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  1. Anastas JN, Shi Y. Histone Serotonylation: Can the Brain Have "Happy" Chromatin?. Mol Cell. 2019 May 2;74(3):418-420. doi: 10.1016/j.molcel.2019.04.017. PubMed PMID: 31051139; PubMed Central PMCID: PMC6662934.
  2. Sheng W, LaFleur MW, Nguyen TH, Chen S, Chakravarthy A, Conway JR, Li Y, Chen H, Yang H, Hsu PH, Van Allen EM, Freeman GJ, De Carvalho DD, He HH, Sharpe AH, Shi Y. LSD1 Ablation Stimulates Anti-tumor Immunity and Enables Checkpoint Blockade. Cell. 2018 Jul 26;174(3):549-563.e19. doi: 10.1016/j.cell.2018.05.052. Epub 2018 Jun 21. PubMed PMID: 29937226; PubMed Central PMCID: PMC6063761.
  3. Li H, Liefke R, Jiang J, Kurland JV, Tian W, Deng P, Zhang W, He Q, Patel DJ, Bulyk ML, Shi Y, Wang Z. Polycomb-like proteins link the PRC2 complex to CpG islands. Nature. 2017 Sep 14;549(7671):287-291. doi: 10.1038/nature23881. Epub 2017 Sep 6. PubMed PMID: 28869966; PubMed Central PMCID: PMC5937281.
  4. Xiang Y, Laurent B, Hsu CH, Nachtergaele S, Lu Z, Sheng W, Xu C, Chen H, Ouyang J, Wang S, Ling D, Hsu PH, Zou L, Jambhekar A, He C, Shi Y. RNA m6A methylation regulates the ultraviolet-induced DNA damage response. Nature. 2017 Mar 23;543(7646):573-576. doi: 10.1038/nature21671. Epub 2017 Mar 15. PubMed PMID: 28297716; PubMed Central PMCID: PMC5490984.
  5. Iberg-Badeaux A, Collombet S, Laurent B, van Oevelen C, Chin KK, Thieffry D, Graf T, Shi Y. A Transcription Factor Pulse Can Prime Chromatin for Heritable Transcriptional Memory. Mol Cell Biol. 2017 Feb 15;37(4). doi: 10.1128/MCB.00372-16. Print 2017 Feb 15. PubMed PMID: 27920256; PubMed Central PMCID: PMC5288571.
  6. Jambhekar A, Anastas JN, Shi Y. Histone Lysine Demethylase Inhibitors. Cold Spring Harb Perspect Med. 2017 Jan 3;7(1). doi: 10.1101/cshperspect.a026484. Review. PubMed PMID: 28049654; PubMed Central PMCID: PMC5204329.
  7. Liefke R, Karwacki-Neisius V, Shi Y. EPOP Interacts with Elongin BC and USP7 to Modulate the Chromatin Landscape. Mol Cell. 2016 Nov 17;64(4):659-672. doi: 10.1016/j.molcel.2016.10.019. PubMed PMID: 27863226; PubMed Central PMCID: PMC5210178.
  8. Ma C, Karwacki-Neisius V, Tang H, Li W, Shi Z, Hu H, Xu W, Wang Z, Kong L, Lv R, Fan Z, Zhou W, Yang P, Wu F, Diao J, Tan L, Shi YG, Lan F, Shi Y. Nono, a Bivalent Domain Factor, Regulates Erk Signaling and Mouse Embryonic Stem Cell Pluripotency. Cell Rep. 2016 Oct 18;17(4):997-1007. doi: 10.1016/j.celrep.2016.09.078. PubMed PMID: 27760330; PubMed Central PMCID: PMC5086807.
  9. Shen H, Xu W, Guo R, Rong B, Gu L, Wang Z, He C, Zheng L, Hu X, Hu Z, Shao ZM, Yang P, Wu F, Shi YG, Shi Y, Lan F. Suppression of Enhancer Overactivation by a RACK7-Histone Demethylase Complex. Cell. 2016 Apr 7;165(2):331-42. doi: 10.1016/j.cell.2016.02.064. PubMed PMID: 27058665; PubMed Central PMCID: PMC4826479.
