Gregory E. Crawford | Scholars@Duke

Gregory E. Crawford
Associate 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 DNase I hypersensitive 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

Associate Professor in Pediatrics, Pediatrics, Medical Genetics, Pediatrics 2015
Associate Professor in Molecular Genetics and Microbiology, Molecular Genetics and Microbiology, Basic Science Departments 2015

Contact Information

Box 3382 Med Ctr, Durham, NC 27710
Room 2363B 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 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
- 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
- Effects of perfluorobutane sulfonate (PFBS) exposure on adverse pregnancy outcomes and fetal development awarded by National Institutes of Health 2017 - 2022
- 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
- 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
- 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
- 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
- Genetic epidemiology of rare and regulatory variants for metabolic traits awarded by University of North Carolina - Chapel Hill 2017 - 2018
- The function and regulation of the novel pregnancy-specific hexokinase HKDC1 awarded by University of Illinois at Chicago 2017 - 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
- Systems Toxicogenomics of Endocrine Disrupting Chemicals in Brain awarded by North Carolina State University 2016 - 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
- 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
- Journal Articles
  - 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 (Accepted)." Molecular Psychiatry (March 8, 2018): 1-16. Full Text
  - 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
  - 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-. 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-. 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-. 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, and Jiang, Y et al. "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
  - Hilton, IB, D'Ippolito, AM, Vockley, CM, Thakore, PI, Crawford, GE, Reddy, TE, and Gersbach, CA. "Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers." Nature biotechnology 33, no. 5 (May 2015): 510-517. Full Text
  - Ding, Z, Ni, Y, Timmer, SW, Lee, B-K, Battenhouse, A, Louzada, S, Yang, F, Dunham, I, Crawford, GE, Lieb, JD, Durbin, R, Iyer, VR, and Birney, E. "Correction: Quantitative Genetics of CTCF Binding Reveal Local Sequence Effects and Different Modes of X-Chromosome Association." PLOS Genetics 11, no. 4 (April 28, 2015): e1005177-e1005177. Full Text
  - Raposo, AASF, Vasconcelos, FF, Drechsel, D, Marie, C, Johnston, C, Dolle, D, Bithell, A, Gillotin, S, van den Berg, DLC, Ettwiller, L, Flicek, P, Crawford, GE, Parras, CM, Berninger, B, Buckley, NJ, Guillemot, F, and Castro, DS. "Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis." Cell reports (March 4, 2015). Full Text
  - Hsiung, CC-S, Morrissey, CS, Udugama, M, Frank, CL, Keller, CA, Baek, S, Giardine, B, Crawford, GE, Sung, M-H, Hardison, RC, and Blobel, GA. "Genome accessibility is widely preserved and locally modulated during mitosis." Genome research 25, no. 2 (February 2015): 213-225. Full Text
  - Su, D, Wang, X, Campbell, MR, Song, L, Safi, A, Crawford, GE, and Bell, DA. "Interactions of chromatin context, binding site sequence content, and sequence evolution in stress-induced p53 occupancy and transactivation." PLoS genetics 11, no. 1 (January 8, 2015): e1004885-. Full Text Open Access Copy
