Gregory E Crawford - Publications

Computational Biology and Bioinformatics Duke University, Durham, NC 

129 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Luo K, Zhong J, Safi A, Hong LK, Tewari AK, Song L, Reddy TE, Ma L, Crawford GE, Hartemink AJ. Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data. Genome Research. PMID 35609992 DOI: 10.1101/gr.272203.120  0.399
2022 Kadur Lakshminarasimha Murthy P, Xi R, Arguijo D, Everitt JI, Kocak DD, Kobayashi Y, Bozec A, Vicent S, Ding S, Crawford GE, Hsu D, Tata PR, Reddy T, Shen X. Epigenetic basis of oncogenic-Kras-mediated epithelial-cellular proliferation and plasticity. Developmental Cell. 57: 310-328.e9. PMID 35134344 DOI: 10.1016/j.devcel.2022.01.006  0.343
2021 Liang D, Elwell AL, Aygün N, Krupa O, Wolter JM, Kyere FA, Lafferty MJ, Cheek KE, Courtney KP, Yusupova M, Garrett ME, Ashley-Koch A, Crawford GE, Love MI, de la Torre-Ubieta L, et al. Cell-type-specific effects of genetic variation on chromatin accessibility during human neuronal differentiation. Nature Neuroscience. PMID 34017130 DOI: 10.1038/s41593-021-00858-w  0.423
2021 Tung KL, Chen KY, Negrete M, Chen T, Safi A, Aljamal AA, Song L, Crawford GE, Ding S, Hsu DS, Shen X. Integrated chromatin and transcriptomic profiling of patient-derived colon cancer organoids identifies personalized drug targets to overcome oxaliplatin resistance. Genes & Diseases. 8: 203-214. PMID 33997167 DOI: 10.1016/J.Gendis.2019.10.012  0.318
2020 Sakabe NJ, Aneas I, Knoblauch N, Sobreira DR, Clark N, Paz C, Horth C, Ziffra R, Kaur H, Liu X, Anderson R, Morrison J, Cheung VC, Grotegut C, Reddy TE, ... ... Crawford GE, et al. Transcriptome and regulatory maps of decidua-derived stromal cells inform gene discovery in preterm birth. Science Advances. 6. PMID 33268355 DOI: 10.1126/sciadv.abc8696  0.323
2020 Thompson JD, Ou J, Lee N, Shin K, Cigliola V, Song L, Crawford GE, Kang J, Poss KD. Identification and requirements of enhancers that direct gene expression during zebrafish fin regeneration. Development (Cambridge, England). PMID 32665240 DOI: 10.1242/Dev.191262  0.454
2020 Keele GR, Quach BC, Israel JW, Chappell GA, Lewis L, Safi A, Simon JM, Cotney P, Crawford GE, Valdar W, Rusyn I, Furey TS. Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation. Plos Genetics. 16: e1008537. PMID 31961859 DOI: 10.1371/Journal.Pgen.1008537  0.71
2019 Edsall LE, Berrio A, Majoros WH, Swain-Lenz D, Morrow S, Shibata Y, Safi A, Wray GA, Crawford GE, Allen AS. Evaluating chromatin accessibility differences across multiple primate species using a joint modelling approach. Genome Biology and Evolution. PMID 31599933 DOI: 10.1093/Gbe/Evz218  0.463
2019 Swain-Lenz D, Berrio A, Safi A, Crawford GE, Wray GA. Comparative analyses of chromatin landscape in white adipose tissue suggest humans may have less beigeing potential than other primates. Genome Biology and Evolution. PMID 31233101 DOI: 10.1093/Gbe/Evz134  0.368
2019 Cannon ME, Currin KW, Young KL, Perrin HJ, Vadlamudi S, Safi A, Song L, Wu Y, Wabitsch M, Laakso M, Crawford GE, Mohlke KL. Open Chromatin Profiling in Adipose Tissue Marks Genomic Regions with Functional Roles in Cardiometabolic Traits. G3 (Bethesda, Md.). PMID 31186305 DOI: 10.1534/G3.119.400294  0.396
2018 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, ... ... Crawford GE, et al. Comprehensive functional genomic resource and integrative model for the human brain. Science (New York, N.Y.). 362. PMID 30545857 DOI: 10.1126/Science.Aat8464  0.431
2018 Amiri A, Coppola G, Scuderi S, Wu F, Roychowdhury T, Liu F, Pochareddy S, Shin Y, Safi A, Song L, Zhu Y, Sousa AMM, Gerstein M, Crawford GE, et al. Transcriptome and epigenome landscape of human cortical development modeled in organoids. Science (New York, N.Y.). 362. PMID 30545853 DOI: 10.1126/Science.Aat6720  0.446
2018 Lee D, Kapoor A, Safi A, Song L, Halushka MK, Crawford GE, Chakravarti A. Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants. Genome Research. PMID 30139769 DOI: 10.1101/Gr.234633.118  0.502
