Harvard Catalyst Profiles

Contact, publication, and social network information about Harvard faculty and fellows.

Yang Shi, Ph.D.

Other Positions

The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. R35CA210104 (SHI, YANG) Aug 25, 2017 - Jul 31, 2024
    Epigenetic regulation of cellular plasticity and cancer cell fate
    Role: Principal Investigator
  2. R21AI130737 (SHI, YANG) Jan 18, 2017 - Dec 31, 2018
    Investigation into the epigenetic mechanisms of trained immunity?
    Role: Principal Investigator
  3. R01GM117264 (SHI, YANG) Aug 19, 2016 - Jul 31, 2020
    Investigation of roles and mechanisms of DNA and histone modification networks in trans-generational epigenetic inheritance
    Role: Principal Investigator
  4. R01MH096066 (SHI, YANG) Aug 10, 2012 - Feb 28, 2023
    Novel epigenetic mechanisms in neuronal development and cognitive function
    Role: Principal Investigator
  5. R01CA118487 (SHI, YANG) Dec 1, 2005 - Jun 30, 2021
    Histone demethylases and regulation of chromatin and transcription in eukaryotes
    Role: Principal Investigator

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Sendinc E, Jambhekar A, Shi Y. Remodeling Your Way out of Cell Cycle. Cell. 2015 Jul 16; 162(2):237-238. PMID: 26186182.
    Citations: 2     Fields:    Translation:Animals
  2. 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 07; 161(4):868-78. PMID: 25936839.
    Citations: 88     Fields:    Translation:AnimalsCells
  3. Murn J, Zarnack K, Yang YJ, Durak O, Murphy EA, Cheloufi S, Gonzalez DM, Teplova M, Curk T, Zuber J, Patel DJ, Ule J, Luscombe NM, Tsai LH, Walsh CA, Shi Y. Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt. Genes Dev. 2015 Mar 01; 29(5):501-12. PMID: 25737280.
    Citations: 7     Fields:    Translation:HumansAnimalsCells
  4. 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. PMID: 25684206.
    Citations: 47     Fields:    Translation:HumansCells
  5. 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. PMID: 25666439.
    Citations: 10     Fields:    Translation:HumansCells
  6. Lan F, Shi Y. Histone H3.3 and cancer: A potential reader connection. Proc Natl Acad Sci U S A. 2015 Jun 02; 112(22):6814-9. PMID: 25453099.
    Citations: 5     Fields:    Translation:HumansCells
  7. Brookes E, Shi Y. Diverse epigenetic mechanisms of human disease. Annu Rev Genet. 2014; 48:237-68. PMID: 25195505.
    Citations: 26     Fields:    Translation:HumansCells
  8. 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 08; 157(4):869-81. PMID: 24813610.
    Citations: 27     Fields:    Translation:HumansAnimalsCells
  9. 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. PMID: 24685137.
    Citations: 32     Fields:    Translation:AnimalsCells
  10. Greer EL, Shi Y. What's the Mtrr with your grandparents? Cell Metab. 2013 Oct 01; 18(4):457-9. PMID: 24093670.
    Citations:    Fields:    Translation:Animals
  11. 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. PMID: 24035498.
    Citations: 24     Fields:    Translation:HumansCells
  12. 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. PMID: 23979597.
    Citations: 17     Fields:    Translation:HumansCells
  13. 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. PMID: 23847782.
    Citations: 1     Fields:    Translation:HumansAnimalsCells
  14. 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. PMID: 23524488.
    Citations: 93     Fields:    Translation:HumansCells
  15. 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. PMID: 23178126.
    Citations: 31     Fields:    Translation:HumansAnimalsCells
  16. Chen S, Shi Y. A new horizon for epigenetic medicine? Cell Res. 2013 Mar; 23(3):326-8. PMID: 22986503.
    Citations: 4     Fields:    Translation:HumansCells
  17. 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. PMID: 22770980.
    Citations: 20     Fields:    Translation:HumansAnimalsCells
  18. 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. PMID: 22711985.
    Citations: 23     Fields:    Translation:HumansAnimalsCells
  19. 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. PMID: 22713873.
    Citations: 53     Fields:    Translation:HumansCells
  20. 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 04; 15(4):505-17. PMID: 22482732.
    Citations: 34     Fields:    Translation:HumansAnimalsCells
  21. Greer EL, Shi Y. Histone methylation: a dynamic mark in health, disease and inheritance. Nat Rev Genet. 2012 Apr 03; 13(5):343-57. PMID: 22473383.
    Citations: 445     Fields:    Translation:HumansAnimalsCells
  22. 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 04; 44(3):373-84. PMID: 22055184.
    Citations: 49     Fields:    Translation:HumansAnimalsCells
  23. 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 02; 108(31):12805-10. PMID: 21768382.
    Citations: 29     Fields:    Translation:AnimalsCells
  24. Iwase S, Xiang B, Ghosh S, Ren T, Lewis PW, Cochrane JC, Allis CD, Picketts DJ, Patel DJ, Li H, Shi Y. ATRX ADD domain links an atypical histone methylation recognition mechanism to human mental-retardation syndrome. Nat Struct Mol Biol. 2011 Jun 12; 18(7):769-76. PMID: 21666679.
