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 at 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

  • Epigenomic Reprogramming in Patient Derived Models of Colorectal Cancer awarded by National Institutes of Health 2018 - 2023
  • Summer Scholars Program in Genome Sciences and Medicine awarded by National Institutes of Health 2017 - 2022
  • Deciphering the regulation of gene expression in the etiology of LOAD awarded by National Institutes of Health 2017 - 2022
  • Postdoctoral Training in Genomic Medicine Research awarded by National Institutes of Health 2017 - 2022
  • Chromatin Mechanisms of Neuronal Maturation awarded by National Institutes of Health 2017 - 2022
  • Effects of perfluorobutane sulfonate (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
  • 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
  • Cellular and Molecular Systems Biology of Preterm Birth awarded by University of Chicago 2015 - 2020
  • 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
  • Epigenome Editing Technologies to Control Diverse Biological Functions awarded by Allen Institute for Brain Science 2017 - 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
  • Exploring the Role of Dynamic Chromatin Occupancy in Transcriptional Regulation - Non-competing renewal II awarded by National Institutes of Health 2016 - 2020
  • 3/3 Chromatin regulation during brain development and in ASD awarded by National Institutes of Health 2018 - 2019
  • Genetic epidemiology of rare and regulatory variants for metabolic traits awarded by University of North Carolina - Chapel Hill 2017 - 2019
  • The function and regulation of the novel pregnancy-specific hexokinase HKDC1 awarded by University of Illinois at Chicago 2017 - 2019
  • Decoding schizophrenia-From GWAS to functional regulatory variants awarded by National Institutes of Health 2014 - 2019
  • Systems Toxicogenomics of Endocrine Disrupting Chemicals in Brain awarded by North Carolina State University 2016 - 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
• Publications & Artistic Works
• 

  Selected Publications

  • Academic Articles

    • Crowley, JJ, Szatkiewicz, J, Kähler, AK, Giusti-Rodriguez, P, Ancalade, N, Booker, JK, Carr, JL, Crawford, GE, Losh, M, Stockmeier, CA, Taylor, AK, Piven, J, and Sullivan, PF. "Common-variant associations with fragile X syndrome." Molecular Psychiatry 24, no. 3 (March 2019): 338-344.  Full Text
    • Coleman, JRI, Bryois, J, Gaspar, HA, Jansen, PR, Savage, JE, Skene, N, Plomin, R, Muñoz-Manchado, AB, Linnarsson, S, Crawford, G, Hjerling-Leffler, J, Sullivan, PF, Posthuma, D, and Breen, G. "Biological annotation of genetic loci associated with intelligence in a meta-analysis of 87,740 individuals." Molecular Psychiatry 24, no. 2 (February 2019): 182-197.  Full Text
    • Barbu, MC, Zeng, Y, Shen, X, Cox, SR, Clarke, TK, Gibson, J, Adams, MJ, Johnstone, M, Haley, CS, Lawrie, SM, Deary, IJ, Wray, NR, Ripke, S, Mattheisen, M, Trzaskowski, M, Byrne, EM, Abdellaoui, A, Agerbo, E, Air, TM, Andlauer, TFM, Bacanu, SA, Bækvad-Hansen, M, Beekman, ATF, Bigdeli, TB, Binder, EB, Blackwood, DHR, Bryois, J, Buttenschøn, HN, Bybjerg-Grauholm, J, Cai, N, Castelao, E, Christensen, JH, Coleman, JRI, Colodro-Conde, L, Couvy-Duchesne, B, Craddock, N, Crawford, GE, Davies, G, Degenhardt, F, Derks, EM, Direk, N, Dolan, CV, Dunn, EC, Eley, TC, Escott-Price, V, Hassan Kiadeh, FF, Finucane, HK, Forstner, AJ, Frank, J, Gaspar, HA, Gill, M, Goes, FS, Gordon, SD, Grove, J, Hall, LS, Hansen, CS, Hansen, TF, Herms, S, Hickie, IB, Hoffmann, P, Homuth, G, Horn, C, Hottenga, JJ, Hougaard, DM, Ising, M, Jansen, R, Jorgenson, E, Knowles, JA, Kohane, IS, Kraft, J, Kretzschmar, WW, Krogh, J, Kutalik, Z, Li, Y, Lind, PA, MacIntyre, DJ, MacKinnon, DF, Maier, RM, Maier, W, Marchini, J, Mbarek, H, McGrath, P, McGuffin, P, Medland, SE, Mehta, D, Middeldorp, CM, Mihailov, E, Milaneschi, Y, Milani, L, Mondimore, FM, Montgomery, GW, Mostafavi, S, Mullins, N, Nauck, M, Ng, B, and Nivard, MG. "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.  Full Text
