Publications from the Chuong lab. Lab member names in bold. Asterisk (*) marks equal contributions. For a complete and updated list of publications, please see the Google Scholar link


  1. Regulation of human interferon signaling by transposon exonization
    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
    bioRxiv 2023

  2. Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer
    Ivancevic A, Simpson DM, Joyner OM, Bagby SM, Nguyen LL, Bitler BG, Pitts TM, Chuong EB​
    bioRxiv 2023
  3. Combinatory EHMT and PARP inhibition induces an interferon response and a CD8 T cell-dependent tumor regression in PARP inhibitor-resistant models
    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 B*
    bioRxiv 2023

Published research articles

  1. An intronic LINE-1 regulates IFNAR1 expression in human immune cells
    Buttler CA, Ramirez D, Dowell RD, Chuong EB
    Mobile DNA 2023
  2. Nascent transcription upon interferon-α2 stimulation on human and rhesus macaque lymphoblastoid cell lines
    Ramirez D, Chuong EB, Dowell RD
    BMC Research Notes 2023
  3. Mouse B2 SINE elements function as IFN-inducible enhancers
    Horton I*, Kelly CJ*, Dziulko A, Simpson DM, Chuong EB
    eLIFE 2023
  4. ATF6-Mediated Signaling Contributes to PARP Inhibitor Resistance in Ovarian Cancer
    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
    Molecular Cancer Research 2023 
  5. Ruminant-specific retrotransposons shape regulatory evolution of bovine immunity
    Kelly CJ, Chitko-McKown C, Chuong EB
    Genome Research 2022
  6. Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells
    Pasquesi GIM, Kelly CJ, Ordonez AD, Chuong EB
    Mobile DNA 2022
  7. Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate
    Raviram R, Rocha PP, Luo VM, Swanzey E, Miraldi ER, Chuong EB, Feschotte C, Bonneau R, Skok JA
    Genome Biology (2018)
  8. Molecular conservation of marsupial and eutherian placentation and lactation 
    Guernsey MW, Chuong EB, Cornelis G, Renfree MB*, Baker JC*
    eLIFE (2017)
  9. Disruption of promoter memory by a long noncoding RNA
    Yu Y, Yarrington RM, Chuong EB, Elde NC, Stillman DJ
    PNAS (2016)
  10. Regulatory evolution of innate immunity through co-option of endogenous retroviruses
    Chuong EB, Elde NC*, Feschotte C*
    Science (2016)
  11. Copy number variation is a fundamental aspect of the placental genome
    Hannibal RL, Chuong EB, Mulia JR, Gilbert DM, Valouev A, Baker JC
    PLOS Genetics (2014)
  12. Chromatin immunoprecipitation and deep sequencing in Xenopus tropicalis and Xenopus laevis
    Wills AE, Gupta R, Chuong EB, Baker JC
    Methods (2014)
  13. Endogenous retroviruses function as species-specific enhancer elements in the placenta
    Chuong EB, Rumi MA, Soares MJ, Baker JC
    Nature Genetics (2013)
  14. HEB and E2A function as SMAD/FOXH1 cofactors
    Yoon SJ, Wills AE, Chuong EB, Gupta R, Baker JC
    Genes and Development (2011)
  15. Chromatin and transcriptional signatures for Nodal signaling during endoderm formation in hESCs
    Kim SW*, Yoon SJ*, Chuong EB*, Oyolu CB, Wills AE, Gupta R, Baker JC
    Developmental Biology (2011) 
  16. Maternal-fetal conflict: Rapidly evolving proteins in the rodent placenta
    Chuong EB, Tong W, Hoekstra HE
    Molecular Biology and Evolution (2010)
  17. Comparative analysis of testis protein evolution in rodents
    Turner LM, Chuong EB, Hoekstra HE
    Genetics (2008)*equal contribution

Reviews and Commentaries

  1. Emerging roles for endogenous retroviruses in immune epigenetic regulation
    Buttler CA, Chuong EB
    Immunological Reviews (2021)
  2. Transposable elements teach T cells new tricks
    Ivancevic A, Chuong EB
    PNAS (2020)
  3. The placenta goes viral: retroviruses control gene expression in pregnancy
    Chuong EB
    PLOS Biology (2018)
  4. Regulatory activities of transposable elements: from conflicts to benefits
    Chuong EB, Elde NC, Feschotte C.
    Nature Reviews Genetics (2016)
  5. Perspective: Transposons up the dosage
    Chuong EBFeschotte C.
    Science (2013)
  6. Evolutionary perspectives into placental biology and disease
    Chuong EB, Hannibal RL, Green SL, Baker JC
    Applied & Translational Genomics (2013)
  7.  Retroviruses facilitate the rapid evolution of the mammalian placenta
    Chuong EB
    Bioessays (2013) highlighted article