    Citations: 86     Fields:    Translation:HumansCells
  25. Rahman S, Sowa ME, Ottinger M, Smith JA, Shi Y, Harper JW, Howley PM. The Brd4 extraterminal domain confers transcription activation independent of pTEFb by recruiting multiple proteins, including NSD3. Mol Cell Biol. 2011 Jul; 31(13):2641-52. PMID: 21555454.
    Citations: 137     Fields:    Translation:HumansCells
  26. Xu Y, Wu F, Tan L, Kong L, Xiong L, Deng J, Barbera AJ, Zheng L, Zhang H, Huang S, Min J, Nicholson T, Chen T, Xu G, Shi Y, Zhang K, Shi YG. Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. Mol Cell. 2011 May 20; 42(4):451-64. PMID: 21514197.
    Citations: 222     Fields:    Translation:AnimalsCells
  27. Iwase S, Shi Y. Histone and DNA modifications in mental retardation. Prog Drug Res. 2011; 67:147-73. PMID: 21141729.
    Citations: 3     Fields:    Translation:HumansAnimalsCells
  28. Fang R, Barbera AJ, Xu Y, Rutenberg M, Leonor T, Bi Q, Lan F, Mei P, Yuan GC, Lian C, Peng J, Cheng D, Sui G, Kaiser UB, Shi Y, Shi YG. Human LSD2/KDM1b/AOF1 regulates gene transcription by modulating intragenic H3K4me2 methylation. Mol Cell. 2010 Jul 30; 39(2):222-33. PMID: 20670891.
    Citations: 74     Fields:    Translation:HumansCells
  29. Qi HH, Sarkissian M, Hu GQ, Wang Z, Bhattacharjee A, Gordon DB, Gonzales M, Lan F, Ongusaha PP, Huarte M, Yaghi NK, Lim H, Garcia BA, Brizuela L, Zhao K, Roberts TM, Shi Y. Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development. Nature. 2010 Jul 22; 466(7305):503-7. PMID: 20622853.
    Citations: 101     Fields:    Translation:HumansAnimalsCells
  30. Mosammaparast N, Shi Y. Reversal of histone methylation: biochemical and molecular mechanisms of histone demethylases. Annu Rev Biochem. 2010; 79:155-79. PMID: 20373914.
    Citations: 192     Fields:    Translation:HumansAnimalsCells
  31. Wang B, Li S, Qi HH, Chowdhury D, Shi Y, Novina CD. Distinct passenger strand and mRNA cleavage activities of human Argonaute proteins. Nat Struct Mol Biol. 2009 Dec; 16(12):1259-66. PMID: 19946268.
    Citations: 64     Fields:    Translation:Humans
  32. Wu S, Hu YC, Liu H, Shi Y. Loss of YY1 impacts the heterochromatic state and meiotic double-strand breaks during mouse spermatogenesis. Mol Cell Biol. 2009 Dec; 29(23):6245-56. PMID: 19786570.
    Citations: 25     Fields:    Translation:AnimalsCells
  33. Nottke A, Colaiácovo MP, Shi Y. Developmental roles of the histone lysine demethylases. Development. 2009 Mar; 136(6):879-89. PMID: 19234061.
    Citations: 64     Fields:    Translation:HumansAnimalsCells
  34. Chen S, Whetstine JR, Ghosh S, Hanover JA, Gali RR, Grosu P, Shi Y. The conserved NAD(H)-dependent corepressor CTBP-1 regulates Caenorhabditis elegans life span. Proc Natl Acad Sci U S A. 2009 Feb 03; 106(5):1496-501. PMID: 19164523.
    Citations: 21     Fields:    Translation:AnimalsCells
  35. Mulligan P, Westbrook TF, Ottinger M, Pavlova N, Chang B, Macia E, Shi YJ, Barretina J, Liu J, Howley PM, Elledge SJ, Shi Y. CDYL bridges REST and histone methyltransferases for gene repression and suppression of cellular transformation. Mol Cell. 2008 Dec 05; 32(5):718-26. PMID: 19061646.
    Citations: 54     Fields:    Translation:HumansCells
  36. Ongusaha PP, Qi HH, Raj L, Kim YB, Aaronson SA, Davis RJ, Shi Y, Liao JK, Lee SW. Identification of ROCK1 as an upstream activator of the JIP-3 to JNK signaling axis in response to UVB damage. Sci Signal. 2008 Nov 25; 1(47):ra14. PMID: 19036714.
    Citations: 20     Fields:    Translation:HumansAnimalsCellsPHPublic Health
  37. Kim HG, Kurth I, Lan F, Meliciani I, Wenzel W, Eom SH, Kang GB, Rosenberger G, Tekin M, Ozata M, Bick DP, Sherins RJ, Walker SL, Shi Y, Gusella JF, Layman LC. Mutations in CHD7, encoding a chromatin-remodeling protein, cause idiopathic hypogonadotropic hypogonadism and Kallmann syndrome. Am J Hum Genet. 2008 Oct; 83(4):511-9. PMID: 18834967.
    Citations: 94     Fields:    Translation:HumansCells
  38. Qi HH, Ongusaha PP, Myllyharju J, Cheng D, Pakkanen O, Shi Y, Lee SW, Peng J, Shi Y. Prolyl 4-hydroxylation regulates Argonaute 2 stability. Nature. 2008 Sep 18; 455(7211):421-4. PMID: 18690212.