  10. Iwase S, Brookes E, Agarwal S, Badeaux AI, Ito H, Vallianatos CN, Tomassy GS, Kasza T, Lin G, Thompson A, Gu L, Kwan KY, Chen C, Sartor MA, Egan B, Xu J, Shi Y. A Mouse Model of X-linked Intellectual Disability Associated with Impaired Removal of Histone Methylation. Cell Rep. 2016 Feb 9;14(5):1000-1009. doi: 10.1016/j.celrep.2015.12.091. Epub 2016 Jan 21. PubMed PMID: 26804915; PubMed Central PMCID: PMC4749408.
  11. Greer EL, Becker B, Latza C, Antebi A, Shi Y. Mutation of C. elegans demethylase spr-5 extends transgenerational longevity. Cell Res. 2016 Feb;26(2):229-38. doi: 10.1038/cr.2015.148. Epub 2015 Dec 22. PubMed PMID: 26691751; PubMed Central PMCID: PMC4746603.
  12. Murn J, Teplova M, Zarnack K, Shi Y, Patel DJ. Recognition of distinct RNA motifs by the clustered CCCH zinc fingers of neuronal protein Unkempt. Nat Struct Mol Biol. 2016 Jan;23(1):16-23. doi: 10.1038/nsmb.3140. Epub 2015 Dec 7. PubMed PMID: 26641712; PubMed Central PMCID: PMC4703518.
  13. Cheloufi S, Elling U, Hopfgartner B, Jung YL, Murn J, Ninova M, Hubmann M, Badeaux AI, Euong Ang C, Tenen D, Wesche DJ, Abazova N, Hogue M, Tasdemir N, Brumbaugh J, Rathert P, Jude J, Ferrari F, Blanco A, Fellner M, Wenzel D, Zinner M, Vidal SE, Bell O, Stadtfeld M, Chang HY, Almouzni G, Lowe SW, Rinn J, Wernig M, Aravin A, Shi Y, Park PJ, Penninger JM, Zuber J, Hochedlinger K. The histone chaperone CAF-1 safeguards somatic cell identity. Nature. 2015 Dec 10;528(7581):218-24. doi: 10.1038/nature15749. PubMed PMID: 26659182; PubMed Central PMCID: PMC4866648.
  14. Luo GZ, Blanco MA, Greer EL, He C, Shi Y. DNA N(6)-methyladenine: a new epigenetic mark in eukaryotes?. Nat Rev Mol Cell Biol. 2015 Dec;16(12):705-10. doi: 10.1038/nrm4076. Epub 2015 Oct 28. Review. PubMed PMID: 26507168; PubMed Central PMCID: PMC4763336.
  15. Chen M, Zhu N, Liu X, Laurent B, Tang Z, Eng R, Shi Y, Armstrong SA, Roeder RG. JMJD1C is required for the survival of acute myeloid leukemia by functioning as a coactivator for key transcription factors. Genes Dev. 2015 Oct 15;29(20):2123-39. doi: 10.1101/gad.267278.115. PubMed PMID: 26494788; PubMed Central PMCID: PMC4617977.
  16. van Oevelen C, Collombet S, Vicent G, Hoogenkamp M, Lepoivre C, Badeaux A, Bussmann L, Sardina JL, Thieffry D, Beato M, Shi Y, Bonifer C, Graf T. C/EBPα Activates Pre-existing and De Novo Macrophage Enhancers during Induced Pre-B Cell Transdifferentiation and Myelopoiesis. Stem Cell Reports. 2015 Aug 11;5(2):232-47. doi: 10.1016/j.stemcr.2015.06.007. Epub 2015 Jul 30. PubMed PMID: 26235892; PubMed Central PMCID: PMC4618662.
  17. Sendinc E, Jambhekar A, Shi Y. Remodeling Your Way out of Cell Cycle. Cell. 2015 Jul 16;162(2):237-238. doi: 10.1016/j.cell.2015.06.050. PubMed PMID: 26186182.
