Complete List of 48 Publication: https://www.ncbi.nlm.nih.gov/myncbi/yarui.diao.1/bibliography/public/
1. Wei X*, Xu Y*, Yang D*, Kim K, Yi L, Luo W, Lin X, Xiang Y, Williams AB, Wang X, Srivas S, Tan C, Zhang K, Li W, Li YE, Yue F, Huang J, Jung I#, Diao Y#. Ultra-high throughput tri-modal single-cell profiling of transcriptome, epigenome, and 3D genome in complex tissues with scHiCAR. Accepted by Nature Biotechnology
2. Sun T, Xu Y, Angel N, Meng Z, Varghese S, Diao Y. A Subset of Transposable Elements as Mechano-Response Enhancer Elements in Controlling Human Embryonic Stem Cell Fate. Nature Cell Biology. 2025 Oct;27(10):1785-1796
3. Dai Q, Wan C, Xu Y, Fei K, Olivere LA, Garrett B, Akers L, Peters D, Otto J, Kontos CD, Ji Z, Diao Y#, Southerland KW#. Vascular adhesion molecule 1+ fibro-adipogenic progenitors mark fatty infiltration in chronic limb-threatening ischemia. JVS-Vascular Science. 2025 Aug 05
4. Southerland KW*, Xu Y*, Peters DT*, Lin X, Wei X, Xiang Y, Fei K, Olivere LA, Morowitz JM, Otto J, Dai Q, Kontos CD, Diao Y. Skeletal muscle regeneration failure in ischemic-damaged limbs is associated with pro-inflammatory macrophages and premature differentiation of satellite cells. Genome Med. 2023 Nov 10;15(1):95. PMCID: PMC10636829
5. Wei X*, Tran D*, Diao Y. HiCAR: Analysis of Open Chromatin Associated Long-range Chromatin Interaction Using Low-Input Materials. Curr Protoc. 2023 Oct;3(10):e899. PMCID: PMC10575683
6. Okafor AE*, Lin X*, Situ C, Wei X, Xiang Y, Wei X, Wu Z, Diao Y. Single-cell chromatin accessibility profiling reveals a self-renewing muscle satellite cell state. J Cell Biol. 2023 Aug 7;222(8). PMCID: PMC10309185.
7. Sun T, Xu Y, Xiang Y, Ou J, Soderblom EJ, Diao Y. Crosstalk between RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells. Nature Genetics. 2023 Aug;55(8):1324–1335. PMCID: PMC10766344. Spotlight by Molecular Cell (PMID: 39983671)
8. Wei X*, Xiang Y*, Peters DT, Marius C, Sun T, Shan R, Ou J, Lin X, Yue F, Li W, Southerland KW, Diao Y. HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization. Molecular Cell. 2022 Mar 17;82(6):1225–1238.e6. PMCID: PMC8934281. "Best of Technology 2022" by Molecular Cell, Preview by Cell Genomics (PMID: 36776526)
9. Li B, Chen PB, Diao Y. CRISPR-SE: a brute force search engine for CRISPR design. NAR Genom Bioinform. 2021 Mar;3(1):lqab013. PMCID: PMC7902234
10. Chen X, Wan J, Yu B, Diao Y#, Zhang W#. PIP5K1α promotes myogenic differentiation via AKT activation and calcium release. Stem Cell Res Ther. 2018;9(1):33. PMCID: PMC5806439
11. Jung I*, Schmitt A*, Diao Y*, Lee AJ, Liu T, Yang D, Tan C, Eom J, Chan M, Chee S, Chiang Z, Kim C, Masliah E, Barr CL, Li B, Kuan S, Kim D, Ren B. A compendium of promoter-centered long-range chromatin interactions in the human genome. Nature Genet. 2019 Oct;51(10):1442–1449. PMCID: PMC6778519
12. Diao Y, Fang R, Li B, Meng Z, Yu J, Qiu Y, Lin KC, Huang H, Liu T, Marina RJ, Jung I, Shen Y, Guan KL, Ren B. A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells. Nature Methods. 2017 Jun;14(6):629–635. PMCID: PMC5490986
13. An Y*, Wang G*, Diao Y*, Long Y, Fu X, Weng M, Zhou L, Sun K, Cheung TH, Ip NY, Sun H, Wang H, Wu Z. A Molecular Switch Regulating Cell Fate Choice between Muscle Progenitor Cells and Brown Adipocytes. Developmental Cell. 2017 May 22;41(4):382–391.e5. PMID: 28535373
14. Diao Y*, Li B, Meng Z, Jung I, Lee AY, Dixon J, Maliskova L, Guan KL, Shen Y*,#, Ren B#. A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening. Genome Res. 2016 Mar;26(3):397–405. PMCID: PMC4772021
15. Diao Y, Guo X, Jiang L, Wang G, Zhang C, Wan J, Jin Y, Wu Z. miR-203, a tumor suppressor frequently down-regulated by promoter hypermethylation in rhabdomyosarcoma. J Biol Chem. 2014 Jan 3;289(1):529–539. PMCID: PMC3879574
