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| 1 | Integrative analyses elucidate transcriptional regulatory functions of risk alleles for metabolic liver disease. (Zhu B, He N, Xiao Y, Chen B, Li C, Mandla R, Liu Y, Zhang J, Chang X, Yu F, Vujkovic M, Lynch JA, Chang KM, VA Million Veteran Program, Pasaniuc B, Rader DJ, Lazar MA, Hu W) Nat Genet 2026 Jun;58(6):1280-1294 1 Citation |
| 1 | szKendall: spatial-structural-zero-aware dissimilarity measures for subtype discovery using single cell Hi-C data. (Liu Y, Lee SW, Kim T, Jin V, Lin S) Nat Commun 2026 Apr 24;17(1) |
| 2 | High-resolution Hi-C profiling of human breast tissues using an optimized protocol for clinical samples. (Choppavarapu L, Fang K, Eacker S, Langford K, Rader JS, Jin VX) STAR Protoc 2026 Mar 20;7(1):104327 |
| 1 | cellSTAAR: incorporating single-cell-sequencing-based functional data to boost power in rare variant association testing of noncoding regions. (Van Buren E, Zhang Y, Li X, Selvaraj MS, Li Z, Zhou H, Palmer ND, Arnett DK, Blangero J, Boerwinkle E, Cade BE, Carlson JC, Carson AP, Chen YI, Curran J, Duggirala R, Fornage M, Franceschini N, Graff M, Gu C, Guo X, He J, Heard-Cosa N, Hou L, Hung YJ, Kalyani RR, Kardia SLR, Kenny E, Kooperberg C, Kral BG, Lange L, Levy D, Li C, Liu S, Lloyd-Jones D, Loos RJF, Manichaikul AW, Martin LW, Mathias R, Minster RL, Mitchell BD, Mychaleckyj JC, Naseri T, North K, O'Connell J, Perry JA, Peyser PA, Psaty BM, Raffield LM, Vasan RS, Redline S, Reiner AP, Rich SS, Smith JA, Spitzer B, Tang H, Taylor KD, Tracy R, Viali S, Yanek L, Zhao W, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Rotter JI, Peloso GM, Natarajan P, Lin X) Nat Methods 2026 Feb;23(2):338-349 1 Citation |
| 1 | TOP2B modulates DNA supercoiling and chromatin contacts during transcriptional induction. (Terrón-Bautista J, Bejarano-Franco M, Del Mar Martínez-Sánchez M, López-Hernández L, Díaz-Maldonado H, Santiago-Gómez A, Kidane S, Jaguva Vasudevan AA, García-Domínguez M, Williams RS, Aguilera A, Millán-Zambrano G, Cortés-Ledesma F) Sci Adv 2025 Nov 28;11(48):eadu6524 1 Citation |
| 2 | Chromatin interaction maps of human arterioles reveal mechanisms for the genetic regulation of blood pressure. (Liu Y, Pandey R, Qiu Q, Liu P, Xue H, Wang J, Therani B, Ying R, Usa K, Grzybowski M, Yang C, Mishra MK, Greene AS, Cowley AW Jr, Rao S, Geurts AM, Widlansky ME, Liang M) Nat Commun 2025 Jul 17;16(1):6577 3 Citations |
| 1 | Conserved chromatin regulators control the transcriptional immune response to intracellular pathogens in Caenorhabditis elegans. (Tecle E, Warushavithana P, Li S, Blanchard MJ, Chhan CB, Bui T, Underwood RS, Bakowski MA, Troemel ER, Lažetić V) PLoS Genet 2025 Apr;21(4):e1011444 4 Citations |
| 2 | Hi-C profiling in tissues reveals 3D chromatin-regulated breast tumor heterogeneity informing a looping-mediated therapeutic avenue. (Choppavarapu L, Fang K, Liu T, Ohihoin AG, Jin VX) Cell Rep 2025 Apr 22;44(4):115450 7 Citations |
| 6 | Chromatin State Maps of Blood Pressure-Relevant Renal Segments Reveal Potential Regulatory Role for SNPs. (Ray A, Yang C, Stelloh C, Tutaj M, Liu P, Liu Y, Qiu Q, Auer PL, Lin CW, Widlansky ME, Geurts AM, Cowley AW Jr, Liang M, Kwitek AE, Greene AS, Rao S) Hypertension 2025 Mar;82(3):476-488 |