  18. Brookes E, Laurent B, Õunap K, Carroll R, Moeschler JB, Field M, Schwartz CE, Gecz J, Shi Y. Mutations in the intellectual disability gene KDM5C reduce protein stability and demethylase activity. Hum Mol Genet. 2015 May 15;24(10):2861-72. doi: 10.1093/hmg/ddv046. Epub 2015 Feb 9. PubMed PMID: 25666439; PubMed Central PMCID: PMC4406297.
  19. Greer EL, Blanco MA, Gu L, Sendinc E, Liu J, Aristizábal-Corrales D, Hsu CH, Aravind L, He C, Shi Y. DNA Methylation on N6-Adenine in C. elegans. Cell. 2015 May 7;161(4):868-78. doi: 10.1016/j.cell.2015.04.005. Epub 2015 Apr 30. PubMed PMID: 25936839; PubMed Central PMCID: PMC4427530.
  20. Laurent B, Ruitu L, Murn J, Hempel K, Ferrao R, Xiang Y, Liu S, Garcia BA, Wu H, Wu F, Steen H, Shi Y. A specific LSD1/KDM1A isoform regulates neuronal differentiation through H3K9 demethylation. Mol Cell. 2015 Mar 19;57(6):957-970. doi: 10.1016/j.molcel.2015.01.010. Epub 2015 Feb 12. PubMed PMID: 25684206; PubMed Central PMCID: PMC4369399.
  21. Guo R, Zheng L, Park JW, Lv R, Chen H, Jiao F, Xu W, Mu S, Wen H, Qiu J, Wang Z, Yang P, Wu F, Hui J, Fu X, Shi X, Shi YG, Xing Y, Lan F, Shi Y. BS69/ZMYND11 reads and connects histone H3.3 lysine 36 trimethylation-decorated chromatin to regulated pre-mRNA processing. Mol Cell. 2014 Oct 23;56(2):298-310. doi: 10.1016/j.molcel.2014.08.022. Epub 2014 Sep 25. PubMed PMID: 25263594; PubMed Central PMCID: PMC4363072.
  22. Brookes E, Shi Y. Diverse epigenetic mechanisms of human disease. Annu Rev Genet. 2014;48:237-68. doi: 10.1146/annurev-genet-120213-092518. Epub 2014 Sep 5. Review. PubMed PMID: 25195505.
  23. Tsai CL, Shi Y, Tainer JA. How substrate specificity is imposed on a histone demethylase--lessons from KDM2A. Genes Dev. 2014 Aug 15;28(16):1735-8. doi: 10.1101/gad.249755.114. PubMed PMID: 25128493; PubMed Central PMCID: PMC4197959.
  24. Alpatov R, Lesch BJ, Nakamoto-Kinoshita M, Blanco A, Chen S, Stützer A, Armache KJ, Simon MD, Xu C, Ali M, Murn J, Prisic S, Kutateladze TG, Vakoc CR, Min J, Kingston RE, Fischle W, Warren ST, Page DC, Shi Y. A chromatin-dependent role of the fragile X mental retardation protein FMRP in the DNA damage response. Cell. 2014 May 8;157(4):869-81. doi: 10.1016/j.cell.2014.03.040. PubMed PMID: 24813610; PubMed Central PMCID: PMC4038154.
  25. Greer EL, Beese-Sims SE, Brookes E, Spadafora R, Zhu Y, Rothbart SB, Aristizábal-Corrales D, Chen S, Badeaux AI, Jin Q, Wang W, Strahl BD, Colaiácovo MP, Shi Y. A histone methylation network regulates transgenerational epigenetic memory in C. elegans. Cell Rep. 2014 Apr 10;7(1):113-26. doi: 10.1016/j.celrep.2014.02.044. Epub 2014 Mar 27. PubMed PMID: 24685137; PubMed Central PMCID: PMC4012616.
