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Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations.
Nat Genet. 2019 Dec;51(12):1664-1669. doi: 10.1038/s41588-019-0538-0. Epub 2019 Nov 29.
Nat Genet. 2019.
PMID: 31784727
Free PMC article.
Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features.
Ray JP, de Boer CG, Fulco CP, Lareau CA, Kanai M, Ulirsch JC, Tewhey R, Ludwig LS, Reilly SK, Bergman DT, Engreitz JM, Issner R, Finucane HK, Lander ES, Regev A, Hacohen N.
Ray JP, et al. Among authors: bergman dt.
Nat Commun. 2020 Mar 6;11(1):1237. doi: 10.1038/s41467-020-15022-4.
Nat Commun. 2020.
PMID: 32144282
Free PMC article.
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HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes.
Marshall JL, Doughty BR, Subramanian V, Guckelberger P, Wang Q, Chen LM, Rodriques SG, Zhang K, Fulco CP, Nasser J, Grinkevich EJ, Noel T, Mangiameli S, Bergman DT, Greka A, Lander ES, Chen F, Engreitz JM.
Marshall JL, et al. Among authors: bergman dt.
Proc Natl Acad Sci U S A. 2020 Dec 29;117(52):33404-33413. doi: 10.1073/pnas.2010738117. Epub 2020 Dec 21.
Proc Natl Acad Sci U S A. 2020.
PMID: 33376219
Free PMC article.
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Genome-wide enhancer maps link risk variants to disease genes.
Nasser J, Bergman DT, Fulco CP, Guckelberger P, Doughty BR, Patwardhan TA, Jones TR, Nguyen TH, Ulirsch JC, Lekschas F, Mualim K, Natri HM, Weeks EM, Munson G, Kane M, Kang HY, Cui A, Ray JP, Eisenhaure TM, Collins RL, Dey K, Pfister H, Price AL, Epstein CB, Kundaje A, Xavier RJ, Daly MJ, Huang H, Finucane HK, Hacohen N, Lander ES, Engreitz JM.
Nasser J, et al. Among authors: bergman dt.
Nature. 2021 May;593(7858):238-243. doi: 10.1038/s41586-021-03446-x. Epub 2021 Apr 7.
Nature. 2021.
PMID: 33828297
Free PMC article.
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Compatibility rules of human enhancer and promoter sequences.
Bergman DT, Jones TR, Liu V, Ray J, Jagoda E, Siraj L, Kang HY, Nasser J, Kane M, Rios A, Nguyen TH, Grossman SR, Fulco CP, Lander ES, Engreitz JM.
Bergman DT, et al.
Nature. 2022 Jul;607(7917):176-184. doi: 10.1038/s41586-022-04877-w. Epub 2022 May 20.
Nature. 2022.
PMID: 35594906
Free PMC article.
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Convergence of coronary artery disease genes onto endothelial cell programs.
Schnitzler GR, Kang H, Fang S, Angom RS, Lee-Kim VS, Ma XR, Zhou R, Zeng T, Guo K, Taylor MS, Vellarikkal SK, Barry AE, Sias-Garcia O, Bloemendal A, Munson G, Guckelberger P, Nguyen TH, Bergman DT, Hinshaw S, Cheng N, Cleary B, Aragam K, Lander ES, Finucane HK, Mukhopadhyay D, Gupta RM, Engreitz JM.
Schnitzler GR, et al. Among authors: bergman dt.
Nature. 2024 Feb;626(8000):799-807. doi: 10.1038/s41586-024-07022-x. Epub 2024 Feb 7.
Nature. 2024.
PMID: 38326615
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Genome-Scale DNA Methylation Analysis Identifies Repeat Element Alterations that Modulate the Genomic Stability of Melanocytic Nevi.
Muse ME, Bergman DT, Salas LA, Tom LN, Tan JM, Laino A, Lambie D, Sturm RA, Schaider H, Soyer HP, Christensen BC, Stark MS.
Muse ME, et al. Among authors: bergman dt.
J Invest Dermatol. 2022 Jul;142(7):1893-1902.e7. doi: 10.1016/j.jid.2021.11.025. Epub 2021 Dec 3.
J Invest Dermatol. 2022.
PMID: 34871578
Free PMC article.
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Genomic profile of Pancoast syndrome due to hepatocellular carcinoma: A case report.
Bergman DT, Zaki L, Pettus JR, Zaki BI, Amin M.
Bergman DT, et al.
Thorac Cancer. 2023 Jun;14(18):1789-1792. doi: 10.1111/1759-7714.14923. Epub 2023 May 9.
Thorac Cancer. 2023.
PMID: 37160416
Free PMC article.
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