    • Amiri, A, Coppola, G, Scuderi, S, Wu, F, Roychowdhury, T, Liu, F, Pochareddy, S, Shin, Y, Safi, A, Song, L, Zhu, Y, Sousa, AMM, PsychENCODE Consortium, , Gerstein, M, Crawford, GE, Sestan, N, Abyzov, A, and Vaccarino, FM. "Transcriptome and epigenome landscape of human cortical development modeled in organoids." Science (New York, N.Y.) 362, no. 6420 (December 2018).  Full Text
    • Wang, D, Liu, S, Warrell, J, Won, H, Shi, X, Navarro, FCP, Clarke, D, Gu, M, Emani, P, Yang, YT, Xu, M, Gandal, MJ, Lou, S, Zhang, J, Park, JJ, Yan, C, Rhie, SK, Manakongtreecheep, K, Zhou, H, Nathan, A, Peters, M, Mattei, E, Fitzgerald, D, Brunetti, T, Moore, J, Jiang, Y, Girdhar, K, Hoffman, GE, Kalayci, S, Gümüş, ZH, Crawford, GE, PsychENCODE Consortium, , Roussos, P, Akbarian, S, Jaffe, AE, White, KP, Weng, Z, Sestan, N, Geschwind, DH, Knowles, JA, and Gerstein, MB. "Comprehensive functional genomic resource and integrative model for the human brain." Science (New York, N.Y.) 362, no. 6420 (December 2018).  Full Text
    • Lee, D, Kapoor, A, Safi, A, Song, L, Halushka, MK, Crawford, GE, and Chakravarti, A. "Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants." Genome Research 28, no. 10 (October 2018): 1577-1588.  Full Text
    • Whitley, SK, Balasubramani, A, Zindl, CL, Sen, R, Shibata, Y, Crawford, GE, Weathington, NM, Hatton, RD, and Weaver, CT. "IL-1R signaling promotes STAT3 and NF-κB factor recruitment to distal cis-regulatory elements that regulate Il17a/f transcription." The Journal of Biological Chemistry 293, no. 41 (October 2018): 15790-15800.  Full Text
    • McDowell, IC, Barrera, A, D'Ippolito, AM, Vockley, CM, Hong, LK, Leichter, SM, Bartelt, LC, Majoros, WH, Song, L, Safi, A, Koçak, DD, Gersbach, CA, Hartemink, AJ, Crawford, GE, Engelhardt, BE, and Reddy, TE. "Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding." Genome Res 28, no. 9 (September 2018): 1272-1284.  Full Text  Link to Item
    • Bryois, J, Garrett, ME, Song, L, Safi, A, Giusti-Rodriguez, P, Johnson, GD, Shieh, AW, Buil, A, Fullard, JF, Roussos, P, Sklar, P, Akbarian, S, Haroutunian, V, Stockmeier, CA, Wray, GA, White, KP, Liu, C, Reddy, TE, Ashley-Koch, A, Sullivan, PF, and Crawford, GE. "Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia." Nature Communications 9, no. 1 (August 7, 2018): 3121-null.  Full Text
    • D'Ippolito, AM, McDowell, IC, Barrera, A, Hong, LK, Leichter, SM, Bartelt, LC, Vockley, CM, Majoros, WH, Safi, A, Song, L, Gersbach, CA, Crawford, GE, and Reddy, TE. "Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids." Cell Systems 7, no. 2 (August 2018): 146-160.e7.  Full Text
    • Peyrot, WJ, Van der Auwera, S, Milaneschi, Y, Dolan, CV, Madden, PAF, Sullivan, PF, Strohmaier, J, Ripke, S, Rietschel, M, Nivard, MG, Mullins, N, Montgomery, GW, Henders, AK, Heat, AC, Fisher, HL, Dunn, EC, Byrne, EM, Air, TA, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, , Baune, BT, Breen, G, Levinson, DF, Lewis, CM, Martin, NG, Nelson, EN, Boomsma, DI, Grabe, HJ, Wray, NR, and Penninx, BWJH. "Does Childhood Trauma Moderate Polygenic Risk for Depression? A Meta-analysis of 5765 Subjects From the Psychiatric Genomics Consortium." Biological Psychiatry 84, no. 2 (July 2018): 138-147.  Full Text
    • Wray, NR, Ripke, S, Mattheisen, M, Trzaskowski, M, Byrne, EM, Abdellaoui, A, Adams, MJ, Agerbo, E, Air, TM, Andlauer, TMF, Bacanu, S-A, Bækvad-Hansen, M, Beekman, AFT, Bigdeli, TB, Binder, EB, Blackwood, DRH, Bryois, J, Buttenschøn, HN, Bybjerg-Grauholm, J, Cai, N, Castelao, E, Christensen, JH, Clarke, T-K, Coleman, JIR, Colodro-Conde, L, Couvy-Duchesne, B, Craddock, N, Crawford, GE, Crowley, CA, Dashti, HS, Davies, G, Deary, IJ, Degenhardt, F, Derks, EM, Direk, N, Dolan, CV, Dunn, EC, Eley, TC, Eriksson, N, Escott-Price, V, Kiadeh, FHF, Finucane, HK, Forstner, AJ, Frank, J, Gaspar, HA, Gill, M, Giusti-Rodríguez, P, Goes, FS, Gordon, SD, Grove, J, Hall, LS, Hannon, E, Hansen, CS, Hansen, TF, Herms, S, Hickie, IB, Hoffmann, P, Homuth, G, Horn, C, Hottenga, J-J, Hougaard, DM, Hu, M, Hyde, CL, Ising, M, Jansen, R, Jin, F, Jorgenson, E, Knowles, JA, Kohane, IS, Kraft, J, Kretzschmar, WW, Krogh, J, Kutalik, Z, Lane, JM, Li, Y, Li, Y, Lind, PA, Liu, X, Lu, L, MacIntyre, DJ, MacKinnon, DF, Maier, RM, Maier, W, Marchini, J, Mbarek, H, McGrath, P, McGuffin, P, Medland, SE, Mehta, D, Middeldorp, CM, Mihailov, E, Milaneschi, Y, Milani, L, Mill, J, Mondimore, FM, Montgomery, GW, Mostafavi, S, Mullins, N, Nauck, M, Ng, B, Nivard, MG, Nyholt, DR, O'Reilly, PF, Oskarsson, H, Owen, MJ, Painter, JN, Pedersen, CB, Pedersen, MG, Peterson, RE, Pettersson, E, Peyrot, WJ, Pistis, G, Posthuma, D, Purcell, SM, Quiroz, JA, Qvist, P, Rice, JP, Riley, BP, Rivera, M, Saeed Mirza, S, Saxena, R, Schoevers, R, Schulte, EC, Shen, L, Shi, J, Shyn, SI, Sigurdsson, E, Sinnamon, GBC, Smit, JH, Smith, DJ, Stefansson, H, Steinberg, S, Stockmeier, CA, Streit, F, Strohmaier, J, Tansey, KE, Teismann, H, Teumer, A, Thompson, W, Thomson, PA, Thorgeirsson, TE, Tian, C, Traylor, M, Treutlein, J, Trubetskoy, V, Uitterlinden, AG, Umbricht, D, Van der Auwera, S, van Hemert, AM, Viktorin, A, Visscher, PM, Wang, Y, Webb, BT, Weinsheimer, SM, Wellmann, J, Willemsen, G, Witt, SH, Wu, Y, Xi, HS, Yang, J, Zhang, F, eQTLGen, , 23andMe, , Arolt, V, Baune, BT, Berger, K, Boomsma, DI, Cichon, S, Dannlowski, U, de Geus, ECJ, DePaulo, JR, Domenici, E, Domschke, K, Esko, T, Grabe, HJ, Hamilton, SP, Hayward, C, Heath, AC, Hinds, DA, Kendler, KS, Kloiber, S, Lewis, G, Li, QS, Lucae, S, Madden, PFA, Magnusson, PK, Martin, NG, McIntosh, AM, Metspalu, A, Mors, O, Mortensen, PB, Müller-Myhsok, B, Nordentoft, M, Nöthen, MM, O'Donovan, MC, Paciga, SA, Pedersen, NL, Penninx, BWJH, Perlis, RH, Porteous, DJ, Potash, JB, Preisig, M, Rietschel, M, Schaefer, C, Schulze, TG, Smoller, JW, Stefansson, K, Tiemeier, H, Uher, R, Völzke, H, Weissman, MM, Werge, T, Winslow, AR, Lewis, CM, Levinson, DF, Breen, G, Børglum, AD, Sullivan, PF, and Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, . "Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression." Nature Genetics 50, no. 5 (May 2018): 668-681.  Full Text
    • Gusev, A, Mancuso, N, Won, H, Kousi, M, Finucane, HK, Reshef, Y, Song, L, Safi, A, Schizophrenia Working Group of the Psychiatric Genomics Consortium, , McCarroll, S, Neale, BM, Ophoff, RA, O'Donovan, MC, Crawford, GE, Geschwind, DH, Katsanis, N, Sullivan, PF, Pasaniuc, B, and Price, AL. "Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights." Nature Genetics 50, no. 4 (April 9, 2018): 538-548.  Full Text
    • Pizzollo, J, Nielsen, WJ, Shibata, Y, Safi, A, Crawford, GE, Wray, GA, and Babbitt, CC. "Comparative Serum Challenges Show Divergent Patterns of Gene Expression and Open Chromatin in Human and Chimpanzee." Genome Biology and Evolution 10, no. 3 (March 2018): 826-839.  Full Text  Open Access Copy
    • Wang, T, Pehrsson, EC, Purushotham, D, Li, D, Zhuo, X, Zhang, B, Lawson, HA, Province, MA, Krapp, C, Lan, Y, Coarfa, C, Katz, TA, Tang, WY, Wang, Z, Biswal, S, Rajagopalan, S, Colacino, JA, Tsai, ZT-Y, Sartor, MA, Neier, K, Dolinoy, DC, Pinto, J, Hamanaka, RB, Mutlu, GM, Patisaul, HB, Aylor, DL, Crawford, GE, Wiltshire, T, Chadwick, LH, Duncan, CG, Garton, AE, McAllister, KA, TaRGET II Consortium, , Bartolomei, MS, Walker, CL, and Tyson, FL. "The NIEHS TaRGET II Consortium and environmental epigenomics." Nature Biotechnology 36, no. 3 (March 2018): 225-227.  Full Text
    • Israel, JW, Chappell, GA, Simon, JM, Pott, S, Safi, A, Lewis, L, Cotney, P, Boulos, HS, Bodnar, W, Lieb, JD, Crawford, GE, Furey, TS, and Rusyn, I. "Tissue- and strain-specific effects of a genotoxic carcinogen 1,3-butadiene on chromatin and transcription." Mammalian Genome : Official Journal of the International Mammalian Genome Society 29, no. 1-2 (February 10, 2018): 153-167.  Full Text
