The Experts below are selected from a list of 226692 Experts worldwide ranked by ideXlab platform
Katelynn R Kazane - One of the best experts on this subject based on the ideXlab platform.
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enhancer connectome in primary human cells identifies target Genes of disease associated dna elements
Nature Genetics, 2017Co-Authors: Maxwell R Mumbach, Ansuman T Satpathy, Evan A Boyle, Chao Dai, Benjamin G Gowen, Seung Woo Cho, Michelle L T Nguyen, Adam J Rubin, Jeffrey M Granja, Katelynn R KazaneAbstract:The challenge of linking intergenic mutations to target Genes has limited molecular understanding of human diseases. Here we show that H3K27ac HiChIP Generates high-resolution contact maps of active enhancers and target Genes in rare primary human T cell subtypes and coronary artery smooth muscle cells. Differentiation of naive T cells into T helper 17 cells or regulatory T cells creates subtype-specific enhancer-promoter interactions, specifically at regions of shared DNA accessibility. These data provide a principled means of assigning molecular functions to autoimmune and cardiovascular disease risk variants, linking hundreds of noncoding variants to Putative Gene targets. Target Genes identified with HiChIP are further supported by CRISPR interference and activation at linked enhancers, by the presence of expression quantitative trait loci, and by allele-specific enhancer loops in patient-derived primary cells. The majority of disease-associated enhancers contact Genes beyond the nearest Gene in the linear genome, leading to a fourfold increase in the number of potential target Genes for autoimmune and cardiovascular diseases.
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enhancer connectome in primary human cells reveals target Genes of disease associated dna elements
bioRxiv, 2017Co-Authors: Maxwell R Mumbach, Ansuman T Satpathy, Evan A Boyle, Chao Dai, Benjamin G Gowen, Seung Woo Cho, Michelle L T Nguyen, Adam J Rubin, Jeffrey M Granja, Katelynn R KazaneAbstract:The challenge of linking intergenic mutations to target Genes has limited molecular understanding of diverse human diseases. Here, we show H3K27ac HiChIP Generates high-resolution contact maps of active enhancers and target Genes in rare primary human T cell subtypes and coronary artery smooth muscle cells. Differentiation of naive T cells to either T helper 17 cells or regulatory T cells create subtype-specific enhancer-promoter interactions, specifically at regions of shared DNA accessibility. These data provide a principled means of assigning molecular functions to autoimmune and cardiovascular disease risk variants, linking hundreds of noncoding variants to Putative Gene targets. Target Genes identified with HiChIP are further supported by CRISPR interference and activation at linked enhancers, by the presence of expression quantitative trait loci, and by allele-specific enhancer loops in patient-derived primary cells. The majority of disease-associated enhancers contact Genes beyond the nearest Gene in the linear genome, leading to a four-fold increase of potential target Genes for autoimmune and cardiovascular diseases.
Hugues Roest Crollius - One of the best experts on this subject based on the ideXlab platform.
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genomicus update 2015 karyoview and matrixview provide a genome wide perspective to multispecies comparative genomics
Nucleic Acids Research, 2015Co-Authors: Alexandra Louis, Nga Nguyen, Matthieu Muffato, Hugues Roest CrolliusAbstract:The Genomicus web server (http://www.genomicus.biologie.ens.fr/genomicus) is a visualization tool allowing comparative genomics in four different phyla (Vertebrate, Fungi, Metazoan and Plants). It provides access to genomic information from extant species, as well as ancestral Gene content and Gene order for vertebrates and flowering plants. Here we present the new features available for vertebrate genome with a focus on new graphical tools. The interface to enter the database has been improved, two pairwise genome comparison tools are now available (KaryoView and MatrixView) and the multiple genome comparison tools (PhyloView and AlignView) propose three new kinds of representation and a more intuitive menu. These new developments have been implemented for Genomicus portal dedicated to vertebrates. This allows the analysis of 68 extant animal genomes, as well as 58 ancestral reconstructed genomes. The Genomicus server also provides access to ancestral Gene orders, to facilitate evolutionary and comparative genomics studies, as well as computationally predicted regulatory interactions, thanks to the representation of conserved non-coding elements with their Putative Gene targets.
Duy An Duong - One of the best experts on this subject based on the ideXlab platform.
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Draft Genome Assembly of the Entomopathogenic Bacterium Photorhabdus luminescens subsp. sonorensis Caborca.
Microbiology resource announcements, 2019Co-Authors: Duy An Duong, Rousel A Orozco, Istvan Molnar, Patricia Espinosa-artiles, S. Patricia StockAbstract:ABSTRACT Photorhabdus luminescens subsp. sonorensis strain Caborca is an entomopathogenic bacterium with a dual lifestyle, namely, as a mutualist of the Heterorhabditis sonorensis nematode and a pathogen to a wide range of insect species. The genome assembly, in 231 contigs, is 5.2 Mbp long and includes 25 Putative Gene clusters for secondary metabolism.