| 1 | Spatial, transcriptomic, and epigenomic analyses link dorsal horn neurons to chronic pain genetic predisposition. (Arokiaraj CM, Leone MJ, Kleyman M, Chamessian A, Noh MC, Phan BN, Lopes BC, Corrigan KA, Cherupally VK, Yeramosu D, Franusich ME, Podder R, Lele S, Shiers S, Kang B, Kennedy MM, Chen V, Chen Z, Mathys H, Dum RP, Lewis DA, Qadri Y, Price TJ, Pfenning AR, Seal RP) Cell Rep 2024 Nov 26;43(11):114876 16 Citations |
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| 1 | Histone oxidation as a new mechanism of metabolic control over gene expression. (Gantner BN, Palma FR, Kayzuka C, Lacchini R, Foltz DR, Backman V, Kelleher N, Shilatifard A, Bonini MG) Trends Genet 2024 Sep;40(9):739-746 22 Citations |
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| 1 | Temporally specific gene expression and chromatin remodeling programs regulate a conserved Pdyn enhancer. (Phillips RA, Wan E, Tuscher JJ, Reid D, Drake OR, Ianov L, Day JJ) Elife 2023 Nov 08;12 10 Citations |
| 1 | A Deeply Quiescent Subset of CML LSC depend on FAO yet Avoid Deleterious ROS by Suppressing Mitochondrial Complex I. (Chimge NO, Chen MH, Nguyen C, Zhao Y, Wu X, Gonzalez PG, Ogana H, Hurwitz S, Teo JL, Chen X, Du J, Jin V, Kim YM, Ono M, Argüello RJ, Kahn M) Curr Mol Pharmacol 2024;17:e060923220758 2 Citations |
| 1 | Prediction accuracy of regulatory elements from sequence varies by functional sequencing technique. (Nowling RJ, Njoya K, Peters JG, Riehle MM) Front Cell Infect Microbiol 2023;13:1182567 |
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| 1 | CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines. (Luo ZH, Shi MW, Zhang Y, Wang DY, Tong YB, Pan XL, Cheng S) Database (Oxford) 2023 May 18;2023 7 Citations |
| 1 | ATP-Dependent Chromatin Remodellers in Inner Ear Development. (Chohra I, Chung K, Giri S, Malgrange B) Cells 2023 Feb 07;12(4) 7 Citations |
| 1 | Structure and functional determinants of Rad6-Bre1 subunits in the histone H2B ubiquitin-conjugating complex. (Shukla PK, Bissell JE, Kumar S, Pokhrel S, Palani S, Radmall KS, Obidi O, Parnell TJ, Brasch J, Shrieve DC, Chandrasekharan MB) Nucleic Acids Res 2023 Mar 21;51(5):2117-2136 21 Citations |
| 1 | Critical Role for the Human Cytomegalovirus Major Immediate Early Proteins in Recruitment of RNA Polymerase II and H3K27Ac To an Enhancer-Like Element in OriLyt. (Forte E, Li M, Ayaloglu Butun F, Hu Q, Borst EM, Schipma MJ, Piunti A, Shilatifard A, Terhune SS, Abecassis M, Meier JL, Hummel M) Microbiol Spectr 2023 Feb 14;11(1):e0314422 7 Citations |
| 1 | G9a Modulates Lipid Metabolism in CD4 T Cells to Regulate Intestinal Inflammation. (Ramos GP, Bamidele AO, Klatt EE, Sagstetter MR, Kurdi AT, Hamdan FH, Kosinsky RL, Gaballa JM, Nair A, Sun Z, Dasari S, Lanza IR, Rozeveld CN, Schott MB, Urrutia G, Westphal MS, Clarkson BD, Howe CL, Marietta EV, Luckey DH, Murray JA, Gonzalez M, Braga Neto MB, Gibbons HR, Smyrk TC, Johnsen S, Lomberk G, Faubion WA) Gastroenterology 2023 Feb;164(2):256-271.e10 32 Citations |
| 4 | Selective and Cell-Active PBRM1 Bromodomain Inhibitors Discovered through NMR Fragment Screening. (Shishodia S, Nuñez R, Strohmier BP, Bursch KL, Goetz CJ, Olp MD, Jensen DR, Fenske TG, Ordonez-Rubiano SC, Blau ME, Roach MK, Peterson FC, Volkman BF, Dykhuizen EC, Smith BC) J Med Chem 2022 Oct 27;65(20):13714-13735 19 Citations |