    • Arnau-Soler, A, Adams, MJ, Generation Scotland, , Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, , Hayward, C, and Thomson, PA. "Genome-wide interaction study of a proxy for stress-sensitivity and its prediction of major depressive disorder." Plos One 13, no. 12 (January 2018): e0209160-null.  Full Text
    • Klann, TS, Crawford, GE, Reddy, TE, and Gersbach, CA. "Screening Regulatory Element Function with CRISPR/Cas9-based Epigenome Editing." Methods in Molecular Biology (Clifton, N.J.) 1767 (January 2018): 447-480.  Full Text
    • Milaneschi, Y, Lamers, F, Peyrot, WJ, Baune, BT, Breen, G, Dehghan, A, Forstner, AJ, Grabe, HJ, Homuth, G, Kan, C, Lewis, C, Mullins, N, Nauck, M, Pistis, G, Preisig, M, Rivera, M, Rietschel, M, Streit, F, Strohmaier, J, Teumer, A, Van der Auwera, S, Wray, NR, Boomsma, DI, Penninx, BWJH, and CHARGE Inflammation Working Group and the Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, . "Genetic Association of Major Depression With Atypical Features and Obesity-Related Immunometabolic Dysregulations." Jama Psychiatry 74, no. 12 (December 2017): 1214-1225.  Full Text
    • Manandhar, D, Song, L, Kabadi, A, Kwon, JB, Edsall, LE, Ehrlich, M, Tsumagari, K, Gersbach, CA, Crawford, GE, and Gordân, R. "Incomplete MyoD-induced transdifferentiation is associated with chromatin remodeling deficiencies." Nucleic Acids Research 45, no. 20 (November 2017): 11684-11699.  Full Text
    • Chappell, GA, Israel, JW, Simon, JM, Pott, S, Safi, A, Eklund, K, Sexton, KG, Bodnar, W, Lieb, JD, Crawford, GE, Rusyn, I, and Furey, TS. "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." Environmental Health Perspectives 125, no. 10 (October 16, 2017): 107006-null.  Full Text
    • Lewis, L, Crawford, GE, Furey, TS, and Rusyn, I. "Genetic and epigenetic determinants of inter-individual variability in responses to toxicants." Current Opinion in Toxicology 6 (October 2017): 50-59.  Full Text
    • Davison, JM, Lickwar, CR, Song, L, Breton, G, Crawford, GE, and Rawls, JF. "Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha." Genome research 27, no. 7 (July 2017): 1195-1206.  Full Text
    • Klann, TS, Black, JB, Chellappan, M, Safi, A, Song, L, Hilton, IB, Crawford, GE, Reddy, TE, and Gersbach, CA. "CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome." Nature Biotechnology 35, no. 6 (June 2017): 561-568.  Full Text
    • Montefiori, L, Hernandez, L, Zhang, Z, Gilad, Y, Ober, C, Crawford, G, Nobrega, M, and Jo Sakabe, N. "Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9." Scientific Reports 7, no. 1 (May 26, 2017): 2451-null.  Full Text
    • Maatouk, DM, Natarajan, A, Shibata, Y, Song, L, Crawford, GE, Ohler, U, and Capel, B. "Genome-wide identification of regulatory elements in Sertoli cells." Development (Cambridge, England) 144, no. 4 (February 2017): 720-730.  Full Text
    • Gopinath, C, Law, WD, Rodríguez-Molina, JF, Prasad, AB, Song, L, Crawford, GE, Mullikin, JC, Svaren, J, and Antonellis, A. "Stringent comparative sequence analysis reveals SOX10 as a putative inhibitor of glial cell differentiation." BMC genomics 17, no. 1 (November 7, 2016): 887-.  Full Text
    • Vockley, CM, D'Ippolito, AM, McDowell, IC, Majoros, WH, Safi, A, Song, L, Crawford, GE, and Reddy, TE. "Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome." Cell 166, no. 5 (August 2016): 1269-1281.e19.  Full Text
    • Scott, LJ, Erdos, MR, Huyghe, JR, Welch, RP, Beck, AT, Wolford, BN, Chines, PS, Didion, JP, Narisu, N, Stringham, HM, Taylor, DL, Jackson, AU, Vadlamudi, S, Bonnycastle, LL, Kinnunen, L, Saramies, J, Sundvall, J, Albanus, RD, Kiseleva, A, Hensley, J, Crawford, GE, Jiang, H, Wen, X, Watanabe, RM, Lakka, TA, Mohlke, KL, Laakso, M, Tuomilehto, J, Koistinen, HA, Boehnke, M, Collins, FS, and Parker, SCJ. "The genetic regulatory signature of type 2 diabetes in human skeletal muscle." Nature Communications 7 (June 29, 2016): 11764-null.  Full Text
    • Yang, R, Kerschner, JL, Gosalia, N, Neems, D, Gorsic, LK, Safi, A, Crawford, GE, Kosak, ST, Leir, S-H, and Harris, A. "Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus." Nucleic Acids Research 44, no. 7 (April 2016): 3082-3094.  Full Text