    Citations: 88     Fields:    Translation:HumansAnimalsCells
  39. Lan F, Nottke AC, Shi Y. Mechanisms involved in the regulation of histone lysine demethylases. Curr Opin Cell Biol. 2008 Jun; 20(3):316-25. PMID: 18440794.
    Citations: 86     Fields:    Translation:HumansAnimalsCells
  40. Westbrook TF, Hu G, Ang XL, Mulligan P, Pavlova NN, Liang A, Leng Y, Maehr R, Shi Y, Harper JW, Elledge SJ. SCFbeta-TRCP controls oncogenic transformation and neural differentiation through REST degradation. Nature. 2008 Mar 20; 452(7185):370-4. PMID: 18354483.
    Citations: 138     Fields:    Translation:HumansAnimalsCells
  41. Matthews AG, Kuo AJ, Ramón-Maiques S, Han S, Champagne KS, Ivanov D, Gallardo M, Carney D, Cheung P, Ciccone DN, Walter KL, Utz PJ, Shi Y, Kutateladze TG, Yang W, Gozani O, Oettinger MA. RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination. Nature. 2007 Dec 13; 450(7172):1106-10. PMID: 18033247.
    Citations: 202     Fields:    Translation:HumansAnimalsCells
  42. Wu S, Shi Y, Mulligan P, Gay F, Landry J, Liu H, Lu J, Qi HH, Wang W, Nickoloff JA, Wu C, Shi Y. A YY1-INO80 complex regulates genomic stability through homologous recombination-based repair. Nat Struct Mol Biol. 2007 Dec; 14(12):1165-72. PMID: 18026119.
    Citations: 72     Fields:    Translation:HumansAnimalsCells
  43. Shi Y. Histone lysine demethylases: emerging roles in development, physiology and disease. Nat Rev Genet. 2007 Nov; 8(11):829-33. PMID: 17909537.
    Citations: 171     Fields:    Translation:HumansAnimalsCells
  44. Lan F, Bayliss PE, Rinn JL, Whetstine JR, Wang JK, Chen S, Iwase S, Alpatov R, Issaeva I, Canaani E, Roberts TM, Chang HY, Shi Y. A histone H3 lysine 27 demethylase regulates animal posterior development. Nature. 2007 Oct 11; 449(7163):689-94. PMID: 17851529.
    Citations: 252     Fields:    Translation:HumansAnimalsCells
  45. Lan F, Collins RE, De Cegli R, Alpatov R, Horton JR, Shi X, Gozani O, Cheng X, Shi Y. Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression. Nature. 2007 Aug 09; 448(7154):718-22. PMID: 17687328.
    Citations: 168     Fields:    Translation:HumansCells
  46. Huarte M, Lan F, Kim T, Vaughn MW, Zaratiegui M, Martienssen RA, Buratowski S, Shi Y. The fission yeast Jmj2 reverses histone H3 Lysine 4 trimethylation. J Biol Chem. 2007 Jul 27; 282(30):21662-70. PMID: 17550896.
    Citations: 15     Fields:    Translation:AnimalsCells
  47. Liu H, Schmidt-Supprian M, Shi Y, Hobeika E, Barteneva N, Jumaa H, Pelanda R, Reth M, Skok J, Rajewsky K, Shi Y. Yin Yang 1 is a critical regulator of B-cell development. Genes Dev. 2007 May 15; 21(10):1179-89. PMID: 17504937.
    Citations: 95     Fields:    Translation:AnimalsCells
  48. Lan F, Zaratiegui M, Villén J, Vaughn MW, Verdel A, Huarte M, Shi Y, Gygi SP, Moazed D, Martienssen RA, Shi Y. S. pombe LSD1 homologs regulate heterochromatin propagation and euchromatic gene transcription. Mol Cell. 2007 Apr 13; 26(1):89-101. PMID: 17434129.
    Citations: 40     Fields:    Translation:AnimalsCells
  49. Horwitz AA, Affar el B, Heine GF, Shi Y, Parvin JD. A mechanism for transcriptional repression dependent on the BRCA1 E3 ubiquitin ligase. Proc Natl Acad Sci U S A. 2007 Apr 17; 104(16):6614-9. PMID: 17420471.
    Citations: 18     Fields:    Translation:HumansCells
  50. Iwase S, Lan F, Bayliss P, de la Torre-Ubieta L, Huarte M, Qi HH, Whetstine JR, Bonni A, Roberts TM, Shi Y. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell. 2007 Mar 23; 128(6):1077-88. PMID: 17320160.
    Citations: 243     Fields:    Translation:HumansAnimalsCells
  51. Shi Y, Whetstine JR. Dynamic regulation of histone lysine methylation by demethylases. Mol Cell. 2007 Jan 12; 25(1):1-14. PMID: 17218267.
    Citations: 215     Fields:    Translation:HumansAnimalsCells
  52. Luke MP, Sui G, Liu H, Shi Y. Yin Yang 1 physically interacts with Hoxa11 and represses Hoxa11-dependent transcription. J Biol Chem. 2006 Nov 03; 281(44):33226-32. PMID: 16963455.
    Citations: 12     Fields:    Translation:HumansAnimalsCells
  53. Affar el B, Gay F, Shi Y, Liu H, Huarte M, Wu S, Collins T, Li E, Shi Y. Essential dosage-dependent functions of the transcription factor yin yang 1 in late embryonic development and cell cycle progression. Mol Cell Biol. 2006 May; 26(9):3565-81. PMID: 16611997.