  - Mateo, JL, van den Berg, DLC, Haeussler, M, Drechsel, D, Gaber, ZB, Castro, DS, Robson, P, Lu, QR, Crawford, GE, Flicek, P, Ettwiller, L, Wittbrodt, J, Guillemot, F, and Martynoga, B. "Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal." Genome research 25, no. 1 (January 2015): 41-56. Full Text
  - Browne, JA, Yang, R, Song, L, Crawford, GE, Leir, S-H, and Harris, A. "Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function." Molecular human reproduction 20, no. 12 (December 2014): 1198-1207. Full Text
  - Ding, Z, Ni, Y, Timmer, SW, Lee, B-K, Battenhouse, A, Louzada, S, Yang, F, Dunham, I, Crawford, GE, Lieb, JD, Durbin, R, Iyer, VR, and Birney, E. "Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association." PLoS genetics 10, no. 11 (November 20, 2014): e1004798-. Full Text Open Access Copy
  - Yardımcı, GG, Frank, CL, Crawford, GE, and Ohler, U. "Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection." Nucleic acids research 42, no. 19 (October 7, 2014): 11865-11878. Full Text Open Access Copy
  - Bing, Z, Day, DS, Ho, J, Lingyun, S, Seidman, JG, Crawford, GE, Park, PJ, and Pu, WT. "VEGF changes chromatin landscape in endothelial cell." ANGIOGENESIS 17, no. 4 (October 2014): 957-957. Link to Item
  - Camp, JG, Frank, CL, Lickwar, CR, Guturu, H, Rube, T, Wenger, AM, Chen, J, Bejerano, G, Crawford, GE, and Rawls, JF. "Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape." Genome research 24, no. 9 (September 2014): 1504-1516. Full Text
  - Kellis, M, Wold, B, Snyder, MP, Bernstein, BE, Kundaje, A, Marinov, GK, Ward, LD, Birney, E, Crawford, GE, Dekker, J, Dunham, I, Elnitski, LL, Farnham, PJ, Feingold, EA, Gerstein, M, Giddings, MC, Gilbert, DM, Gingeras, TR, Green, ED, Guigo, R, Hubbard, T, Kent, J, Lieb, JD, Myers, RM, Pazin, MJ, Ren, B, Stamatoyannopoulos, J, Weng, Z, White, KP, and Hardison, RC. "Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease." Proceedings of the National Academy of Sciences of the United States of America 111, no. 33 (August 2014): E3366-. (Letter) Full Text
  - Factor, DC, Corradin, O, Zentner, GE, Saiakhova, A, Song, L, Chenoweth, JG, McKay, RD, Crawford, GE, Scacheri, PC, and Tesar, PJ. "Epigenomic comparison reveals activation of "seed" enhancers during transition from naive to primed pluripotency." Cell stem cell 14, no. 6 (June 2014): 854-863. Full Text
  - Terragni, J, Zhang, G, Sun, Z, Pradhan, S, Song, L, Crawford, GE, Lacey, M, and Ehrlich, M. "Notch signaling genes: myogenic DNA hypomethylation and 5-hydroxymethylcytosine." Epigenetics 9, no. 6 (June 2014): 842-850. Full Text
  - Kellis, M, Wold, B, Snyder, MP, Bernstein, BE, Kundaje, A, Marinov, GK, Ward, LD, Birney, E, Crawford, GE, Dekker, J, Dunham, I, Elnitski, LL, Farnham, PJ, Feingold, EA, Gerstein, M, Giddings, MC, Gilbert, DM, Gingeras, TR, Green, ED, Guigo, R, Hubbard, T, Kent, J, Lieb, JD, Myers, RM, Pazin, MJ, Ren, B, Stamatoyannopoulos, JA, Weng, Z, White, KP, and Hardison, RC. "Defining functional DNA elements in the human genome." Proceedings of the National Academy of Sciences of the United States of America 111, no. 17 (April 21, 2014): 6131-6138. (Review) Full Text
  - Balasubramani, A, Winstead, CJ, Turner, H, Janowski, KM, Harbour, SN, Shibata, Y, Crawford, GE, Hatton, RD, and Weaver, CT. "Deletion of a conserved cis-element in the Ifng locus highlights the role of acute histone acetylation in modulating inducible gene transcription." PLoS Genet 10, no. 1 (January 2014): e1003969-. Full Text Link to Item