    • Zhong, J, Luo, K, Winter, PS, Crawford, GE, Iversen, ES, and Hartemink, AJ. "Mapping nucleosome positions using DNase-seq." Genome Research 26, no. 3 (March 2016): 351-364.  Full Text
    • Frank, CL, Manandhar, D, Gordân, R, and Crawford, GE. "HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells." Epigenetics & chromatin 9 (January 2016): 15-.  Full Text  Open Access Copy
    • PsychENCODE Consortium, , Akbarian, S, Liu, C, Knowles, JA, Vaccarino, FM, Farnham, PJ, Crawford, GE, Jaffe, AE, Pinto, D, Dracheva, S, Geschwind, DH, Mill, J, Nairn, AC, Abyzov, A, Pochareddy, S, Prabhakar, S, Weissman, S, Sullivan, PF, State, MW, Weng, Z, Peters, MA, White, KP, Gerstein, MB, Amiri, A, Armoskus, C, Ashley-Koch, AE, Bae, T, Beckel-Mitchener, A, Berman, BP, Coetzee, GA, Coppola, G, Francoeur, N, Fromer, M, Gao, R, Grennan, K, Herstein, J, Kavanagh, DH, Ivanov, NA, Jiang, Y, Kitchen, RR, Kozlenkov, A, Kundakovic, M, Li, M, Li, Z, Liu, S, Mangravite, LM, Mattei, E, Markenscoff-Papadimitriou, E, Navarro, FCP, North, N, Omberg, L, Panchision, D, Parikshak, N, Poschmann, J, Price, AJ, Purcaro, M, Reddy, TE, Roussos, P, Schreiner, S, Scuderi, S, Sebra, R, Shibata, M, Shieh, AW, Skarica, M, Sun, W, Swarup, V, Thomas, A, Tsuji, J, van Bakel, H, Wang, D, Wang, Y, Wang, K, Werling, DM, Willsey, AJ, Witt, H, Won, H, Wong, CCY, Wray, GA, Wu, EY, Xu, X, Yao, L, Senthil, G, Lehner, T, Sklar, P, and Sestan, N. "The PsychENCODE project." Nature Neuroscience 18, no. 12 (December 2015): 1707-1712. (Review)  Full Text  Open Access Copy
    • Thakore, PI, D'Ippolito, AM, Song, L, Safi, A, Shivakumar, NK, Kabadi, AM, Reddy, TE, Crawford, GE, and Gersbach, CA. "Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements." Nature Methods 12, no. 12 (December 2015): 1143-1149.  Full Text
    • Hauser, MA, Aboobakar, IF, Liu, Y, Miura, S, Whigham, BT, Challa, P, Wheeler, J, Williams, A, Santiago-Turla, C, Qin, X, Rautenbach, RM, Ziskind, A, Ramsay, M, Uebe, S, Song, L, Safi, A, Vithana, EN, Mizoguchi, T, Nakano, S, Kubota, T, Hayashi, K, Manabe, S-I, Kazama, S, Mori, Y, Miyata, K, Yoshimura, N, Reis, A, Crawford, GE, Pasutto, F, Carmichael, TR, Williams, SEI, Ozaki, M, Aung, T, Khor, C-C, Stamer, WD, Ashley-Koch, AE, and Allingham, RR. "Genetic variants and cellular stressors associated with exfoliation syndrome modulate promoter activity of a lncRNA within the LOXL1 locus." Human Molecular Genetics 24, no. 22 (November 2015): 6552-6563.  Full Text
    • Fufa, TD, Harris, ML, Watkins-Chow, DE, Levy, D, Gorkin, DU, Gildea, DE, Song, L, Safi, A, Crawford, GE, Sviderskaya, EV, Bennett, DC, Mccallion, AS, Loftus, SK, and Pavan, WJ. "Genomic analysis reveals distinct mechanisms and functional classes of SOX10-regulated genes in melanocytes." Human molecular genetics 24, no. 19 (October 2015): 5433-5450.  Full Text
    • Polstein, LR, Perez-Pinera, P, Kocak, DD, Vockley, CM, Bledsoe, P, Song, L, Safi, A, Crawford, GE, Reddy, TE, and Gersbach, CA. "Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators." Genome Research 25, no. 8 (August 2015): 1158-1169.  Full Text
    • Polstein, LR, Perez-Pinera, P, Kocak, DD, Vockley, CM, Bledsoe, P, Song, L, Safi, A, Crawford, GE, Reddy, TE, and Gersbach, CA. "Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators." GENOME RESEARCH 25, no. 8 (August 2015): 1158-1169.  Full Text  Link to Item
    • Frank, CL, Liu, F, Wijayatunge, R, Song, L, Biegler, MT, Yang, MG, Vockley, CM, Safi, A, Gersbach, CA, Crawford, GE, and West, AE. "Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum." Nature Neuroscience 18, no. 5 (May 2015): 647-656.  Full Text
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    • Bina, M, Wyss, P, Lazarus, SA, Shah, SR, Ren, W, Szpankowski, W, Crawford, GE, Park, SP, and Song, XC. "Discovering sequences with potential regulatory characteristics." Genomics 93, no. 4 (April 2009): 314-322.  Full Text  Link to Item