16. Diao Y, Guo X, Li Y, Sun K, Lu L, Jiang L, Fu X, Zhu H, Sun H, Wang H, Wu Z. Pax3/7BP is a Pax7- and Pax3-binding protein that regulates the proliferation of muscle precursor cells by an epigenetic mechanism. Cell Stem Cell. 2012 Aug 3;11(2):231–241. PMID: 22862948
17. Diao Y, Liu W, Wong CCL, Wang X, Lee K, Cheung PY, Pan L, Xu T, Han J, Yates JR 3rd, Zhang M, Wu Z. Oxidation-induced intramolecular disulfide bond inactivates mitogen-activated protein kinase kinase 6 by inhibiting ATP binding. Proc Natl Acad Sci U S A. 2010 Dec 7;107(49):20974–20979. PMCID: PMC3000308
18. Diao Y, Wang X, Wu Z. SOCS1, SOCS3, and PIAS1 promote myogenic differentiation by inhibiting the leukemia inhibitory factor-induced JAK1/STAT1/STAT3 pathway. Mol Cell Biol. 2009 Sep;29(18):5084–5093. PMCID: PMC2738280
1. Park S, Park H, Byun YG, Wei X, Eom J, Joo J, Lee AJ, Diao Y, Chung WS, Jung I. NR3C1-mediated epigenetic regulation suppresses astrocytic immune responses in mice. Nat Commun. 2025 Sep 22;16(1):8330. PMCID: PMC12454645
2. Cosgrove BD, Bounds LR, Taylor CK, Su AL, Rizzo AJ, Barrera A, Sun T, Safi A, Song L, Whitlow T, Tata A, Iglesias N, Diao Y, Tata PR, Hoffman BD, Crawford GE, Gersbach CA. Mechanosensitive genomic enhancers potentiate the cellular response to matrix stiffness. Science. American Association for the Advancement of Science (AAAS); 2025 Sep 25;(eadl1988):eadl1988. PMID: 40997217
3. Anglen T, Kaplow IM, Choi B, Dewars E, Perelli RM, Hagy KT, Tran D, Ramaker ME, Shah SH, Jung I, Landstrom AP, Karra R, Diao Y, Gersbach CA. A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress. Genome Res. Cold Spring Harbor Laboratory; 2025 Oct 22; PMID: 41125440
4. Ban GI, Puviindran V, Xiang Y, Nadesan P, Tang J, Ou J, Guardino N, Nakagawa M, Browne M, Wallace A, Ishikawa K, Shimada E, Martin JT, Diao Y, Kirsch DG, Alman BA. The COMPASS complex maintains the metastatic capacity imparted by a subpopulation of cells in UPS. iScience. 2024 Jul 19;27(7):110187. PMCID: PMC11233968
5. Lee MJ, Hammouda MB, Miao W, Okafor AE, Jin YJ, Sun H, Jain V, Markovtsov V, Diao Y, Gregory SG, Zhang JY. UBE2N Is Essential for Maintenance of Skin Homeostasis and Suppression of Inflammation. J Invest Dermatol. 2024 May 23; Available from: http://dx.doi.org/10.1016/j.jid.2024.04.017 PMID: 38796140
6. Song B, Liu D, Dai W, McMyn NF, Wang Q, Yang D, Krejci A, Vasilyev A, Untermoser N, Loregger A, Song D, Williams B, Rosen B, Cheng X, Chao L, Kale HT, Zhang H, Diao Y, Bürckstümmer T, Siliciano JD, Li JJ, Siliciano RF, Huangfu D, Li W. Decoding heterogeneous single-cell perturbation responses. Nat Cell Biol. 2025 Mar;27(3):493–504. PMCID: PMC11906366
7. Huang B, Zeng Z, Kim S, Fausto CC, Koppitch K, Li H, Li Z, Chen X, Guo J, Zhang CC, Ma T, Medina P, Schreiber ME, Xia MW, Vonk AC, Xiang T, Patel T, Li Y, Parvez RK, Der B, Chen JH, Liu Z, Thornton ME, Grubbs BH, Diao Y, Dou Y, Gnedeva K, Ying Q, Pastor-Soler NM, Fei T, Hallows KR, Lindström NO, McMahon AP, Li Z. Long-term expandable mouse and human-induced nephron progenitor cells enable kidney organoid maturation and modeling of plasticity and disease. Cell Stem Cell. 2024 Jun 6;31(6):921–939.e17. PMCID: PMC11162329
8. Ando K, Ou J, Thompson JD, Welsby J, Bangru S, Shen J, Wei X, Diao Y, Poss KD. A screen for regeneration-associated silencer regulatory elements in zebrafish. Dev Cell. 2024 Mar 11;59(5):676–691.e5. PMCID: PMC10939760
9. Zheng C, Wei Y, Zhang P, Lin K, He D, Teng H, Manyam G, Zhang Z, Liu W, Lee HRL, Tang X, He W, Islam N, Jain A, Chiu Y, Cao S, Diao Y, Meyer-Gauen S, Höök M, Malovannaya A, Li W, Hu M, Wang W, Xu H, Kopetz S, Chen Y. CRISPR-Cas9-based functional interrogation of unconventional translatome reveals human cancer dependency on cryptic non-canonical open reading frames. Nat Struct Mol Biol. 2023 Dec;30(12):1878–1892. PMCID: PMC10716047