  26. Mosammaparast N, Kim H, Laurent B, Zhao Y, Lim HJ, Majid MC, Dango S, Luo Y, Hempel K, Sowa ME, Gygi SP, Steen H, Harper JW, Yankner B, Shi Y. The histone demethylase LSD1/KDM1A promotes the DNA damage response. J Cell Biol. 2013 Nov 11;203(3):457-70. doi: 10.1083/jcb.201302092. PubMed PMID: 24217620; PubMed Central PMCID: PMC3824007.
  27. Lim HJ, Dimova NV, Tan MK, Sigoillot FD, King RW, Shi Y. The G2/M regulator histone demethylase PHF8 is targeted for degradation by the anaphase-promoting complex containing CDC20. Mol Cell Biol. 2013 Nov;33(21):4166-80. doi: 10.1128/MCB.00689-13. Epub 2013 Aug 26. PubMed PMID: 23979597; PubMed Central PMCID: PMC3811896.
  28. Tan MK, Lim HJ, Bennett EJ, Shi Y, Harper JW. Parallel SCF adaptor capture proteomics reveals a role for SCFFBXL17 in NRF2 activation via BACH1 repressor turnover. Mol Cell. 2013 Oct 10;52(1):9-24. doi: 10.1016/j.molcel.2013.08.018. Epub 2013 Sep 12. PubMed PMID: 24035498; PubMed Central PMCID: PMC3981468.
  29. Greer EL, Shi Y. What's the Mtrr with your grandparents?. Cell Metab. 2013 Oct 1;18(4):457-9. doi: 10.1016/j.cmet.2013.09.016. PubMed PMID: 24093670; PubMed Central PMCID: PMC3947785.
  30. Medvedovic J, Ebert A, Tagoh H, Tamir IM, Schwickert TA, Novatchkova M, Sun Q, Huis In 't Veld PJ, Guo C, Yoon HS, Denizot Y, Holwerda SJ, de Laat W, Cogné M, Shi Y, Alt FW, Busslinger M. Flexible long-range loops in the VH gene region of the Igh locus facilitate the generation of a diverse antibody repertoire. Immunity. 2013 Aug 22;39(2):229-44. doi: 10.1016/j.immuni.2013.08.011. PubMed PMID: 23973221; PubMed Central PMCID: PMC4810778.
  31. Pan X, Papasani M, Hao Y, Calamito M, Wei F, Quinn Iii WJ, Basu A, Wang J, Hodawadekar S, Zaprazna K, Liu H, Shi Y, Allman D, Cancro M, Atchison ML. YY1 controls Igκ repertoire and B-cell development, and localizes with condensin on the Igκ locus. EMBO J. 2013 Apr 17;32(8):1168-82. doi: 10.1038/emboj.2013.66. Epub 2013 Mar 26. PubMed PMID: 23531880; PubMed Central PMCID: PMC3630362.
  32. Tan L, Xiong L, Xu W, Wu F, Huang N, Xu Y, Kong L, Zheng L, Schwartz L, Shi Y, Shi YG. Genome-wide comparison of DNA hydroxymethylation in mouse embryonic stem cells and neural progenitor cells by a new comparative hMeDIP-seq method. Nucleic Acids Res. 2013 Apr;41(7):e84. doi: 10.1093/nar/gkt091. Epub 2013 Feb 13. PubMed PMID: 23408859; PubMed Central PMCID: PMC3627583.
  33. Badeaux AI, Shi Y. Emerging roles for chromatin as a signal integration and storage platform. Nat Rev Mol Cell Biol. 2013 Apr;14(4):211-24. doi: 10.1038/nrm3545. Review. PubMed PMID: 23524488; PubMed Central PMCID: PMC4082330.
  34. Chen S, Shi Y. A new horizon for epigenetic medicine?. Cell Res. 2013 Mar;23(3):326-8. doi: 10.1038/cr.2012.136. Epub 2012 Sep 18. PubMed PMID: 22986503; PubMed Central PMCID: PMC3587697.
