Scholars@Duke

• Background
• 

  Education, Training, & Certifications

  • Postdoctoral Research Fellow, National Human Genome Research Institute, National Institutes of Health 2001 - 2006
  • Ph.D., University of Michigan, Ann Arbor 2001
• 

  Duke Appointment History

  • Associate Professor in Pediatrics, Pediatrics, Medical Genetics, Pediatrics 2015 - 2020
  • Associate Professor in Pediatrics, Pediatrics, Medical Genetics, Pediatrics 2011 - 2015
  • Assistant Professor in Molecular Genetics and Microbiology, Molecular Genetics and Microbiology, Basic Science Departments 2006 - 2015
  • Assistant Professor in Pediatrics, Pediatrics, Medical Genetics, Pediatrics 2006 - 2011
• Recognition
• 

  In the News

  • OCT 3, 2018

    Duke Med Alumni News

    From Innovation to Impact

  • APR 9, 2018

    Faculty Startup Sold to Belgian Pharma for $30 Million

  • MAY 17, 2017

    Microbes Seen Controlling Action of Hosts Genes

  • AUG 25, 2016

    Hormone Activation Of Genes Takes Teamwork

  • JAN 6, 2015

    Genomics Team Wins $5.9 Million Grant
• Research
• 

  Selected Grants

  • Genetic and Genomics Training Grant awarded by National Institutes of Health 2020 - 2025
  • Lewy body neuropathologies and SNCA gene: variants expression and splicing awarded by National Institutes of Health 2020 - 2025
  • Epigenomic Reprogramming in Patient Derived Models of Colorectal Cancer awarded by National Institutes of Health 2018 - 2023
  • The Duke FUNCTION Center: Pioneering the comprehensive identification of combinatorial noncoding causes of disease awarded by National Institutes of Health 2020 - 2023
  • Chromatin regulation during brain development and in ASD awarded by Yale University 2019 - 2023
  • Quantifying the genetic diversity of human regulatory element activity awarded by National Institutes of Health 2019 - 2023
  • Preparing Genetic Counselors for Genomic Medicine Research awarded by National Institutes of Health 2017 - 2022
  • IRES Track 1 IRTG Engaged in Dissecting and Reengineering the Regulatory Genome awarded by  National Science Foundation 2019 - 2022
  • Chromatin Mechanisms of Neuronal Maturation awarded by National Institutes of Health 2017 - 2022
  • Effects of PFBS exposure on adverse pregnancy outcomes and fetal development awarded by National Institutes of Health 2017 - 2022
  • Mapping Epigenetic Memory of Exposure New To Observe (MEMENTO) awarded by Defense Advanced Research Projects Agency 2019 - 2021
  • To support research on the development of CRISPR-based epigenome editing tools to refine genome wide association studies awarded by Open Philanthropy Project 2018 - 2021
  • Epigenome Editing Technologies to Control Diverse Biological Functions awarded by Allen Institute for Brain Science 2017 - 2021
  • 3/3 Chromatin regulation during brain development and in ASD awarded by National Institutes of Health 2018 - 2021
  • Regulatory Mechanisms of CD4+ T Cell Differentiation awarded by National Institutes of Health 2017 - 2021
  • Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
  • Identifying Pathogenic Non-Coding Mutations in Rare Mendelian Disease awarded by National Institutes of Health 2019 - 2021
  • Genetic epidemiology of rare and regulatory variants for metabolic traits awarded by University of North Carolina - Chapel Hill 2017 - 2021
  • Postdoctoral Training in Genomic Medicine Research awarded by National Institutes of Health 2017 - 2021
  • Systems Toxicogenomics of Endocrine Disrupting Chemicals in Brain awarded by North Carolina State University 2016 - 2021
  • HARDAC-M: Enabling memory-intensive computation for genomics awarded by North Carolina Biotechnology Center 2020 - 2021
  • Thwarting Influenza with RNA-powered Modulators (ThIRM) awarded by Georgia Institute of Technology 2019 - 2021
  • Exploring the Role of Dynamic Chromatin Occupancy in Transcriptional Regulation - Non-competing renewal III awarded by National Institutes of Health 2016 - 2021
  • Identification and application of regulatory elements for heart regeneration awarded by National Institutes of Health 2016 - 2020
  • New methods for quantitative modeling of protein-DNA interactions awarded by National Institutes of Health 2015 - 2020
  • Genetics Training Grant awarded by National Institutes of Health 1979 - 2020
  • Organization and Function of Cellular Structure awarded by National Institutes of Health 1975 - 2020
  • The function and regulation of the novel pregnancy-specific hexokinase HKDC1 awarded by University of Illinois at Chicago 2017 - 2020
  • Cellular and Molecular Systems Biology of Preterm Birth awarded by University of Chicago 2015 - 2019
  • Decoding schizophrenia-From GWAS to functional regulatory variants awarded by National Institutes of Health 2014 - 2019
  • Decoding and Reprogramming the Corticosteroid Transcriptional Regulatory Network awarded by National Institutes of Health 2015 - 2018
  • Engineering Targeted Epigenetic Modifiers for Precise Control of Gene Regulation awarded by National Institutes of Health 2013 - 2018
  • Genes, genomes, and genotoxicity: in vivo epigenetic toxicology of 1,3-butadiene awarded by University of North Carolina - Chapel Hill 2013 - 2018
  • GWAS TO GENE FUNCTION: NOS1AP AND OTHER QT INTERVAL GENES awarded by Johns Hopkins University 2014 - 2017
  • The function and regulation of the novel pregnancy-specific hexokinase HKDC1 awarded by Northwestern University 2015 - 2016
  • Genome-Wide Mapping of Enhancer Elements for Neuronal Differentiation Genes awarded by National Institutes of Health 2013 - 2016
  • Microbial Regulation of Nuclear Receptor Activity in the Intestinal Epithelium awarded by Baylor College of Medicine 2014 - 2016
  • Comprehensive Identification of Active Functional Elements in Human Chromatin awarded by National Institutes of Health 2007 - 2013
  • Identification of Disease-Causing Mutations in SCID Using Exome-Wide Sequencing awarded by National Institutes of Health 2009 - 2012
  • High-performance Computing System for Bioinformatics awarded by National Institutes of Health 2009 - 2010
  • Generation of a genome-wide DNAse hypersensitive library awarded by National Institutes of Health 2006 - 2010
• 

