Publication: An integrated encyclopedia of DNA elements in the human genome

Citation: ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57-74. doi:10.1038/nature11247

Funding: The Consortium is funded by grants from the NHGRI as follows: Production Grants: U54HG004570 (Bernstein); U01HG004695 (Birney); U54HG004563 (Crawford); U54HG004557 (Gingeras); U54HG004555 (Hubbard); U41HG004568 (Kent); U54HG004576 (Myers); U54HG004558 (Snyder); U54HG004592 (Stamatoyannopoulos). Pilot Grants: R01HG003143 (Dekker); RC2HG005591 and R01HG003700 (Giddings); R01HG004456-03 (Ruan); U01HG004571 (Tenenbaum); U01HG004561 (Weng); RC2HG005679 (White). This project was supported in part by American Recovery and Reinvestment Act (ARRA) funds from the NHGRI through grants U54HG004570, U54HG004563, U41HG004568, U54HG004592, R01HG003143, RC2HG005591, R01HG003541, U01HG004561, RC2HG005679 and R01HG003988 (PI: Pennacchio). In addition, work from NHGRI Groups was supported by the Intramural Research Program of the NHGRI (Elnitski, ZIAHG200323; Margulies, ZIAHG200341). Research in the Pennachio lab was performed at Lawrence Berkeley National Laboratory and at the United States Department of Energy Joint Genome Institute, Department of Energy Contract DE-AC02-05CH11231, University of California.

Publication: Data navigation on the ENCODE portal

Citation: Kagda MS, Lam B, Litton C, et al. Data navigation on the ENCODE portal. Nat Commun. 2025;16(1):9592. Published 2025 Oct 30. doi:10.1038/s41467-025-64343-9

Funding: All the figures in the manuscript are prepared using the free academic licence version of Tableau Desktop 2023.1. The authors would like to thank Salesforce for providing us with a free academic version. In addition, we would like to thank all the past and present members of the ENCODE and affiliated consortia. National Human Genome Research Institute, National Institutes of Health [U24 HG009397].

Publication: New developments on the Encyclopedia of DNA Elements (ENCODE) data portal

Citation: Luo Y, Hitz BC, Gabdank I, et al. New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. Nucleic Acids Res. 2020;48(D1):D882-D889. doi:10.1093/nar/gkz1062

Funding: National Human Genome Research Institute, National Institutes of Health [U24 HG009397]. The content is solely theresponsibility of the authors and does not necessarily represent the official views of the National Human Genome Research Institute or the National Institutes of Health. The funders had no role in design, data processing, implementation, decision to publish, or preparation of the manuscript. Funding for open access charge: National Human Genome Research Institute, National Institutes of Health [U24 HG009397].

Publication: Brain cell type-specific enhancer-promoter interactome maps and disease-risk association

Citation: Nott A, Holtman IR, Coufal NG, et al. Brain cell type-specific enhancer-promoter interactome maps and disease-risk association. Science. 2019;366(6469):1134-1139. doi:10.1126/science.aay0793

Funding: Support was provided by NIH grants R01 NS096170, RF1 AG061060-01, R01 AG056511-01A1, R01 AG057706-01, a Cure Alzheimer’s Fund Gifford Neuroinflammation Consortium, and UCSD Shiley-Marcos ADRC 1P30AG062429. A.N. was supported by the Alzheimer’s Association (AARF-18-531498) and the Altman Clinical & Translational Research Institute at UCSD (National Center for Advancing Translational Sciences, NIH KL2TR001444). I.R.H. was supported by the VENI research program, which is financed by the Netherlands Organization for Scientific Research. N.G.C. was funded by NIH K08 NS109200-01 and The Hartwell Foundation. C.Z.H. is supported by the Cancer Research Institute Irvington Postdoctoral Fellowship Program. C.O. was funded by NIHNCI CCSG: P30 014195 and S10-OD023689. Salk facilities are supported by the Salk Cancer Center (NCI grant: P30-CA014195). F.H.G. was supported by the JPB Foundation, The Engman Foundation, The AHA/ Allen Award, and the Dolby Foundation. J.B.B. and R.A.S. were supported by AG062429-01.

Publication: The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions

Citation: Wang Y, Song F, Zhang B, et al. The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions. Genome Biol. 2018;19(1):151. Published 2018 Oct 4. doi:10.1186/s13059-018-1519-9

Funding: This work was supported by NIH grants R35GM124820, R01HG009906, and U01CA200060 (F.Y.). F.Y. is also supported by Leukemia Research Foundation, PhRMA Foundation, and Penn State CTSI. T.W. is also supported by NIH grants R01HG007175, R01HG007354, R01ES024992, U24ES026699, and U01HG009391. M.H. is partially supported by NIH U54DK107977. Y.L. is partially supported by NIH R01HG006292 and R01HL129132.

Publication: PubMed: 25788621

Citation: Teng L, He B, Wang J, Tan K. 4DGenome: a comprehensive database of chromatin interactions. Bioinformatics. 2015;31(15):2560-2564. doi:10.1093/bioinformatics/btv158

Funding: This study was supported by the National Institutes of Health grants [HG006130], [GM108716] and [GM104369] to K.T.