  35. Chen H, Ma H, Inuzuka H, Diao J, Lan F, Shi YG, Wei W, Shi Y. DNA damage regulates UHRF1 stability via the SCF(β-TrCP) E3 ligase. Mol Cell Biol. 2013 Mar;33(6):1139-48. doi: 10.1128/MCB.01191-12. Epub 2013 Jan 7. PubMed PMID: 23297342; PubMed Central PMCID: PMC3592027.
  36. Ballaré C, Lange M, Lapinaite A, Martin GM, Morey L, Pascual G, Liefke R, Simon B, Shi Y, Gozani O, Carlomagno T, Benitah SA, Di Croce L. Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity. Nat Struct Mol Biol. 2012 Dec;19(12):1257-65. doi: 10.1038/nsmb.2434. Epub 2012 Oct 28. PubMed PMID: 23104054; PubMed Central PMCID: PMC3926938.
  37. Yang YJ, Baltus AE, Mathew RS, Murphy EA, Evrony GD, Gonzalez DM, Wang EP, Marshall-Walker CA, Barry BJ, Murn J, Tatarakis A, Mahajan MA, Samuels HH, Shi Y, Golden JA, Mahajnah M, Shenhav R, Walsh CA. Microcephaly gene links trithorax and REST/NRSF to control neural stem cell proliferation and differentiation. Cell. 2012 Nov 21;151(5):1097-112. doi: 10.1016/j.cell.2012.10.043. PubMed PMID: 23178126; PubMed Central PMCID: PMC3567437.
  38. Blättler SM, Verdeguer F, Liesa M, Cunningham JT, Vogel RO, Chim H, Liu H, Romanino K, Shirihai OS, Vazquez F, Rüegg MA, Shi Y, Puigserver P. Defective mitochondrial morphology and bioenergetic function in mice lacking the transcription factor Yin Yang 1 in skeletal muscle. Mol Cell Biol. 2012 Aug;32(16):3333-46. doi: 10.1128/MCB.00337-12. Epub 2012 Jun 18. PubMed PMID: 22711985; PubMed Central PMCID: PMC3434543.
  39. Kim HG, Kim HT, Leach NT, Lan F, Ullmann R, Silahtaroglu A, Kurth I, Nowka A, Seong IS, Shen Y, Talkowski ME, Ruderfer D, Lee JH, Glotzbach C, Ha K, Kjaergaard S, Levin AV, Romeike BF, Kleefstra T, Bartsch O, Elsea SH, Jabs EW, MacDonald ME, Harris DJ, Quade BJ, Ropers HH, Shaffer LG, Kutsche K, Layman LC, Tommerup N, Kalscheuer VM, Shi Y, Morton CC, Kim CH, Gusella JF. Translocations disrupting PHF21A in the Potocki-Shaffer-syndrome region are associated with intellectual disability and craniofacial anomalies. Am J Hum Genet. 2012 Jul 13;91(1):56-72. doi: 10.1016/j.ajhg.2012.05.005. Epub 2012 Jul 5. PubMed PMID: 22770980; PubMed Central PMCID: PMC3397276.
  40. Chen S, Ma J, Wu F, Xiong LJ, Ma H, Xu W, Lv R, Li X, Villen J, Gygi SP, Liu XS, Shi Y. The histone H3 Lys 27 demethylase JMJD3 regulates gene expression by impacting transcriptional elongation. Genes Dev. 2012 Jun 15;26(12):1364-75. doi: 10.1101/gad.186056.111. PubMed PMID: 22713873; PubMed Central PMCID: PMC3387663.
  41. Blättler SM, Cunningham JT, Verdeguer F, Chim H, Haas W, Liu H, Romanino K, Rüegg MA, Gygi SP, Shi Y, Puigserver P. Yin Yang 1 deficiency in skeletal muscle protects against rapamycin-induced diabetic-like symptoms through activation of insulin/IGF signaling. Cell Metab. 2012 Apr 4;15(4):505-17. doi: 10.1016/j.cmet.2012.03.008. PubMed PMID: 22482732; PubMed Central PMCID: PMC3324784.
