Dynamic changes in the epigenomic landscape regulate human organogenesis and link to developmental disorders

[1]  Michael D. Wilson,et al.  Sufu- and Spop-mediated downregulation of Hedgehog signaling promotes beta cell differentiation through organ-specific niche signals , 2019, Nature Communications.

[2]  N. Hanley,et al.  A Human Stem Cell Model of Fabry Disease Implicates LIMP-2 Accumulation in Cardiomyocyte Pathology , 2019, Stem cell reports.

[3]  Kornel Labun,et al.  CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing , 2019, Nucleic Acids Res..

[4]  Joan,et al.  Prevalence and architecture of de novo mutations in developmental disorders , 2017, Nature.

[5]  James D Stephenson,et al.  Quantifying the contribution of recessive coding variation to developmental disorders , 2017, Science.

[6]  J. Noonan,et al.  High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development , 2018, Cell reports.

[7]  Damian Smedley,et al.  The 100 000 Genomes Project: bringing whole genome sequencing to the NHS , 2018, British Medical Journal.

[8]  Caroline F. Wright,et al.  De novo mutations in regulatory elements in neurodevelopmental disorders , 2018, Nature.

[9]  Tyler H. Garvin,et al.  Ultraconserved Enhancers Are Required for Normal Development , 2018, Cell.

[10]  Xuedong Zhou,et al.  Bivalent Histone Modifications and Development. , 2017, Current stem cell research & therapy.

[11]  Fabian J Theis,et al.  The Human Cell Atlas , 2017, bioRxiv.

[12]  Michael C. Ostrowski,et al.  The ETS family of oncogenic transcription factors in solid tumours , 2017, Nature Reviews Cancer.

[13]  Deciphering Developmental Disorders Study,et al.  Prevalence and architecture of de novo mutations in developmental disorders , 2017, Nature.

[14]  Helen E. Parkinson,et al.  The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog) , 2016, Nucleic Acids Res..

[15]  J. Knight,et al.  XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits , 2016, Genome Medicine.

[16]  Daning Lu,et al.  Chromosome conformation elucidates regulatory relationships in developing human brain , 2016, Nature.

[17]  Dave T. Gerrard,et al.  An integrative transcriptomic atlas of organogenesis in human embryos , 2016, eLife.

[18]  Guangchuang Yu,et al.  ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. , 2016, Molecular bioSystems.

[19]  Aaron T. L. Lun,et al.  csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows , 2015, Nucleic acids research.

[20]  Eran Meshorer,et al.  Chromatin remodeling and bivalent histone modifications in embryonic stem cells , 2015, EMBO reports.

[21]  Gabor T. Marth,et al.  A global reference for human genetic variation , 2015, Nature.

[22]  Dave T. Gerrard,et al.  Human pancreas development , 2015, Development.

[23]  R. Passier,et al.  Expansion and patterning of cardiovascular progenitors derived from human pluripotent stem cells , 2015, Nature Biotechnology.

[24]  N. Hanley,et al.  TEAD and YAP regulate the enhancer network of human embryonic pancreatic progenitors , 2015, Nature Cell Biology.

[25]  Jing Leng,et al.  Evolutionary changes in promoter and enhancer activity during human corticogenesis , 2015, Science.

[26]  Michael Q. Zhang,et al.  Integrative analysis of 111 reference human epigenomes , 2015, Nature.

[27]  Andrew R. Gehrke,et al.  Deep conservation of wrist and digit enhancers in fish , 2014, Proceedings of the National Academy of Sciences.

[28]  Elhanan Borenstein,et al.  Conservation of trans-acting circuitry during mammalian regulatory evolution , 2014, Nature.

[29]  M. Looso,et al.  RBM24 is a major regulator of muscle-specific alternative splicing. , 2014, Developmental cell.

[30]  D. Page,et al.  Poised chromatin in the mammalian germ line , 2014, Development.

[31]  David G. Robinson,et al.  subSeq: Determining Appropriate Sequencing Depth Through Efficient Read Subsampling , 2014, Bioinform..

[32]  A. Hattersley,et al.  GATA4 Mutations Are a Cause of Neonatal and Childhood-Onset Diabetes , 2014, Diabetes.

[33]  Eric Nestler,et al.  ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases , 2014, BMC Genomics.

[34]  T. Meehan,et al.  An atlas of active enhancers across human cell types and tissues , 2014, Nature.

[35]  Anna Murray,et al.  Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis , 2013, Nature Genetics.

[36]  A. Visel,et al.  Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development , 2013, Cell.

[37]  C. Mummery,et al.  PGC-1α and Reactive Oxygen Species Regulate Human Embryonic Stem Cell-Derived Cardiomyocyte Function , 2013, Stem cell reports.

[38]  T. Hearn,et al.  Development of the Human Pancreas From Foregut to Endocrine Commitment , 2013, Diabetes.

[39]  Laura E. DeMare,et al.  The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb , 2013, Cell.

[40]  V. Christoffels,et al.  A molecular and genetic outline of cardiac morphogenesis , 2013, Acta physiologica.

[41]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[42]  Bronwen L. Aken,et al.  GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.

[43]  Manolis Kellis,et al.  ChromHMM: automating chromatin-state discovery and characterization , 2012, Nature Methods.

[44]  S. Mundlos,et al.  Deletions in PITX1 cause a spectrum of lower-limb malformations including mirror-image polydactyly , 2012, European Journal of Human Genetics.

[45]  A. Hattersley,et al.  GATA6 haploinsufficiency causes pancreatic agenesis in humans , 2011, Nature Genetics.

[46]  R. Passier,et al.  NKX2-5eGFP/w hESCs for isolation of human cardiac progenitors and cardiomyocytes , 2011, Nature Methods.

[47]  Brent S. Pedersen,et al.  BioStar: An Online Question & Answer Resource for the Bioinformatics Community , 2011, PLoS Comput. Biol..

[48]  H. Firth,et al.  The Deciphering Developmental Disorders (DDD) study , 2011, Developmental medicine and child neurology.

[49]  Timothy J. Durham,et al.  Systematic analysis of chromatin state dynamics in nine human cell types , 2011, Nature.

[50]  M. Palassini,et al.  Derepression of Polycomb targets during pancreatic organogenesis allows insulin-producing beta-cells to adopt a neural gene activity program. , 2010, Genome research.

[51]  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.

[52]  Michael D. Wilson,et al.  Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding , 2010, Science.

[53]  K. Pollard,et al.  Detection of nonneutral substitution rates on mammalian phylogenies. , 2010, Genome research.

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

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

[56]  D. Haussler,et al.  Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. , 2005, Genome research.

[57]  Klaudia Walter,et al.  Open access, freely available online PLoS BIOLOGY Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development , 2022 .

[58]  K. Kawakami,et al.  A transposon-mediated gene trap approach identifies developmentally regulated genes in zebrafish. , 2004, Developmental cell.

[59]  O. Madsen,et al.  Expression patterns of Wnts, Frizzleds, sFRPs, and misexpression in transgenic mice suggesting a role for Wnts in pancreas and foregut pattern formation , 2002, Developmental dynamics : an official publication of the American Association of Anatomists.