    • Ott, CJ, Suszko, M, Blackledge, NP, Wright, JE, Crawford, GE, and Harris, A. "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): 680-692.  Open Access Copy  Link to Item
    • Schnetz, MP, Bartels, CF, Shastri, K, Balasubramanian, D, Zentner, GE, Balaji, R, Zhang, X, Song, L, Wang, Z, Laframboise, T, Crawford, GE, and Scacheri, PC. "Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns." Genome Res 19, no. 4 (April 2009): 590-601.  Full Text  Link to Item
    • Shibata, Y, and Crawford, GE. "Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip)." Methods Mol Biol 556 (2009): 177-190.  Full Text  Link to Item
    • Boyle, AP, Guinney, J, Crawford, GE, and Furey, TS. "F-Seq: a feature density estimator for high-throughput sequence tags." Bioinformatics (Oxford, England) 24, no. 21 (November 2008): 2537-2538.  Full Text
    • Boyle, AP, Davis, S, Shulha, HP, Meltzer, P, Margulies, EH, Weng, Z, Furey, TS, and Crawford, GE. "High-resolution mapping and characterization of open chromatin across the genome." Cell 132, no. 2 (January 2008): 311-322.  Full Text
    • Eguchi, J, Yan, Q-W, Schones, DE, Kamal, M, Hsu, C-H, Zhang, MQ, Crawford, GE, and Rosen, ED. "Interferon regulatory factors are transcriptional regulators of adipogenesis." Cell Metabolism 7, no. 1 (January 2008): 86-94.  Full Text
    • Xi, H, Shulha, HP, Lin, JM, Vales, TR, Fu, Y, Bodine, DM, McKay, RDG, Chenoweth, JG, Tesar, PJ, Furey, TS, Ren, B, Weng, Z, and Crawford, GE. "Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome." Plos Genetics 3, no. 8 (August 2007): e136-null.  Full Text
    • ENCODE Project Consortium, , Birney, E, Stamatoyannopoulos, JA, Dutta, A, Guigó, R, Gingeras, TR, Margulies, EH, Weng, Z, Snyder, M, Dermitzakis, ET, Thurman, RE, Kuehn, MS, Taylor, CM, Neph, S, Koch, CM, Asthana, S, Malhotra, A, Adzhubei, I, Greenbaum, JA, Andrews, RM, Flicek, P, Boyle, PJ, Cao, H, Carter, NP, Clelland, GK, Davis, S, Day, N, Dhami, P, Dillon, SC, Dorschner, MO, Fiegler, H, Giresi, PG, Goldy, J, Hawrylycz, M, Haydock, A, Humbert, R, James, KD, Johnson, BE, Johnson, EM, Frum, TT, Rosenzweig, ER, Karnani, N, Lee, K, Lefebvre, GC, Navas, PA, Neri, F, Parker, SCJ, Sabo, PJ, Sandstrom, R, Shafer, A, Vetrie, D, Weaver, M, Wilcox, S, Yu, M, Collins, FS, Dekker, J, Lieb, JD, Tullius, TD, Crawford, GE, Sunyaev, S, Noble, WS, Dunham, I, Denoeud, F, Reymond, A, Kapranov, P, Rozowsky, J, Zheng, D, Castelo, R, Frankish, A, Harrow, J, Ghosh, S, Sandelin, A, Hofacker, IL, Baertsch, R, Keefe, D, Dike, S, Cheng, J, Hirsch, HA, Sekinger, EA, Lagarde, J, Abril, JF, Shahab, A, Flamm, C, Fried, C, Hackermüller, J, Hertel, J, Lindemeyer, M, Missal, K, Tanzer, A, Washietl, S, Korbel, J, Emanuelsson, O, Pedersen, JS, Holroyd, N, Taylor, R, Swarbreck, D, Matthews, N, Dickson, MC, Thomas, DJ, Weirauch, MT, Gilbert, J, Drenkow, J, Bell, I, Zhao, X, Srinivasan, KG, Sung, W-K, Ooi, HS, Chiu, KP, Foissac, S, Alioto, T, Brent, M, Pachter, L, Tress, ML, Valencia, A, Choo, SW, Choo, CY, Ucla, C, Manzano, C, Wyss, C, Cheung, E, Clark, TG, Brown, JB, Ganesh, M, Patel, S, Tammana, H, Chrast, J, Henrichsen, CN, Kai, C, Kawai, J, Nagalakshmi, U, Wu, J, Lian, Z, Lian, J, Newburger, P, Zhang, X, Bickel, P, Mattick, JS, Carninci, P, Hayashizaki, Y, Weissman, S, Hubbard, T, Myers, RM, Rogers, J, Stadler, PF, Lowe, TM, Wei, C-L, Ruan, Y, Struhl, K, Gerstein, M, Antonarakis, SE, Fu, Y, Green, ED, Karaöz, U, Siepel, A, Taylor, J, Liefer, LA, Wetterstrand, KA, Good, PJ, Feingold, EA, Guyer, MS, Cooper, GM, Asimenos, G, Dewey, CN, Hou, M, Nikolaev, S, Montoya-Burgos, JI, Löytynoja, A, Whelan, S, Pardi, F, Massingham, T, Huang, H, Zhang, NR, Holmes, I, Mullikin, JC, Ureta-Vidal, A, Paten, B, Seringhaus, M, Church, D, Rosenbloom, K, Kent, WJ, Stone, EA, NISC Comparative Sequencing Program, , Baylor College of Medicine Human Genome Sequencing Center, , Washington University Genome Sequencing Center, , Broad Institute, , Children's Hospital Oakland