  External Relationships

  • Element Genomics
• Publications & Artistic Works
• 

  Selected Publications

  • Academic Articles

    • Crowley, James J., Jin Szatkiewicz, Anna K. Kähler, Paola Giusti-Rodriguez, NaEshia Ancalade, Jessica K. Booker, Jennifer L. Carr, et al. “Correction: Common-variant associations with fragile X syndrome.” Mol Psychiatry 25, no. 12 (December 2020): 3450. https://doi.org/10.1038/s41380-019-0526-x.
       Full Text  Link to Item
    • Sakabe, Noboru J., Ivy Aneas, Nicholas Knoblauch, Debora R. Sobreira, Nicole Clark, Cristina Paz, Cynthia Horth, et al. “Transcriptome and regulatory maps of decidua-derived stromal cells inform gene discovery in preterm birth.” Sci Adv 6, no. 49 (December 2020). https://doi.org/10.1126/sciadv.abc8696.
       Full Text  Link to Item
    • Keele, Gregory R., Bryan C. Quach, Jennifer W. Israel, Grace A. Chappell, Lauren Lewis, Alexias Safi, Jeremy M. Simon, et al. “Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation.” Plos Genet 16, no. 1 (January 2020): e1008537. https://doi.org/10.1371/journal.pgen.1008537.
       Full Text  Link to Item
    • Edsall, Lee E., Alejandro Berrio, William H. Majoros, Devjanee Swain-Lenz, Shauna Morrow, Yoichiro Shibata, Alexias Safi, Gregory A. Wray, Gregory E. Crawford, and Andrew S. Allen. “Evaluating Chromatin Accessibility Differences Across Multiple Primate Species Using a Joint Modeling Approach.” Genome Biol Evol 11, no. 10 (October 1, 2019): 3035–53. https://doi.org/10.1093/gbe/evz218.
       Full Text  Link to Item
    • Cannon, Maren E., Kevin W. Currin, Kristin L. Young, Hannah J. Perrin, Swarooparani Vadlamudi, Alexias Safi, Lingyun Song, et al. “Open Chromatin Profiling in Adipose Tissue Marks Genomic Regions with Functional Roles in Cardiometabolic Traits.” G3 (Bethesda) 9, no. 8 (August 8, 2019): 2521–33. https://doi.org/10.1534/g3.119.400294.
       Full Text  Link to Item
    • Swain-Lenz, Devjanee, Alejandro Berrio, Alexias Safi, Gregory E. Crawford, and Gregory A. Wray. “Comparative Analyses of Chromatin Landscape in White Adipose Tissue Suggest Humans May Have Less Beigeing Potential than Other Primates.” Genome Biol Evol 11, no. 7 (July 1, 2019): 1997–2008. https://doi.org/10.1093/gbe/evz134.
       Full Text  Link to Item
    • Crowley, James J., Jin Szatkiewicz, Anna K. Kähler, Paola Giusti-Rodriguez, NaEshia Ancalade, Jessica K. Booker, Jennifer L. Carr, et al. “Common-variant associations with fragile X syndrome.” Mol Psychiatry 24, no. 3 (March 2019): 338–44. https://doi.org/10.1038/s41380-018-0290-3.
       Full Text  Link to Item
    • Coleman, Jonathan R. I., Julien Bryois, Héléna A. Gaspar, Philip R. Jansen, Jeanne E. Savage, Nathan Skene, Robert Plomin, et al. “Biological annotation of genetic loci associated with intelligence in a meta-analysis of 87,740 individuals.” Mol Psychiatry 24, no. 2 (February 2019): 182–97. https://doi.org/10.1038/s41380-018-0040-6.
       Full Text  Link to Item
    • Barbu, M. C., Y. Zeng, X. Shen, S. R. Cox, T. K. Clarke, J. Gibson, M. J. Adams, et al. “Association of Whole-Genome and NETRIN1 Signaling Pathway–Derived Polygenic Risk Scores for Major Depressive Disorder and White Matter Microstructure in the UK Biobank.” Biological Psychiatry: Cognitive Neuroscience and Neuroimaging 4, no. 1 (January 1, 2019): 91–100. https://doi.org/10.1016/j.bpsc.2018.07.006.
       Full Text
    • Tung, K. L., K. Y. Chen, M. Negrete, T. Chen, A. Safi, A. A. Aljamal, L. Song, et al. “Integrated chromatin and transcriptomic profiling of patient-derived colon cancer organoids identifies personalized drug targets to overcome oxaliplatin resistance.” Genes and Diseases, January 1, 2019. https://doi.org/10.1016/j.gendis.2019.10.012.
       Full Text
    • Amiri, Anahita, Gianfilippo Coppola, Soraya Scuderi, Feinan Wu, Tanmoy Roychowdhury, Fuchen Liu, Sirisha Pochareddy, et al. “Transcriptome and epigenome landscape of human cortical development modeled in organoids.” Science 362, no. 6420 (December 14, 2018). https://doi.org/10.1126/science.aat6720.
       Full Text  Link to Item
    • Wang, Daifeng, Shuang Liu, Jonathan Warrell, Hyejung Won, Xu Shi, Fabio C. P. Navarro, Declan Clarke, et al. “Comprehensive functional genomic resource and integrative model for the human brain.” Science 362, no. 6420 (December 14, 2018). https://doi.org/10.1126/science.aat8464.
       Full Text  Link to Item
    • Whitley, Sarah K., Anand Balasubramani, Carlene L. Zindl, Ranjan Sen, Yoichiro Shibata, Gregory E. Crawford, Nathaniel M. Weathington, Robin D. Hatton, and Casey T. Weaver. “IL-1R signaling promotes STAT3 and NF-κB factor recruitment to distal cis-regulatory elements that regulate Il17a/f transcription.” J Biol Chem 293, no. 41 (October 12, 2018): 15790–800. https://doi.org/10.1074/jbc.RA118.002721.
       Full Text  Link to Item
    • Lee, Dongwon, Ashish Kapoor, Alexias Safi, Lingyun Song, Marc K. Halushka, Gregory E. Crawford, and Aravinda Chakravarti. “Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants.” Genome Res 28, no. 10 (October 2018): 1577–88. https://doi.org/10.1101/gr.234633.118.
       Full Text  Link to Item
    • McDowell, Ian C., Alejandro Barrera, Anthony M. D’Ippolito, Christopher M. Vockley, Linda K. Hong, Sarah M. Leichter, Luke C. Bartelt, et al. “Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding.” Genome Res 28, no. 9 (September 2018): 1272–84. https://doi.org/10.1101/gr.233346.117.
       Full Text  Link to Item
    • D’Ippolito, Anthony M., Ian C. McDowell, Alejandro Barrera, Linda K. Hong, Sarah M. Leichter, Luke C. Bartelt, Christopher M. Vockley, et al. “Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids.” Cell Syst 7, no. 2 (August 22, 2018): 146-160.e7. https://doi.org/10.1016/j.cels.2018.06.007.
       Full Text  Link to Item
    • Bryois, Julien, Melanie E. Garrett, Lingyun Song, Alexias Safi, Paola Giusti-Rodriguez, Graham D. Johnson, Annie W. Shieh, et al. “Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia.” Nat Commun 9, no. 1 (August 7, 2018): 3121. https://doi.org/10.1038/s41467-018-05379-y.
       Full Text  Link to Item
    • Peyrot, Wouter J., Sandra Van der Auwera, Yuri Milaneschi, Conor V. Dolan, Pamela A. F. Madden, Patrick F. Sullivan, Jana Strohmaier, et al. “Does Childhood Trauma Moderate Polygenic Risk for Depression? A Meta-analysis of 5765 Subjects From the Psychiatric Genomics Consortium.” Biol Psychiatry 84, no. 2 (July 15, 2018): 138–47. https://doi.org/10.1016/j.biopsych.2017.09.009.
       Full Text  Link to Item
    • Wray, Naomi R., Stephan Ripke, Manuel Mattheisen, Maciej Trzaskowski, Enda M. Byrne, Abdel Abdellaoui, Mark J. Adams, et al. “Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression.” Nat Genet 50, no. 5 (May 2018): 668–81. https://doi.org/10.1038/s41588-018-0090-3.
       Full Text  Link to Item
    • Gusev, Alexander, Nicholas Mancuso, Hyejung Won, Maria Kousi, Hilary K. Finucane, Yakir Reshef, Lingyun Song, et al. “Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights.” Nat Genet 50, no. 4 (April 2018): 538–48. https://doi.org/10.1038/s41588-018-0092-1.
       Full Text  Link to Item
    • Wang, Ting, Erica C. Pehrsson, Deepak Purushotham, Daofeng Li, Xiaoyu Zhuo, Bo Zhang, Heather A. Lawson, et al. “The NIEHS TaRGET II Consortium and environmental epigenomics.” Nat Biotechnol 36, no. 3 (March 6, 2018): 225–27. https://doi.org/10.1038/nbt.4099.
       Full Text  Link to Item