  - Balasubramani, A, Winstead, CJ, Turner, H, Janowski, KM, Harbour, SN, Shibata, Y, Crawford, GE, Hatton, RD, and Weaver, CT. "Deletion of a Conserved cis-Element in the Ifng Locus Highlights the Role of Acute Histone Acetylation in Modulating Inducible Gene Transcription." PLoS Genetics 10, no. 1 (January 1, 2014). Full Text
  - Wortham, M, Guo, C, Zhang, M, Song, L, Lee, B-K, Iyer, VR, Furey, TS, Crawford, GE, Yan, H, and He, Y. "Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma." PloS one 9, no. 9 (January 2014): e107156-. Full Text Open Access Copy
  - Bischof, JM, Gillen, AE, Song, L, Gosalia, N, London, D, Furey, TS, Crawford, GE, and Harris, A. "A Genome-Wide Analysis of Open Chromatin in Human Epididymis Epithelial Cells Reveals Candidate Regulatory Elements for Genes Coordinating Epididymal Function." BIOLOGY OF REPRODUCTION 89, no. 4 (October 2013). Full Text Link to Item
  - Perez-Pinera, P, Kocak, DD, Vockley, CM, Adler, AF, Kabadi, AM, Polstein, LR, Thakore, PI, Glass, KA, Ousterout, DG, Leong, KW, Guilak, F, Crawford, GE, Reddy, TE, and Gersbach, CA. "RNA-guided gene activation by CRISPR-Cas9-based transcription factors." Nat Methods 10, no. 10 (October 2013): 973-976. Full Text Link to Item
  - Tsumagari, K, Baribault, C, Terragni, J, Chandra, S, Renshaw, C, Sun, Z, Song, L, Crawford, GE, Pradhan, S, Lacey, M, and Ehrlich, M. "DNA methylation and differentiation: HOX genes in muscle cells." EPIGENETICS & CHROMATIN 6 (August 2, 2013). Full Text Link to Item
  - Winter, DR, Song, L, Mukherjee, S, Furey, TS, and Crawford, GE. "DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types." Genome Res 23, no. 7 (July 2013): 1118-1129. Full Text Link to Item
  - Sheffield, NC, Thurman, RE, Song, L, Safi, A, Stamatoyannopoulos, JA, Lenhard, B, Crawford, GE, and Furey, TS. "Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions." Genome Res 23, no. 5 (May 2013): 777-788. Full Text 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 human gene activation by combinations of synthetic transcription factors." Nat Methods 10, no. 3 (March 2013): 239-242. Full Text Link to Item
  - Tsumagari, K, Baribault, C, Terragni, J, Varley, KE, Gertz, J, Pradhan, S, Badoo, M, Crain, CM, Song, L, Crawford, GE, Myers, RM, Lacey, M, and Ehrlich, M. "Early de novo DNA methylation and prolonged demethylation in the muscle lineage." EPIGENETICS 8, no. 3 (March 2013): 317-332. Full Text Link to Item
  - Varley, KE, Gertz, J, Bowling, KM, Parker, SL, Reddy, TE, Pauli-Behn, F, Cross, MK, Williams, BA, Stamatoyannopoulos, JA, Crawford, GE, Absher, DM, Wold, BJ, and Myers, RM. "Dynamic DNA methylation across diverse human cell lines and tissues." GENOME RESEARCH 23, no. 3 (March 2013): 555-567. Full Text Link to Item
  - Gertz, J, Savic, D, Varley, KE, Partridge, EC, Safi, A, Jain, P, Cooper, GM, Reddy, TE, Crawford, GE, and Myers, RM. "Distinct properties of cell-type-specific and shared transcription factor binding sites." Molecular Cell 52, no. 1 (2013): 25-36. Full Text
  - Gertz, J, Savic, D, Varley, KE, Partridge, EC, Safi, A, Jain, P, Cooper, GM, Reddy, TE, Crawford, GE, and Myers, RM. "Distinct Properties of Cell-Type-Specific and Shared Transcription Factor Binding Sites." Molecular Cell (2013). Full Text
  - Perez-Pinera, P, Kocak, DD, Vockley, CM, Adler, AF, Kabadi, AM, Polstein, LR, Thakore, PI, Glass, KA, Ousterout, DG, Leong, KW, Guilak, F, Crawford, GE, Reddy, TE, and Gersbach, CA. "RNA-guided gene activation by CRISPR-Cas9-based transcription factors." Nature Methods 10, no. 10 (2013): 973-976. Full Text