2018 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, et al. Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding. Genome Research. PMID 30097539 DOI: 10.1101/Gr.233346.117  0.433
2018 Whitley SK, Balasubramani A, Zindl C, Sen R, Shibata Y, Crawford GE, Weathington NM, Hatton RD, Weaver CT. IL-1R signaling promotes STAT3 and NF-κB factor recruitment to distal cis-regulatory elements that regulate transcription. The Journal of Biological Chemistry. PMID 30093408 DOI: 10.1074/Jbc.Ra118.002721  0.305
2018 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, ... ... Crawford GE, et al. Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia. Nature Communications. 9: 3121. PMID 30087329 DOI: 10.1038/S41467-018-05379-Y  0.351
2018 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, Reddy TE. Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids. Cell Systems. PMID 30031775 DOI: 10.1016/J.Cels.2018.06.007  0.465
2018 Gusev A, Mancuso N, Won H, Kousi M, Finucane HK, Reshef Y, Song L, Safi A, McCarroll S, Neale BM, Ophoff RA, O'Donovan MC, Crawford GE, Geschwind DH, et al. Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights. Nature Genetics. 50: 538-548. PMID 29632383 DOI: 10.1038/S41588-018-0092-1  0.431
2018 Pizzollo J, Nielsen WJ, Shibata Y, Safi A, Crawford GE, Wray GA, Babbitt CC. Comparative Serum Challenges Show Divergent Patterns of Gene Expression and Open Chromatin in Human and Chimpanzee. Genome Biology and Evolution. 10: 826-839. PMID 29608722 DOI: 10.1093/Gbe/Evy041  0.46
2018 Klann TS, Crawford GE, Reddy TE, Gersbach CA. Screening Regulatory Element Function with CRISPR/Cas9-based Epigenome Editing. Methods in Molecular Biology (Clifton, N.J.). 1767: 447-480. PMID 29524151 DOI: 10.1007/978-1-4939-7774-1_25  0.434
2018 Israel JW, Chappell GA, Simon JM, Pott S, Safi A, Lewis L, Cotney P, Boulos HS, Bodnar W, Lieb JD, Crawford GE, Furey TS, 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. PMID 29429127 DOI: 10.1007/S00335-018-9739-6  0.669
2017 Lewis L, Crawford GE, Furey TS, Rusyn I. Genetic and epigenetic determinants of inter-individual variability in responses to toxicants. Current Opinion in Toxicology. 6: 50-59. PMID 29276797 DOI: 10.1016/J.Cotox.2017.08.006  0.662
2017 Chappell GA, Israel JW, Simon JM, Pott S, Safi A, Eklund K, Sexton KG, Bodnar W, Lieb JD, Crawford GE, Rusyn I, 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: 107006. PMID 29038090 DOI: 10.1289/Ehp1937  0.676
2017 Manandhar D, Song L, Kabadi A, Kwon JB, Edsall LE, Ehrlich M, Tsumagari K, Gersbach CA, Crawford GE, Gordân R. Incomplete MyoD-induced transdifferentiation is associated with chromatin remodeling deficiencies. Nucleic Acids Research. PMID 28977539 DOI: 10.1093/Nar/Gkx773  0.529
2017 Montefiori L, Hernandez L, Zhang Z, Gilad Y, Ober C, Crawford G, Nobrega M, Jo Sakabe N. Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9. Scientific Reports. 7: 2451. PMID 28550296 DOI: 10.1038/S41598-017-02547-W  0.364
2017 Davison JM, Lickwar CR, Song L, Breton G, Crawford GE, Rawls JF. Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha. Genome Research. PMID 28385711 DOI: 10.1101/Gr.220111.116  0.465
2017 Klann TS, Black JB, Chellappan M, Safi A, Song L, Hilton IB, Crawford GE, Reddy TE, Gersbach CA. CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome. Nature Biotechnology. PMID 28369033 DOI: 10.1038/Nbt.3853  0.468
2017 Maatouk DM, Natarajan A, Shibata Y, Song L, Crawford GE, Ohler U, Capel B. Genome-wide identification of regulatory elements in Sertoli cells. Development (Cambridge, England). PMID 28087634 DOI: 10.1242/Dev.142554  0.559
2016 Gopinath C, Law WD, Rodríguez-Molina JF, Prasad AB, Song L, Crawford GE, Mullikin JC, Svaren J, Antonellis A. Stringent comparative sequence analysis reveals SOX10 as a putative inhibitor of glial cell differentiation. Bmc Genomics. 17: 887. PMID 27821050 DOI: 10.1186/S12864-016-3167-3  0.445
2016 Vockley CM, D'Ippolito AM, McDowell IC, Majoros WH, Safi A, Song L, Crawford GE, Reddy TE. Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome. Cell. 166: 1269-1281.e19. PMID 27565349 DOI: 10.1016/J.Cell.2016.07.049  0.457