Research Institute, , Batzoglou, S, Goldman, N, Hardison, RC, Haussler, D, Miller, W, Sidow, A, Trinklein, ND, Zhang, ZD, Barrera, L, Stuart, R, King, DC, Ameur, A, Enroth, S, Bieda, MC, Kim, J, Bhinge, AA, Jiang, N, Liu, J, Yao, F, Vega, VB, Lee, CWH, Ng, P, Yang, A, Moqtaderi, Z, Zhu, Z, Xu, X, Squazzo, S, Oberley, MJ, Inman, D, Singer, MA, Richmond, TA, Munn, KJ, Rada-Iglesias, A, Wallerman, O, Komorowski, J, Fowler, JC, Couttet, P, Bruce, AW, Dovey, OM, Ellis, PD, Langford, CF, Nix, DA, Euskirchen, G, Hartman, S, Urban, AE, Kraus, P, Van Calcar, S, Heintzman, N, Kim, TH, Wang, K, Qu, C, Hon, G, Luna, R, Glass, CK, Rosenfeld, MG, Aldred, SF, Cooper, SJ, Halees, A, Lin, JM, Shulha, HP, Zhang, X, Xu, M, Haidar, JNS, Yu, Y, Iyer, VR, Green, RD, Wadelius, C, Farnham, PJ, Ren, B, Harte, RA, Hinrichs, AS, Trumbower, H, Clawson, H, Hillman-Jackson, J, Zweig, AS, Smith, K, Thakkapallayil, A, Barber, G, Kuhn, RM, Karolchik, D, Armengol, L, Bird, CP, de Bakker, PIW, Kern, AD, Lopez-Bigas, N, Martin, JD, Stranger, BE, Woodroffe, A, Davydov, E, Dimas, A, Eyras, E, Hallgrímsdóttir, IB, Huppert, J, Zody, MC, Abecasis, GR, Estivill, X, Bouffard, GG, Guan, X, Hansen, NF, Idol, JR, Maduro, VVB, Maskeri, B, McDowell, JC, Park, M, Thomas, PJ, Young, AC, Blakesley, RW, Muzny, DM, Sodergren, E, Wheeler, DA, Worley, KC, Jiang, H, Weinstock, GM, Gibbs, RA, Graves, T, Fulton, R, Mardis, ER, Wilson, RK, Clamp, M, Cuff, J, Gnerre, S, Jaffe, DB, Chang, JL, Lindblad-Toh, K, Lander, ES, Koriabine, M, Nefedov, M, Osoegawa, K, Yoshinaga, Y, Zhu, B, and de Jong, PJ. "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project." Nature 447, no. 7146 (June 2007): 799-816.  Full Text
    • Heintzman, ND, Stuart, RK, Hon, G, Fu, Y, Ching, CW, Hawkins, RD, Barrera, LO, Van Calcar, S, Qu, C, Ching, KA, Wang, W, Weng, Z, Green, RD, Crawford, GE, and Ren, B. "Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome." Nature Genetics 39, no. 3 (March 2007): 311-318.  Full Text
    • Nagel, S, Scherr, M, Kel, A, Hornischer, K, Crawford, GE, Kaufmann, M, Meyer, C, Drexler, HG, and MacLeod, RAF. "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 Research 67, no. 4 (February 2007): 1461-1471.  Full Text
    • Xi, H, Shulha, HP, Lin, JM, Vales, TR, Fu, Y, Bodine, DM, McKay, RDG, Chenoweth, JG, Tesar, PJ, Furey, TS, Ren, B, Weng, Z, and Crawford, GE. "Identification and Characterization of Cell Type–Specific and Ubiquitous Chromatin Regulatory Structures in the Human Genome." Plos Genetics 3, no. 8 (2007): e136-e136.  Full Text
    • Bernat, JA, Crawford, GE, Ogurtsov, AY, Collins, FS, Ginsburg, D, and Kondrashov, AS. "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.  Full Text  Link to Item
    • Crawford, GE, Davis, S, Scacheri, PC, Renaud, G, Halawi, MJ, Erdos, MR, Green, R, Meltzer, PS, Wolfsberg, TG, and Collins, FS. "DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays." Nature Methods 3, no. 7 (July 2006): 503-509.  Full Text
    • Lewinski, MK, Yamashita, M, Emerman, M, Ciuffi, A, Marshall, H, Crawford, G, Collins, F, Shinn, P, Leipzig, J, Hannenhalli, S, Berry, CC, Ecker, JR, and Bushman, FD. "Retroviral DNA integration: viral and cellular determinants of target-site selection." Plos Pathogens 2, no. 6 (June 23, 2006): e60-null.  Full Text
    • Scacheri, PC, Davis, S, Odom, DT, Crawford, GE, Perkins, S, Halawi, MJ, Agarwal, SK, Marx, SJ, Spiegel, AM, Meltzer, PS, and Collins, FS. "Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis." Plos Genetics 2, no. 4 (April 7, 2006): e51-null.  Full Text
    • Crawford, GE, Holt, IE, Whittle, J, Webb, BD, Tai, D, Davis, S, Margulies, EH, Chen, Y, Bernat, JA, Ginsburg, D, Zhou, D, Luo, S, Vasicek, TJ, Daly, MJ, Wolfsberg, TG, and Collins, FS. "Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)." Genome Research 16, no. 1 (January 2006): 123-131.  Full Text