  - Zhang, B, Day, DS, Ho, JW, Song, L, Cao, J, Christodoulou, D, Seidman, JG, Crawford, GE, Park, PJ, and Pu, WT. "A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity." Genome Research 23, no. 6 (2013): 917-927. Full Text
  - Tewari, AK, Yardimci, GG, Shibata, Y, Sheffield, NC, Song, L, Taylor, BS, Georgiev, SG, Coetzee, GA, Ohler, U, Furey, TS, Crawford, GE, and Febbo, PG. "Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity. (Published online)" Genome Biol 13, no. 10 (October 3, 2012): R88-. Full Text Link to Item
  - ENCODE Project Consortium, . "An integrated encyclopedia of DNA elements in the human genome." Nature 489, no. 7414 (September 6, 2012): 57-74. Full Text Link to Item
  - Natarajan, A, Yardimci, GG, Sheffield, NC, Crawford, GE, and Ohler, U. "Predicting cell-type-specific gene expression from regions of open chromatin." Genome Res 22, no. 9 (September 2012): 1711-1722. Full Text Link to Item
  - Shibata, Y, Sheffield, NC, Fedrigo, O, Babbitt, CC, Wortham, M, Tewari, AK, London, D, Song, L, Lee, B-K, Iyer, VR, Parker, SCJ, Margulies, EH, Wray, GA, Furey, TS, and Crawford, GE. "Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection." PLoS Genet 8, no. 6 (June 2012): e1002789-. Full Text Link to Item
  - Balasubramanian, D, Akhtar-Zaidi, B, Song, L, Bartels, CF, Veigl, M, Beard, L, Myeroff, L, Guda, K, Lutterbaugh, J, Willis, J, Crawford, GE, Markowitz, SD, and Scacheri, PC. "H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island-containing start sites. (Published online)" Genome Med 4, no. 5 (May 28, 2012): 47-. Full Text Link to Item
  - Bischof, JM, Ott, CJ, Leir, S-H, Gosalia, N, Song, L, London, D, Furey, TS, Cotton, CU, Crawford, GE, and Harris, A. "A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function." Thorax 67, no. 5 (May 2012): 385-391. Full Text Link to Item
  - Reddy, TE, Gertz, J, Pauli, F, Kucera, KS, Varley, KE, Newberry, KM, Marinov, GK, Mortazavi, A, Williams, BA, Song, L, Crawford, GE, Wold, B, Willard, HF, and Myers, RM. "Effects of sequence variation on differential allelic transcription factor occupancy and gene expression." Genome Res 22, no. 5 (May 2012): 860-869. Full Text Link to Item
  - Degner, JF, Pai, AA, Pique-Regi, R, Veyrieras, J-B, Gaffney, DJ, Pickrell, JK, De Leon, S, Michelini, K, Lewellen, N, Crawford, GE, Stephens, M, Gilad, Y, and Pritchard, JK. "DNase I sensitivity QTLs are a major determinant of human expression variation. (Published online)" Nature 482, no. 7385 (February 5, 2012): 390-394. Full Text Link to Item
  - Gaffney, DJ, Veyrieras, J-B, Degner, JF, Pique-Regi, R, Pai, AA, Crawford, GE, Stephens, M, Gilad, Y, and Pritchard, JK. "Dissecting the regulatory architecture of gene expression QTLs. (Published online)" Genome Biol 13, no. 1 (January 31, 2012): R7-. Full Text Link to Item
  - Calabrese, JM, Sun, W, Song, L, Mugford, JW, Williams, L, Yee, D, Starmer, J, Mieczkowski, P, Crawford, GE, and Magnuson, T. "Site-specific silencing of regulatory elements as a mechanism of x inactivation." Cell 151, no. 5 (2012): 951-963. Full Text
  - Lee, B-K, Bhinge, AA, Battenhouse, A, McDaniell, RM, Liu, Z, Song, L, Ni, Y, Birney, E, Lieb, JD, Furey, TS, Crawford, GE, and Iyer, VR. "Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells." Genome Res 22, no. 1 (January 2012): 9-24. Full Text Link to Item
  - Parker, SCJ, Gartner, J, Cardenas-Navia, I, Wei, X, Abaan, HO, Ajay, SS, Hansen, NF, Song, L, Bhanot, UK, Killian, JK, Gindin, Y, Walker, RL, Meltzer, PS, Mullikin, JC, Furey, TS, Crawford, GE, Rosenberg, SA, Samuels, Y, and Margulies, EH. "Mutational Signatures of De-Differentiation in Functional Non-Coding Regions of Melanoma Genomes." PLoS Genetics 8, no. 8 (2012). Full Text