    • Pizzollo, Jason, William J. Nielsen, Yoichiro Shibata, Alexias Safi, Gregory E. Crawford, Gregory A. Wray, and Courtney C. Babbitt. “Comparative Serum Challenges Show Divergent Patterns of Gene Expression and Open Chromatin in Human and Chimpanzee.” Genome Biol Evol 10, no. 3 (March 1, 2018): 826–39. https://doi.org/10.1093/gbe/evy041.
       Full Text  Open Access Copy  Link to Item
    • Israel, Jennifer W., Grace A. Chappell, Jeremy M. Simon, Sebastian Pott, Alexias Safi, Lauren Lewis, Paul Cotney, et al. “Tissue- and strain-specific effects of a genotoxic carcinogen 1,3-butadiene on chromatin and transcription.” Mamm Genome 29, no. 1–2 (February 2018): 153–67. https://doi.org/10.1007/s00335-018-9739-6.
       Full Text  Link to Item
    • Arnau-Soler, Aleix, Mark J. Adams, Mark J. Generation Scotland, Mark J. Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Caroline Hayward, and Pippa A. Thomson. “Genome-wide interaction study of a proxy for stress-sensitivity and its prediction of major depressive disorder.” Plos One 13, no. 12 (2018): e0209160. https://doi.org/10.1371/journal.pone.0209160.
       Full Text  Link to Item
    • Klann, Tyler S., Gregory E. Crawford, Timothy E. Reddy, and Charles A. Gersbach. “Screening Regulatory Element Function with CRISPR/Cas9-based Epigenome Editing.” Methods Mol Biol 1767 (2018): 447–80. https://doi.org/10.1007/978-1-4939-7774-1_25.
       Full Text  Link to Item
    • Milaneschi, Yuri, Femke Lamers, Wouter J. Peyrot, Bernhard T. Baune, Gerome Breen, Abbas Dehghan, Andreas J. Forstner, et al. “Genetic Association of Major Depression With Atypical Features and Obesity-Related Immunometabolic Dysregulations.” Jama Psychiatry 74, no. 12 (December 1, 2017): 1214–25. https://doi.org/10.1001/jamapsychiatry.2017.3016.
       Full Text  Link to Item
    • Manandhar, Dinesh, Lingyun Song, Ami Kabadi, Jennifer B. Kwon, Lee E. Edsall, Melanie Ehrlich, Koji Tsumagari, Charles A. Gersbach, Gregory E. Crawford, and Raluca Gordân. “Incomplete MyoD-induced transdifferentiation is associated with chromatin remodeling deficiencies.” Nucleic Acids Res 45, no. 20 (November 16, 2017): 11684–99. https://doi.org/10.1093/nar/gkx773.
       Full Text  Link to Item
    • Chappell, Grace A., Jennifer W. Israel, Jeremy M. Simon, Sebastian Pott, Alexias Safi, Karl Eklund, Kenneth G. Sexton, et al. “Variation 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 Perspect 125, no. 10 (October 16, 2017): 107006. https://doi.org/10.1289/EHP1937.
       Full Text  Link to Item
    • Lewis, Lauren, Gregory E. Crawford, Terrence S. Furey, and Ivan Rusyn. “Genetic and epigenetic determinants of inter-individual variability in responses to toxicants.” Curr Opin Toxicol 6 (October 2017): 50–59. https://doi.org/10.1016/j.cotox.2017.08.006.
       Full Text  Link to Item
    • Davison, James M., Colin R. Lickwar, Lingyun Song, Ghislain Breton, Gregory E. Crawford, and John F. Rawls. “Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha.” Genome Res 27, no. 7 (July 2017): 1195–1206. https://doi.org/10.1101/gr.220111.116.
       Full Text  Link to Item
    • Klann, Tyler S., Joshua B. Black, Malathi Chellappan, Alexias Safi, Lingyun Song, Isaac B. Hilton, Gregory E. Crawford, Timothy E. Reddy, and Charles A. Gersbach. “CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome.” Nat Biotechnol 35, no. 6 (June 2017): 561–68. https://doi.org/10.1038/nbt.3853.
       Full Text  Link to Item
    • Montefiori, Lindsey, Liana Hernandez, Zijie Zhang, Yoav Gilad, Carole Ober, Gregory Crawford, Marcelo Nobrega, and Noboru Jo Sakabe. “Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9.” Sci Rep 7, no. 1 (May 26, 2017): 2451. https://doi.org/10.1038/s41598-017-02547-w.
       Full Text  Link to Item
    • Maatouk, Danielle M., Anirudh Natarajan, Yoichiro Shibata, Lingyun Song, Gregory E. Crawford, Uwe Ohler, and Blanche Capel. “Genome-wide identification of regulatory elements in Sertoli cells.” Development 144, no. 4 (February 15, 2017): 720–30. https://doi.org/10.1242/dev.142554.
       Full Text  Link to Item
    • Gopinath, Chetna, William D. Law, José F. Rodríguez-Molina, Arjun B. Prasad, Lingyun Song, Gregory E. Crawford, James C. Mullikin, John Svaren, and Anthony Antonellis. “Stringent comparative sequence analysis reveals SOX10 as a putative inhibitor of glial cell differentiation.” Bmc Genomics 17, no. 1 (November 7, 2016): 887. https://doi.org/10.1186/s12864-016-3167-3.
       Full Text  Link to Item
    • Vockley, Christopher M., Anthony M. D’Ippolito, Ian C. McDowell, William H. Majoros, Alexias Safi, Lingyun Song, Gregory E. Crawford, and Timothy E. Reddy. “Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome.” Cell 166, no. 5 (August 25, 2016): 1269-1281.e19. https://doi.org/10.1016/j.cell.2016.07.049.
       Full Text  Link to Item
    • Scott, Laura J., Michael R. Erdos, Jeroen R. Huyghe, Ryan P. Welch, Andrew T. Beck, Brooke N. Wolford, Peter S. Chines, et al. “The genetic regulatory signature of type 2 diabetes in human skeletal muscle.” Nat Commun 7 (June 29, 2016): 11764. https://doi.org/10.1038/ncomms11764.
       Full Text  Link to Item
    • Yang, Rui, Jenny L. Kerschner, Nehal Gosalia, Daniel Neems, Lidija K. Gorsic, Alexias Safi, Gregory E. Crawford, Steven T. Kosak, Shih-Hsing Leir, and Ann Harris. “Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus.” Nucleic Acids Res 44, no. 7 (April 20, 2016): 3082–94. https://doi.org/10.1093/nar/gkv1358.
       Full Text  Link to Item
    • Zhong, Jianling, Kaixuan Luo, Peter S. Winter, Gregory E. Crawford, Edwin S. Iversen, and Alexander J. Hartemink. “Mapping nucleosome positions using DNase-seq.” Genome Res 26, no. 3 (March 2016): 351–64. https://doi.org/10.1101/gr.195602.115.
       Full Text  Link to Item
    • Frank, Christopher L., Dinesh Manandhar, Raluca Gordân, and Gregory E. Crawford. “HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells.” Epigenetics Chromatin 9 (2016): 15. https://doi.org/10.1186/s13072-016-0065-5.
       Full Text  Open Access Copy  Link to Item
    • PsychENCODE Consortium, Nenad, Schahram Akbarian, Chunyu Liu, James A. Knowles, Flora M. Vaccarino, Peggy J. Farnham, Gregory E. Crawford, et al. “The PsychENCODE project.” Nat Neurosci 18, no. 12 (December 2015): 1707–12. https://doi.org/10.1038/nn.4156.
       Full Text  Open Access Copy  Link to Item
    • Thakore, Pratiksha I., Anthony M. D’Ippolito, Lingyun Song, Alexias Safi, Nishkala K. Shivakumar, Ami M. Kabadi, Timothy E. Reddy, Gregory E. Crawford, and Charles A. Gersbach. “Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements.” Nat Methods 12, no. 12 (December 2015): 1143–49. https://doi.org/10.1038/nmeth.3630.
       Full Text  Link to Item
    • Hauser, Michael A., Inas F. Aboobakar, Yutao Liu, Shiroh Miura, Benjamin T. Whigham, Pratap Challa, Joshua Wheeler, et al. “Genetic variants and cellular stressors associated with exfoliation syndrome modulate promoter activity of a lncRNA within the LOXL1 locus.” Hum Mol Genet 24, no. 22 (November 15, 2015): 6552–63. https://doi.org/10.1093/hmg/ddv347.
       Full Text  Link to Item
    • Fufa, Temesgen D., Melissa L. Harris, Dawn E. Watkins-Chow, Denise Levy, David U. Gorkin, Derek E. Gildea, Lingyun Song, et al. “Genomic analysis reveals distinct mechanisms and functional classes of SOX10-regulated genes in melanocytes.” Hum Mol Genet 24, no. 19 (October 1, 2015): 5433–50. https://doi.org/10.1093/hmg/ddv267.
