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For: Quang DX, Erdos MR, Parker SCJ, Collins FS. Motif signatures in stretch enhancers are enriched for disease-associated genetic variants. Epigenetics Chromatin 2015;8:23. [PMID: 26180553 DOI: 10.1186/s13072-015-0015-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 07/01/2015] [Indexed: 02/07/2023]  Open
Number Cited by Other Article(s)
1
Varshney A, Manickam N, Orchard P, Tovar A, Ventresca C, Zhang Z, Feng F, Mears J, Erdos MR, Narisu N, Nishino K, Rai V, Stringham HM, Jackson AU, Tamsen T, Gao C, Yang M, Koues OI, Welch JD, Burant CF, Williams LK, Jenkinson C, DeFronzo RA, Norton L, Saramies J, Lakka TA, Laakso M, Tuomilehto J, Mohlke KL, Kitzman JO, Koistinen HA, Liu J, Boehnke M, Collins FS, Scott LJ, Parker SCJ. Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.15.571696. [PMID: 38168419 PMCID: PMC10760134 DOI: 10.1101/2023.12.15.571696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
2
Ivancevic A, Simpson DM, Joyner OM, Bagby SM, Nguyen LL, Bitler BG, Pitts TM, Chuong EB. Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer. SCIENCE ADVANCES 2024;10:eado1218. [PMID: 39018396 PMCID: PMC466953 DOI: 10.1126/sciadv.ado1218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/13/2024] [Indexed: 07/19/2024]
3
Tovar A, Kyono Y, Nishino K, Bose M, Varshney A, Parker SCJ, Kitzman JO. Using a modular massively parallel reporter assay to discover context-specific regulatory grammars in type 2 diabetes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.08.561391. [PMID: 37873175 PMCID: PMC10592691 DOI: 10.1101/2023.10.08.561391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
4
Kravchuk EV, Ashniev GA, Gladkova MG, Orlov AV, Vasileva AV, Boldyreva AV, Burenin AG, Skirda AM, Nikitin PI, Orlova NN. Experimental Validation and Prediction of Super-Enhancers: Advances and Challenges. Cells 2023;12:cells12081191. [PMID: 37190100 DOI: 10.3390/cells12081191] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023]  Open
5
Orchard P, Manickam N, Ventresca C, Vadlamudi S, Varshney A, Rai V, Kaplan J, Lalancette C, Mohlke KL, Gallagher K, Burant CF, Parker SCJ. Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits. Genome Res 2021;31:2258-2275. [PMID: 34815310 PMCID: PMC8647829 DOI: 10.1101/gr.268482.120] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/16/2021] [Indexed: 12/12/2022]
6
Varshney A, Kyono Y, Elangovan VR, Wang C, Erdos MR, Narisu N, Albanus RD, Orchard P, Stitzel ML, Collins FS, Kitzman JO, Parker SCJ. A Transcription Start Site Map in Human Pancreatic Islets Reveals Functional Regulatory Signatures. Diabetes 2021;70:1581-1591. [PMID: 33849996 PMCID: PMC8336006 DOI: 10.2337/db20-1087] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 04/09/2021] [Indexed: 12/21/2022]
7
Ohnmacht J, May P, Sinkkonen L, Krüger R. Missing heritability in Parkinson's disease: the emerging role of non-coding genetic variation. J Neural Transm (Vienna) 2020;127:729-748. [PMID: 32248367 PMCID: PMC7242266 DOI: 10.1007/s00702-020-02184-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/24/2020] [Indexed: 02/01/2023]
8
Quang D, Xie X. FactorNet: A deep learning framework for predicting cell type specific transcription factor binding from nucleotide-resolution sequential data. Methods 2019;166:40-47. [PMID: 30922998 PMCID: PMC6708499 DOI: 10.1016/j.ymeth.2019.03.020] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 03/05/2019] [Accepted: 03/20/2019] [Indexed: 01/08/2023]  Open
9
Lee HK, Willi M, Shin HY, Liu C, Hennighausen L. Progressing super-enhancer landscape during mammary differentiation controls tissue-specific gene regulation. Nucleic Acids Res 2019;46:10796-10809. [PMID: 30285185 PMCID: PMC6237736 DOI: 10.1093/nar/gky891] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 09/20/2018] [Indexed: 12/15/2022]  Open
10
Jia Y, Chng WJ, Zhou J. Super-enhancers: critical roles and therapeutic targets in hematologic malignancies. J Hematol Oncol 2019;12:77. [PMID: 31311566 PMCID: PMC6636097 DOI: 10.1186/s13045-019-0757-y] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/14/2019] [Indexed: 12/11/2022]  Open
