Author details

Full Name

Thomas A Down

Affiliation

ORCID

Career Start Year

2002

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
27791097	Stable <i>Caenorhabditis elegans</i> chromatin domains separate broadly expressed and developmentally regulated genes.	Proc Natl Acad Sci U S A	2016
26578572	WormBase 2016: expanding to enable helminth genomic research.	Nucleic Acids Res	2016
26315906	An interactive genome browser of association results from the UK10K cohorts project.	Bioinformatics	2015
24653213	Extreme HOT regions are CpG-dense promoters in C. elegans and humans.	Genome Research	2014
24810143	A comparison of peak callers used for DNase-Seq data.	PLoS ONE	2014
23706135	Inactive or moderately active human promoters are enriched for inter-individual epialleles.	Genome Biol	2013
24371807	Synergistic mechanisms of DNA demethylation during transition to ground-state pluripotency.	Stem Cell Reports	2013
23966877	Binding of TFIIIC to sine elements controls the relocation of activity-dependent neuronal genes to transcription factories.	PLoS Genetics	2013
23922824	Chromatin accessibility data sets show bias due to sequence specificity of the DNase I enzyme.	PLoS ONE	2013
23223451	Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine.	Science	2013
23550086	The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures.	Genome Res	2013
23727884	The epigenetic regulator PLZF represses L1 retrotransposition in germ and progenitor cells.	EMBO Journal	2013
22479372	Genome wide analysis of acute myeloid leukemia reveal leukemia specific methylome and subtype specific hypomethylation of repeats.	PLoS One	2012
22919074	Guthrie card methylomics identifies temporally stable epialleles that are present at birth in humans.	Genome Res	2012
22826509	A functional methylome map of ulcerative colitis.	Genome Res	2012
22479388	Genomic targets of Brachyury (T) in differentiating mouse embryonic stem cells.	PLoS One	2012
21980303	Identification of type 1 diabetes-associated DNA methylation variable positions that precede disease diagnosis.	PLoS Genet	2011
21252075	Dalliance: interactive genome viewing on the web.		2011
21324880	Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors.	Genome Res	2011
21747404	Epigenome-wide association studies for common human diseases.	Nat Rev Genet	2011
22025602	Distinct epigenomic features in end-stage failing human hearts.	Circulation	2011
21940836	Comparative methylomics reveals gene-body H3K36me3 in Drosophila predicts DNA methylation and CpG landscapes in other invertebrates.	Genome Res	2011
21646344	Systematic bias in high-throughput sequencing data and its correction by BEADS.	Nucleic Acids Research	2011
20579334	Metamotifs--a generative model for building families of nucleotide position weight matrices.	BMC Bioinformatics	2010
21124985	Integrated genetic and epigenetic analysis identifies haplotype-specific methylation in the FTO type 2 diabetes and obesity susceptibility locus.	PLoS One	2010
21152003	Assessing computational methods of cis-regulatory module prediction.	PLoS Comput Biol	2010
20875111	Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated.	BMC Genomics	2010
20975942	Genome-wide identification of targets and function of individual MicroRNAs in mouse embryonic stem cells.	PLoS Genet	2010
20084101	Differential DNA methylation correlates with differential expression of angiogenic factors in human heart failure.	PLoS ONE	2010
20219945	Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains.	Genome Res	2010
20071334	DNA methylation-mediated down-regulation of DNA methyltransferase-1 (DNMT1) is coincident with, but not essential for, global hypomethylation in human placenta.	J Biol Chem	2010
20106815	iMotifs: an integrated sequence motif visualization and analysis environment.		2010
19783735	Smicl is required for phosphorylation of RNA polymerase II and affects 3'-end processing of RNA at the midblastula transition in Xenopus.	Development (Cambridge)	2009
19182803	Differential chromatin marking of introns and expressed exons by H3K36me3.	Nature Genetics	2009
19401398	Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level.	Genome Res	2009
19237542	Placenta-specific methylation of the vitamin D 24-hydroxylase gene: implications for feedback autoregulation of active vitamin D levels at the fetomaternal interface.	J Biol Chem	2009
18708652	Specific tumour-associated methylation in normal human term placenta and first-trimester cytotrophoblasts.	Mol Hum Reprod	2008
18000006	Ensembl 2008.	Nucleic Acids Res	2008
18689808	BioJava: an open-source framework for bioinformatics.	Bioinformatics	2008
18577705	An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs).	Genome Res	2008
18673527	Integrating biological data--the Distributed Annotation System.	BMC Bioinformatics	2008
18194537	NestedMICA as an ab initio protein motif discovery tool.	BMC Bioinformatics	2008
18612301	A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.	Nat Biotechnol	2008
17238282	Large-scale discovery of promoter motifs in Drosophila melanogaster.	PLoS Comput Biol	2007
17850653	Integrating sequence and structural biology with DAS.	BMC Bioinformatics	2007
17148474	Ensembl 2007.	Nucleic Acids Res	2007
16522222	Multi-genome biology.		2006
17072317	DNA methylation profiling of human chromosomes 6, 20 and 22.	Nat Genet	2006
17002805	A machine learning strategy to identify candidate binding sites in human protein-coding sequence.	BMC Bioinformatics	2006
16381931	Ensembl 2006.	Nucleic Acids Res	2006