    • Lewinski, MK, Yamashita, M, Emerman, M, Ciuffi, A, Marshall, H, Crawford, G, Collins, F, Shinn, P, Leipzig, J, Hannenhalli, S, Berry, CC, Ecker, JR, and Bushman, FD. "Retroviral DNA integration: Viral and cellular determinants of target-site selection." PLoS Pathogens 2, no. 6 (2006): 0611-0622.  Full Text
    • Scacheri, PC, Crawford, GE, and Davis, S. "Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays." Methods Enzymol 411 (2006): 270-282. (Review)  Full Text  Link to Item
    • Scacheri, PC, Davis, S, Odom, DT, Crawford, GE, Perkins, S, Halawi, MJ, Agarwal, SK, Marx, SJ, Spiegel, AM, Meltzer, PS, and Collins, FS. "Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis." PLoS genetics 2, no. 4 (2006): e51-.  Full Text
    • Yan, J, Xu, L, Crawford, G, Wang, Z, and Burgess, SM. "The forkhead transcription factor FoxI1 remains bound to condensed mitotic chromosomes and stably remodels chromatin structure." Molecular and Cellular Biology 26, no. 1 (January 2006): 155-168.  Full Text
    • ENCODE Project Consortium, . "The ENCODE (ENCyclopedia Of DNA Elements) Project." Science (New York, N.Y.) 306, no. 5696 (October 2004): 636-640.  Full Text
    • Crawford, GE, Holt, IE, Mullikin, JC, Tai, D, Blakesley, R, Bouffard, G, Young, A, Masiello, C, Green, ED, Wolfsberg, TG, Collins, FS, and National Institutes Of Health Intramural Sequencing Center, . "Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites." Proceedings of the National Academy of Sciences of the United States of America 101, no. 4 (January 19, 2004): 992-997.  Full Text
    • Crawford, GE, Lu, QL, Partridge, TA, and Chamberlain, JS. "Suppression of revertant fibers in mdx mice by expression of a functional dystrophin." Hum Mol Genet 10, no. 24 (November 15, 2001): 2745-2750.  Link to Item
    • Crawford, GE, Faulkner, JA, Crosbie, RH, Campbell, KP, Froehner, SC, and Chamberlain, JS. "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.  Link to Item
    • Lumeng, C, Phelps, S, Crawford, GE, Walden, PD, Barald, K, and Chamberlain, JS. "Interactions between beta 2-syntrophin and a family of microtubule-associated serine/threonine kinases." Nature Neuroscience 2, no. 7 (July 1999): 611-617.  Full Text

  • Conference Papers

    • Thakore, PI, D'Ippolito, A, Song, L, Safi, A, Shivakumar, NK, Kabadi, AM, Bledsoe, P, Reddy, TE, Crawford, GE, and Gersbach, CA. "485. Targeted Epigenome Editing by CRISPR/Cas9-Based Repressors for Silencing of Distal Regulatory Elements." May 2015.  Full Text
    • Babbitt, CC, Pfefferle, LW, Crawford, GE, and Wray, GA. "Evolution of gene expression network underlying a disease state." April 2015.  Link to Item
    • Hsiung, CCS, Morrissey, C, Udugama, M, Frank, C, Keller, CA, Baek, S, Giardine, B, Crawford, GE, Sung, M-H, Raj, A, Hardison, RC, and Blobel, GA. "Epigenetics of Cellular Memory: Insights from the Chromatin Accessibility Landscape of the Mitotic Genome." December 6, 2014.  Link to Item
    • Thakore, PI, Ousterout, DG, Kabadi, AM, Deneke, VE, Crawford, GE, Reddy, TE, and Gersbach, CA. "CRISPR/Cas9-Based Transcriptional Repressors for Control of Human Gene Expression." May 2014.  Link to Item
    • Perez-Pinera, P, Ousterout, DG, Brunger, JM, Farin, AM, Glass, KA, Guilak, F, Crawford, GE, Hartemink, AJ, and Gersbach, CA. "Synergistic and Tunable Gene Activation by Combinations of Synthetic Transcription Factors." June 2013.  Link to Item
    • Ehrlich, M, Tsumagari, K, Chang, S-C, Lacey, M, Baribault, C, Chittur, SV, Sowden, J, Tawil, R, Varley, KE, Gertz, J, Myers, RM, Song, L, and Crawford, GE. "FINDING TARGETS FOR FSH DYSTROPHY THERAPY." 2011.  Link to Item
    • Nagel, S, Scherr, M, Kel, A, Hornischer, K, Crawford, GE, Kaufmann, M, Meyer, C, Drexler, HG, and MacLeod, RAF. "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." 48th Annual Meeting of the American-Society-of-Hematology. Orlando, FL. December 9, 2006 - December 12, 2006.: AMER SOC HEMATOLOGY, November 16, 2006.  Link to Item
• Teaching & Mentoring
• 

  Recent Courses

  • 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

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