| 1 | Activation of γ-globin expression by hypoxia-inducible factor 1α. (Feng R, Mayuranathan T, Huang P, Doerfler PA, Li Y, Yao Y, Zhang J, Palmer LE, Mayberry K, Christakopoulos GE, Xu P, Li C, Cheng Y, Blobel GA, Simon MC, Weiss MJ) Nature 2022 Oct;610(7933):783-790 66 Citations |
| 1 | Group 3 innate lymphoid cells require BATF to regulate gut homeostasis in mice. (Wu X, Khatun A, Kasmani MY, Chen Y, Zheng S, Atkinson S, Nguyen C, Burns R, Taparowsky EJ, Salzman NH, Hand TW, Cui W) J Exp Med 2022 Nov 07;219(11) 23 Citations |
| 1 | The Drosophila BEAF insulator protein interacts with the polybromo subunit of the PBAP chromatin remodeling complex. (McKowen JK, Avva SVSP, Maharjan M, Duarte FM, Tome JM, Judd J, Wood JL, Negedu S, Dong Y, Lis JT, Hart CM) G3 (Bethesda) 2022 Nov 04;12(11) 6 Citations |
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| 1 | HiCImpute: A Bayesian hierarchical model for identifying structural zeros and enhancing single cell Hi-C data. (Xie Q, Han C, Jin V, Lin S) PLoS Comput Biol 2022 Jun;18(6):e1010129 15 Citations |
| 1 | Combination of the modulators of epigenetic machinery and specific cell signaling pathways as a promising approach for cell reprogramming. (Alexanian AR) Mol Cell Biochem 2022 Oct;477(10):2309-2317 3 Citations |
| 1 | Single-Cell Transcriptomic and Epigenetic Analyses of Mouse Mammary Development Starting with the Embryo. (Ma Z, Lytle NK, Ramos C, Naeem RF, Wahl GM) Methods Mol Biol 2022;2471:49-82 2 Citations |
| 2 | Histone H3 and H4 tails play an important role in nucleosome phase separation. (Hammonds EF, Harwig MC, Paintsil EA, Tillison EA, Hill RB, Morrison EA) Biophys Chem 2022 Apr;283:106767 17 Citations |
| 3 | KrasG12D induces changes in chromatin territories that differentially impact early nuclear reprogramming in pancreatic cells. (Mathison AJ, Kerketta R, de Assuncao TM, Leverence E, Zeighami A, Urrutia G, Stodola TJ, di Magliano MP, Iovanna JL, Zimmermann MT, Lomberk G, Urrutia R) Genome Biol 2021 Oct 14;22(1):289 13 Citations |
| 1 | SMARCA4: Implications of an Altered Chromatin-Remodeling Gene for Cancer Development and Therapy. (Mardinian K, Adashek JJ, Botta GP, Kato S, Kurzrock R) Mol Cancer Ther 2021 Dec;20(12):2341-2351 187 Citations |
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| 1 | E2A-regulated epigenetic landscape promotes memory CD8 T cell differentiation. (Schauder DM, Shen J, Chen Y, Kasmani MY, Kudek MR, Burns R, Cui W) Proc Natl Acad Sci U S A 2021 Apr 20;118(16) 32 Citations |
| 1 | Nucleosome composition regulates the histone H3 tail conformational ensemble and accessibility. (Morrison EA, Baweja L, Poirier MG, Wereszczynski J, Musselman CA) Nucleic Acids Res 2021 May 07;49(8):4750-4767 41 Citations |
| 1 | A cohesive look at leukemogenesis: The cohesin complex and other driving mutations in AML. (Heimbruch KE, Meyer AE, Agrawal P, Viny AD, Rao S) Neoplasia 2021 Mar;23(3):337-347 20 Citations |
| 1 | Modeling and analysis of Hi-C data by HiSIF identifies characteristic promoter-distal loops. (Zhou Y, Cheng X, Yang Y, Li T, Li J, Huang TH, Wang J, Lin S, Jin VX) Genome Med 2020 Aug 12;12(1):69 10 Citations |