11
Hamdan FH, Johnsen SA. Perturbing Enhancer Activity in Cancer Therapy. Cancers (Basel) 2019;11:cancers11050634. [PMID: 31067678 PMCID: PMC6563029 DOI: 10.3390/cancers11050634] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/26/2019] [Accepted: 05/05/2019] [Indexed: 02/07/2023]  Open
12
Varshney A, VanRenterghem H, Orchard P, Boyle AP, Stitzel ML, Ucar D, Parker SCJ. Cell Specificity of Human Regulatory Annotations and Their Genetic Effects on Gene Expression. Genetics 2019;211:549-562. [PMID: 30593493 PMCID: PMC6366912 DOI: 10.1534/genetics.118.301525] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 12/09/2018] [Indexed: 12/19/2022]  Open
13
Khan A, Mathelier A, Zhang X. Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers. Epigenetics 2018;13:910-922. [PMID: 30169995 DOI: 10.1080/15592294.2018.1514231] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]  Open
14
Developmental Control of NRAMP1 (SLC11A1) Expression in Professional Phagocytes. BIOLOGY 2017;6:biology6020028. [PMID: 28467369 PMCID: PMC5485475 DOI: 10.3390/biology6020028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/25/2017] [Accepted: 04/25/2017] [Indexed: 12/11/2022]
15
Keating ST, Plutzky J, El-Osta A. Epigenetic Changes in Diabetes and Cardiovascular Risk. Circ Res 2017;118:1706-22. [PMID: 27230637 DOI: 10.1161/circresaha.116.306819] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 04/30/2016] [Indexed: 01/03/2023]
16
Expression of long non-coding RNAs in autoimmunity and linkage to enhancer function and autoimmune disease risk genetic variants. J Autoimmun 2017;81:99-109. [PMID: 28420548 DOI: 10.1016/j.jaut.2017.03.014] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/29/2017] [Accepted: 03/31/2017] [Indexed: 01/19/2023]
17
Pierce S, Coetzee GA. Parkinson's disease-associated genetic variation is linked to quantitative expression of inflammatory genes. PLoS One 2017;12:e0175882. [PMID: 28407015 PMCID: PMC5391096 DOI: 10.1371/journal.pone.0175882] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 03/31/2017] [Indexed: 12/11/2022]  Open
18
Lawlor N, Khetan S, Ucar D, Stitzel ML. Genomics of Islet (Dys)function and Type 2 Diabetes. Trends Genet 2017;33:244-255. [PMID: 28245910 DOI: 10.1016/j.tig.2017.01.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 01/30/2017] [Indexed: 12/28/2022]
19
Genetic regulatory signatures underlying islet gene expression and type 2 diabetes. Proc Natl Acad Sci U S A 2017;114:2301-2306. [PMID: 28193859 DOI: 10.1073/pnas.1621192114] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
20
Ehrlich KC, Paterson HL, Lacey M, Ehrlich M. DNA Hypomethylation in Intragenic and Intergenic Enhancer Chromatin of Muscle-Specific Genes Usually Correlates with their Expression. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2016;89:441-455. [PMID: 28018137 PMCID: PMC5168824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
21
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, Parker SCJ. The genetic regulatory signature of type 2 diabetes in human skeletal muscle. Nat Commun 2016;7:11764. [PMID: 27353450 PMCID: PMC4931250 DOI: 10.1038/ncomms11764] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 04/27/2016] [Indexed: 12/11/2022]  Open
22
Quang D, Xie X. DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences. Nucleic Acids Res 2016;44:e107. [PMID: 27084946 PMCID: PMC4914104 DOI: 10.1093/nar/gkw226] [Citation(s) in RCA: 454] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 02/27/2016] [Accepted: 03/22/2016] [Indexed: 01/19/2023]  Open
23
Super Enhancers in Cancers, Complex Disease, and Developmental Disorders. Genes (Basel) 2015;6:1183-200. [PMID: 26569311 PMCID: PMC4690034 DOI: 10.3390/genes6041183] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 10/24/2015] [Accepted: 10/26/2015] [Indexed: 11/17/2022]  Open
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