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Author Details

Alexias Safi
Center for Genomic and Computational Biology, Duke University Medical Center
2003
38
23
Nathan Sheffield (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
35179181Identification of enhancer regulatory elements that direct epicardial gene expression during zebrafish heart regeneration.Development2022
35609992Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data.Genome Res2022
35513710Enhancer selection dictates gene expression responses in remote organs during tissue regeneration.Nat Cell Biol2022
34216551Targeted long-read sequencing identifies missing disease-causing variation.Am J Hum Genet2021
34429139Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer's disease brains.Mol Neurodegener2021
31961859Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation.PLoS Genet2020
31599933Evaluating Chromatin Accessibility Differences Across Multiple Primate Species Using a Joint Modeling Approach.Genome Biol Evol2019
33997167Integrated chromatin and transcriptomic profiling of patient-derived colon cancer organoids identifies personalized drug targets to overcome oxaliplatin resistance.Genes Dis2019
31186305Open Chromatin Profiling in Adipose Tissue Marks Genomic Regions with Functional Roles in Cardiometabolic Traits.G3 (Bethesda)2019
31233101Comparative Analyses of Chromatin Landscape in White Adipose Tissue Suggest Humans May Have Less Beigeing Potential than Other Primates.Genome Biol Evol2019
29429127Tissue- and strain-specific effects of a genotoxic carcinogen 1,3-butadiene on chromatin and transcription.Mamm Genome2018
30097539Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding.Genome Res2018
30139769Human cardiac <i>cis</i>-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants.Genome Res2018
30087329Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia.Nat Commun2018
30031775Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids.Cell Syst2018
30545853Transcriptome and epigenome landscape of human cortical development modeled in organoids.Science2018
29632383Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights.Nat Genet2018
29608722Comparative Serum Challenges Show Divergent Patterns of Gene Expression and Open Chromatin in Human and Chimpanzee.Genome Biol Evol2018
29038090Variation in DNA-Damage Responses to an Inhalational Carcinogen (1,3-Butadiene) in Relation to Strain-Specific Differences in Chromatin Accessibility and Gene Transcription Profiles in C57BL/6J and CAST/EiJ Mice.Environ Health Perspect2017
28369033CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome.Nat Biotechnol2017
27565349Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome.Cell2016
26673704Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus.Nucleic Acids Res2016
25569532Interactions of chromatin context, binding site sequence content, and sequence evolution in stress-induced p53 occupancy and transactivation.PLoS Genet2015
26501517Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements.Nat Methods2015
26307087Genetic variants and cellular stressors associated with exfoliation syndrome modulate promoter activity of a lncRNA within the LOXL1 locus.Hum Mol Genet2015
26206884Genomic analysis reveals distinct mechanisms and functional classes of SOX10-regulated genes in melanocytes.Hum Mol Genet2015
25849986Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum.Nat Neurosci2015
26025803Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators.Genome Res2015
23482648Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.Genome Res2013
24076218Distinct properties of cell-type-specific and shared transcription factor binding sites.Mol Cell2013
22955617The accessible chromatin landscape of the human genome.Nature2012
21546544A region of the nucleosome required for multiple types of transcriptional silencing in Saccharomyces cerevisiae.Genetics2011
18268008Evolution of new function through a single amino acid change in the yeast repressor Sum1p.Mol Cell Biol2008
16481744Autophosphorylation of Ser66 on Xenopus Myt1 is a prerequisite for meiotic inactivation of Myt1.Cell Cycle2006
16342947Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate.Biochemistry2005
14729969Role for the pleckstrin homology domain-containing protein CKIP-1 in phosphatidylinositol 3-kinase-regulated muscle differentiation.Mol Cell Biol2004
15534213Remote hot spots mediate protein substrate recognition for the Cdc25 phosphatase.Proc Natl Acad Sci U S A2004
12801222Inhibition of Cdc25 phosphatases by indolyldihydroxyquinones.J Med Chem2003
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Collaborators

Center for Genomic & Computational Biology, Duke University
Co-authored papers 31
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Co-authored papers 22
Co-authored papers 10
University of North Carolina at Chapel Hill
Co-authored papers 5
Duke University
Co-authored papers 4
University of North Carolina
Co-authored papers 4
Co-authored papers 3
Co-authored papers 3
The University of Chicago
Co-authored papers 3
University of Virginia
Co-authored papers 2
University of North Carolina at Chapel Hill
Co-authored papers 2
Center for Genomic and Computational Biology, Duke University.
Co-authored papers 2
MRC London Institute of Medical Sciences
Co-authored papers 2
University of Washington
Co-authored papers 2
Co-authored papers 2
Altius Institute for Biomedical Sciences
Co-authored papers 2
Duke University School of Medicine
Co-authored papers 2
Cancer Research Center, University at Albany, State University of New York
Co-authored papers 1
Co-authored papers 1
Co-authored papers 1
Altius Institute for Biomedical Sciences
Co-authored papers 1
Harvard Medical School
Co-authored papers 1
University of Michigan Medical School ann arbor
Co-authored papers 1
Center for Epigenomics, University of California San Diego
Co-authored papers 1
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National Human Genome Research Institute, National Institutes of Health
Co-authored papers 1
Johns Hopkins University School of Medicine
Co-authored papers 1
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University of Washington
Co-authored papers 1