| 1 | Determinants and role of chromatin organization in acute leukemia. (Fang C, Rao S, Crispino JD, Ntziachristos P) Leukemia 2020 Oct;34(10):2561-2575 20 Citations |
| 1 | Discovering How Heme Controls Genome Function Through Heme-omics. (Liao R, Zheng Y, Liu X, Zhang Y, Seim G, Tanimura N, Wilson GM, Hematti P, Coon JJ, Fan J, Xu J, Keles S, Bresnick EH) Cell Rep 2020 Jun 30;31(13):107832 26 Citations |
| 2 | Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. (Akdemir KC, Le VT, Chandran S, Li Y, Verhaak RG, Beroukhim R, Campbell PJ, Chin L, Dixon JR, Futreal PA, PCAWG Structural Variation Working Group, PCAWG Consortium) Nat Genet 2020 Mar;52(3):294-305 218 Citations |
| 1 | Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling. (Bersini S, Lytle NK, Schulte R, Huang L, Wahl GM, Hetzer MW) Life Sci Alliance 2020 Jan;3(1) 48 Citations |
| 1 | Ligand-induced IFNGR1 down-regulation calibrates myeloid cell IFNγ responsiveness. (Crisler WJ, Eshleman EM, Lenz LL) Life Sci Alliance 2019 Oct;2(5) 8 Citations |
| 2 | Regeneration Rosetta: An Interactive Web Application To Explore Regeneration-Associated Gene Expression and Chromatin Accessibility. (Rau A, Dhara SP, Udvadia AJ, Auer PL) G3 (Bethesda) 2019 Dec 03;9(12):3953-3959 3 Citations |
| 1 | Tet inactivation disrupts YY1 binding and long-range chromatin interactions during embryonic heart development. (Fang S, Li J, Xiao Y, Lee M, Guo L, Han W, Li T, Hill MC, Hong T, Mo W, Xu R, Zhang P, Wang F, Chang J, Zhou Y, Sun D, Martin JF, Huang Y) Nat Commun 2019 Sep 20;10(1):4297 75 Citations |
| 1 | BRCA1 mutations attenuate super-enhancer function and chromatin looping in haploinsufficient human breast epithelial cells. (Zhang X, Wang Y, Chiang HC, Hsieh YP, Lu C, Park BH, Jatoi I, Jin VX, Hu Y, Li R) Breast Cancer Res 2019 Apr 17;21(1):51 21 Citations |
| 1 | Temporal dynamic reorganization of 3D chromatin architecture in hormone-induced breast cancer and endocrine resistance. (Zhou Y, Gerrard DL, Wang J, Li T, Yang Y, Fritz AJ, Rajendran M, Fu X, Stein G, Schiff R, Lin S, Frietze S, Jin VX) Nat Commun 2019 Apr 03;10(1):1522 67 Citations |
| 1 | Three-dimensional analysis reveals altered chromatin interaction by enhancer inhibitors harbors TCF7L2-regulated cancer gene signature. (Gerrard DL, Wang Y, Gaddis M, Zhou Y, Wang J, Witt H, Lin S, Farnham PJ, Jin VX, Frietze SE) J Cell Biochem 2019 Mar;120(3):3056-3070 9 Citations |
| 1 | A CHAF1B-Dependent Molecular Switch in Hematopoiesis and Leukemia Pathogenesis. (Volk A, Liang K, Suraneni P, Li X, Zhao J, Bulic M, Marshall S, Pulakanti K, Malinge S, Taub J, Ge Y, Rao S, Bartom E, Shilatifard A, Crispino JD) Cancer Cell 2018 Nov 12;34(5):707-723.e7 75 Citations |
| 1 | A cancer-associated polymorphism in ESCRT-III disrupts the abscission checkpoint and promotes genome instability. (Sadler JBA, Wenzel DM, Strohacker LK, Guindo-Martínez M, Alam SL, Mercader JM, Torrents D, Ullman KS, Sundquist WI, Martin-Serrano J) Proc Natl Acad Sci U S A 2018 Sep 18;115(38):E8900-E8908 59 Citations |
| 1 | FoxO1 and FoxA1/2 form a complex on DNA and cooperate to open chromatin at insulin-regulated genes. (Schill D, Nord J, Cirillo LA) Biochem Cell Biol 2019 Apr;97(2):118-129 9 Citations |