10. Zhao S, Lu J, Pan B, Fan H, Byrum SD, Xu C, Kim A, Guo Y, Kanchi KL, Gong W, Sun T, Storey AJ, Burkholder NT, Mackintosh SG, Kuhlers PC, Edmondson RD, Strahl BD, Diao Y, Tackett AJ, Raab JR, Cai L, Song J, Wang GG. TNRC18 engages H3K9me3 to mediate silencing of endogenous retrotransposons. Nature. 2023 Nov;623(7987):633–642. PMCID: 9099300
11. Wang X, He Q, Zhou C, Xu Y, Liu D, Fujiwara N, Kubota N, Click A, Henderson P, Vancil J, Marquez CA, Gunasekaran G, Schwartz ME, Tabrizian P, Sarpel U, Fiel MI, Diao Y, Sun B, Hoshida Y, Liang S, Zhong Z. Prolonged hypernutrition impairs TREM2-dependent efferocytosis to license chronic liver inflammation and NASH development. Immunity. 2023 Jan 10;56(1):58–77.e11. PMCID: PMC9839616
12. Bara AM, Chen L, Ma C, Underwood J, Moreci RS, Sumigray K, Sun T, Diao Y, Verzi M, Lechler T. Maf family transcription factors are required for nutrient uptake in the mouse neonatal gut. Development. 2022 Dec 1;149(23). Available from: http://dx.doi.org/10.1242/dev.201251 PMCID: PMC10112929
13. Xu J, Song F, Lyu H, Kobayashi M, Zhang B, Zhao Z, Hou Y, Wang X, Luan Y, Jia B, Stasiak L, Wong JHY, Wang Q, Jin Q, Jin Q, Fu Y, Yang H, Hardison RC, Dovat S, Platanias LC, Diao Y, Yang Y, Yamada T, Viny AD, Levine RL, Claxton D, Broach JR, Zheng H, Yue F. Subtype-specific 3D genome alteration in acute myeloid leukaemia. Nature. 2022 Oct 26; Available from: http://dx.doi.org/10.1038/s41586-022-05365-x PMID: 36289338
14. Meng Z, Li FL, Fang C, Yeoman B, Qiu Y, Wang Y, Cai X, Lin KC, Yang D, Luo M, Fu V, Ma X, Diao Y, Giancotti FG, Ren B, Engler AJ, Guan KL. The Hippo pathway mediates Semaphorin signaling. Sci Adv. 2022 May 27;8(21):eabl9806. PMCID: PMC9132450
15. Wang J, Broer T, Chavez T, Zhou CJ, Tran S, Xiang Y, Khodabukus A, Diao Y, Bursac N. Myoblast deactivation within engineered human skeletal muscle creates a transcriptionally heterogeneous population of quiescent satellite-like cells. Biomaterials. 2022 May;284:121508. PMCID: PMC9289780
16. Tang YJ, Puviindran V, Xiang Y, Yahara Y, Zhang H, Nadesan P, Diao Y, Kirsch DG, Alman BA. Tumor-propagating side population cells are a dynamic subpopulation in undifferentiated pleomorphic sarcoma. JCI Insight; 2021 Nov 22;6(22).
17. Fan H, Lu J, Guo Y, Li D, Zhang ZM, Tsai YH, Pi WC, Ahn JH, Gong W, Xiang Y, Allison DF, Geng H, He S, Diao Y, Chen WY, Strahl BD, Cai L, Song J, Wang GG. BAHCC1 binds H3K27me3 via a conserved BAH module to mediate gene silencing and oncogenesis. Nat Genet. 2020 Dec;52(12):1384–1396. PMID: 33139953
18. Yahara Y, Barrientos T, Tang YJ, Puviindran V, Nadesan P, Zhang H, Gibson JR, Gregory SG, Diao Y, Xiang Y, Qadri YJ, Souma T, Shinohara ML, Alman BA. Erythromyeloid progenitors give rise to a population of osteoclasts that contribute to bone homeostasis and repair. Nat Cell Biol. 2020 Jan;22(1):49–59. PMCID: PMC6953622
19. Wisdom AJ, Hong CS, Lin AJ, Xiang Y, Cooper DE, Zhang J, Xu ES, Kuo HC, Mowery YM, Carpenter DJ, Kadakia KT, Himes JE, Luo L, Ma Y, Williams N, Cardona DM, Haldar M, Diao Y, Markovina S, Schwarz JK, Kirsch DG. Neutrophils promote tumor resistance to radiation therapy. Proc Natl Acad Sci U S A. 2019 Sep 10;116(37):18584–18589. PMCID: PMC6744874
20. Gao Y, Hisey E, Bradshaw TWA, Erata E, Brown WE, Courtland JL, Uezu A, Xiang Y, Diao Y, Soderling SH. Plug-and-Play Protein Modification Using Homology-Independent Universal Genome Engineering. Neuron. 2019 Aug 21;103(4):583–597.e8. PMCID: PMC7200071
(* Co-first author; # Co-corresponding author)