Gregory E. Crawford | Scholars@Duke

Gregory E. Crawford
Professor in Pediatrics

My research involves identifying gene regulatory elements across the genome to help us understand how chromatin structure dictates cell function and fate. For the last 30 years, mapping chromatin accessible sites has been the gold standard method to identify the location of active regulatory elements, including promoters, enhancers, silencers, and locus control regions. I have developed technologies that can identify most DNase I hypersensitive sites from potentially any cell type from any species with a sequenced genome. We are combining this data with other wet-lab and computational data types to better understand how these regulatory regions control global gene expression in a set of diverse tissues (normal and diseased) representative of the human body.

Current Appointments & Affiliations

Professor in Pediatrics, Pediatrics, Medical Genetics, Pediatrics 2020
Associate Professor in Molecular Genetics and Microbiology, Molecular Genetics and Microbiology, Basic Science Departments 2015
Affiliate of the Duke Regeneration Center, Regeneration Next Initiative, Basic Science Departments 2021

Contact Information

Box 3382 Med Ctr, Durham, NC 27710
Room 2353B CIEMAS, Durham, NC 27708
greg.crawford@duke.edu (919) 684-8196
Crawford Lab Website

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
Previous Appointments & Affiliations
- 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
- JAN 6, 2015 Duke Today
  