  - Reddy, TE, Gertz, J, Crawford, GE, Garabedian, MJ, and Myers, RM. "The hypersensitive glucocorticoid response specifically regulates period 1 and expression of circadian genes." Molecular and Cellular Biology 32, no. 18 (2012): 3756-3767. Full Text
  - Stamatoyannopoulos, JA, Snyder, M, Hardison, R, Ren, B, Gingeras, T, Gilbert, DM, Groudine, M, Bender, M, Kaul, R, Canfield, T, Giste, E, Johnson, A, Zhang, M, Balasundaram, G, Byron, R, Roach, V, Sabo, PJ, Sandstrom, R, Stehling, AS, Thurman, RE, Weissman, SM, Cayting, P, Hariharan, M, Lian, J, Cheng, Y, Landt, SG, Ma, Z, Wold, BJ, Dekker, J, Crawford, GE, Keller, CA, Wu, W, Morrissey, C, Kumar, SA, Mishra, T, Jain, D, Byrska-Bishop, M, Blankenberg, D, Lajoie, BR, Jain, G, Sanyal, A, and Chen, K-B et al. "An encyclopedia of mouse DNA elements (Mouse ENCODE)." Genome Biology (2012): 418--. Full Text
  - Stamatoyannopoulos, JA, Snyder, M, Hardison, R, Ren, B, Gingeras, T, Gilbert, DM, Groudine, M, Bender, M, Kaul, R, Canfield, T, Giste, E, Johnson, A, Zhang, M, Balasundaram, G, Byron, R, Roach, V, Sabo, PJ, Sandstrom, R, Stehling, AS, Thurman, RE, Weissman, SM, Cayting, P, Hariharan, M, Lian, J, Cheng, Y, Landt, SG, Ma, Z, Wold, BJ, Dekker, J, Crawford, GE, Keller, CA, Wu, W, Morrissey, C, Kumar, SA, Mishra, T, Jain, D, Byrska-Bishop, M, Blankenberg, D, Lajoiel, BR, Jain, G, and Sanyal, A et al. "An encyclopedia of mouse DNA elements (Mouse ENCODE)." Genome Biology 13, no. 8 (2012). Full Text
  - Thurman, RE, Rynes, E, Humbert, R, Vierstra, J, Maurano, MT, Haugen, E, Sheffield, NC, Stergachis, AB, Wang, H, Vernot, B, Garg, K, John, S, Sandstrom, R, Bates, D, Boatman, L, Canfield, TK, Diegel, M, Dunn, D, Ebersol, AK, Frum, T, Giste, E, Johnson, AK, Johnson, EM, Kutyavin, T, Lajoie, B, Lee, B-K, Lee, K, London, D, Lotakis, D, Neph, S, Neri, F, Nguyen, ED, Qu, H, Reynolds, AP, Roach, V, Safi, A, Sanchez, ME, Sanyal, A, Shafer, A, Simon, JM, Song, L, Vong, S, Weaver, M, Yan, Y, and Zhang, Z et al. "The accessible chromatin landscape of the human genome." Nature 489, no. 7414 (2012): 75-82. Full Text
  - Zhang, W, Wu, Y, Schnable, JC, Zeng, Z, Freeling, M, Crawford, GE, and Jiang, J. "High-resolution mapping of open chromatin in the rice genome." Genome Res 22, no. 1 (January 2012): 151-162. Full Text Link to Item
  - Song, L, Zhang, Z, Grasfeder, LL, Boyle, AP, Giresi, PG, Lee, B-K, Sheffield, NC, Gräf, S, Huss, M, Keefe, D, Liu, Z, London, D, McDaniell, RM, Shibata, Y, Showers, KA, Simon, JM, Vales, T, Wang, T, Winter, D, Zhang, Z, Clarke, ND, Birney, E, Iyer, VR, Crawford, GE, Lieb, JD, and Furey, TS. "Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity." Genome Res 21, no. 10 (October 2011): 1757-1767. Full Text Link to Item
  - Wu, W, Cheng, Y, Keller, CA, Ernst, J, Kumar, SA, Mishra, T, Morrissey, C, Dorman, CM, Chen, K-B, Drautz, D, Giardine, B, Shibata, Y, Song, L, Pimkin, M, Crawford, GE, Furey, TS, Kellis, M, Miller, W, Taylor, J, Schuster, SC, Zhang, Y, Chiaromonte, F, Blobel, GA, Weiss, MJ, and Hardison, RC. "Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration." Genome Res 21, no. 10 (October 2011): 1659-1671. Full Text Link to Item
  - Tsumagari, K, Chang, S-C, Lacey, M, Baribault, C, Chittur, SV, Sowden, J, Tawil, R, Crawford, GE, and Ehrlich, M. "Gene expression during normal and FSHD myogenesis. (Published online)" BMC Med Genomics 4 (September 27, 2011): 67-. Full Text Link to Item
