,et al.  The 5-methylcytosine content of DNA from human tumors. , 1983, Nucleic acids research.

[100]  A. Feinberg,et al.  Hypomethylation distinguishes genes of some human cancers from their normal counterparts , 1983, Nature.

[101]  R. Holliday,et al.  A new theory of carcinogenesis , 1979, British Journal of Cancer.

[102]  Arthur D. Riggs,et al.  X inactivation, differentiation, and DNA methylation. , 1975, Cytogenetics and cell genetics.

[103]  D. L. Nanney,et al.  EPIGENETIC CONTROL SYSTEMS. , 1958, Proceedings of the National Academy of Sciences of the United States of America.

[104]  C. Waddington,et al.  The strategy of the genes , 1957 .

[105]  C. Waddington.  Organisers and genes. , 1943 .