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Edward Boyi Chuong

TitleAssistant Professor
InstitutionUniversity of Colorado Boulder
DepartmentBiology-MCD Instruction

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    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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    1. Ivancevic A, Sankovitz M, Allen H, Joyner O, Chuong EB, Ramsey SD. De novo genome assemblies of the dwarf honey bee subgenus Micrapis : Apis andreniformis and Apis florea. bioRxiv. 2025 Apr 06. PMID: 40236222.
      View in: PubMed
    2. Hunt DR, Allen H, Martin TG, Feghali SN, Chuong EB, Leinwand LA. Genome Report: First whole genome assembly of Python regius (ball python), a model of extreme physiological and metabolic plasticity. bioRxiv. 2025 Feb 06. PMID: 39975114.
      View in: PubMed
    3. Witt KC, Dziulko A, An J, Pekovic F, Cheng AX, Liu GY, Lee OV, Turner DJ, Lari A, Gaidt MM, Chavez R, Fattinger SA, Abraham P, Dhaliwal H, Lee AY, Kotov DI, Coscoy L, Glaunsinger BA, Valkov E, Chuong EB, Vance RE. The SP140-RESIST pathway regulates interferon mRNA stability and antiviral immunity. bioRxiv. 2025 Jan 29. PMID: 39974928.
      View in: PubMed
    4. Pasquesi GIM, Allen H, Ivancevic A, Barbachano-Guerrero A, Joyner O, Guo K, Simpson DM, Gapin K, Horton I, Nguyen LL, Yang Q, Warren CJ, Florea LD, Bitler BG, Santiago ML, Sawyer SL, Chuong EB. Regulation of human interferon signaling by transposon exonization. Cell. 2024 Dec 26; 187(26):7621-7636.e19. PMID: 39672162.
      View in: PubMed
    5. Nguyen LL, Watson ZL, Ortega R, Woodruff ER, Jordan KR, Iwanaga R, Yamamoto TM, Bailey CA, To F, Lin S, Villagomez FR, Jeong AD, Guntupalli SR, Behbakht K, Gibaja V, Arnoult N, Chuong EB, Bitler BG. EHMT1/2 Inhibition Promotes Regression of Therapy-Resistant Ovarian Cancer Tumors in a CD8 T-cell-Dependent Manner. Mol Cancer Res. 2024 12 03; 22(12):1117-1127. PMID: 39136655.
      View in: PubMed
    6. Hsieh J, Danis EP, Owens CR, Parrish JK, Nowling NL, Wolin AR, Purdy SC, Rosenbaum SR, Ivancevic AM, Chuong EB, Ford HL, Jedlicka P. Dependence of PAX3-FOXO1 chromatin occupancy on ETS1 at important disease-promoting genes exposes new targetable vulnerability in Fusion-Positive Rhabdomyosarcoma. Oncogene. 2025 Jan; 44(1):19-29. PMID: 39448867.
      View in: PubMed
    7. Dziulko AK, Allen H, Chuong EB. An endogenous retrovirus regulates tumor-specific expression of the immune transcriptional regulator SP140. Hum Mol Genet. 2024 08 06; 33(16):1454-1464. PMID: 38751339.
      View in: PubMed
    8. Kalbfleisch TS, McKay SD, Murdoch BM, Adelson DL, Almansa-Villa D, Becker G, Beckett LM, Ben?tez-Galeano MJ, Biase F, Casey T, Chuong E, Clark E, Clarke S, Cockett N, Couldrey C, Davis BW, Elsik CG, Faraut T, Gao Y, Genet C, Grady P, Green J, Green R, Guan D, Hagen D, Hartley GA, Heaton M, Hoyt SJ, Huang W, Jarvis E, Kalleberg J, Khatib H, Koepfi KP, Koltes J, Koren S, Kuehn C, Leeb T, Leonard A, Liu GE, Low WY, McConnell H, McRae K, Miga K, Mousel M, Neibergs H, Olagunju T, Pennell M, Petry B, Pewsner M, Phillippy AM, Pickett BD, Pineda P, Potapova T, Rachagani S, Rhie A, Rijnkels M, Robic A, Rodriguez Osorio N, Safonova Y, Schettini G, Schnabel RD, Sirpu Natesh N, Stegemiller M, Storer J, Stothard P, Stull C, Tosser-Klopp G, Traglia GM, Tuggle CK, Van Tassell CP, Watson C, Weikard R, Wimmers K, Xie S, Yang L, Smith TPL, O'Neill RJ, Rosen BD. The Ruminant Telomere-to-Telomere (RT2T) Consortium. Nat Genet. 2024 Aug; 56(8):1566-1573. PMID: 39103649.
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    9. Ivancevic A, Simpson DM, Joyner OM, Bagby SM, Nguyen LL, Bitler BG, Pitts TM, Chuong EB. Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer. Sci Adv. 2024 Jul 19; 10(29):eado1218. PMID: 39018396.