  - Boyle, AP, Song, L, Lee, B-K, London, D, Keefe, D, Birney, E, Iyer, VR, Crawford, GE, and Furey, TS. "High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells." Genome Res 21, no. 3 (March 2011): 456-464. Full Text Link to Item
  - Myers, RM, Stamatoyannopoulos, J, Snyder, M, Dunham, I, Hardison, RC, Bernstein, BE, Gingeras, TR, Kent, WJ, Birney, E, Wold, B, Crawford, GE, Bernstein, BE, Epstein, CB, Shoresh, N, Ernst, J, Mikkelsen, TS, Kheradpour, P, Zhang, X, Wang, L, Issner, R, Coyne, MJ, Durham, T, Ku, M, Truong, T, Ward, LD, Altshuler, RC, Lin, MF, Kellis, M, Gingeras, TR, Davis, CA, Kapranov, P, Dobin, A, Zaleski, C, Schlesinger, F, Batut, P, Chakrabortty, S, Jha, S, Lin, W, Drenkow, J, Wang, H, Bell, K, and Gao, H et al. "A user's guide to the Encyclopedia of DNA elements (ENCODE)." PLoS Biology 9, no. 4 (2011). Full Text
  - Stitzel, ML, Sethupathy, P, Pearson, DS, Chines, PS, Song, L, Erdos, MR, Welch, R, Parker, SCJ, Boyle, AP, Scott, LJ, NISC Comparative Sequencing Program, , Margulies, EH, Boehnke, M, Furey, TS, Crawford, GE, and Collins, FS. "Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci." Cell Metab 12, no. 5 (November 3, 2010): 443-455. Full Text Link to Item
  - Birney, E, Lieb, JD, Furey, TS, Crawford, GE, and Iyer, VR. "Allele-specific and heritable chromatin signatures in humans." Hum Mol Genet 19, no. R2 (October 15, 2010): R204-R209. (Review) Full Text Link to Item
  - Balasubramani, A, Shibata, Y, Crawford, GE, Baldwin, AS, Hatton, RD, and Weaver, CT. "Modular utilization of distal cis-regulatory elements controls Ifng gene expression in T cells activated by distinct stimuli." Immunity 33, no. 1 (July 23, 2010): 35-47. Full Text Link to Item
  - Schnetz, MP, Handoko, L, Akhtar-Zaidi, B, Bartels, CF, Pereira, CF, Fisher, AG, Adams, DJ, Flicek, P, Crawford, GE, Laframboise, T, Tesar, P, Wei, C-L, and Scacheri, PC. "CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. (Published online)" PLoS Genet 6, no. 7 (July 15, 2010): e1001023-. Full Text Open Access Copy Link to Item
  - Mukasa, R, Balasubramani, A, Lee, YK, Whitley, SK, Weaver, BT, Shibata, Y, Crawford, GE, Hatton, RD, and Weaver, CT. "Epigenetic instability of cytokine and transcription factor gene loci underlies plasticity of the T helper 17 cell lineage." Immunity 32, no. 5 (May 28, 2010): 616-627. Full Text Link to Item
  - McDaniell, R, Lee, B-K, Song, L, Liu, Z, Boyle, AP, Erdos, MR, Scott, LJ, Morken, MA, Kucera, KS, Battenhouse, A, Keefe, D, Collins, FS, Willard, HF, Lieb, JD, Furey, TS, Crawford, GE, Iyer, VR, and Birney, E. "Heritable individual-specific and allele-specific chromatin signatures in humans." Science 328, no. 5975 (April 9, 2010): 235-239. Full Text Link to Item
  - Song, L, and Crawford, GE. "DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells." Cold Spring Harb Protoc 2010, no. 2 (February 2010): pdb.prot5384-. Full Text Link to Item
  - Schnetz, MP, Handoko, L, Akhtar-Zaidi, B, Bartels, CF, Pereira, CF, Fisher, AG, Adams, DJ, Flicek, P, Crawford, GE, LaFramboise, T, Tesar, P, Wei, C-L, and Scacheri, PC. "CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression." PLoS Genetics 6, no. 7 (2010): 1-15. Full Text
  - Stitzel, ML, Sethupathy, P, Pearson, DS, Chines, PS, Song, L, Erdos, MR, Welch, R, Parker, SCJ, Boyle, AP, Scott, LJ, Program, NCS, Margulies, EH, Boehnke, M, Furey, TS, Crawford, GE, and Collins, FS. "Erratum: Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci (Cell Metabolism (2010) 12 (443-455))." Cell Metabolism 12, no. 6 (2010): 683--. Full Text
