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 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
  • 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
  • Mapping Epigenetic Memory of Exposure New To Observe (MEMENTO) awarded by Defense Advanced Research Projects Agency 2019 - 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

    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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 Res 42, no. 19 (October 29, 2014): 11865–78. https://doi.org/10.1093/nar/gku810.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • ENCODE Project Consortium, Sean D. “The ENCODE (ENCyclopedia Of DNA Elements) Project.” Science 306, no. 5696 (October 22, 2004): 636–40. https://doi.org/10.1126/science.1105136.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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  • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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    • 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.
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• Teaching & Mentoring
• 

  Recent Courses

  • 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
  • BIOLOGY 728B: University Program in Genetics and Genomics Biological Solutions Module Il 2018
  • CMB 778B: University Program in Genetics and Genomics Biological Solutions Module Il 2018
  • MGM 778B: University Program in Genetics and Genomics Biological Solutions Module Il 2018
  • UPGEN 778B: University Program in Genetics and Genomics Biological Solutions Module Il 2018
• Scholarly, Clinical, & Service Activities
• 

  Outreach & Engaged Scholarship

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

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