       Full Text  Link to Item
    • Polstein, Lauren R., Pablo Perez-Pinera, D Dewran Kocak, Christopher M. Vockley, Peggy Bledsoe, Lingyun Song, Alexias Safi, Gregory E. Crawford, Timothy E. Reddy, and Charles A. Gersbach. “Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators.” Genome Res 25, no. 8 (August 2015): 1158–69. https://doi.org/10.1101/gr.179044.114.
       Full Text  Link to Item
    • Frank, Christopher L., Fang Liu, Ranjula Wijayatunge, Lingyun Song, Matthew T. Biegler, Marty G. Yang, Christopher M. Vockley, et al. “Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum.” Nat Neurosci 18, no. 5 (May 2015): 647–56. https://doi.org/10.1038/nn.3995.
       Full Text  Link to Item
    • Hilton, Isaac B., Anthony M. D’Ippolito, Christopher M. Vockley, Pratiksha I. Thakore, Gregory E. Crawford, Timothy E. Reddy, and Charles A. Gersbach. “Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers.” Nat Biotechnol 33, no. 5 (May 2015): 510–17. https://doi.org/10.1038/nbt.3199.
       Full Text  Link to Item
    • Ding, Z., Y. Ni, S. W. Timmer, B. K. Lee, A. Battenhouse, S. Louzada, F. Yang, et al. “Correction: Quantitative Genetics of CTCF Binding Reveal Local Sequence Effects and Different Modes of X-Chromosome Association (PLoS Genet, 11, 4, (2015)).” Plos Genetics 11, no. 4 (April 28, 2015). https://doi.org/10.1371/journal.pgen.1005177.
       Full Text
    • Raposo, Alexandre A. S. F., Francisca F. Vasconcelos, Daniela Drechsel, Corentine Marie, Caroline Johnston, Dirk Dolle, Angela Bithell, et al. “Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis.” Cell Rep 10, no. 9 (March 10, 2015): 1544–56. https://doi.org/10.1016/j.celrep.2015.02.025.
       Full Text  Link to Item
    • Hsiung, Chris C-S, Christapher S. Morrissey, Maheshi Udugama, Christopher L. Frank, Cheryl A. Keller, Songjoon Baek, Belinda Giardine, et al. “Genome accessibility is widely preserved and locally modulated during mitosis.” Genome Res 25, no. 2 (February 2015): 213–25. https://doi.org/10.1101/gr.180646.114.
       Full Text  Link to Item
    • Mateo, Juan L., Debbie L. C. van den Berg, Maximilian Haeussler, Daniela Drechsel, Zachary B. Gaber, Diogo S. Castro, Paul Robson, et al. “Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.” Genome Res 25, no. 1 (January 2015): 41–56. https://doi.org/10.1101/gr.173435.114.
       Full Text  Link to Item
    • Su, Dan, Xuting Wang, Michelle R. Campbell, Lingyun Song, Alexias Safi, Gregory E. Crawford, and Douglas A. Bell. “Interactions of chromatin context, binding site sequence content, and sequence evolution in stress-induced p53 occupancy and transactivation.” Plos Genet 11, no. 1 (January 2015): e1004885. https://doi.org/10.1371/journal.pgen.1004885.
       Full Text  Open Access Copy  Link to Item
    • Browne, James A., Rui Yang, Lingyun Song, Gregory E. Crawford, Shih-Hsing Leir, and Ann Harris. “Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function.” Mol Hum Reprod 20, no. 12 (December 2014): 1198–1207. https://doi.org/10.1093/molehr/gau075.
       Full Text  Link to Item
    • Ding, Zhihao, Yunyun Ni, Sander W. Timmer, Bum-Kyu Lee, Anna Battenhouse, Sandra Louzada, Fengtang Yang, et al. “Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.” Plos Genet 10, no. 11 (November 2014): e1004798. https://doi.org/10.1371/journal.pgen.1004798.
       Full Text  Open Access Copy  Link to Item
    • Yardımcı, Galip Gürkan, Christopher L. Frank, Gregory E. Crawford, and Uwe Ohler. “Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection.” Nucleic Acids Research 42, no. 19 (October 7, 2014): 11865–78. https://doi.org/10.1093/nar/gku810.
       Full Text  Open Access Copy
    • Zhang, Bing, Daniel S. Day, Joshua Ho, Lingyun Song, Jonathan G. Seidman, Gregory E. Crawford, Peter J. Park, and William T. Pu. “VEGF changes chromatin landscape in endothelial cell.” Angiogenesis 17, no. 4 (October 1, 2014): 957–957.
       Link to Item
    • Camp, J Gray, Christopher L. Frank, Colin R. Lickwar, Harendra Guturu, Tomas Rube, Aaron M. Wenger, Jenny Chen, Gill Bejerano, Gregory E. Crawford, and John F. Rawls. “Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape.” Genome Res 24, no. 9 (September 2014): 1504–16. https://doi.org/10.1101/gr.165845.113.
       Full Text  Link to Item
    • Kellis, Manolis, Barbara Wold, Michael P. Snyder, Bradley E. Bernstein, Anshul Kundaje, Georgi K. Marinov, Lucas D. Ward, et al. “Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.” Proc Natl Acad Sci U S A 111, no. 33 (August 19, 2014): E3366. https://doi.org/10.1073/pnas.1410434111.
       Full Text  Link to Item
    • Factor, Daniel C., Olivia Corradin, Gabriel E. Zentner, Alina Saiakhova, Lingyun Song, Josh G. Chenoweth, Ronald D. McKay, Gregory E. Crawford, Peter C. Scacheri, and Paul J. Tesar. “Epigenomic comparison reveals activation of "seed" enhancers during transition from naive to primed pluripotency.” Cell Stem Cell 14, no. 6 (June 5, 2014): 854–63. https://doi.org/10.1016/j.stem.2014.05.005.
       Full Text  Link to Item
    • Terragni, Jolyon, Guoqiang Zhang, Zhiyi Sun, Sriharsa Pradhan, Lingyun Song, Gregory E. Crawford, Michelle Lacey, and Melanie Ehrlich. “Notch signaling genes: myogenic DNA hypomethylation and 5-hydroxymethylcytosine.” Epigenetics 9, no. 6 (June 2014): 842–50. https://doi.org/10.4161/epi.28597.
       Full Text  Link to Item
    • Kellis, Manolis, Barbara Wold, Michael P. Snyder, Bradley E. Bernstein, Anshul Kundaje, Georgi K. Marinov, Lucas D. Ward, et al. “Defining functional DNA elements in the human genome.” Proc Natl Acad Sci U S A 111, no. 17 (April 29, 2014): 6131–38. https://doi.org/10.1073/pnas.1318948111.
       Full Text  Link to Item
    • Balasubramani, A., C. J. Winstead, H. Turner, K. M. Janowski, S. N. Harbour, Y. Shibata, G. E. Crawford, R. D. Hatton, and C. T. Weaver. “Deletion of a Conserved cis-Element in the Ifng Locus Highlights the Role of Acute Histone Acetylation in Modulating Inducible Gene Transcription.” Plos Genetics 10, no. 1 (January 1, 2014). https://doi.org/10.1371/journal.pgen.1003969.
       Full Text
    • Balasubramani, Anand, Colleen J. Winstead, Henrietta Turner, Karen M. Janowski, Stacey N. Harbour, Yoichiro Shibata, Gregory E. Crawford, Robin D. Hatton, and Casey T. Weaver. “Deletion of a conserved cis-element in the Ifng locus highlights the role of acute histone acetylation in modulating inducible gene transcription.” Plos Genet 10, no. 1 (January 2014): e1003969. https://doi.org/10.1371/journal.pgen.1003969.
       Full Text  Link to Item
    • Wortham, Matthew, Changcun Guo, Monica Zhang, Lingyun Song, Bum-Kyu Lee, Vishwanath R. Iyer, Terrence S. Furey, Gregory E. Crawford, Hai Yan, and Yiping He. “Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma.” Plos One 9, no. 9 (2014): e107156. https://doi.org/10.1371/journal.pone.0107156.
       Full Text  Open Access Copy  Link to Item
    • Gertz, Jason, Daniel Savic, Katherine E. Varley, E Christopher Partridge, Alexias Safi, Preti Jain, Gregory M. Cooper, Timothy E. Reddy, Gregory E. Crawford, and Richard M. Myers. “Distinct properties of cell-type-specific and shared transcription factor binding sites.” Mol Cell 52, no. 1 (October 10, 2013): 25–36. https://doi.org/10.1016/j.molcel.2013.08.037.
       Full Text  Link to Item