  Genomics Team Wins $5.9 Million Grant
Research
Selected Grants
- ATRXmutations,innate immune activation and therapeutic vunerabilityin malignant gliomas awarded by National Institutes of Health 2022 - 2027
- Myovascular Mechanisms of Cardiac Growth and Regeneration awarded by National Institutes of Health 2022 - 2026
- High-Throughput Functional Annotation of Gene Regulatory Elements and Variants Critical to Complex Cellular Phenotypes awarded by National Institutes of Health 2021 - 2026
- Duke Center for Advancement of Child Health (CAtCH). awarded by National Institutes of Health 2021 - 2026
- Beyond GWAS: High Throughput Functional Genomics & Epigenome Editing to Elucidate the Effects of Genetic Associations for Schizophrenia awarded by National Institutes of Health 2021 - 2026
- Genetic and Genomics Training Grant awarded by National Institutes of Health 2020 - 2025
- Untangling the diversity in the genetic architecture of late-onset Alzheimer's disease using single cell multi-omics awarded by National Institutes of Health 2022 - 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
- Genomics, variation, and evolution of cerebellar circuits linked to higher cognitive functions in humans awarded by National Institutes of Health 2021 - 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
- Preparing Genetic Counselors for Genomic Medicine Research awarded by National Institutes of Health 2017 - 2023
- Quantifying the genetic diversity of human regulatory element activity awarded by National Institutes of Health 2019 - 2023
- Postdoctoral Training in Genomic Medicine Research awarded by National Institutes of Health 2017 - 2023
- Discovery and validation of genetic variation impacting the gene regulatory landscape during human cortical development awarded by University of North Carolina - Chapel Hill 2021 - 2023
- IRES Track 1 IRTG Engaged in Dissecting and Reengineering the Regulatory Genome awarded by National Science Foundation 2019 - 2023
- Chromatin Mechanisms of Neuronal Maturation awarded by National Institutes of Health 2017 - 2023
- Thwarting Influenza with RNA-powered Modulators (ThIRM) awarded by Georgia Institute of Technology 2019 - 2023
- To support research on the development of CRISPR-based epigenome editing tools to refine genome wide association studies awarded by Open Philanthropy Project 2018 - 2022
- Regulatory Mechanisms of CD4+ T Cell Differentiation awarded by National Institutes of Health 2017 - 2022
- Identifying Pathogenic Non-Coding Mutations in Rare Mendelian Disease awarded by National Institutes of Health 2019 - 2022
- Genetic epidemiology of rare and regulatory variants for metabolic traits awarded by University of North Carolina - Chapel Hill 2017 - 2022
- Systems Toxicogenomics of Endocrine Disrupting Chemicals in Brain awarded by North Carolina State University 2016 - 2022
- Effects of perfluorobutane sulfonate (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 - 2022
- Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 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
- HARDAC-M: Enabling memory-intensive computation for genomics awarded by North Carolina Biotechnology Center 2020 - 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
- 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
  - Luo, Kaixuan, Jianling Zhong, Alexias Safi, Linda K. Hong, Alok K. Tewari, Lingyun Song, Timothy E. Reddy, Li Ma, Gregory E. Crawford, and Alexander J. Hartemink. “Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data.” Genome Res 32, no. 6 (June 2022): 1183–98. https://doi.org/10.1101/gr.272203.120.
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  - Sun, Fei, Jianhong Ou, Adam R. Shoffner, Yu Luan, Hongbo Yang, Lingyun Song, Alexias Safi, et al. “Enhancer selection dictates gene expression responses in remote organs during tissue regeneration.” Nature Cell Biology 24, no. 5 (May 2022): 685–96. https://doi.org/10.1038/s41556-022-00906-y.
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  - Cao, Yingxi, Yu Xia, Joseph J. Balowski, Jianhong Ou, Lingyun Song, Alexias Safi, Timothy Curtis, Gregory E. Crawford, Kenneth D. Poss, and Jingli Cao. “Identification of enhancer regulatory elements that direct epicardial gene expression during zebrafish heart regeneration.” Development 149, no. 4 (February 15, 2022). https://doi.org/10.1242/dev.200133.
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  - Kadur Lakshminarasimha Murthy, Preetish, Rui Xi, Diana Arguijo, Jeffrey I. Everitt, Dewran D. Kocak, Yoshihiko Kobayashi, Aline Bozec, et al. “Epigenetic basis of oncogenic-Kras-mediated epithelial-cellular proliferation and plasticity.” Dev Cell 57, no. 3 (February 7, 2022): 310-328.e9. https://doi.org/10.1016/j.devcel.2022.01.006.
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  - Gamache, J., J. Barrera, D. Gingerich, M. Garrett, D. Chipman, H. Fradin, A. Ashley-Koch, G. Crawford, and O. Chiba-Falek. “Parallel single-nucleus chromatin accessibility and transcriptomic profiling of human late-onset Alzheimer's disease brains.” Alzheimer’S &Amp; Dementia : The Journal of the Alzheimer’S Association 17 (December 1, 2021): e057261. https://doi.org/10.1002/alz.057261.
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  - Wang, Lihua, Ergang Wang, Jorge Prado Balcazar, Zhenzhen Wu, Kun Xiang, Yi Wang, Qiang Huang, et al. “Chromatin Remodeling of Colorectal Cancer Liver Metastasis is Mediated by an HGF-PU.1-DPP4 Axis.” Adv Sci (Weinh) 8, no. 19 (October 2021): e2004673. https://doi.org/10.1002/advs.202004673.
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  - Barrera, Julio, Lingyun Song, Julia E. Gamache, Melanie E. Garrett, Alexias Safi, Young Yun, Ivana Premasinghe, et al. “Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer's disease brains.” Mol Neurodegener 16, no. 1 (August 24, 2021): 58. https://doi.org/10.1186/s13024-021-00481-0.
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  - Miller, Danny E., Arvis Sulovari, Tianyun Wang, Hailey Loucks, Kendra Hoekzema, Katherine M. Munson, Alexandra P. Lewis, et al. “Targeted long-read sequencing identifies missing disease-causing variation.” Am J Hum Genet 108, no. 8 (August 5, 2021): 1436–49. https://doi.org/10.1016/j.ajhg.2021.06.006.
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  - Liang, Dan, Angela L. Elwell, Nil Aygün, Oleh Krupa, Justin M. Wolter, Felix A. Kyere, Michael J. Lafferty, et al. “Cell-type-specific effects of genetic variation on chromatin accessibility during human neuronal differentiation.” Nature Neuroscience 24, no. 7 (July 2021): 941–53. https://doi.org/10.1038/s41593-021-00858-w.
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  - Tung, Kuei-Ling, Kai-Yuan Chen, Marcos Negrete, Tianyi Chen, Alexias Safi, Abed Alhalim Aljamal, Lingyun Song, et al. “Integrated chromatin and transcriptomic profiling of patient-derived colon cancer organoids identifies personalized drug targets to overcome oxaliplatin resistance.” Genes Dis 8, no. 2 (March 2021): 203–14. https://doi.org/10.1016/j.gendis.2019.10.012.
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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. “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.
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  - 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.
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  - Thompson, John D., Jianhong Ou, Nutishia Lee, Kwangdeok Shin, Valentina Cigliola, Lingyun Song, Gregory E. Crawford, Junsu Kang, and Kenneth D. Poss. “Identification and requirements of enhancers that direct gene expression during zebrafish fin regeneration.” Development 147, no. 14 (July 30, 2020). https://doi.org/10.1242/dev.191262.
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  - 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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  - Cocce, Kimberly J., Jeff S. Jasper, Taylor K. Desautels, Logan Everett, Suzanne Wardell, Thomas Westerling, Robert Baldi, et al. “The Lineage Determining Factor GRHL2 Collaborates with FOXA1 to Establish a Targetable Pathway in Endocrine Therapy-Resistant Breast Cancer.” Cell Rep 29, no. 4 (October 22, 2019): 889-903.e10. https://doi.org/10.1016/j.celrep.2019.09.032.
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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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  - Hoffman, Gabriel E., Jaroslav Bendl, Georgios Voloudakis, Kelsey S. Montgomery, Laura Sloofman, Ying-Chih Wang, Hardik R. Shah, et al. “CommonMind Consortium provides transcriptomic and epigenomic data for Schizophrenia and Bipolar Disorder.” Sci Data 6, no. 1 (September 24, 2019): 180. https://doi.org/10.1038/s41597-019-0183-6.
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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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  - 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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  - 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.
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  - 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.
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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 (Cambridge, England) 144, no. 4 (February 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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  - 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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  - 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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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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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. “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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - ENCODE Project Consortium, E Jane. “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 2022
- UPGEN 778A: University Program in Genetics and Genomics Biological Solutions Module I 2021
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- Bass Connections Faculty Team Member . Enabling Precision Health and Medicine . August 2017 - May 2018 2017 - 2018

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