  - Xu, X, Tsumagari, K, Sowden, J, Tawil, R, Boyle, AP, Song, L, Furey, TS, Crawford, GE, and Ehrlich, M. "DNaseI hypersensitivity at gene-poor, FSH dystrophy-linked 4q35.2." Nucleic Acids Res 37, no. 22 (December 2009): 7381-7393. Full Text Link to Item
  - Ott, CJ, Blackledge, NP, Kerschner, JL, Leir, S-H, Crawford, GE, Cotton, CU, and Harris, A. "Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus." Proc Natl Acad Sci U S A 106, no. 47 (November 24, 2009): 19934-19939. Full Text Link to Item
  - Heintzman, ND, Hon, GC, Hawkins, RD, Kheradpour, P, Stark, A, Harp, LF, Ye, Z, Lee, LK, Stuart, RK, Ching, CW, Ching, KA, Antosiewicz-Bourget, JE, Liu, H, Zhang, X, Green, RD, Lobanenkov, VV, Stewart, R, Thomson, JA, Crawford, GE, Kellis, M, and Ren, B. "Histone modifications at human enhancers reflect global cell-type-specific gene expression." Nature 459, no. 7243 (May 7, 2009): 108-112. Full Text Link to Item
  - 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 24, no. 21 (November 1, 2008): 2537-2538. Full Text Link to Item
  - 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 25, 2008): 311-322. Full Text Link to Item
  - 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 Metab 7, no. 1 (January 2008): 86-94. Full Text Link to Item
  - 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 Genet 3, no. 8 (August 2007): e136-. Full Text Link to Item
  - 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, and Frum, TT 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. Full Text Link to Item
  - 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." Nat Genet 39, no. 3 (March 2007): 311-318. Full Text Link to Item
  - 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 Res 67, no. 4 (February 15, 2007): 1461-1471. Full Text Link to Item
  - 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-. 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." Nat Methods 3, no. 7 (July 2006): 503-509. Full Text Link to Item
  - 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 Pathog 2, no. 6 (June 2006): e60-. 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 Genet 2, no. 4 (April 2006): e51-. Full Text Link to Item
  - 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 Res 16, no. 1 (January 2006): 123-131. Full Text Link to Item
  - 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." Mol Cell Biol 26, no. 1 (January 2006): 155-168. Full Text Link to Item
  - 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." Proc Natl Acad Sci U S A 101, no. 4 (January 27, 2004): 992-997. Full Text Link to Item
  - Feingold, EA, Good, PJ, Guyer, MS, Kamholz, S, Liefer, L, Wetterstrand, K, Collins, FS, Gingeras, TR, Kampa, D, Sekinger, EA, Cheng, J, Hirsch, H, Ghosh, S, Zhu, Z, Patel, S, Piccolboni, A, Yang, A, Tammana, H, Bekiranov, S, Kapranov, P, Harrison, R, Church, G, Struhl, K, Ren, B, Kim, TH, Barrera, LO, Qu, C, Calcar, SV, Luna, R, Glass, CK, Rosenfeld, MG, Guigo, R, Antonarakis, SE, Birney, E, Brent, M, Pachter, L, Reymond, A, Dermitzakis, ET, Dewey, C, Keefe, D, Denoeud, F, and Lagarde, J et al. "The ENCODE (ENCyclopedia of DNA Elements) Project." Science 306, no. 5696 (2004): 636-640. 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." Nat Neurosci 2, no. 7 (July 1999): 611-617. Full Text Link to Item
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- Bass Connections Faculty Team Member . Enabling Precision Health and Medicine . August 2017 - May 2018 2017 - 2018

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