| 1 | Identification of nine new susceptibility loci for endometrial cancer. (O'Mara TA, Glubb DM, Amant F, Annibali D, Ashton K, Attia J, Auer PL, Beckmann MW, Black A, Bolla MK, Brauch H, Brenner H, Brinton L, Buchanan DD, Burwinkel B, Chang-Claude J, Chanock SJ, Chen C, Chen MM, Cheng THT, Clarke CL, Clendenning M, Cook LS, Couch FJ, Cox A, Crous-Bous M, Czene K, Day F, Dennis J, Depreeuw J, Doherty JA, Dörk T, Dowdy SC, Dürst M, Ekici AB, Fasching PA, Fridley BL, Friedenreich CM, Fritschi L, Fung J, García-Closas M, Gaudet MM, Giles GG, Goode EL, Gorman M, Haiman CA, Hall P, Hankison SE, Healey CS, Hein A, Hillemanns P, Hodgson S, Hoivik EA, Holliday EG, Hopper JL, Hunter DJ, Jones A, Krakstad C, Kristensen VN, Lambrechts D, Marchand LL, Liang X, Lindblom A, Lissowska J, Long J, Lu L, Magliocco AM, Martin L, McEvoy M, Meindl A, Michailidou K, Milne RL, Mints M, Montgomery GW, Nassir R, Olsson H, Orlow I, Otton G, Palles C, Perry JRB, Peto J, Pooler L, Prescott J, Proietto T, Rebbeck TR, Risch HA, Rogers PAW, Rübner M, Runnebaum I, Sacerdote C, Sarto GE, Schumacher F, Scott RJ, Setiawan VW, Shah M, Sheng X, Shu XO, Southey MC, Swerdlow AJ, Tham E, Trovik J, Turman C, Tyrer JP, Vachon C, VanDen Berg D, Vanderstichele A, Wang Z, Webb PM, Wentzensen N, Werner HMJ, Winham SJ, Wolk A, Xia L, Xiang YB, Yang HP, Yu H, Zheng W, Pharoah PDP, Dunning AM, Kraft P, De Vivo I, Tomlinson I, Easton DF, Spurdle AB, Thompson DJ) Nat Commun 2018 Aug 09;9(1):3166 233 Citations |
| 1 | CBFβ-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia. (Pulikkan JA, Hegde M, Ahmad HM, Belaghzal H, Illendula A, Yu J, O'Hagan K, Ou J, Muller-Tidow C, Wolfe SA, Zhu LJ, Dekker J, Bushweller JH, Castilla LH) Cell 2018 Jun 28;174(1):172-186.e21 68 Citations |
| 2 | Cyclin-dependent kinase 1 (CDK1) and CDK2 have opposing roles in regulating interactions of splicing factor 3B1 with chromatin. (Murthy T, Bluemn T, Gupta AK, Reimer M Jr, Rao S, Pillai MM, Minella AC) J Biol Chem 2018 Jun 29;293(26):10220-10234 19 Citations |
| 2 | Genome-Wide Association Study to Find Modifiers for Tetralogy of Fallot in the 22q11.2 Deletion Syndrome Identifies Variants in the GPR98 Locus on 5q14.3. (Guo T, Repetto GM, McDonald McGinn DM, Chung JH, Nomaru H, Campbell CL, Blonska A, Bassett AS, Chow EWC, Mlynarski EE, Swillen A, Vermeesch J, Devriendt K, Gothelf D, Carmel M, Michaelovsky E, Schneider M, Eliez S, Antonarakis SE, Coleman K, Tomita-Mitchell A, Mitchell ME, Digilio MC, Dallapiccola B, Marino B, Philip N, Busa T, Kushan-Wells L, Bearden CE, Piotrowicz M, Hawuła W, Roberts AE, Tassone F, Simon TJ, van Duin EDA, van Amelsvoort TA, Kates WR, Zackai E, Johnston HR, Cutler DJ, Agopian AJ, Goldmuntz E, Mitchell LE, Wang T, Emanuel BS, Morrow BE, International 22q11.2 Consortium/Brain and Behavior Consortium*) Circ Cardiovasc Genet 2017 Oct;10(5):e001690 22 Citations |
| 1 | RUNX1 is required for oncogenic Myb and Myc enhancer activity in T-cell acute lymphoblastic leukemia. (Choi A, Illendula A, Pulikkan JA, Roderick JE, Tesell J, Yu J, Hermance N, Zhu LJ, Castilla LH, Bushweller JH, Kelliher MA) Blood 2017 Oct 12;130(15):1722-1733 78 Citations |
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