2016 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, ... ... Crawford GE, et al. The genetic regulatory signature of type 2 diabetes in human skeletal muscle. Nature Communications. 7: 11764. PMID 27353450 DOI: 10.1038/Ncomms11764  0.497
2016 Frank CL, Manandhar D, Gordân R, Crawford GE. HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells. Epigenetics & Chromatin. 9: 15. PMID 27087856 DOI: 10.1186/S13072-016-0065-5  0.375
2016 Zhong J, Luo K, Winter PS, Crawford GE, Iversen ES, Hartemink AJ. Mapping nucleosome positions using DNase-seq. Genome Research. PMID 26772197 DOI: 10.1101/Gr.195602.115  0.45
2015 Yang R, Kerschner JL, Gosalia N, Neems D, Gorsic LK, Safi A, Crawford GE, Kosak ST, Leir SH, Harris A. Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus. Nucleic Acids Research. PMID 26673704 DOI: 10.1093/Nar/Gkv1358  0.52
2015 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, et al. The PsychENCODE project. Nature Neuroscience. 18: 1707-1712. PMID 26605881 DOI: 10.1038/Nn.4156  0.56
2015 Thakore PI, D'Ippolito AM, Song L, Safi A, Shivakumar NK, Kabadi AM, Reddy TE, Crawford GE, Gersbach CA. Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nature Methods. PMID 26501517 DOI: 10.1038/Nmeth.3630  0.494
2015 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, ... ... Crawford GE, et al. Genetic Variants and Cellular Stressors Associated with Exfoliation Syndrome Modulate Promoter Activity of a lncRNA within the LOXL1 Locus. Human Molecular Genetics. PMID 26307087 DOI: 10.1093/Hmg/Ddv347  0.398
2015 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, Pavan WJ. Genomic analysis reveals distinct mechanisms and functional classes of SOX10-regulated genes in melanocytes. Human Molecular Genetics. 24: 5433-50. PMID 26206884 DOI: 10.1093/Hmg/Ddv267  0.567
2015 Polstein LR, Perez-Pinera P, Kocak DD, Vockley CM, Bledsoe P, Song L, Safi A, Crawford GE, Reddy TE, Gersbach CA. Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators. Genome Research. PMID 26025803 DOI: 10.1101/Gr.179044.114  0.548
2015 Ding Z, Ni Y, Timmer SW, Lee BK, Battenhouse A, Louzada S, Yang F, Dunham I, Crawford GE, Lieb JD, Durbin R, Iyer VR, Birney E. Correction: Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association. Plos Genetics. 11: e1005177. PMID 25919664 DOI: 10.1371/Journal.Pgen.1005177  0.301
2015 Frank CL, Liu F, Wijayatunge R, Song L, Biegler MT, Yang MG, Vockley CM, Safi A, Gersbach CA, Crawford GE, West AE. Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum. Nature Neuroscience. 18: 647-56. PMID 25849986 DOI: 10.1038/Nn.3995  0.462
2015 Hilton IB, D'Ippolito AM, Vockley CM, Thakore PI, Crawford GE, Reddy TE, Gersbach CA. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nature Biotechnology. 33: 510-7. PMID 25849900 DOI: 10.1038/Nbt.3199  0.493
2015 Raposo AA, Vasconcelos FF, Drechsel D, Marie C, Johnston C, Dolle D, Bithell A, Gillotin S, van den Berg DL, Ettwiller L, Flicek P, Crawford GE, Parras CM, Berninger B, Buckley NJ, et al. Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis. Cell Reports. PMID 25753420 DOI: 10.1016/J.Celrep.2015.02.025  0.516
2015 Su D, Wang X, Campbell MR, Song L, Safi A, Crawford GE, Bell DA. Interactions of chromatin context, binding site sequence content, and sequence evolution in stress-induced p53 occupancy and transactivation. Plos Genetics. 11: e1004885. PMID 25569532 DOI: 10.1371/Journal.Pgen.1004885  0.475
2015 Hsiung CC, Morrissey CS, Udugama M, Frank CL, Keller CA, Baek S, Giardine B, Crawford GE, Sung MH, Hardison RC, Blobel GA. Genome accessibility is widely preserved and locally modulated during mitosis. Genome Research. 25: 213-25. PMID 25373146 DOI: 10.1101/Gr.180646.114  0.515
2015 Mateo JL, van den Berg DL, Haeussler M, Drechsel D, Gaber ZB, Castro DS, Robson P, Crawford GE, Flicek P, Ettwiller L, Wittbrodt J, Guillemot F, Martynoga B. Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal. Genome Research. 25: 41-56. PMID 25294244 DOI: 10.1101/Gr.173435.114  0.465