Publication: HIPPIE2: a method for fine-scale identification of physically interacting chromatin regions

Citation: Kuksa PP, Amlie-Wolf A, Hwang YC, Valladares O, Gregory BD, Wang LS. HIPPIE2: a method for fine-scale identification of physically interacting chromatin regions. NAR Genom Bioinform. 2020;2(2):lqaa022. doi:10.1093/nargab/lqaa022

Funding: National Institute of General Medical Sciences [R01-GM099962]; National Institute on Aging [U54-AG052427, U24-AG041689, T32-AG00255]. Funding for open access charge: National Institute on Aging [U24-AG041689, U54-AG052427].

Publication: Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

Citation: Javierre BM, Burren OS, Wilder SP, et al. Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters. Cell. 2016;167(5):1369-1384.e19. doi:10.1016/j.cell.2016.09.037

Funding: This work was supported by the following grants: UK Medical Research Council (MR/L007150/1, MC_UP_1302/1, MC_UP_1302/3, MC_UP_1302/5), UK Biotechnology and Biological Sciences Research Council (BB/J004480/1), ERC (DEVOCHROMO advanced grant), JDRF (9-2011-253, 5-SRA-2015-130), Wellcome Trust (089989, 091157, 095908, 100140, 107212, 107881), European Union 7th Framework Programme (FP7/2007-2013, grant agreements 241447 [NAIMIT] and 282510 [BLUEPRINT]), NHS Blood and Transplant, NIHR (PG-0310-1002), and BHF (RG/09/12/28096). K.D. is funded by NHS Health Education England. M.F. is supported by the BHF Cambridge Centre of Excellence (RE/13/6/30180). S.P.W., M.K., D.R.Z., and O.S. are funded by the European Molecular Biology Laboratory. We gratefully acknowledge the participation of all NIHR Cambridge BioResource volunteers and thank the NIHR Cambridge BioResource centre and staff for their contribution.

Publication: A compendium of promoter-centered long-range chromatin interactions in the human genome

Citation: Jung I, Schmitt A, Diao Y, et al. A compendium of promoter-centered long-range chromatin interactions in the human genome. Nat Genet. 2019;51(10):1442-1449. doi:10.1038/s41588-019-0494-8

Funding: This work was funded in part by the Ludwig Institute for Cancer Research (to B. Ren), NIH (1R01ES024984, to B. Ren), the Ministry of Science, ICT, and Future Planning through the National Research Foundation in Republic of Korea (2017R1C1B2008838 to I. Jung), Korean Ministry of Health and Welfare (HI17C0328 to I. Jung), and SUHF Fellowship (to I. Jung).

Publication: Genome-wide enhancer maps link risk variants to disease genes

Citation: Nasser J, Bergman DT, Fulco CP, et al. Genome-wide enhancer maps link risk variants to disease genes. Nature. 2021;593(7858):238-243. doi:10.1038/s41586-021-03446-x

Funding: This work was supported by the Broad Institute (E.S.L.); an NIH Pathway to Independence Award (K99HG009917 and R00HG009917 to J.M.E.); an NHGRI Genomic Innovator Award (R35HG011324 to J.M.E.); the Harvard Society of Fellows (J.M.E.); Gordon and Betty Moore and the BASE Research Initiative at the Lucile Packard Children’s Hospital at Stanford University (J.M.E.); NHGRI P50HG006193 (N.H.); NIDDK P30DK043351 (R.J.X.); NIH U01 CA200059 (F.L. and H.P.); U01 HG009379, R01 MH101244, and R37 MH107649 (A.K.P.); NIDDK K01DK114379 (H.H.); the Zhengxu and Ying He Foundation (H.H.); the Stanley Center for Psychiatric Research (H.H.); NIAID K22AI153648 (J.P.R.); and a Siebel Scholarship (F.L.).

Publication: Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes

Citation: Song M, Yang X, Ren X, et al. Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes. Nat Genet. 2019;51(8):1252-1262. doi:10.1038/s41588-019-0472-1

Funding: We thank Anthony Schmitt and Bing Ren (Ludwig Institute for Cancer Research, University of California, San Diego) for sharing pcHi-C probes and the pcHi-C protocol. Genomic analysis of the WTC11 line in this study was made possible by the whole-genome sequencing data generated by the Allen Institute for Cell Science. We thank the Institute and its founder Paul G. Allen for making this work possible. We thank Gary Hon (University of Texas Southwestern Medical Center) and Steven Henikoff (Fred Hutchinson Cancer Research Center, Howard Hughes Medical Institute) for providing reagents. We acknowledge the ENCODE Consortium and Bradley Bernstein’s laboratory for generating the ChIP-seq data for astrocytes used in this study. We thank N. Ahituv, Y. Guo, R. D. Hawkins, M. McManus, and B. Ren for providing critical feedback on the manuscript. We thank Y. Qu for her contributions to the illustrations for Figure 1. This work was made possible in part by NIH-NEI P30EY002162 (Core Grant for Vision Research and the Research to Prevent Blindness Unrestricted Grant). This work was supported by the National Institutes of Health (NIH) grants R01AG057497 to Y.S., L.G., and H.S., R01EY027789 and UM1HG009402 to Y.S., the UCSF Weill Institute for Neuroscience Innovation Award, the Hillblom Foundation, and the American Federation for Aging Research New Investigator Award in Alzheimer’s Disease to Y.S., R01EY028249, R01HL130533, R01-HL13535801 to B.R.C., P01NS097206 and U19MH106434 to H.S., and R01MH105128, R35NS097370, and U19AI131130 to G.L.M. M.S. is supported by T32GM007175. F.J. is supported by T32GM007309.