    Citations: 69     Fields:    Translation:HumansAnimalsCells
  54. Whetstine JR, Nottke A, Lan F, Huarte M, Smolikov S, Chen Z, Spooner E, Li E, Zhang G, Colaiacovo M, Shi Y. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell. 2006 May 05; 125(3):467-81. PMID: 16603238.
    Citations: 332     Fields:    Translation:HumansAnimalsCells
  55. Affar el B, Luke MP, Gay F, Calvo D, Sui G, Weiss RS, Li E, Shi Y. Targeted ablation of Par-4 reveals a cell type-specific susceptibility to apoptosis-inducing agents. Cancer Res. 2006 Apr 01; 66(7):3456-62. PMID: 16585168.
    Citations: 4     Fields:    Translation:HumansAnimalsCells
  56. Rosendorff A, Sakakibara S, Lu S, Kieff E, Xuan Y, DiBacco A, Shi Y, Shi Y, Gill G. NXP-2 association with SUMO-2 depends on lysines required for transcriptional repression. Proc Natl Acad Sci U S A. 2006 Apr 04; 103(14):5308-13. PMID: 16567619.
    Citations: 46     Fields:    Translation:Cells
  57. Bates EA, Victor M, Jones AK, Shi Y, Hart AC. Differential contributions of Caenorhabditis elegans histone deacetylases to huntingtin polyglutamine toxicity. J Neurosci. 2006 Mar 08; 26(10):2830-8. PMID: 16525063.
    Citations: 57     Fields:    Translation:HumansAnimalsCells
  58. Liu LP, Ni JQ, Shi YD, Oakeley EJ, Sun FL. Sex-specific role of Drosophila melanogaster HP1 in regulating chromatin structure and gene transcription. Nat Genet. 2005 Dec; 37(12):1361-6. PMID: 16258543.
    Citations: 37     Fields:    Translation:HumansAnimalsCells
  59. Shi YJ, Matson C, Lan F, Iwase S, Baba T, Shi Y. Regulation of LSD1 histone demethylase activity by its associated factors. Mol Cell. 2005 Sep 16; 19(6):857-64. PMID: 16140033.
    Citations: 266     Fields:    Translation:HumansCells
  60. Park SK, Nguyen MD, Fischer A, Luke MP, Affar el B, Dieffenbach PB, Tseng HC, Shi Y, Tsai LH. Par-4 links dopamine signaling and depression. Cell. 2005 Jul 29; 122(2):275-87. PMID: 16051151.
    Citations: 37     Fields:    Translation:AnimalsCells
  61. Whetstine JR, Ceron J, Ladd B, Dufourcq P, Reinke V, Shi Y. Regulation of tissue-specific and extracellular matrix-related genes by a class I histone deacetylase. Mol Cell. 2005 May 13; 18(4):483-90. PMID: 15893731.
    Citations: 27     Fields:    Translation:AnimalsCells
  62. Sui G, Shi Y. Gene silencing by a DNA vector-based RNAi technology. Methods Mol Biol. 2005; 309:205-18. PMID: 15990402.
    Citations: 25     Fields:    Translation:HumansCells
  63. Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR, Cole PA, Casero RA, Shi Y. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell. 2004 Dec 29; 119(7):941-53. PMID: 15620353.
    Citations: 1055     Fields:    Translation:HumansCells
  64. Alpatov R, Munguba GC, Caton P, Joo JH, Shi Y, Shi Y, Hunt ME, Sugrue SP. Nuclear speckle-associated protein Pnn/DRS binds to the transcriptional corepressor CtBP and relieves CtBP-mediated repression of the E-cadherin gene. Mol Cell Biol. 2004 Dec; 24(23):10223-35. PMID: 15542832.
    Citations: 26     Fields:    Translation:HumansAnimalsCells
  65. Xiang R, Shi Y, Dillon DA, Negin B, Horváth C, Wilkins JA. 2D LC/MS analysis of membrane proteins from breast cancer cell lines MCF7 and BT474. J Proteome Res. 2004 Nov-Dec; 3(6):1278-83. PMID: 15595738.
    Citations: 8     Fields:    Translation:HumansCells
  66. Shi Y, Shi Y. Metabolic enzymes and coenzymes in transcription--a direct link between metabolism and transcription? Trends Genet. 2004 Sep; 20(9):445-52. PMID: 15313554.
    Citations: 23     Fields:    Translation:HumansAnimalsCells
  67. Sui G, Affar el B, Shi Y, Brignone C, Wall NR, Yin P, Donohoe M, Luke MP, Calvo D, Grossman SR, Shi Y. Yin Yang 1 is a negative regulator of p53. Cell. 2004 Jun 25; 117(7):859-72. PMID: 15210108.
    Citations: 147     Fields:    Translation:HumansAnimalsCells
  68. Chen J, Wall NR, Kocher K, Duclos N, Fabbro D, Neuberg D, Griffin JD, Shi Y, Gilliland DG. Stable expression of small interfering RNA sensitizes TEL-PDGFbetaR to inhibition with imatinib or rapamycin. J Clin Invest. 2004 Jun; 113(12):1784-91. PMID: 15199413.