    • Bischof, Jared M., Austin E. Gillen, Lingyun Song, Nehal Gosalia, Darin London, Terrence S. Furey, Gregory E. Crawford, and Ann Harris. “A genome-wide analysis of open chromatin in human epididymis epithelial cells reveals candidate regulatory elements for genes coordinating epididymal function.” Biol Reprod 89, no. 4 (October 2013): 104. https://doi.org/10.1095/biolreprod.113.110403.
       Full Text  Link to Item
    • Perez-Pinera, Pablo, D Dewran Kocak, Christopher M. Vockley, Andrew F. Adler, Ami M. Kabadi, Lauren R. Polstein, Pratiksha I. Thakore, et al. “RNA-guided gene activation by CRISPR-Cas9-based transcription factors.” Nat Methods 10, no. 10 (October 2013): 973–76. https://doi.org/10.1038/nmeth.2600.
       Full Text  Link to Item
    • Tsumagari, Koji, Carl Baribault, Jolyon Terragni, Sruti Chandra, Chloe Renshaw, Zhiyi Sun, Lingyun Song, et al. “DNA methylation and differentiation: HOX genes in muscle cells.” Epigenetics Chromatin 6, no. 1 (August 2, 2013): 25. https://doi.org/10.1186/1756-8935-6-25.
       Full Text  Link to Item
    • Winter, Deborah R., Lingyun Song, Sayan Mukherjee, Terrence S. Furey, and Gregory E. Crawford. “DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types.” Genome Res 23, no. 7 (July 2013): 1118–29. https://doi.org/10.1101/gr.150482.112.
       Full Text  Link to Item
    • Zhang, Bing, Daniel S. Day, Joshua W. Ho, Lingyun Song, Jingjing Cao, Danos Christodoulou, Jonathan G. Seidman, Gregory E. Crawford, Peter J. Park, and William T. Pu. “A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity.” Genome Res 23, no. 6 (June 2013): 917–27. https://doi.org/10.1101/gr.149674.112.
       Full Text  Link to Item
    • Sheffield, Nathan C., Robert E. Thurman, Lingyun Song, Alexias Safi, John A. Stamatoyannopoulos, Boris Lenhard, Gregory E. Crawford, and Terrence S. Furey. “Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.” Genome Res 23, no. 5 (May 2013): 777–88. https://doi.org/10.1101/gr.152140.112.
       Full Text  Link to Item
    • Perez-Pinera, Pablo, David G. Ousterout, Jonathan M. Brunger, Alicia M. Farin, Katherine A. Glass, Farshid Guilak, Gregory E. Crawford, Alexander J. Hartemink, and Charles A. Gersbach. “Synergistic and tunable human gene activation by combinations of synthetic transcription factors.” Nat Methods 10, no. 3 (March 2013): 239–42. https://doi.org/10.1038/nmeth.2361.
       Full Text  Link to Item
    • Tsumagari, Koji, Carl Baribault, Jolyon Terragni, Katherine E. Varley, Jason Gertz, Sirharsa Pradhan, Melody Badoo, et al. “Early de novo DNA methylation and prolonged demethylation in the muscle lineage.” Epigenetics 8, no. 3 (March 2013): 317–32. https://doi.org/10.4161/epi.23989.
       Full Text  Link to Item
    • Varley, Katherine E., Jason Gertz, Kevin M. Bowling, Stephanie L. Parker, Timothy E. Reddy, Florencia Pauli-Behn, Marie K. Cross, et al. “Dynamic DNA methylation across diverse human cell lines and tissues.” Genome Res 23, no. 3 (March 2013): 555–67. https://doi.org/10.1101/gr.147942.112.
       Full Text  Link to Item
    • Perez-Pinera, P., D. D. Kocak, C. M. Vockley, A. F. Adler, A. M. Kabadi, L. R. Polstein, P. I. Thakore, et al. “RNA-guided gene activation by CRISPR-Cas9-based transcription factors.” Nature Methods 10, no. 10 (2013): 973–76. https://doi.org/10.1038/nmeth.2600.
       Full Text
    • Calabrese, J Mauro, Wei Sun, Lingyun Song, Joshua W. Mugford, Lucy Williams, Della Yee, Joshua Starmer, Piotr Mieczkowski, Gregory E. Crawford, and Terry Magnuson. “Site-specific silencing of regulatory elements as a mechanism of X inactivation.” Cell 151, no. 5 (November 21, 2012): 951–63. https://doi.org/10.1016/j.cell.2012.10.037.
       Full Text  Link to Item
    • Tewari, Alok K., Galip Gürkan Yardimci, Yoichiro Shibata, Nathan C. Sheffield, Lingyun Song, Barry S. Taylor, Stoyan G. Georgiev, et al. “Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity.” Genome Biol 13, no. 10 (October 3, 2012): R88. https://doi.org/10.1186/gb-2012-13-10-r88.
       Full Text  Link to Item
    • ENCODE Project Consortium, Serge. “An integrated encyclopedia of DNA elements in the human genome.” Nature 489, no. 7414 (September 6, 2012): 57–74. https://doi.org/10.1038/nature11247.
       Full Text  Link to Item
    • Thurman, Robert E., Eric Rynes, Richard Humbert, Jeff Vierstra, Matthew T. Maurano, Eric Haugen, Nathan C. Sheffield, et al. “The accessible chromatin landscape of the human genome.” Nature 489, no. 7414 (September 6, 2012): 75–82. https://doi.org/10.1038/nature11232.
       Full Text  Link to Item
    • Natarajan, Anirudh, Galip Gürkan Yardimci, Nathan C. Sheffield, Gregory E. Crawford, and Uwe Ohler. “Predicting cell-type-specific gene expression from regions of open chromatin.” Genome Res 22, no. 9 (September 2012): 1711–22. https://doi.org/10.1101/gr.135129.111.
       Full Text  Link to Item
    • Reddy, Timothy E., Jason Gertz, Gregory E. Crawford, Michael J. Garabedian, and Richard M. Myers. “The hypersensitive glucocorticoid response specifically regulates period 1 and expression of circadian genes.” Mol Cell Biol 32, no. 18 (September 2012): 3756–67. https://doi.org/10.1128/MCB.00062-12.
       Full Text  Link to Item
    • Mouse ENCODE Consortium, Leslie B., John A. Stamatoyannopoulos, Michael Snyder, Ross Hardison, Bing Ren, Thomas Gingeras, David M. Gilbert, et al. “An encyclopedia of mouse DNA elements (Mouse ENCODE).” Genome Biol 13, no. 8 (August 13, 2012): 418. https://doi.org/10.1186/gb-2012-13-8-418.
       Full Text  Link to Item
    • Stamatoyannopoulos, J. A., M. Snyder, R. Hardison, B. Ren, T. Gingeras, D. M. Gilbert, M. Groudine, et al. “An encyclopedia of mouse DNA elements (Mouse ENCODE) (Accepted).” Genome Biology, August 13, 2012, 418. https://doi.org/10.1186/gb4035.
       Full Text
    • Shibata, Yoichiro, Nathan C. Sheffield, Olivier Fedrigo, Courtney C. Babbitt, Matthew Wortham, Alok K. Tewari, Darin London, et al. “Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection.” Plos Genet 8, no. 6 (June 2012): e1002789. https://doi.org/10.1371/journal.pgen.1002789.
       Full Text  Link to Item
    • Balasubramanian, Dheepa, Batool Akhtar-Zaidi, Lingyun Song, Cynthia F. Bartels, Martina Veigl, Lydia Beard, Lois Myeroff, et al. “H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island-containing start sites.” Genome Med 4, no. 5 (May 28, 2012): 47. https://doi.org/10.1186/gm346.
       Full Text  Link to Item
    • Bischof, Jared M., Christopher J. Ott, Shih-Hsing Leir, Nehal Gosalia, Lingyun Song, Darin London, Terrence S. Furey, Calvin U. Cotton, Gregory E. Crawford, and Ann Harris. “A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function.” Thorax 67, no. 5 (May 2012): 385–91. https://doi.org/10.1136/thoraxjnl-2011-200880.
       Full Text  Link to Item
    • Reddy, Timothy E., Jason Gertz, Florencia Pauli, Katerina S. Kucera, Katherine E. Varley, Kimberly M. Newberry, Georgi K. Marinov, et al. “Effects of sequence variation on differential allelic transcription factor occupancy and gene expression.” Genome Res 22, no. 5 (May 2012): 860–69. https://doi.org/10.1101/gr.131201.111.
       Full Text  Link to Item
    • Tewari, Alok K., Galip G. Yardimci, Gregory E. Crawford, and Phillip G. Febbo. “Abstract 2923: Androgen receptor activation changes chromatin structure and transcriptional activation.” Endocrinology, April 15, 2012. https://doi.org/10.1158/1538-7445.am2012-2923.
       Full Text