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    10. Nguyen LL, Watson ZL, Ortega R, Woodruff ER, Jordan KR, Iwanaga R, Yamamoto TM, Bailey CA, To F, Jeong AD, Guntupalli SR, Behbakht K, Gibaja V, Arnoult N, Cocozaki A, Chuong EB, Bitler BG. Combining EHMT and PARP Inhibition: A Strategy to Diminish Therapy-Resistant Ovarian Cancer Tumor Growth while Stimulating Immune Activation. Mol Cancer Ther. 2024 Jun 12; OF1-OF16. PMID: 38863225.
      View in: PubMed
    11. Nguyen LL, Watson ZL, Ortega R, Woodruff ER, Jordan KR, Iwanaga R, Yamamoto TM, Bailey CA, To F, Jeong AD, Guntupalli SR, Behbakht K, Gibaja V, Arnoult N, Cocozaki A, Chuong EB, Bitler BG. Combining EHMT and PARP Inhibition: A Strategy to Diminish Therapy-Resistant Ovarian Cancer Tumor Growth while Stimulating Immune Activation. Mol Cancer Ther. 2024 May 08. PMID: 38714351.
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    12. Buttler CA, Ramirez D, Dowell RD, Chuong EB. An intronic LINE-1 regulates IFNAR1 expression in human immune cells. Mob DNA. 2023 Nov 30; 14(1):20. PMID: 38037122.
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    13. Arkhipova IR, Burns KH, Chiappinelli KB, Chuong EB, Goubert C, Guarn? A, Larracuente AM, Lee EA, Levin HL. Meeting report: transposable elements at the crossroads of evolution, health and disease 2023. Mob DNA. 2023 Nov 27; 14(1):19. PMID: 38012685.
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    14. Pasquesi GIM, Allen H, Ivancevic A, Barbachano-Guerrero A, Joyner O, Guo K, Simpson DM, Gapin K, Horton I, Nguyen L, Yang Q, Warren CJ, Florea LD, Bitler BG, Santiago ML, Sawyer SL, Chuong EB. Regulation of human interferon signaling by transposon exonization. bioRxiv. 2023 Sep 15. PMID: 37745311.
      View in: PubMed
    15. Horton I, Kelly CJ, Dziulko A, Simpson DM, Chuong EB. Mouse B2 SINE elements function as IFN-inducible enhancers. Elife. 2023 05 09; 12. PMID: 37158599.
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    16. Nguyen LL, Watson ZL, Ortega R, Woodruff ER, Jordan KR, Iwanaga R, Yamamoto TM, Bailey CA, Jeong AD, Guntupalli SR, Behbakht K, Gbaja V, Arnoult N, Chuong EB, Bitler BG. Combinatory EHMT and PARP inhibition induces an interferon response and a CD8 T cell-dependent tumor regression in PARP inhibitor-resistant models. bioRxiv. 2023 Feb 23. PMID: 36865165.
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    17. McMellen A, Yamamoto TM, Qamar L, Sanders BE, Nguyen LL, Ortiz Chavez D, Bapat J, Berning A, Post MD, Johnson J, Behbakht K, Nurmemmedov E, Chuong EB, Bitler BG. ATF6-Mediated Signaling Contributes to PARP Inhibitor Resistance in Ovarian Cancer. Mol Cancer Res. 2023 01 03; 21(1):3-13. PMID: 36149636.
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    18. Simpson DM, Chuong EB. Genetic Knockout of TE Insertions by CRISPR-Cas9. Methods Mol Biol. 2023; 2607:369-379. PMID: 36449171.
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    19. Pasquesi GIM, Kelly CJ, Ordonez AD, Chuong EB. Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells. Mob DNA. 2022 Sep 06; 13(1):22. PMID: 36068622.
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    20. Kelly CJ, Chitko-McKown CG, Chuong EB. Ruminant-specific retrotransposons shape regulatory evolution of bovine immunity. Genome Res. 2022 Aug 25; 32(8):1474-1486. PMID: 35948370.
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    21. Perry BW, Gopalan SS, Pasquesi GIM, Schield DR, Westfall AK, Smith CF, Koludarov I, Chippindale PT, Pellegrino MW, Chuong EB, Mackessy SP, Castoe TA. Snake venom gene expression is coordinated by novel regulatory architecture and the integration of multiple co-opted vertebrate pathways. Genome Res. 2022 06; 32(6):1058-1073. PMID: 35649579.
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    22. Buttler CA, Chuong EB. Emerging roles for endogenous retroviruses in immune epigenetic regulation. Immunol Rev. 2022 01; 305(1):165-178. PMID: 34816452.
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    23. Cable J, Heard E, Hirose T, Prasanth KV, Chen LL, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, Chen CK, Wilusz JE, Lempradl A, McGeary SE, Wahba L, Pyle AM, Hargrove AE, Simon MD, Marcia M, Przanowska RK, Chang HY, Jaffrey SR, Contreras LM, Chen Q, Shi J, Mendell JT, He L, Song E, Rinn JL, Lalwani MK, Kalem MC, Chuong EB, Maquat LE, Liu X. Noncoding RNAs: biology and applications-a Keystone Symposia report. Ann N Y Acad Sci. 2021 12; 1506(1):118-141. PMID: 34791665.