2015 Loftus S, Cronin J, Fufa T, McCallion A, Crawford G, Pavan W. Abstract A23: Epigenetic Cis-regulatory interactions in HIF1a-activated melanocytes Cancer Research. 75. DOI: 10.1158/1538-7445.Mel2014-A23  0.518
2015 Thakore PI, D'Ippolito A, Song L, Safi A, Shivakumar NK, Kabadi AM, Bledsoe P, Reddy TE, Crawford GE, Gersbach CA. 485. Targeted Epigenome Editing by CRISPR/Cas9-Based Repressors for Silencing of Distal Regulatory Elements Molecular Therapy. 23: S192-S193. DOI: 10.1016/S1525-0016(16)34094-1  0.521
2014 Ding Z, Ni Y, Timmer SW, Lee BK, Battenhouse A, Louzada S, Yang F, Dunham I, Crawford GE, Lieb JD, Durbin R, Iyer VR, Birney E. Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association. Plos Genetics. 10: e1004798. PMID 25411781 DOI: 10.1371/Journal.Pgen.1004798  0.412
2014 Yard?mc? GGü, Frank CL, Crawford GE, Ohler U. Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection Nucleic Acids Research. 42: 11865-11878. PMID 25294828 DOI: 10.1093/Nar/Gku810  0.452
2014 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, et al. 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: E3366. PMID 25275169 DOI: 10.1073/Pnas.1410434111  0.515
2014 Wortham M, Guo C, Zhang M, Song L, Lee BK, Iyer VR, Furey TS, Crawford GE, Yan H, He Y. Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma. Plos One. 9: e107156. PMID 25198066 DOI: 10.1371/Journal.Pone.0107156  0.728
2014 Browne JA, Yang R, Song L, Crawford GE, Leir SH, Harris A. Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function. Molecular Human Reproduction. 20: 1198-207. PMID 25180270 DOI: 10.1093/Molehr/Gau075  0.56
2014 Camp JG, Frank CL, Lickwar CR, Guturu H, Rube T, Wenger AM, Chen J, Bejerano G, Crawford GE, Rawls JF. Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape. Genome Research. 24: 1504-16. PMID 24963153 DOI: 10.1101/Gr.165845.113  0.504
2014 Factor DC, Corradin O, Zentner GE, Saiakhova A, Song L, Chenoweth JG, McKay RD, Crawford GE, Scacheri PC, Tesar PJ. Epigenomic comparison reveals activation of "seed" enhancers during transition from naive to primed pluripotency. Cell Stem Cell. 14: 854-63. PMID 24905169 DOI: 10.1016/J.Stem.2014.05.005  0.464
2014 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, et al. Defining functional DNA elements in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 111: 6131-8. PMID 24753594 DOI: 10.1073/Pnas.1318948111  0.611
2014 Terragni J, Zhang G, Sun Z, Pradhan S, Song L, Crawford GE, Lacey M, Ehrlich M. Notch signaling genes: myogenic DNA hypomethylation and 5-hydroxymethylcytosine. Epigenetics. 9: 842-50. PMID 24670287 DOI: 10.4161/Epi.28597  0.426
2014 Balasubramani A, Winstead CJ, Turner H, Janowski KM, Harbour SN, Shibata Y, Crawford GE, Hatton RD, 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: e1003969. PMID 24415943 DOI: 10.1371/Journal.Pgen.1003969  0.483
2014 Hsiung CC, Morrissey C, Udugama M, Frank C, Keller CA, Baek S, Giardine B, Crawford GE, Sung M, Raj A, Hardison RC, Blobel GA. Epigenetics of Cellular Memory: Insights from the Chromatin Accessibility Landscape of the Mitotic Genome Blood. 124: 4342-4342. DOI: 10.1182/Blood.V124.21.4342.4342  0.543
2014 Browne JA, Yang R, Song L, Crawford GE, Leir SH, Harris A. Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function Molecular Human Reproduction. 20: 1198-1207. DOI: 10.1093/molehr/gau075  0.464
2013 Gertz J, Savic D, Varley KE, Partridge EC, Safi A, Jain P, Cooper GM, Reddy TE, Crawford GE, Myers RM. Distinct properties of cell-type-specific and shared transcription factor binding sites. Molecular Cell. 52: 25-36. PMID 24076218 DOI: 10.1016/J.Molcel.2013.08.037  0.504
2013 Bischof JM, Gillen AE, Song L, Gosalia N, London D, Furey TS, Crawford GE, 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: 104. PMID 24006278 DOI: 10.1095/Biolreprod.113.110403  0.739
2013 Tsumagari K, Baribault C, Terragni J, Chandra S, Renshaw C, Sun Z, Song L, Crawford GE, Pradhan S, Lacey M, Ehrlich M. DNA methylation and differentiation: HOX genes in muscle cells. Epigenetics & Chromatin. 6: 25. PMID 23916067 DOI: 10.1186/1756-8935-6-25  0.396