    Citations: 13     Fields:    Translation:HumansAnimalsCells
  69. Lo MC, Gay F, Odom R, Shi Y, Lin R. Phosphorylation by the beta-catenin/MAPK complex promotes 14-3-3-mediated nuclear export of TCF/POP-1 in signal-responsive cells in C. elegans. Cell. 2004 Apr 02; 117(1):95-106. PMID: 15066285.
    Citations: 65     Fields:    Translation:AnimalsCells
  70. Walker AK, Shi Y, Blackwell TK. An extensive requirement for transcription factor IID-specific TAF-1 in Caenorhabditis elegans embryonic transcription. J Biol Chem. 2004 Apr 09; 279(15):15339-47. PMID: 14726532.
    Citations: 8     Fields:    Translation:HumansAnimalsCells
  71. Lin X, Liang YY, Sun B, Liang M, Shi Y, Brunicardi FC, Shi Y, Feng XH. Smad6 recruits transcription corepressor CtBP to repress bone morphogenetic protein-induced transcription. Mol Cell Biol. 2003 Dec; 23(24):9081-93. PMID: 14645520.
    Citations: 27     Fields:    Translation:HumansAnimalsCells
  72. Shi Y, Blackwell TK. A two-tiered transcription regulation mechanism that protects germ cell identity. Mol Cell. 2003 Nov; 12(5):1062-4. PMID: 14636565.
    Citations:    Fields:    Translation:AnimalsCells
  73. Wall NR, Shi Y. Small RNA: can RNA interference be exploited for therapy? Lancet. 2003 Oct 25; 362(9393):1401-3. PMID: 14585643.
    Citations: 32     Fields:    Translation:HumansAnimalsCells
  74. Ding H, Schwarz DS, Keene A, Affar el B, Fenton L, Xia X, Shi Y, Zamore PD, Xu Z. Selective silencing by RNAi of a dominant allele that causes amyotrophic lateral sclerosis. Aging Cell. 2003 08; 2(4):209-17. PMID: 12934714.
    Citations: 46     Fields:    Translation:HumansAnimals
  75. Brooks JT, Shapiro RL, Kumar L, Wells JG, Phillips-Howard PA, Shi YP, Vulule JM, Hoekstra RM, Mintz E, Slutsker L. Epidemiology of sporadic bloody diarrhea in rural Western Kenya. Am J Trop Med Hyg. 2003 Jun; 68(6):671-7. PMID: 12892051.
    Citations: 14     Fields:    Translation:HumansCellsPHPublic Health
  76. Shi Y, Sawada J, Sui G, Affar el B, Whetstine JR, Lan F, Ogawa H, Luke MP, Nakatani Y, Shi Y. Coordinated histone modifications mediated by a CtBP co-repressor complex. Nature. 2003 Apr 17; 422(6933):735-8. PMID: 12700765.
    Citations: 267     Fields:    Translation:HumansCells
  77. Mayo MW, Denlinger CE, Broad RM, Yeung F, Reilly ET, Shi Y, Jones DR. Ineffectiveness of histone deacetylase inhibitors to induce apoptosis involves the transcriptional activation of NF-kappa B through the Akt pathway. J Biol Chem. 2003 May 23; 278(21):18980-9. PMID: 12649266.
    Citations: 50     Fields:    Translation:HumansCells
  78. Gay F, Calvo D, Lo MC, Ceron J, Maduro M, Lin R, Shi Y. Acetylation regulates subcellular localization of the Wnt signaling nuclear effector POP-1. Genes Dev. 2003 Mar 15; 17(6):717-22. PMID: 12651889.
    Citations: 18     Fields:    Translation:HumansAnimalsCells
  79. Shi Y. Mammalian RNAi for the masses. Trends Genet. 2003 Jan; 19(1):9-12. PMID: 12493242.
    Citations: 55     Fields:    Translation:HumansAnimals
  80. Gaudilliere B, Shi Y, Bonni A. RNA interference reveals a requirement for myocyte enhancer factor 2A in activity-dependent neuronal survival. J Biol Chem. 2002 Nov 29; 277(48):46442-6. PMID: 12235147.
    Citations: 36     Fields:    Translation:AnimalsCells
  81. Shim EY, Walker AK, Shi Y, Blackwell TK. CDK-9/cyclin T (P-TEFb) is required in two postinitiation pathways for transcription in the C. elegans embryo. Genes Dev. 2002 Aug 15; 16(16):2135-46. PMID: 12183367.
    Citations: 81     Fields:    Translation:AnimalsCells
  82. Rafiee P, Shi Y, Kong X, Pritchard KA, Tweddell JS, Litwin SB, Mussatto K, Jaquiss RD, Su J, Baker JE. Activation of protein kinases in chronically hypoxic infant human and rabbit hearts: role in cardioprotection. Circulation. 2002 Jul 09; 106(2):239-45. PMID: 12105165.
    Citations: 13     Fields:    Translation:HumansAnimalsCells
  83. Dufourcq P, Victor M, Gay F, Calvo D, Hodgkin J, Shi Y. Functional requirement for histone deacetylase 1 in Caenorhabditis elegans gonadogenesis. Mol Cell Biol. 2002 May; 22(9):3024-34. PMID: 11940660.
    Citations: 25     Fields:    Translation:HumansAnimalsCells
  84. Sui G, Soohoo C, Affar el B, Gay F, Shi Y, Forrester WC, Shi Y. A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc Natl Acad Sci U S A. 2002 Apr 16; 99(8):5515-20. PMID: 11960009.
