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
Preprints
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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 - 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
- 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
Science Advances 2024 - An endogenous retrovirus regulates tumor-specific expression of the immune transcriptional regulator SP140
Dziulko AK, Allen H, Chuong EB
Human Molecular Genetics 2024 - Combining EHMT and PARP Inhibition: A Strategy to Diminish Therapy-Resistant Ovarian Cancer Tumor Growth while Stimulating Immune Activation
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*
Molecular Cancer Therapeutics 2024 - An intronic LINE-1 regulates IFNAR1 expression in human immune cells
Buttler CA, Ramirez D, Dowell RD, Chuong EB
Mobile DNA 2023 - Nascent transcription upon interferon-α2 stimulation on human and rhesus macaque lymphoblastoid cell lines
Ramirez D, Chuong EB, Dowell RD
BMC Research Notes 2023 - Mouse B2 SINE elements function as IFN-inducible enhancers
Horton I*, Kelly CJ*, Dziulko A, Simpson DM, Chuong EB
eLIFE 2023 - 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 - Ruminant-specific retrotransposons shape regulatory evolution of bovine immunity
Kelly CJ, Chitko-McKown C, Chuong EB
Genome Research 2022 - 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 - 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) - Molecular conservation of marsupial and eutherian placentation and lactation
Guernsey MW, Chuong EB, Cornelis G, Renfree MB*, Baker JC*
eLIFE (2017) - Disruption of promoter memory by a long noncoding RNA
Yu Y, Yarrington RM, Chuong EB, Elde NC, Stillman DJ
PNAS (2016) - Regulatory evolution of innate immunity through co-option of endogenous retroviruses
Chuong EB, Elde NC*, Feschotte C*
Science (2016) - 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) - Chromatin immunoprecipitation and deep sequencing in Xenopus tropicalis and Xenopus laevis
Wills AE, Gupta R, Chuong EB, Baker JC
Methods (2014) - Endogenous retroviruses function as species-specific enhancer elements in the placenta
Chuong EB, Rumi MA, Soares MJ, Baker JC
Nature Genetics (2013) - HEB and E2A function as SMAD/FOXH1 cofactors
Yoon SJ, Wills AE, Chuong EB, Gupta R, Baker JC
Genes and Development (2011) - 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) - Maternal-fetal conflict: Rapidly evolving proteins in the rodent placenta
Chuong EB, Tong W, Hoekstra HE
Molecular Biology and Evolution (2010) - Comparative analysis of testis protein evolution in rodents
Turner LM, Chuong EB, Hoekstra HE
Genetics (2008)*equal contribution
Reviews and Commentaries
- Emerging roles for endogenous retroviruses in immune epigenetic regulation
Buttler CA, Chuong EB
Immunological Reviews (2021) - Transposable elements teach T cells new tricks
Ivancevic A, Chuong EB
PNAS (2020) - The placenta goes viral: retroviruses control gene expression in pregnancy
Chuong EB
PLOS Biology (2018) - Regulatory activities of transposable elements: from conflicts to benefits
Chuong EB, Elde NC, Feschotte C.
Nature Reviews Genetics (2016) - Perspective: Transposons up the dosage
Chuong EB, Feschotte C.
Science (2013) - Evolutionary perspectives into placental biology and disease
Chuong EB, Hannibal RL, Green SL, Baker JC
Applied & Translational Genomics (2013) - Retroviruses facilitate the rapid evolution of the mammalian placenta
Chuong EB
Bioessays (2013) highlighted article