Christine Cheng

Title(s)Associate Professor In Residence, Psychiatry
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
ORCID ORCID Icon0000-0001-5345-8427 Additional info
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    Collapse Biography 
    Collapse Education and Training
    University of California, San Diego, La JollaPhD03/2011Bioinformatics and Systems Biology
    Stanford University, Palo AltoMS03/2001Computer Science
    National Taiwan University, TaiwanBS06/1996Plant Biology
    Collapse Awards and Honors
    Boston University2018  - 2020Data Science Faculty Fellow
    National Institute of Health2012  - 2015NIH L. Kirschstein NRSA Individual Postdoctoral Fellowship (F32)
    Department of Defence2005  - 2008DOD Army Breast Cancer Predoctoral Traineeship

    Collapse Overview 
    Collapse Overview
    Dr. Cheng’s laboratory at UCSD includes both wet-lab (experimental) and dry-lab (computational) research. Dr. Cheng’s research program studies transcriptional regulatory network and aims to develop a comprehensive understanding of how aberrant regulatory circuits contribute to human disease. Dr. Cheng’s lab utilizes single cell droplet-based technology enabled by microfluidic device to simultaneously profile the transcriptom and epigenome of thousands of single cells at the same time. The main focus of her lab is to utilize single cell resolution functional genomic assays and computational methods to study heterogeneous clinical tissue samples and blood immune cell populations in patient samples. Current projects focus on applying single-cell transcriptomics and epigenetics in Alzheimer’s disease, opioid use disorder patient samples, with the goal of finding diagnostic markers and therapeutic targets.

    Dr. Cheng received her Master’s degree in Computer Science from Stanford University and she received her doctorate degree in Bioinformatics and Systems Biology from University of California, San Diego. After completing her doctoral research, Dr. Cheng did her postdoctoral training with Dr. Aviv Regev at the Broad Institute of MIT and Harvard.
    Collapse Websites

    Collapse Research 
    Collapse Research Activities and Funding
    Single Cell Transcriptomics of the Cocaine Use Disorder in the Context of HIV
    NIH U01DA05006Jun 15, 2022 - Mar 31, 2027
    Role: Principal Investigator
    Exploring the Pathophysiology of AD and ADRDs with 3D Asteroid Models
    NIH R56AG074591Sep 15, 2021 - Aug 31, 2022
    Role: Principal Investigator
    Single Cell Transcriptomics of the Opioid Use Disorder and HIV Syndemic in the Human Brain
    NIH UM1DA051411Sep 1, 2020 - Aug 31, 2025
    Role: Principal Investigator
    Synergistic Mechanisms of chronic Innate Immune Activation in Microglia by Opiates and HIV Infection
    NIH R01DA051889Jul 15, 2020 - Apr 30, 2025
    Role: Principal Investigator
    Effect of opioid use disorder on HIV latent reservoirs and immune dysfunction assessed by single-cell transcriptomics
    NIH R33DA047032Aug 15, 2018 - May 24, 2023
    Role: Principal Investigator
    Effect of opioid use disorder on HIV latent reservoirs and immune dysfunction assessed by single-cell transcriptomics
    NIH R61DA047032Aug 15, 2018 - May 31, 2021
    Role: Principal Investigator
    Mapping the transcriptional regulatory circuits of human hematopoiesis
    NIH F32CA168253Apr 1, 2012 - Mar 31, 2015
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Featured Publications