    • Degner, Jacob F., Athma A. Pai, Roger Pique-Regi, Jean-Baptiste Veyrieras, Daniel J. Gaffney, Joseph K. Pickrell, Sherryl De Leon, et al. “DNase I sensitivity QTLs are a major determinant of human expression variation.” Nature 482, no. 7385 (February 5, 2012): 390–94. https://doi.org/10.1038/nature10808.
       Full Text  Link to Item
    • Gaffney, Daniel J., Jean-Baptiste Veyrieras, Jacob F. Degner, Roger Pique-Regi, Athma A. Pai, Gregory E. Crawford, Matthew Stephens, Yoav Gilad, and Jonathan K. Pritchard. “Dissecting the regulatory architecture of gene expression QTLs.” Genome Biol 13, no. 1 (January 31, 2012): R7. https://doi.org/10.1186/gb-2012-13-1-r7.
       Full Text  Link to Item
    • Lee, Bum-Kyu, Akshay A. Bhinge, Anna Battenhouse, Ryan M. McDaniell, Zheng Liu, Lingyun Song, Yunyun Ni, et al. “Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells.” Genome Res 22, no. 1 (January 2012): 9–24. https://doi.org/10.1101/gr.127597.111.
       Full Text  Link to Item
    • Parker, Stephen C. J., Jared Gartner, Isabel Cardenas-Navia, Xiaomu Wei, Hatice Ozel Abaan, Subramanian S. Ajay, Nancy F. Hansen, et al. “Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes.” Plos Genet 8, no. 8 (2012): e1002871. https://doi.org/10.1371/journal.pgen.1002871.
       Full Text  Link to Item
    • Zhang, Wenli, Yufeng Wu, James C. Schnable, Zixian Zeng, Michael Freeling, Gregory E. Crawford, and Jiming Jiang. “High-resolution mapping of open chromatin in the rice genome.” Genome Res 22, no. 1 (January 2012): 151–62. https://doi.org/10.1101/gr.131342.111.
       Full Text  Link to Item
    • Song, Lingyun, Zhancheng Zhang, Linda L. Grasfeder, Alan P. Boyle, Paul G. Giresi, Bum-Kyu Lee, Nathan C. Sheffield, et al. “Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.” Genome Res 21, no. 10 (October 2011): 1757–67. https://doi.org/10.1101/gr.121541.111.
       Full Text  Link to Item
    • Wu, Weisheng, Yong Cheng, Cheryl A. Keller, Jason Ernst, Swathi Ashok Kumar, Tejaswini Mishra, Christapher Morrissey, et al. “Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration.” Genome Res 21, no. 10 (October 2011): 1659–71. https://doi.org/10.1101/gr.125088.111.
       Full Text  Link to Item
    • Tsumagari, Koji, Shao-Chi Chang, Michelle Lacey, Carl Baribault, Sridar V. Chittur, Janet Sowden, Rabi Tawil, Gregory E. Crawford, and Melanie Ehrlich. “Gene expression during normal and FSHD myogenesis.” Bmc Med Genomics 4 (September 27, 2011): 67. https://doi.org/10.1186/1755-8794-4-67.
       Full Text  Link to Item
    • ENCODE Project Consortium, Vijay. “A user's guide to the encyclopedia of DNA elements (ENCODE).” Plos Biol 9, no. 4 (April 2011): e1001046. https://doi.org/10.1371/journal.pbio.1001046.
       Full Text  Link to Item
    • Boyle, Alan P., Lingyun Song, Bum-Kyu Lee, Darin London, Damian Keefe, Ewan Birney, Vishwanath R. Iyer, Gregory E. Crawford, and Terrence S. Furey. “High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.” Genome Res 21, no. 3 (March 2011): 456–64. https://doi.org/10.1101/gr.112656.110.
       Full Text  Link to Item
    • Stitzel, M. L., P. Sethupathy, D. S. Pearson, P. S. Chines, L. Song, M. R. Erdos, R. Welch, et al. “Erratum: Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci (Cell Metabolism (2010) 12 (443-455)).” Cell Metabolism 12, no. 6 (December 1, 2010): 683. https://doi.org/10.1016/j.cmet.2010.11.013.
       Full Text
    • Stitzel, Michael L., Praveen Sethupathy, Daniel S. Pearson, Peter S. Chines, Lingyun Song, Michael R. Erdos, Ryan Welch, et al. “Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci.” Cell Metab 12, no. 5 (November 3, 2010): 443–55. https://doi.org/10.1016/j.cmet.2010.09.012.
       Full Text  Link to Item
    • Birney, Ewan, Jason D. Lieb, Terrence S. Furey, Gregory E. Crawford, and Vishwanath R. Iyer. “Allele-specific and heritable chromatin signatures in humans.” Hum Mol Genet 19, no. R2 (October 15, 2010): R204–9. https://doi.org/10.1093/hmg/ddq404.
       Full Text  Link to Item
    • Balasubramani, Anand, Yoichiro Shibata, Gregory E. Crawford, Albert S. Baldwin, Robin D. Hatton, and Casey T. Weaver. “Modular utilization of distal cis-regulatory elements controls Ifng gene expression in T cells activated by distinct stimuli.” Immunity 33, no. 1 (July 23, 2010): 35–47. https://doi.org/10.1016/j.immuni.2010.07.004.
       Full Text  Link to Item
    • Schnetz, Michael P., Lusy Handoko, Batool Akhtar-Zaidi, Cynthia F. Bartels, C Filipe Pereira, Amanda G. Fisher, David J. Adams, et al. “CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression.” Plos Genet 6, no. 7 (July 15, 2010): e1001023. https://doi.org/10.1371/journal.pgen.1001023.
       Full Text  Open Access Copy  Link to Item
    • Schnetz, M. P., L. Handoko, B. Akhtar-Zaidi, C. F. Bartels, C. F. Pereira, A. G. Fisher, D. J. Adams, et al. “CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression.” Plos Genetics 6, no. 7 (July 1, 2010).
    • Mukasa, Ryuta, Anand Balasubramani, Yun Kyung Lee, Sarah K. Whitley, Benjamin T. Weaver, Yoichiro Shibata, Gregory E. Crawford, Robin D. Hatton, and Casey T. Weaver. “Epigenetic instability of cytokine and transcription factor gene loci underlies plasticity of the T helper 17 cell lineage.” Immunity 32, no. 5 (May 28, 2010): 616–27. https://doi.org/10.1016/j.immuni.2010.04.016.
       Full Text  Link to Item
    • McDaniell, Ryan, Bum-Kyu Lee, Lingyun Song, Zheng Liu, Alan P. Boyle, Michael R. Erdos, Laura J. Scott, et al. “Heritable individual-specific and allele-specific chromatin signatures in humans.” Science 328, no. 5975 (April 9, 2010): 235–39. https://doi.org/10.1126/science.1184655.
       Full Text  Link to Item
    • Song, Lingyun, and Gregory E. Crawford. “DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells.” Cold Spring Harb Protoc 2010, no. 2 (February 2010): pdb.prot5384. https://doi.org/10.1101/pdb.prot5384.
       Full Text  Link to Item
    • Xu, Xueqing, Koji Tsumagari, Janet Sowden, Rabi Tawil, Alan P. Boyle, Lingyun Song, Terrence S. Furey, Gregory E. Crawford, and Melanie Ehrlich. “DNaseI hypersensitivity at gene-poor, FSH dystrophy-linked 4q35.2.” Nucleic Acids Res 37, no. 22 (December 2009): 7381–93. https://doi.org/10.1093/nar/gkp833.
       Full Text  Link to Item
    • Ott, Christopher J., Neil P. Blackledge, Jenny L. Kerschner, Shih-Hsing Leir, Gregory E. Crawford, Calvin U. Cotton, and Ann Harris. “Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus.” Proc Natl Acad Sci U S A 106, no. 47 (November 24, 2009): 19934–39. https://doi.org/10.1073/pnas.0900946106.
       Full Text  Link to Item
    • Heintzman, Nathaniel D., Gary C. Hon, R David Hawkins, Pouya Kheradpour, Alexander Stark, Lindsey F. Harp, Zhen Ye, et al. “Histone modifications at human enhancers reflect global cell-type-specific gene expression.” Nature 459, no. 7243 (May 7, 2009): 108–12. https://doi.org/10.1038/nature07829.
       Full Text  Link to Item
    • Bina, Minou, Phillip Wyss, Sheryl A. Lazarus, Syed R. Shah, Wenhui Ren, Wojciech Szpankowski, Gregory E. Crawford, Sang P. Park, and Xiaohui C. Song. “Discovering sequences with potential regulatory characteristics.” Genomics 93, no. 4 (April 2009): 314–22. https://doi.org/10.1016/j.ygeno.2008.11.008.
       Full Text  Link to Item
    • Ott, Christopher J., Magdalena Suszko, Neil P. Blackledge, Jane E. Wright, Gregory E. Crawford, and Ann Harris. “A complex intronic enhancer regulates expression of the CFTR gene by direct interaction with the promoter.” J Cell Mol Med 13, no. 4 (April 2009): 680–92. https://doi.org/10.1111/j.1582-4934.2008.00621.x.
