Dennis J. Yuan, PhD

Dennis J. Yuan, PhD

Postdoctoral Fellow
Weill Cornell Medicine & New York Genome Center
dyuan (at) nygenome.org

About

I am a postdoctoral fellow in the Landau Lab at Weill Cornell Medicine and the New York Genome Center, where I develop single-cell technologies that link mutations and cell states.

I trained as a biomedical engineer. My doctoral work at Columbia used engineered materials to probe how mechanical cues shape T cell activation, which is where my interest in single-cell heterogeneity started.

Research

1Single-cell genotype-to-phenotype mapping in normal tissues

Somatic mutations accumulate in every tissue as we age, but a mutation is only interesting if you can see what it does to the cell carrying it. Sequencing DNA and RNA from the same single cell has been the bottleneck. We built scG2P, which co-captures somatic DNA mutations and mRNA transcripts from the same cell at scale. Applied to esophageal tissue from older adults, more than half of over 10,000 cells carried clonal driver mutations, predominantly in NOTCH1 and TP53. NOTCH1-mutant clones disproportionately occupy immature differentiation states, staying in the tissue and continuing to divide instead of maturing and shedding from the surface.

  • Genotype-to-phenotype mapping of somatic clonal mosaicism via single-cell co-capture of DNA mutations and mRNA transcripts Cancer Discov 2026 PaperPreprintPress

2Retracing evolutionary histories in aging and pre-cancerous tissues

Normal tissue is a competition between clones playing out over decades. Using large-scale single-cell phylogenetics, we reconstruct when clones arose, how fast they expanded, and which ones displaced their neighbors, turning a static snapshot of mutations into a history of the tissue.

  • A comprehensive view of somatic mosaicism by single-cell DNA analysis bioRxiv 2025 Preprint
  • Large-scale single-cell phylogenetic mapping of clonal evolution in the human aging esophagus bioRxiv 2025 Preprint

3Earlier work — T cell mechanobiology

My doctoral work at Columbia asked how the physical properties of an antigen-presenting surface shape a T cell’s response. T cell activation turns out to be biphasic in substrate stiffness, and soft elastomer fiber scaffolds can expand T cells from patients whose cells expand poorly by conventional methods — a route to personalizing cell therapy manufacturing.

  • Biphasic response of T cell activation to substrate stiffness Biomaterials 2021 Paper
  • Enhanced activation and expansion of T cells using mechanically soft elastomer fibers Adv Biosyst 2018 Paper
  • Improving T cell expansion with a soft touch Nano Lett 2017 Paper

News

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Publications

Full list, newest first. Also on Google Scholar.

  1. Genotype-to-phenotype mapping of somatic clonal mosaicism via single-cell co-capture of DNA mutations and mRNA transcripts
    Yuan DJ, Zinno J, Botella T, Dhingra D, Wang S, Hawkins AG, Swett A, Sotelo J, Raviram R, Hughes C, Potenski C, Godfrey KD, Ainsworth KM, Xu S, Que J, Abrams JA, Yokoyama A, Kakiuchi N, Ogawa S, Landau DA
    Cancer Discovery, 2026
    PaperPreprintPress
  2. A comprehensive view of somatic mosaicism by single-cell DNA analysis
    Luquette LJ, Coorens THH, Natu A, Suvakov M, Caplin A, Jun MS, Mo A, Pelt J, Anderson L, Berselli M, Bhamidipati S, Blanchard T, Brew J, Chun HE, Chun H, Dehankar MK, Feng WC, Furatero R, Grochowski CM, Ho E, Jang Y, Kottapalli K, Leonard MK, Lim NS, Lindsay T, Nicholson S, Raimondi I, Runnels A, Scharlee C, Shin J, Veit AD, VonDran M, Wang Y, Yuan DJ, Zhao Y, SMaHT Single Cell Focus Group, Bell TJ, Ardlie K, Doddapaneni H, Fulton R, Germer S, Landau D, Oh JW, Park PJ, Vaccarino FM, Walsh C, Abyzov A
    bioRxiv (preprint), 2025
    Preprint
  3. Large-scale single-cell phylogenetic mapping of clonal evolution in the human aging esophagus
    Prieto T, Yuan DJ, Zinno J, Hughes C, Midler N, Kao S, Huuhtanen J, Raviram R, Fotopoulou F, Ruthen N, Rajagopalan S, Schiffman JS, D'Avino AR, Yoon SH, Sotelo J, Omans ND, Wheeler N, Garces A, Pradhan B, Cheng AP, Robine N, Potenski C, Godfrey K, Kakiuchi N, Yokoyama A, Ogawa S, Abrams J, Raimondi I, Landau DA
    bioRxiv (preprint), 2025
    Preprint
  4. Paired plus-minus sequencing is an ultra-high throughput and accurate method for dual strand sequencing of DNA molecules
    Cheng AP, Rusinek I, Sossin A, Widman AJ, Meiri E, Krieger G, Hirschberg O, Tov DS, Gilad S, Jaimovich A, Barad O, Avaylon S, Rajagopalan S, Potenski C, Prieto T, Yuan DJ, et al., Faltas BM, Landau DA
    bioRxiv (preprint), 2025
    Preprint
  5. Biphasic response of T cell activation to substrate stiffness
    Yuan DJ, Shi L, Kam LC
    Biomaterials, 273:120797, 2021
    Paper
  6. Enhanced activation and expansion of T cells using mechanically soft elastomer fibers
    Dang A, De Leo S, Bogdanowicz DR, Yuan DJ, Fernandes SM, Brown JR, Lu HH, Kam LC
    Advanced Biosystems, 2(2):1700167, 2018
    Paper
  7. Improving T cell expansion with a soft touch
    Lambert L, Goebrecht GKE, De Leo SE, O'Connor RS, Nunez-Cruz S, Li T, Yuan J, Milone MC, Kam LC
    Nano Letters, 17(2):821-826, 2017
    Paper
  8. Astrocyte elevated gene-1 (AEG-1) induces epithelial-mesenchymal transition in lung cancer through activating Wnt/beta-catenin signaling
    He W, He S, Wang Z, Shen H, Fang W, Zhang Y, Qian W, Lin M, Yuan J, Wang J, Huang W, Wang L, Ke Z
    BMC Cancer, 15(1):107, 2015
    Paper

Background

Appointments

  • 2021–presentPostdoctoral Fellow
    Weill Cornell Medicine & New York Genome Center
    Landau Lab (Dan Landau, MD PhD)
  • 2017–2020TL1 Precision Medicine Fellow
    Irving Institute for Clinical and Translational Research, CUIMC

Education

  • 2015–2021PhD, Biomedical Engineering
    Columbia University
    Thesis: Mechanical regulation of T cell activation (Lance Kam, PhD)
  • 2015–2017MSc, Biomedical Engineering
    Columbia University
  • 2011–2015BSc, Bioengineering, magna cum laude
    University of California, Los Angeles

Awards

  • 2026–2028MacMillan Postdoctoral Fellow
    MacMillan Center for the Study of the Non-coding Cancer Genome, New York Genome Center
  • 2025Outstanding Contribution by a Postdoctoral Fellow
    New York Genome Center
  • 2017–2020NIH/NCATS TL1 Precision Medicine Fellowship

Contact

dyuan@nygenome.org
New York Genome Center, 101 Avenue of the Americas, New York, NY 10013

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