2013 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, Gersbach CA. RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nature Methods. 10: 973-6. PMID 23892895 DOI: 10.1038/Nmeth.2600  0.4
2013 Winter DR, Song L, Mukherjee S, Furey TS, Crawford GE. DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types. Genome Research. 23: 1118-29. PMID 23657885 DOI: 10.1101/Gr.150482.112  0.726
2013 Zhang B, Day DS, Ho JW, Song L, Cao J, Christodoulou D, Seidman JG, Crawford GE, Park PJ, Pu WT. A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity. Genome Research. 23: 917-27. PMID 23547170 DOI: 10.1101/Gr.149674.112  0.478
2013 Sheffield NC, Thurman RE, Song L, Safi A, Stamatoyannopoulos JA, Lenhard B, Crawford GE, Furey TS. Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions. Genome Research. 23: 777-88. PMID 23482648 DOI: 10.1101/Gr.152140.112  0.734
2013 Tsumagari K, Baribault C, Terragni J, Varley KE, Gertz J, Pradhan S, Badoo M, Crain CM, Song L, Crawford GE, Myers RM, Lacey M, Ehrlich M. Early de novo DNA methylation and prolonged demethylation in the muscle lineage. Epigenetics : Official Journal of the Dna Methylation Society. 8: 317-32. PMID 23417056 DOI: 10.4161/Epi.23989  0.403
2013 Perez-Pinera P, Ousterout DG, Brunger JM, Farin AM, Glass KA, Guilak F, Crawford GE, Hartemink AJ, Gersbach CA. Synergistic and tunable human gene activation by combinations of synthetic transcription factors. Nature Methods. 10: 239-42. PMID 23377379 DOI: 10.1038/Nmeth.2361  0.495
2013 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, Myers RM. Dynamic DNA methylation across diverse human cell lines and tissues. Genome Research. 23: 555-67. PMID 23325432 DOI: 10.1101/Gr.147942.112  0.448
2012 Calabrese JM, Sun W, Song L, Mugford JW, Williams L, Yee D, Starmer J, Mieczkowski P, Crawford GE, Magnuson T. Site-specific silencing of regulatory elements as a mechanism of x inactivation Cell. 151: 951-963. PMID 23178118 DOI: 10.1016/J.Cell.2012.10.037  0.488
2012 Tewari AK, Yardimci GG, Shibata Y, Sheffield NC, Song L, Taylor BS, Georgiev SG, Coetzee GA, Ohler U, Furey TS, Crawford GE, Febbo PG. Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity. Genome Biology. 13: R88. PMID 23034120 DOI: 10.1186/Gb-2012-13-10-R88  0.711
2012 Natarajan A, Yardimci GG, Sheffield NC, Crawford GE, Ohler U. Predicting cell-type-specific gene expression from regions of open chromatin. Genome Research. 22: 1711-22. PMID 22955983 DOI: 10.1101/Gr.135129.111  0.554
2012 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, ... ... Crawford GE, et al. The accessible chromatin landscape of the human genome. Nature. 489: 75-82. PMID 22955617 DOI: 10.1038/Nature11232  0.749
2012 Parker SC, Gartner J, Cardenas-Navia I, Wei X, Ozel Abaan H, Ajay SS, Hansen NF, Song L, Bhanot UK, Killian JK, Gindin Y, Walker RL, Meltzer PS, Mullikin JC, Furey TS, ... Crawford GE, et al. Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes. Plos Genetics. 8: e1002871. PMID 22912592 DOI: 10.1371/Journal.Pgen.1002871  0.666
2012 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, ... ... Crawford GE, et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biology. 13: 418. PMID 22889292 DOI: 10.1186/Gb-2012-13-8-418  0.626
2012 Reddy TE, Gertz J, Crawford GE, Garabedian MJ, Myers RM. The hypersensitive glucocorticoid response specifically regulates period 1 and expression of circadian genes. Molecular and Cellular Biology. 32: 3756-67. PMID 22801371 DOI: 10.1128/Mcb.00062-12  0.503
2012 Shibata Y, Sheffield NC, Fedrigo O, Babbitt CC, Wortham M, Tewari AK, London D, Song L, Lee BK, Iyer VR, Parker SC, Margulies EH, Wray GA, Furey TS, Crawford GE. Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. Plos Genetics. 8: e1002789. PMID 22761590 DOI: 10.1371/Journal.Pgen.1002789  0.749
2012 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, Scacheri PC. H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island-containing start sites. Genome Medicine. 4: 47. PMID 22640407 DOI: 10.1186/Gm346  0.473