       Full Text  Open Access Copy  Link to Item
    • Schnetz, Michael P., Cynthia F. Bartels, Kuntal Shastri, Dheepa Balasubramanian, Gabriel E. Zentner, Ravishankar Balaji, Xiaodong Zhang, et al. “Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns.” Genome Res 19, no. 4 (April 2009): 590–601. https://doi.org/10.1101/gr.086983.108.
       Full Text  Link to Item
    • Shibata, Yoichiro, and Gregory E. Crawford. “Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip).” Methods Mol Biol 556 (2009): 177–90. https://doi.org/10.1007/978-1-60327-192-9_13.
       Full Text  Link to Item
    • Boyle, Alan P., Justin Guinney, Gregory E. Crawford, and Terrence S. Furey. “F-Seq: a feature density estimator for high-throughput sequence tags.” Bioinformatics 24, no. 21 (November 1, 2008): 2537–38. https://doi.org/10.1093/bioinformatics/btn480.
       Full Text  Link to Item
    • Boyle, Alan P., Sean Davis, Hennady P. Shulha, Paul Meltzer, Elliott H. Margulies, Zhiping Weng, Terrence S. Furey, and Gregory E. Crawford. “High-resolution mapping and characterization of open chromatin across the genome.” Cell 132, no. 2 (January 25, 2008): 311–22. https://doi.org/10.1016/j.cell.2007.12.014.
       Full Text  Link to Item
    • Eguchi, Jun, Qing-Wu Yan, Dustin E. Schones, Michael Kamal, Chung-Hsin Hsu, Michael Q. Zhang, Gregory E. Crawford, and Evan D. Rosen. “Interferon regulatory factors are transcriptional regulators of adipogenesis.” Cell Metab 7, no. 1 (January 2008): 86–94. https://doi.org/10.1016/j.cmet.2007.11.002.
       Full Text  Link to Item
    • Xi, Hualin, Hennady P. Shulha, Jane M. Lin, Teresa R. Vales, Yutao Fu, David M. Bodine, Ronald D. G. McKay, et al. “Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome.” Plos Genet 3, no. 8 (August 2007): e136. https://doi.org/10.1371/journal.pgen.0030136.
       Full Text  Link to Item
    • ENCODE Project Consortium, Pieter J., Ewan Birney, John A. Stamatoyannopoulos, Anindya Dutta, Roderic Guigó, Thomas R. Gingeras, Elliott H. Margulies, et al. “Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.” Nature 447, no. 7146 (June 14, 2007): 799–816. https://doi.org/10.1038/nature05874.
       Full Text  Link to Item
    • Heintzman, Nathaniel D., Rhona K. Stuart, Gary Hon, Yutao Fu, Christina W. Ching, R David Hawkins, Leah O. Barrera, et al. “Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.” Nat Genet 39, no. 3 (March 2007): 311–18. https://doi.org/10.1038/ng1966.
       Full Text  Link to Item
    • Nagel, Stefan, Michaela Scherr, Alexander Kel, Klaus Hornischer, Gregory E. Crawford, Maren Kaufmann, Corinna Meyer, Hans G. Drexler, and Roderick A. F. MacLeod. “Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU.1 and HMGA1.” Cancer Res 67, no. 4 (February 15, 2007): 1461–71. https://doi.org/10.1158/0008-5472.CAN-06-2615.
       Full Text  Link to Item
    • Xi, H., H. P. Shulha, J. M. Lin, T. R. Vales, Y. Fu, D. M. Bodine, R. D. G. McKay, et al. “Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome.” Plos Genetics 3, no. 8 (2007): e136. https://doi.org/10.1371/journal.pgen.0030136.
       Full Text
    • Bernat, John A., Gregory E. Crawford, Aleksey Y. Ogurtsov, Francis S. Collins, David Ginsburg, and Alexey S. Kondrashov. “Distant conserved sequences flanking endothelial-specific promoters contain tissue-specific DNase-hypersensitive sites and over-represented motifs.” Hum Mol Genet 15, no. 13 (July 1, 2006): 2098–2105. https://doi.org/10.1093/hmg/ddl133.
       Full Text  Link to Item
    • Crawford, Gregory E., Sean Davis, Peter C. Scacheri, Gabriel Renaud, Mohamad J. Halawi, Michael R. Erdos, Roland Green, Paul S. Meltzer, Tyra G. Wolfsberg, and Francis S. Collins. “DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays.” Nat Methods 3, no. 7 (July 2006): 503–9. https://doi.org/10.1038/nmeth888.
       Full Text  Link to Item
    • Lewinski, Mary K., Masahiro Yamashita, Michael Emerman, Angela Ciuffi, Heather Marshall, Gregory Crawford, Francis Collins, et al. “Retroviral DNA integration: viral and cellular determinants of target-site selection.” Plos Pathog 2, no. 6 (June 2006): e60. https://doi.org/10.1371/journal.ppat.0020060.
       Full Text  Link to Item
    • Scacheri, Peter C., Sean Davis, Duncan T. Odom, Gregory E. Crawford, Stacie Perkins, Mohamad J. Halawi, Sunita K. Agarwal, et al. “Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis.” Plos Genet 2, no. 4 (April 2006): e51. https://doi.org/10.1371/journal.pgen.0020051.
       Full Text  Link to Item
    • Crawford, Gregory E., Ingeborg E. Holt, James Whittle, Bryn D. Webb, Denise Tai, Sean Davis, Elliott H. Margulies, et al. “Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS).” Genome Res 16, no. 1 (January 2006): 123–31. https://doi.org/10.1101/gr.4074106.
       Full Text  Link to Item
    • Lewinski, M. K., M. Yamashita, M. Emerman, A. Ciuffi, H. Marshall, G. Crawford, F. Collins, et al. “Retroviral DNA integration: Viral and cellular determinants of target-site selection.” Plos Pathogens 2, no. 6 (2006): 0611–22. https://doi.org/10.1371/journal.ppat.0020060.
       Full Text
    • Scacheri, P. C., S. Davis, D. T. Odom, G. E. Crawford, S. Perkins, M. J. Halawi, S. K. Agarwal, et al. “Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis.” Plos Genetics 2, no. 4 (2006): e51. https://doi.org/10.1371/journal.pgen.0020051.
       Full Text
    • Scacheri, Peter C., Gregory E. Crawford, and Sean Davis. “Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays.” Methods Enzymol 411 (2006): 270–82. https://doi.org/10.1016/S0076-6879(06)11014-9.
       Full Text  Link to Item
    • Yan, Jizhou, Lisha Xu, Gregory Crawford, Zenfeng Wang, and Shawn M. Burgess. “The forkhead transcription factor FoxI1 remains bound to condensed mitotic chromosomes and stably remodels chromatin structure.” Mol Cell Biol 26, no. 1 (January 2006): 155–68. https://doi.org/10.1128/MCB.26.1.155-168.2006.
       Full Text  Link to Item
    • ENCODE Project Consortium, Anthony J. “The ENCODE (ENCyclopedia Of DNA Elements) Project.” Science 306, no. 5696 (October 22, 2004): 636–40. https://doi.org/10.1126/science.1105136.
       Full Text  Link to Item
    • Crawford, Gregory E., Ingeborg E. Holt, James C. Mullikin, Denise Tai, Robert Blakesley, Gerard Bouffard, Alice Young, et al. “Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites.” Proc Natl Acad Sci U S A 101, no. 4 (January 27, 2004): 992–97. https://doi.org/10.1073/pnas.0307540100.
       Full Text  Link to Item
    • Crawford, G. E., Q. L. Lu, T. A. Partridge, and J. S. Chamberlain. “Suppression of revertant fibers in mdx mice by expression of a functional dystrophin.” Hum Mol Genet 10, no. 24 (November 15, 2001): 2745–50. https://doi.org/10.1093/hmg/10.24.2745.
       Full Text  Link to Item
    • Crawford, G. E., J. A. Faulkner, R. H. Crosbie, K. P. Campbell, S. C. Froehner, and J. S. Chamberlain. “Assembly of the dystrophin-associated protein complex does not require the dystrophin COOH-terminal domain.” J Cell Biol 150, no. 6 (September 18, 2000): 1399–1410. https://doi.org/10.1083/jcb.150.6.1399.
       Full Text  Link to Item
    • Lumeng, C., S. Phelps, G. E. Crawford, P. D. Walden, K. Barald, and J. S. Chamberlain. “Interactions between beta 2-syntrophin and a family of microtubule-associated serine/threonine kinases.” Nat Neurosci 2, no. 7 (July 1999): 611–17. https://doi.org/10.1038/10165.
       Full Text  Link to Item