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    Altmetrics Details 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. Nuclear morphology is shaped by loop-extrusion programs. Nature. 2024 Mar; 627(8002):196-203. Patta I, Zand M, Lee L, Mishra S, Bortnick A, Lu H, Prusty A, McArdle S, Mikulski Z, Wang HY, Cheng CS, Fisch KM, Hu M, Murre C. PMID: 38355805.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    2. Single cell transcriptomic profiling of a neuron-astrocyte assembloid tauopathy model. Nat Commun. 2022 10 21; 13(1):6275. Rickner HD, Jiang L, Hong R, O'Neill NK, Mojica CA, Snyder BJ, Zhang L, Shaw D, Medalla M, Wolozin B, Cheng CS. PMID: 36271092; PMCID: PMC9587045.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    3. FOXR1 regulates stress response pathways and is necessary for proper brain development. PLoS Genet. 2021 11; 17(11):e1009854. Mota A, Waxman HK, Hong R, Lagani GD, Niu SY, Bertherat FL, Wolfe L, Malicdan CM, Markello TC, Adams DR, Gahl WA, Cheng CS, Beffert U, Ho A. PMID: 34723967; PMCID: PMC8559929.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    4. Single cell transcriptomics reveals opioid usage evokes widespread suppression of antiviral gene program. Nat Commun. 2020 05 26; 11(1):2611. Karagiannis TT, Cleary JP, Gok B, Henderson AJ, Martin NG, Yajima M, Nelson EC, Cheng CS. PMID: 32457298; PMCID: PMC7250875.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    5. ATAC-seq Assay with Low Mitochondrial DNA Contamination from Primary Human CD4+ T Lymphocytes. J Vis Exp. 2019 03 22; (145). Rickner HD, Niu SY, Cheng CS. PMID: 30958473; PMCID: PMC7203994.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    6. Genetic determinants of co-accessible chromatin regions in activated T cells across humans. Nat Genet. 2018 08; 50(8):1140-1150. Gate RE, Cheng CS, Aiden AP, Siba A, Tabaka M, Lituiev D, Machol I, Gordon MG, Subramaniam M, Shamim M, Hougen KL, Wortman I, Huang SC, Durand NC, Feng T, De Jager PL, Chang HY, Aiden EL, Benoist C, Beer MA, Ye CJ, Regev A. PMID: 29988122; PMCID: PMC6097927.
      View in: PubMed   Mentions: 72     Fields:    Translation:HumansCells
    7. Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus. Cell. 2018 07 26; 174(3):744-757.e24. Quinodoz SA, Ollikainen N, Tabak B, Palla A, Schmidt JM, Detmar E, Lai MM, Shishkin AA, Bhat P, Takei Y, Trinh V, Aznauryan E, Russell P, Cheng C, Jovanovic M, Chow A, Cai L, McDonel P, Garber M, Guttman M. PMID: 29887377; PMCID: PMC6548320.
      View in: PubMed   Mentions: 345     Fields:    Translation:HumansAnimalsCells
    8. Genome-scale identification of transcription factors that mediate an inflammatory network during breast cellular transformation. Nat Commun. 2018 05 25; 9(1):2068. Ji Z, He L, Rotem A, Janzer A, Cheng CS, Regev A, Struhl K. PMID: 29802342; PMCID: PMC5970197.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    9. PHF6 regulates phenotypic plasticity through chromatin organization within lineage-specific genes. Genes Dev. 2017 05 15; 31(10):973-989. Soto-Feliciano YM, Bartlebaugh JME, Liu Y, Sánchez-Rivera FJ, Bhutkar A, Weintraub AS, Buenrostro JD, Cheng CS, Regev A, Jacks TE, Young RA, Hemann MT. PMID: 28607179; PMCID: PMC5495126.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    10. Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression. Cell Rep. 2017 04 25; 19(4):875-889. Fiziev P, Akdemir KC, Miller JP, Keung EZ, Samant NS, Sharma S, Natale CA, Terranova CJ, Maitituoheti M, Amin SB, Martinez-Ledesma E, Dhamdhere M, Axelrad JB, Shah A, Cheng CS, Mahadeshwar H, Seth S, Barton MC, Protopopov A, Tsai KY, Davies MA, Garcia BA, Amit I, Chin L, Ernst J, Rai K. PMID: 28445736; PMCID: PMC5473172.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansCells
    11. Iterative Modeling Reveals Evidence of Sequential Transcriptional Control Mechanisms. Cell Syst. 2017 03 22; 4(3):330-343.e5. Cheng CS, Behar MS, Suryawanshi GW, Feldman KE, Spreafico R, Hoffmann A. PMID: 28237795; PMCID: PMC5434763.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansAnimalsCells
    12. Semiconductor-based DNA sequencing of histone modification states. Nat Commun. 2013; 4:2672. Cheng CS, Rai K, Garber M, Hollinger A, Robbins D, Anderson S, Macbeth A, Tzou A, Carneiro MO, Raychowdhury R, Russ C, Hacohen N, Gershenwald JE, Lennon N, Nusbaum C, Chin L, Regev A, Amit I. PMID: 24157732; PMCID: PMC3917140.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    13. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol Cell. 2012 Sep 14; 47(5):810-22. Garber M, Yosef N, Goren A, Raychowdhury R, Thielke A, Guttman M, Robinson J, Minie B, Chevrier N, Itzhaki Z, Blecher-Gonen R, Bornstein C, Amann-Zalcenstein D, Weiner A, Friedrich D, Meldrim J, Ram O, Cheng C, Gnirke A, Fisher S, Friedman N, Wong B, Bernstein BE, Nusbaum C, Hacohen N, Regev A, Amit I. PMID: 22940246; PMCID: PMC3873101.
      View in: PubMed   Mentions: 207     Fields:    Translation:AnimalsCells
    14. Mechanisms establishing TLR4-responsive activation states of inflammatory response genes. PLoS Genet. 2011 Dec; 7(12):e1002401. Escoubet-Lozach L, Benner C, Kaikkonen MU, Lozach J, Heinz S, Spann NJ, Crotti A, Stender J, Ghisletti S, Reichart D, Cheng CS, Luna R, Ludka C, Sasik R, Garcia-Bassets I, Hoffmann A, Subramaniam S, Hardiman G, Rosenfeld MG, Glass CK. PMID: 22174696; PMCID: PMC3234212.
      View in: PubMed   Mentions: 80     Fields:    Translation:HumansAnimalsCells
    15. The specificity of innate immune responses is enforced by repression of interferon response elements by NF-κB p50. Sci Signal. 2011 Feb 22; 4(161):ra11. Cheng CS, Feldman KE, Lee J, Verma S, Huang DB, Huynh K, Chang M, Ponomarenko JV, Sun SC, Benedict CA, Ghosh G, Hoffmann A. PMID: 21343618; PMCID: PMC3096068.
      View in: PubMed   Mentions: 55     Fields:    Translation:HumansAnimalsCells
    16. A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell. 2009 Jul 10; 138(1):114-28. Ramirez-Carrozzi VR, Braas D, Bhatt DM, Cheng CS, Hong C, Doty KR, Black JC, Hoffmann A, Carey M, Smale ST. PMID: 19596239; PMCID: PMC2712736.
      View in: PubMed   Mentions: 315     Fields:    Translation:HumansAnimalsCells
    17. Epigenetic control: slow and global, nimble and local. Genes Dev. 2008 May 01; 22(9):1110-4. Cheng CS, Johnson TL, Hoffmann A. PMID: 18451102; PMCID: PMC2732403.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    18. Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters. Proc Natl Acad Sci U S A. 2007 Mar 20; 104(12):4852-7. Kwon YS, Garcia-Bassets I, Hutt KR, Cheng CS, Jin M, Liu D, Benner C, Wang D, Ye Z, Bibikova M, Fan JB, Duan L, Glass CK, Rosenfeld MG, Fu XD. PMID: 17360330; PMCID: PMC1821125.
      View in: PubMed   Mentions: 65     Fields:    Translation:HumansCells
    19. Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptors. Cell. 2007 Feb 09; 128(3):505-518. Garcia-Bassets I, Kwon YS, Telese F, Prefontaine GG, Hutt KR, Cheng CS, Ju BG, Ohgi KA, Wang J, Escoubet-Lozach L, Rose DW, Glass CK, Fu XD, Rosenfeld MG. PMID: 17289570; PMCID: PMC1994663.
      View in: PubMed   Mentions: 239     Fields:    Translation:HumansCells
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