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Draft Genome Assembly of the Entomopathogenic Bacterium Photorhabdus luminescens subsp. sonorensis Caborca
'American Society for Microbiology', 2019Co-Authors: Duy An Duong, Espinosa-artiles Patricia, Orozco, Rousel A, Molnár István, Stock S PatriciaAbstract:Photorhabdus luminescens subsp. sonorensis strain Caborca is an entomopathogenic bacterium with a dual lifestyle, namely, as a mutualist of the Heterorhabditis sonorensis nematode and a pathogen to a wide range of insect species. The genome assembly, in 231 contigs, is 5.2 Mbp long and includes 25 Putative Gene clusters for secondary metabolism.College of Agriculture and Life Sciences (CALS) from the University of Arizona; University of Arizona; PERT, NIHUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [K12GM000708]Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu
Maxwell R Mumbach - One of the best experts on this subject based on the ideXlab platform.
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enhancer connectome in primary human cells identifies target Genes of disease associated dna elements
Nature Genetics, 2017Co-Authors: Maxwell R Mumbach, Ansuman T Satpathy, Evan A Boyle, Chao Dai, Benjamin G Gowen, Seung Woo Cho, Michelle L T Nguyen, Adam J Rubin, Jeffrey M Granja, Katelynn R KazaneAbstract:The challenge of linking intergenic mutations to target Genes has limited molecular understanding of human diseases. Here we show that H3K27ac HiChIP Generates high-resolution contact maps of active enhancers and target Genes in rare primary human T cell subtypes and coronary artery smooth muscle cells. Differentiation of naive T cells into T helper 17 cells or regulatory T cells creates subtype-specific enhancer-promoter interactions, specifically at regions of shared DNA accessibility. These data provide a principled means of assigning molecular functions to autoimmune and cardiovascular disease risk variants, linking hundreds of noncoding variants to Putative Gene targets. Target Genes identified with HiChIP are further supported by CRISPR interference and activation at linked enhancers, by the presence of expression quantitative trait loci, and by allele-specific enhancer loops in patient-derived primary cells. The majority of disease-associated enhancers contact Genes beyond the nearest Gene in the linear genome, leading to a fourfold increase in the number of potential target Genes for autoimmune and cardiovascular diseases.
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enhancer connectome in primary human cells reveals target Genes of disease associated dna elements
bioRxiv, 2017Co-Authors: Maxwell R Mumbach, Ansuman T Satpathy, Evan A Boyle, Chao Dai, Benjamin G Gowen, Seung Woo Cho, Michelle L T Nguyen, Adam J Rubin, Jeffrey M Granja, Katelynn R KazaneAbstract:The challenge of linking intergenic mutations to target Genes has limited molecular understanding of diverse human diseases. Here, we show H3K27ac HiChIP Generates high-resolution contact maps of active enhancers and target Genes in rare primary human T cell subtypes and coronary artery smooth muscle cells. Differentiation of naive T cells to either T helper 17 cells or regulatory T cells create subtype-specific enhancer-promoter interactions, specifically at regions of shared DNA accessibility. These data provide a principled means of assigning molecular functions to autoimmune and cardiovascular disease risk variants, linking hundreds of noncoding variants to Putative Gene targets. Target Genes identified with HiChIP are further supported by CRISPR interference and activation at linked enhancers, by the presence of expression quantitative trait loci, and by allele-specific enhancer loops in patient-derived primary cells. The majority of disease-associated enhancers contact Genes beyond the nearest Gene in the linear genome, leading to a four-fold increase of potential target Genes for autoimmune and cardiovascular diseases.
Alexandra Louis - One of the best experts on this subject based on the ideXlab platform.
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genomicus update 2015 karyoview and matrixview provide a genome wide perspective to multispecies comparative genomics
Nucleic Acids Research, 2015Co-Authors: Alexandra Louis, Nga Nguyen, Matthieu Muffato, Hugues Roest CrolliusAbstract:The Genomicus web server (http://www.genomicus.biologie.ens.fr/genomicus) is a visualization tool allowing comparative genomics in four different phyla (Vertebrate, Fungi, Metazoan and Plants). It provides access to genomic information from extant species, as well as ancestral Gene content and Gene order for vertebrates and flowering plants. Here we present the new features available for vertebrate genome with a focus on new graphical tools. The interface to enter the database has been improved, two pairwise genome comparison tools are now available (KaryoView and MatrixView) and the multiple genome comparison tools (PhyloView and AlignView) propose three new kinds of representation and a more intuitive menu. These new developments have been implemented for Genomicus portal dedicated to vertebrates. This allows the analysis of 68 extant animal genomes, as well as 58 ancestral reconstructed genomes. The Genomicus server also provides access to ancestral Gene orders, to facilitate evolutionary and comparative genomics studies, as well as computationally predicted regulatory interactions, thanks to the representation of conserved non-coding elements with their Putative Gene targets.