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    24. Ivancevic A, Chuong EB. Transposable elements teach T cells new tricks. Proc Natl Acad Sci U S A. 2020 04 28; 117(17):9145-9147. PMID: 32312814.
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    25. Branco MR, Chuong EB. Crossroads between transposons and gene regulation. Philos Trans R Soc Lond B Biol Sci. 2020 03 30; 375(1795):20190330. PMID: 32075561.
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    26. Raviram R, Rocha PP, Luo VM, Swanzey E, Miraldi ER, Chuong EB, Feschotte C, Bonneau R, Skok JA. Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate. Genome Biol. 2018 12 13; 19(1):216. PMID: 30541598.
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    27. Chuong EB. The placenta goes viral: Retroviruses control gene expression in pregnancy. PLoS Biol. 2018 10; 16(10):e3000028. PMID: 30300353.
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    28. Guernsey MW, Chuong EB, Cornelis G, Renfree MB, Baker JC. Molecular conservation of marsupial and eutherian placentation and lactation. Elife. 2017 09 12; 6. PMID: 28895534.
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    29. Chuong EB, Elde NC, Feschotte C. Regulatory activities of transposable elements: from conflicts to benefits. Nat Rev Genet. 2017 02; 18(2):71-86. PMID: 27867194.
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    30. Yu Y, Yarrington RM, Chuong EB, Elde NC, Stillman DJ. Disruption of promoter memory by synthesis of a long noncoding RNA. Proc Natl Acad Sci U S A. 2016 08 23; 113(34):9575-80. PMID: 27506791.
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    31. Chuong EB, Elde NC, Feschotte C. Regulatory evolution of innate immunity through co-option of endogenous retroviruses. Science. 2016 Mar 04; 351(6277):1083-7. PMID: 26941318.
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    32. Hannibal RL, Chuong EB, Rivera-Mulia JC, Gilbert DM, Valouev A, Baker JC. Copy number variation is a fundamental aspect of the placental genome. PLoS Genet. 2014 May; 10(5):e1004290. PMID: 24785991.
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    33. Chuong EB, Feschotte C. Evolution. Transposons up the dosage. Science. 2013 Nov 15; 342(6160):812-3. PMID: 24233714.
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    34. Wills AE, Gupta R, Chuong E, Baker JC. Chromatin immunoprecipitation and deep sequencing in Xenopus tropicalis and Xenopus laevis. Methods. 2014 Apr 01; 66(3):410-21. PMID: 24064036.
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    35. Chuong EB, Hannibal RL, Green SL, Baker JC. Evolutionary perspectives into placental biology and disease. Appl Transl Genom. 2013 Dec 01; 2:64-69. PMID: 27896057.
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    36. Chuong EB. Retroviruses facilitate the rapid evolution of the mammalian placenta. Bioessays. 2013 Oct; 35(10):853-61. PMID: 23873343.
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    37. Chuong EB, Rumi MA, Soares MJ, Baker JC. Endogenous retroviruses function as species-specific enhancer elements in the placenta. Nat Genet. 2013 Mar; 45(3):325-9. PMID: 23396136.
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    38. Ackerman WE, Bulmer JN, Carter AM, Chaillet JR, Chamley L, Chen CP, Chuong EB, Coleman SJ, Collet GP, Croy BA, de Mestre AM, Dickinson H, Ducray J, Enders AC, Fogarty NM, Gauster M, Golos T, Haider S, Heazell AE, Holland OJ, Huppertz B, Husebekk A, John RM, Johnsen GM, Jones CJ, Kalionis B, K?nig J, Lorenzon AR, Moffett A, Moreira de Mello JC, Nuzzo AM, Parham P, Parolini O, Petroff MG, Pidoux G, Ram?rez-Pinilla MP, Robinson WP, Rolfo A, Sadovsky Y, Soma H, Southcombe JH, Tilburgs T, Lash GE. IFPA Meeting 2011 workshop report III: Placental immunology; epigenetic and microRNA-dependent gene regulation; comparative placentation; trophoblast differentiation; stem cells. Placenta. 2012 Feb; 33 Suppl:S15-22. PMID: 22154501.
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    39. Yoon SJ, Wills AE, Chuong E, Gupta R, Baker JC. HEB and E2A function as SMAD/FOXH1 cofactors. Genes Dev. 2011 Aug 01; 25(15):1654-61. PMID: 21828274.
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    40. Kim SW, Yoon SJ, Chuong E, Oyolu C, Wills AE, Gupta R, Baker J. Chromatin and transcriptional signatures for Nodal signaling during endoderm formation in hESCs. Dev Biol. 2011 Sep 15; 357(2):492-504. PMID: 21741376.
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    41. Chuong EB, Tong W, Hoekstra HE. Maternal-fetal conflict: rapidly evolving proteins in the rodent placenta. Mol Biol Evol. 2010 Jun; 27(6):1221-5. PMID: 20123797.
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    42. Turner LM, Chuong EB, Hoekstra HE. Comparative analysis of testis protein evolution in rodents. Genetics. 2008 Aug; 179(4):2075-89. PMID: 18689890.
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