2012 Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, Gaffney DJ, Pickrell JK, De Leon S, Michelini K, Lewellen N, Crawford GE, Stephens M, Gilad Y, Pritchard JK. DNase I sensitivity QTLs are a major determinant of human expression variation. Nature. 482: 390-4. PMID 22307276 DOI: 10.1038/Nature10808  0.535
2012 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, Myers RM. Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Research. 22: 860-9. PMID 22300769 DOI: 10.1101/Gr.131201.111  0.546
2012 Gaffney DJ, Veyrieras JB, Degner JF, Pique-Regi R, Pai AA, Crawford GE, Stephens M, Gilad Y, Pritchard JK. Dissecting the regulatory architecture of gene expression QTLs. Genome Biology. 13: R7. PMID 22293038 DOI: 10.1186/Gb-2012-13-1-R7  0.444
2012 Bischof JM, Ott CJ, Leir SH, Gosalia N, Song L, London D, Furey TS, Cotton CU, Crawford GE, Harris A. A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function. Thorax. 67: 385-91. PMID 22169360 DOI: 10.1136/Thoraxjnl-2011-200880  0.731
2012 Zhang W, Wu Y, Schnable JC, Zeng Z, Freeling M, Crawford GE, Jiang J. High-resolution mapping of open chromatin in the rice genome. Genome Research. 22: 151-62. PMID 22110044 DOI: 10.1101/Gr.131342.111  0.528
2012 Lee BK, Bhinge AA, Battenhouse A, McDaniell RM, Liu Z, Song L, Ni Y, Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR. Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Research. 22: 9-24. PMID 22090374 DOI: 10.1101/Gr.127597.111  0.731
2012 Tewari A, Yardimci G, Shibata Y, Sheffield N, Song L, Taylor B, Coetzee G, Furey T, Crawford G, Febbo P. Abstract A12: Chromatin accessibility reveals insight into androgen receptor activation and transcriptional specificity Cancer Research. 72: A12-A12. DOI: 10.1158/1538-7445.Prca2012-A12  0.688
2012 Tewari AK, Yardimci GG, Crawford GE, Febbo PG. Abstract 2923: Androgen receptor activation changes chromatin structure and transcriptional activation Cancer Research. 72: 2923-2923. DOI: 10.1158/1538-7445.Am2012-2923  0.487
2012 Maatouk DM, Natarajan A, Shibata Y, Song L, Crawford G, Capel B. Using Chromatin Architecture to Identify Gene Regulatory Elements Required for Testis Development. Biology of Reproduction. 87: 67-67. DOI: 10.1093/Biolreprod/87.S1.67  0.465
2011 Tsumagari K, Chang SC, Lacey M, Baribault C, Chittur SV, Sowden J, Tawil R, Crawford GE, Ehrlich M. Gene expression during normal and FSHD myogenesis. Bmc Medical Genomics. 4: 67. PMID 21951698 DOI: 10.1186/1755-8794-4-67  0.408
2011 Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D, Giardine B, Shibata Y, Song L, Pimkin M, Crawford GE, et al. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Research. 21: 1659-71. PMID 21795386 DOI: 10.1101/Gr.125088.111  0.716
2011 Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Gräf S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, ... ... Crawford GE, et al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Research. 21: 1757-67. PMID 21750106 DOI: 10.1101/Gr.121541.111  0.816
2011 Boyle AP, Song L, Lee BK, London D, Keefe D, Birney E, Iyer VR, Crawford GE, Furey TS. High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Research. 21: 456-64. PMID 21106903 DOI: 10.1101/Gr.112656.110  0.803
2011 Winter D, Song L, Mukherjee S, Furey T, Crawford G. Analyzing high resolution nucleosome structure by DNase-seq F1000research. 2. DOI: 10.7490/F1000Research.2123.1  0.596
2010 Stitzel ML, Sethupathy P, Pearson DS, Chines PS, Song L, Erdos MR, Welch R, Parker SC, Boyle AP, Scott LJ, Margulies EH, Boehnke M, Furey TS, Crawford GE, et al. Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci. Cell Metabolism. 12: 443-55. PMID 21035756 DOI: 10.1016/J.Cmet.2010.09.012  0.803
2010 Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR. Allele-specific and heritable chromatin signatures in humans. Human Molecular Genetics. 19: R204-9. PMID 20846943 DOI: 10.1093/Hmg/Ddq404  0.716
2010 Schnetz MP, Handoko L, Akhtar-Zaidi B, Bartels CF, Pereira CF, Fisher AG, Adams DJ, Flicek P, Crawford GE, Laframboise T, Tesar P, Wei CL, Scacheri PC. CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. Plos Genetics. 6: e1001023. PMID 20657823 DOI: 10.1371/Journal.Pgen.1001023  0.531