  42. Greer EL, Shi Y. Histone methylation: a dynamic mark in health, disease and inheritance. Nat Rev Genet. 2012 Apr 3;13(5):343-57. doi: 10.1038/nrg3173. Review. PubMed PMID: 22473383; PubMed Central PMCID: PMC4073795.
  43. Ma H, Chen H, Guo X, Wang Z, Sowa ME, Zheng L, Hu S, Zeng P, Guo R, Diao J, Lan F, Harper JW, Shi YG, Xu Y, Shi Y. M phase phosphorylation of the epigenetic regulator UHRF1 regulates its physical association with the deubiquitylase USP7 and stability. Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):4828-33. doi: 10.1073/pnas.1116349109. Epub 2012 Mar 12. PubMed PMID: 22411829; PubMed Central PMCID: PMC3323953.
  44. Wang Y, Kallgren SP, Reddy BD, Kuntz K, López-Maury L, Thompson J, Watt S, Ma C, Hou H, Shi Y, Yates JR 3rd, Bähler J, O'Connell MJ, Jia S. Histone H3 lysine 14 acetylation is required for activation of a DNA damage checkpoint in fission yeast. J Biol Chem. 2012 Feb 3;287(6):4386-93. doi: 10.1074/jbc.M111.329417. Epub 2011 Dec 19. PubMed PMID: 22184112; PubMed Central PMCID: PMC3281674.
  45. Lee MH, Lahusen T, Wang RH, Xiao C, Xu X, Hwang YS, He WW, Shi Y, Deng CX. Yin Yang 1 positively regulates BRCA1 and inhibits mammary cancer formation. Oncogene. 2012 Jan 5;31(1):116-27. doi: 10.1038/onc.2011.217. Epub 2011 Jun 13. PubMed PMID: 21666725.
  46. Wu C, So J, Davis-Dusenbery BN, Qi HH, Bloch DB, Shi Y, Lagna G, Hata A. Hypoxia potentiates microRNA-mediated gene silencing through posttranslational modification of Argonaute2. Mol Cell Biol. 2011 Dec;31(23):4760-74. doi: 10.1128/MCB.05776-11. Epub 2011 Oct 3. PubMed PMID: 21969601; PubMed Central PMCID: PMC3232924.
  47. Dango S, Mosammaparast N, Sowa ME, Xiong LJ, Wu F, Park K, Rubin M, Gygi S, Harper JW, Shi Y. DNA unwinding by ASCC3 helicase is coupled to ALKBH3-dependent DNA alkylation repair and cancer cell proliferation. Mol Cell. 2011 Nov 4;44(3):373-84. doi: 10.1016/j.molcel.2011.08.039. PubMed PMID: 22055184; PubMed Central PMCID: PMC3258846.
  48. Greer EL, Maures TJ, Ucar D, Hauswirth AG, Mancini E, Lim JP, Benayoun BA, Shi Y, Brunet A. Transgenerational epigenetic inheritance of longevity in Caenorhabditis elegans. Nature. 2011 Oct 19;479(7373):365-71. doi: 10.1038/nature10572. PubMed PMID: 22012258; PubMed Central PMCID: PMC3368121.
  49. Nottke AC, Beese-Sims SE, Pantalena LF, Reinke V, Shi Y, Colaiácovo MP. SPR-5 is a histone H3K4 demethylase with a role in meiotic double-strand break repair. Proc Natl Acad Sci U S A. 2011 Aug 2;108(31):12805-10. doi: 10.1073/pnas.1102298108. Epub 2011 Jul 18. PubMed PMID: 21768382; PubMed Central PMCID: PMC3150895.
  50. Rajakumara E, Wang Z, Ma H, Hu L, Chen H, Lin Y, Guo R, Wu F, Li H, Lan F, Shi YG, Xu Y, Patel DJ, Shi Y. PHD finger recognition of unmodified histone H3R2 links UHRF1 to regulation of euchromatic gene expression. Mol Cell. 2011 Jul 22;43(2):275-284. doi: 10.1016/j.molcel.2011.07.006. PubMed PMID: 21777816; PubMed Central PMCID: PMC4691841.