    Citations: 301     Fields:    Translation:HumansAnimalsCells
  85. Victor M, Bei Y, Gay F, Calvo D, Mello C, Shi Y. HAT activity is essential for CBP-1-dependent transcription and differentiation in Caenorhabditis elegans. EMBO Rep. 2002 Jan; 3(1):50-5. PMID: 11751575.
    Citations: 8     Fields:    Translation:AnimalsCells
  86. Calvo D, Victor M, Gay F, Sui G, Luke MP, Dufourcq P, Wen G, Maduro M, Rothman J, Shi Y. A POP-1 repressor complex restricts inappropriate cell type-specific gene transcription during Caenorhabditis elegans embryogenesis. EMBO J. 2001 Dec 17; 20(24):7197-208. PMID: 11742996.
    Citations: 32     Fields:    Translation:AnimalsCells
  87. Walker AK, Rothman JH, Shi Y, Blackwell TK. Distinct requirements for C.elegans TAF(II)s in early embryonic transcription. EMBO J. 2001 Sep 17; 20(18):5269-79. PMID: 11566890.
    Citations: 18     Fields:    Translation:HumansAnimalsCells
  88. Oei SL, Shi Y. Poly(ADP-ribosyl)ation of transcription factor Yin Yang 1 under conditions of DNA damage. Biochem Biophys Res Commun. 2001 Jul 06; 285(1):27-31. PMID: 11437367.
    Citations: 17     Fields:    Translation:HumansCells
  89. Oei SL, Shi Y. Transcription factor Yin Yang 1 stimulates poly(ADP-ribosyl)ation and DNA repair. Biochem Biophys Res Commun. 2001 Jun 08; 284(2):450-4. PMID: 11394900.
    Citations: 17     Fields:    Translation:HumansCells
  90. See RH, Calvo D, Shi Y, Kawa H, Luke MP, Yuan Z, Shi Y. Stimulation of p300-mediated transcription by the kinase MEKK1. J Biol Chem. 2001 May 11; 276(19):16310-7. PMID: 11278389.
    Citations: 24     Fields:    Translation:HumansAnimalsCells
  91. Nasrin N, Ogg S, Cahill CM, Biggs W, Nui S, Dore J, Calvo D, Shi Y, Ruvkun G, Alexander-Bridges MC. DAF-16 recruits the CREB-binding protein coactivator complex to the insulin-like growth factor binding protein 1 promoter in HepG2 cells. Proc Natl Acad Sci U S A. 2000 Sep 12; 97(19):10412-7. PMID: 10973497.
    Citations: 48     Fields:    Translation:HumansCells
  92. Coull JJ, Romerio F, Sun JM, Volker JL, Galvin KM, Davie JR, Shi Y, Hansen U, Margolis DM. The human factors YY1 and LSF repress the human immunodeficiency virus type 1 long terminal repeat via recruitment of histone deacetylase 1. J Virol. 2000 Aug; 74(15):6790-9. PMID: 10888618.
    Citations: 144     Fields:    Translation:HumansCells
  93. Walker AK, See R, Batchelder C, Kophengnavong T, Gronniger JT, Shi Y, Blackwell TK. A conserved transcription motif suggesting functional parallels between Caenorhabditis elegans SKN-1 and Cap'n'Collar-related basic leucine zipper proteins. J Biol Chem. 2000 Jul 21; 275(29):22166-71. PMID: 10764775.
    Citations: 25     Fields:    Translation:AnimalsCells
  94. Sze JY, Victor M, Loer C, Shi Y, Ruvkun G. Food and metabolic signalling defects in a Caenorhabditis elegans serotonin-synthesis mutant. Nature. 2000 Feb 03; 403(6769):560-4. PMID: 10676966.
    Citations: 197     Fields:    Translation:AnimalsCells
  95. Kato Y, Shi Y, He X. Neuralization of the Xenopus embryo by inhibition of p300/ CREB-binding protein function. J Neurosci. 1999 Nov 01; 19(21):9364-73. PMID: 10531441.
    Citations: 15     Fields:    Translation:Animals
  96. Yuan ZM, Huang Y, Ishiko T, Nakada S, Utsugisawa T, Shioya H, Utsugisawa Y, Shi Y, Weichselbaum R, Kufe D. Function for p300 and not CBP in the apoptotic response to DNA damage. Oncogene. 1999 Oct 07; 18(41):5714-7. PMID: 10523850.
    Citations: 20     Fields:    Translation:HumansCells
  97. Donohoe ME, Zhang X, McGinnis L, Biggers J, Li E, Shi Y. Targeted disruption of mouse Yin Yang 1 transcription factor results in peri-implantation lethality. Mol Cell Biol. 1999 Oct; 19(10):7237-44. PMID: 10490658.
    Citations: 106     Fields:    Translation:Animals
  98. Johnstone RW, Tommerup N, Hansen C, Vissing H, Shi Y. Structural organization, tissue expression, and chromosomal localization of Ciao 1, a functional modulator of the Wilms' tumor suppressor, WT1. Immunogenetics. 1999 Sep; 49(10):900-5. PMID: 10438340.