2010 Balasubramani A, Shibata Y, Crawford GE, Baldwin AS, Hatton RD, Weaver CT. Modular utilization of distal cis-regulatory elements controls Ifng gene expression in T cells activated by distinct stimuli. Immunity. 33: 35-47. PMID 20643337 DOI: 10.1016/J.Immuni.2010.07.004  0.391
2010 Mukasa R, Balasubramani A, Lee YK, Whitley SK, Weaver BT, Shibata Y, Crawford GE, Hatton RD, Weaver CT. Epigenetic instability of cytokine and transcription factor gene loci underlies plasticity of the T helper 17 cell lineage. Immunity. 32: 616-27. PMID 20471290 DOI: 10.1016/J.Immuni.2010.04.016  0.402
2010 McDaniell R, Lee BK, 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, et al. Heritable individual-specific and allele-specific chromatin signatures in humans. Science (New York, N.Y.). 328: 235-9. PMID 20299549 DOI: 10.1126/Science.1184655  0.801
2010 Song L, Crawford GE. DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harbor Protocols. 2010: pdb.prot5384. PMID 20150147 DOI: 10.1101/Pdb.Prot5384  0.557
2010 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, et al. Erratum: Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci (Cell Metabolism (2010) 12 (443-455)) Cell Metabolism. 12. DOI: 10.1016/J.Cmet.2010.11.013  0.743
2009 Ott CJ, Blackledge NP, Kerschner JL, Leir SH, Crawford GE, Cotton CU, Harris A. Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus. Proceedings of the National Academy of Sciences of the United States of America. 106: 19934-9. PMID 19897727 DOI: 10.1073/Pnas.0900946106  0.528
2009 Xu X, Tsumagari K, Sowden J, Tawil R, Boyle AP, Song L, Furey TS, Crawford GE, Ehrlich M. DNaseI hypersensitivity at gene-poor, FSH dystrophy-linked 4q35.2. Nucleic Acids Research. 37: 7381-93. PMID 19820107 DOI: 10.1093/Nar/Gkp833  0.775
2009 Shibata Y, Crawford GE. Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip). Methods in Molecular Biology (Clifton, N.J.). 556: 177-90. PMID 19488879 DOI: 10.1007/978-1-60327-192-9_13  0.516
2009 Ott CJ, Suszko M, Blackledge NP, Wright JE, Crawford GE, Harris A. A complex intronic enhancer regulates expression of the CFTR gene by direct interaction with the promoter. Journal of Cellular and Molecular Medicine. 13: 680-92. PMID 19449463 DOI: 10.1111/J.1582-4934.2008.00621.X  0.53
2009 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, ... ... Crawford GE, et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature. 459: 108-12. PMID 19295514 DOI: 10.1038/Nature07829  0.559
2009 Schnetz MP, Bartels CF, Shastri K, Balasubramanian D, Zentner GE, Balaji R, Zhang X, Song L, Wang Z, Laframboise T, Crawford GE, Scacheri PC. Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns. Genome Research. 19: 590-601. PMID 19251738 DOI: 10.1101/Gr.086983.108  0.534
2009 Bina M, Wyss P, Lazarus SA, Shah SR, Ren W, Szpankowski W, Crawford GE, Park SP, Song XC. Discovering sequences with potential regulatory characteristics. Genomics. 93: 314-22. PMID 19084590 DOI: 10.1016/J.Ygeno.2008.11.008  0.484
2009 Tewari AK, Song L, Furey TS, Crawford GE, Febbo PG. Abstract B44: Chromatin structure impacts androgen receptor transcriptional specificity in prostate cancer cell lines Cancer Research. 69. DOI: 10.1158/0008-5472.Fbcr09-B44  0.701
2008 Boyle AP, Guinney J, Crawford GE, Furey TS. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics (Oxford, England). 24: 2537-8. PMID 18784119 DOI: 10.1093/Bioinformatics/Btn480  0.749
2008 Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE. High-resolution mapping and characterization of open chromatin across the genome. Cell. 132: 311-22. PMID 18243105 DOI: 10.1016/J.Cell.2007.12.014  0.807
2008 Eguchi J, Yan QW, Schones DE, Kamal M, Hsu CH, Zhang MQ, Crawford GE, Rosen ED. Interferon regulatory factors are transcriptional regulators of adipogenesis. Cell Metabolism. 7: 86-94. PMID 18177728 DOI: 10.1016/J.Cmet.2007.11.002  0.476
2007 Xi H, Shulha HP, Lin JM, Vales TR, Fu Y, Bodine DM, McKay RD, Chenoweth JG, Tesar PJ, Furey TS, Ren B, Weng Z, Crawford GE. Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. Plos Genetics. 3: e136. PMID 17708682 DOI: 10.1371/Journal.Pgen.0030136  0.731