  • Conference Papers

    • Thakore, Pratiksha I., Anthony D’Ippolito, Lingyun Song, Alexias Safi, Nishkala K. Shivakumar, Ami M. Kabadi, Peggy Bledsoe, Timothy E. Reddy, Gregory E. Crawford, and Charles A. Gersbach. “485. Targeted Epigenome Editing by CRISPR/Cas9-Based Repressors for Silencing of Distal Regulatory Elements.” In Molecular Therapy, 23:S192–93. Elsevier BV, 2015. https://doi.org/10.1016/s1525-0016(16)34094-1.
       Full Text
    • Babbitt, C. C., L. W. Pfefferle, G. E. Crawford, and G. A. Wray. “Evolution of gene expression network underlying a disease state.” In Integrative and Comparative Biology, 55:E7–E7. OXFORD UNIV PRESS INC, 2015.
       Link to Item
    • Hsiung, Chris C. S., Christapher Morrissey, Maheshi Udugama, Christopher Frank, Cheryl A. Keller, Songjoon Baek, Belinda Giardine, et al. “Epigenetics of Cellular Memory: Insights from the Chromatin Accessibility Landscape of the Mitotic Genome.” In Blood, Vol. 124. AMER SOC HEMATOLOGY, 2014.
       Link to Item
    • Thakore, Pratiksha I., David G. Ousterout, Ami M. Kabadi, Victoria E. Deneke, Gregory E. Crawford, Timothy E. Reddy, and Charles A. Gersbach. “CRISPR/Cas9-Based Transcriptional Repressors for Control of Human Gene Expression.” In Molecular Therapy, 22:S214–15. NATURE PUBLISHING GROUP, 2014.
       Link to Item
    • Perez-Pinera, Pablo, David G. Ousterout, Jonathan M. Brunger, Alicia M. Farin, Katherine A. Glass, Farshid Guilak, Gregory E. Crawford, Alexander J. Hartemink, and Charles A. Gersbach. “Synergistic and Tunable Gene Activation by Combinations of Synthetic Transcription Factors.” In Molecular Therapy, 21:S93–S93. NATURE PUBLISHING GROUP, 2013.
       Link to Item
    • Ehrlich, Melanie, Koji Tsumagari, Shao-Chi Chang, Michelle Lacey, Carl Baribault, Sridar V. Chittur, Janet Sowden, et al. “FINDING TARGETS FOR FSH DYSTROPHY THERAPY.” In Journal of Gene Medicine, 13:418–418. WILEY-BLACKWELL, 2011.
       Link to Item
    • Nagel, Stefan, Michaela Scherr, Alexander Kel, Klaus Hornischer, Gregory E. Crawford, Maren Kaufmann, Corinna Meyer, Hans G. Drexler, and Roderick A. F. MacLeod. “Inhibition of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-ALL after Blocking Remote 3′-BCL11B Enhancer Sequences with Matching DNA Oligos Reveals Coregulation by PU.1 and HMGA1.” In Blood, 108:2212–2212. American Society of Hematology, 2006. https://doi.org/10.1182/blood.v108.11.2212.2212.
       Full Text
• Teaching & Mentoring
• 

  Recent Courses

  • UPGEN 778A: University Program in Genetics and Genomics Biological Solutions Module I 2021
  • UPGEN 778A: University Program in Genetics and Genomics Biological Solutions Module I 2020
  • BIOLOGY 728B: University Program in Genetics and Genomics Biological Solutions Module Il 2019
  • CMB 778B: University Program in Genetics and Genomics Biological Solutions Module Il 2019
  • MGM 778B: University Program in Genetics and Genomics Biological Solutions Module Il 2019
  • UPGEN 778B: University Program in Genetics and Genomics Biological Solutions Module Il 2019
• Scholarly, Clinical, & Service Activities
• 

  Outreach & Engaged Scholarship

  • Bass Connections Faculty Team Member . Enabling Precision Health and Medicine . August 2017 - May 2018  2017 - 2018

Some information on this profile has been compiled automatically from Duke databases and external sources. (Our About page explains how this works.) If you see a problem with the information, please write to Scholars@Duke and let us know. We will reply promptly.