    Citations:    Fields:    Translation:HumansAnimalsCells
  99. Cook J, Krishnan S, Ananth S, Sells SF, Shi Y, Walther MM, Linehan WM, Sukhatme VP, Weinstein MH, Rangnekar VM. Decreased expression of the pro-apoptotic protein Par-4 in renal cell carcinoma. Oncogene. 1999 Feb 04; 18(5):1205-8. PMID: 10022126.
    Citations: 30     Fields:    Translation:HumansCells
  100. Yuan ZM, Huang Y, Ishiko T, Nakada S, Utsugisawa T, Shioya H, Utsugisawa Y, Yokoyama K, Weichselbaum R, Shi Y, Kufe D. Role for p300 in stabilization of p53 in the response to DNA damage. J Biol Chem. 1999 Jan 22; 274(4):1883-6. PMID: 9890940.
    Citations: 36     Fields:    Translation:HumansCells
  101. Johnstone RW, Tommerup N, Hansen C, Vissing H, Shi Y. Mapping of the human PAWR (par-4) gene to chromosome 12q21. Genomics. 1998 Oct 15; 53(2):241-3. PMID: 9790775.
    Citations: 13     Fields:    Translation:HumansCells
  102. See RH, Shi Y. Adenovirus E1B 19,000-molecular-weight protein activates c-Jun N-terminal kinase and c-Jun-mediated transcription. Mol Cell Biol. 1998 Jul; 18(7):4012-22. PMID: 9632786.
    Citations: 10     Fields:    Translation:HumansCells
  103. Johnstone RW, Wang J, Tommerup N, Vissing H, Roberts T, Shi Y. Ciao 1 is a novel WD40 protein that interacts with the tumor suppressor protein WT1. J Biol Chem. 1998 May 01; 273(18):10880-7. PMID: 9556563.
    Citations: 13     Fields:    Translation:HumansCells
  104. Bauknecht T, Shi Y. Overexpression of C/EBPbeta represses human papillomavirus type 18 upstream regulatory region activity in HeLa cells by interfering with the binding of TATA-binding protein. J Virol. 1998 Mar; 72(3):2113-24. PMID: 9499067.
    Citations: 10     Fields:    Translation:HumansCells
  105. Kawasaki H, Song J, Eckner R, Ugai H, Chiu R, Taira K, Shi Y, Jones N, Yokoyama KK. p300 and ATF-2 are components of the DRF complex, which regulates retinoic acid- and E1A-mediated transcription of the c-jun gene in F9 cells. Genes Dev. 1998 Jan 15; 12(2):233-45. PMID: 9436983.
    Citations: 36     Fields:    Translation:AnimalsCells
  106. Galvin KM, Shi Y. Multiple mechanisms of transcriptional repression by YY1. Mol Cell Biol. 1997 Jul; 17(7):3723-32. PMID: 9199306.
    Citations: 46     Fields:    Translation:HumansCells
  107. Sells SF, Han SS, Muthukkumar S, Maddiwar N, Johnstone R, Boghaert E, Gillis D, Liu G, Nair P, Monnig S, Collini P, Mattson MP, Sukhatme VP, Zimmer SG, Wood DP, McRoberts JW, Shi Y, Rangnekar VM. Expression and function of the leucine zipper protein Par-4 in apoptosis. Mol Cell Biol. 1997 Jul; 17(7):3823-32. PMID: 9199316.
    Citations: 35     Fields:    Translation:HumansAnimalsCells
  108. Gerritsen ME, Williams AJ, Neish AS, Moore S, Shi Y, Collins T. CREB-binding protein/p300 are transcriptional coactivators of p65. Proc Natl Acad Sci U S A. 1997 Apr 01; 94(7):2927-32. PMID: 9096323.
    Citations: 220     Fields:    Translation:AnimalsCells
  109. Li WW, Hsiung Y, Wong V, Galvin K, Zhou Y, Shi Y, Lee AS. Suppression of grp78 core promoter element-mediated stress induction by the dbpA and dbpB (YB-1) cold shock domain proteins. Mol Cell Biol. 1997 Jan; 17(1):61-8. PMID: 8972186.
    Citations: 17     Fields:    Translation:HumansCells
  110. Johnstone RW, See RH, Sells SF, Wang J, Muthukkumar S, Englert C, Haber DA, Licht JD, Sugrue SP, Roberts T, Rangnekar VM, Shi Y. A novel repressor, par-4, modulates transcription and growth suppression functions of the Wilms' tumor suppressor WT1. Mol Cell Biol. 1996 Dec; 16(12):6945-56. PMID: 8943350.
    Citations: 61     Fields:    Translation:HumansCells
  111. Bauknecht T, See RH, Shi Y. A novel C/EBP beta-YY1 complex controls the cell-type-specific activity of the human papillomavirus type 18 upstream regulatory region. J Virol. 1996 Nov; 70(11):7695-705. PMID: 8892890.
    Citations: 25     Fields:    Translation:HumansCells
  112. Lee JS, See RH, Deng T, Shi Y. Adenovirus E1A downregulates cJun- and JunB-mediated transcription by targeting their coactivator p300. Mol Cell Biol. 1996 Aug; 16(8):4312-26. PMID: 8754832.
    Citations: 33     Fields:    Translation:HumansCells
  113. Lee JS, Zhang X, Shi Y. Differential interactions of the CREB/ATF family of transcription factors with p300 and adenovirus E1A. J Biol Chem. 1996 Jul 26; 271(30):17666-74. PMID: 8663457.