2007 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, ... ... Crawford GE, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.722
2007 Nagel S, Scherr M, Kel A, Hornischer K, Crawford GE, Kaufmann M, Meyer C, Drexler HG, MacLeod RA. 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: 1461-71. PMID 17308084 DOI: 10.1158/0008-5472.Can-06-2615  0.458
2007 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, Ren B. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome Nature Genetics. 39: 311-318. PMID 17277777 DOI: 10.1038/Ng1966  0.52
2006 Crawford GE, Davis S, Scacheri PC, Renaud G, Halawi MJ, Erdos MR, Green R, Meltzer PS, Wolfsberg TG, Collins FS. DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nature Methods. 3: 503-9. PMID 16791207 DOI: 10.1038/Nmeth888  0.605
2006 Lewinski MK, Yamashita M, Emerman M, Ciuffi A, Marshall H, Crawford G, Collins F, Shinn P, Leipzig J, Hannenhalli S, Berry CC, Ecker JR, Bushman FD. Retroviral DNA integration: viral and cellular determinants of target-site selection. Plos Pathogens. 2: e60. PMID 16789841 DOI: 10.1371/Journal.Ppat.0020060  0.48
2006 Bernat JA, Crawford GE, Ogurtsov AY, Collins FS, Ginsburg D, Kondrashov AS. Distant conserved sequences flanking endothelial-specific promoters contain tissue-specific DNase-hypersensitive sites and over-represented motifs. Human Molecular Genetics. 15: 2098-105. PMID 16723375 DOI: 10.1093/Hmg/Ddl133  0.606
2006 Scacheri PC, Davis S, Odom DT, Crawford GE, Perkins S, Halawi MJ, Agarwal SK, Marx SJ, Spiegel AM, Meltzer PS, Collins FS. Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis. Plos Genetics. 2: e51. PMID 16604156 DOI: 10.1371/Journal.Pgen.0020051  0.6
2006 Yan J, Xu L, Crawford G, Wang Z, Burgess SM. The forkhead transcription factor FoxI1 remains bound to condensed mitotic chromosomes and stably remodels chromatin structure. Molecular and Cellular Biology. 26: 155-68. PMID 16354687 DOI: 10.1128/Mcb.26.1.155-168.2006  0.456
2006 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, et al. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Research. 16: 123-31. PMID 16344561 DOI: 10.1101/Gr.4074106  0.62
2006 Nagel S, Scherr M, Kel A, Hornischer K, Crawford GE, Kaufmann M, Meyer C, Drexler HG, 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. Blood. 108: 2212-2212. DOI: 10.1182/Blood.V108.11.2212.2212  0.478
2005 Bernat JA, Kondrashov AS, Crawford GE, Collins FS, Ginsburg D. Comparative Genomic Analysis of the 5′-Upstream Sequences of von Willebrand Factor and 27 Other Endothelial-Specific Genes Identifies Conserved Noncoding Sequences That Are DNase Hypersensitive. Blood. 106: 2650-2650. DOI: 10.1182/Blood.V106.11.2650.2650  0.624
2005 Moratto D, Jagadeesh JG, Konno A, Bosticardo M, Crawford GE, Holt I, Muul LM, Shurman SH, Wolfsberg T, Candotti F. 333. Preferential Targeting of Transcriptional Start Sites after Retroviral-Mediated T-Cell Gene Therapy for Adenosine Deaminase Deficiency Molecular Therapy. 11. DOI: 10.1016/J.Ymthe.2005.06.336  0.474
2004 Crawford GE, Holt IE, Mullikin JC, Tai D, Blakesley R, Bouffard G, Young A, Masiello C, Green ED, Wolfsberg TG, Collins FS. 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: 992-7. PMID 14732688 DOI: 10.1073/Pnas.0307540100  0.633
2002 Crawford GE, Lu QL, Partridge TA, Chamberlain JS. Suppression of revertant fibers in mdx mice by expression of a functional dystrophin. Human Molecular Genetics. 10: 2745-50. PMID 11734539 DOI: 10.1093/Hmg/10.24.2745  0.458
2000 Crawford GE, Faulkner JA, Crosbie RH, Campbell KP, Froehner SC, Chamberlain JS. Assembly of the dystrophin-associated protein complex does not require the dystrophin COOH-terminal domain. The Journal of Cell Biology. 150: 1399-410. PMID 10995444 DOI: 10.1083/Jcb.150.6.1399  0.496
1999 Lumeng C, Phelps S, Crawford GE, Walden PD, Barald K, Chamberlain JS. Interactions between beta 2-syntrophin and a family of microtubule-associated serine/threonine kinases. Nature Neuroscience. 2: 611-7. PMID 10404183 DOI: 10.1038/10165  0.443
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