    Citations: 12     Fields:    Translation:Cells
  114. Wang J, Auger KR, Jarvis L, Shi Y, Roberts TM. Direct association of Grb2 with the p85 subunit of phosphatidylinositol 3-kinase. J Biol Chem. 1995 May 26; 270(21):12774-80. PMID: 7759531.
    Citations: 26     Fields:    Translation:HumansAnimalsCells
  115. Lee JS, Galvin KM, See RH, Eckner R, Livingston D, Moran E, Shi Y. Relief of YY1 transcriptional repression by adenovirus E1A is mediated by E1A-associated protein p300. Genes Dev. 1995 May 15; 9(10):1188-98. PMID: 7758944.
    Citations: 104     Fields:    Translation:HumansCells
  116. Reddy JC, Morris JC, Wang J, English MA, Haber DA, Shi Y, Licht JD. WT1-mediated transcriptional activation is inhibited by dominant negative mutant proteins. J Biol Chem. 1995 May 05; 270(18):10878-84. PMID: 7738027.
    Citations: 33     Fields:    Translation:HumansAnimalsCells
  117. Lee JS, See RH, Galvin KM, Wang J, Shi Y. Functional interactions between YY1 and adenovirus E1A. Nucleic Acids Res. 1995 Mar 25; 23(6):925-31. PMID: 7731805.
    Citations: 30     Fields:    Translation:HumansCells
  118. Bauknecht T, Jundt F, Herr I, Oehler T, Delius H, Shi Y, Angel P, Zur Hausen H. A switch region determines the cell type-specific positive or negative action of YY1 on the activity of the human papillomavirus type 18 promoter. J Virol. 1995 Jan; 69(1):1-12. PMID: 7983700.
    Citations: 24     Fields:    Translation:HumansCells
  119. Mills LK, Shi Y, Millette RL. YY1 is the cellular factor shown previously to bind to regulatory regions of several leaky-late (beta gamma, gamma 1) genes of herpes simplex virus type 1. J Virol. 1994 Feb; 68(2):1234-8. PMID: 8289358.
    Citations: 6     Fields:    Translation:Cells
  120. Riggs KJ, Saleque S, Wong KK, Merrell KT, Lee JS, Shi Y, Calame K. Yin-yang 1 activates the c-myc promoter. Mol Cell Biol. 1993 Dec; 13(12):7487-95. PMID: 8246966.
    Citations: 65     Fields:    Translation:HumansAnimalsCells
  121. Lee JS, Galvin KM, Shi Y. Evidence for physical interaction between the zinc-finger transcription factors YY1 and Sp1. Proc Natl Acad Sci U S A. 1993 Jul 01; 90(13):6145-9. PMID: 8327494.
    Citations: 110     Fields:    Translation:HumansCells
  122. Lee TC, Shi Y, Schwartz RJ. Displacement of BrdUrd-induced YY1 by serum response factor activates skeletal alpha-actin transcription in embryonic myoblasts. Proc Natl Acad Sci U S A. 1992 Oct 15; 89(20):9814-8. PMID: 1409704.
    Citations: 73     Fields:    Translation:AnimalsCells
  123. Seto E, Shi Y, Shenk T. YY1 is an initiator sequence-binding protein that directs and activates transcription in vitro. Nature. 1991 Nov 21; 354(6350):241-5. PMID: 1720509.
    Citations: 156     Fields:    Translation:HumansAnimalsCells
  124. Shi Y, Seto E, Chang LS, Shenk T. Transcriptional repression by YY1, a human GLI-Krüppel-related protein, and relief of repression by adenovirus E1A protein. Cell. 1991 Oct 18; 67(2):377-88. PMID: 1655281.
    Citations: 334     Fields:    Translation:HumansCells
  125. Montalvo EA, Shi Y, Shenk TE, Levine AJ. Negative regulation of the BZLF1 promoter of Epstein-Barr virus. J Virol. 1991 Jul; 65(7):3647-55. PMID: 1645787.
    Citations: 37     Fields:    Translation:HumansAnimalsCells
  126. Shi Y, Rodriguez M, Shahan K, Derman E. Subfamily of submaxillary gland-specific Mup genes: chromosomal linkage and sequence comparison with liver-specific Mup genes. Nucleic Acids Res. 1989 Aug 11; 17(15):6191-203. PMID: 2771644.
    Citations: 5     Fields:    Translation:AnimalsCells
  127. Chang LS, Shi Y, Shenk T. Adeno-associated virus P5 promoter contains an adenovirus E1A-inducible element and a binding site for the major late transcription factor. J Virol. 1989 Aug; 63(8):3479-88. PMID: 2545917.
    Citations: 64     Fields:    Translation:HumansCells
  128. Shi Y, Son HJ, Shahan K, Rodriguez M, Costantini F, Derman E. Silent genes in the mouse major urinary protein gene family. Proc Natl Acad Sci U S A. 1989 Jun; 86(12):4584-8. PMID: 2734309.
    Citations: 10     Fields:    Translation:AnimalsCells
  129. Shahan K, Denaro M, Gilmartin M, Shi Y, Derman E. Expression of six mouse major urinary protein genes in the mammary, parotid, sublingual, submaxillary, and lachrymal glands and in the liver. Mol Cell Biol. 1987 May; 7(5):1947-54. PMID: 3600653.
    Citations: 26     Fields:    Translation:Animals
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.