Portrait of Yi Chen

Edward P. Evans MDS Fellow · Columbia University

M.D.M.Sc.Ph.D.

Physician-scientist decoding how the three-dimensional genome decides the fate of blood stem cells, and what goes wrong in leukemia.

Now obsessed with chromatin loops

0Papers, preprints & abstracts
0Citations on Google Scholar
0h-index
0As first, equal-first or corresponding author
0Journals reviewed for, incl. Nature Communications
0Countries, one research path

Citation metrics from Google Scholar, as of September 2026.

01Research

From the bedside to the base pair.

Trained first as a physician, then in the wet lab, then in code. Four threads run through my work, and all of them start from patients.

01Current focus · Columbia

Chromatin topology & stem cell fate

How does genome folding decide what a hematopoietic stem cell becomes? I lead the computational and multi-omics analyses of STAG2-cohesin in blood formation and myeloid leukemia, integrating 3D genome maps with chromatin accessibility, protein–DNA binding, DNA methylation and single-cell profiles. Key Personnel on an NIH/NCI R37 MERIT Award.

  • Cohesin · STAG2
  • Hi-C
  • ATAC · CUT&RUN · ChIP
  • WGBS
  • scRNA · scATAC
  • AML · MDS

02Ph.D. · Karolinska Institutet

Sarcoma multi-omics

Sarcomas are rare and strikingly heterogeneous. I built end-to-end pipelines integrating transcriptomic, genomic, epigenomic and proteomic data to define molecular subtypes, treatment-resistance mechanisms and prognostic biomarkers in synovial sarcoma, Ewing sarcoma and chondrosarcoma, and lately how epigenetic remodeling opens sarcomas to T cells.

  • Synovial sarcoma
  • Ewing sarcoma
  • Proteomics
  • Integrative clustering
  • Tumor immunity

03Computational oncology

Machine learning & applied AI

Prognostic and multi-modal models that combine multi-omics, clinical and imaging data to predict outcomes, now in myeloid malignancy cohorts. I also build LLM-based, tool-using agents for reproducible analysis pipelines, with retrieval-augmented generation and strict evaluation: unit tests, data-leakage and sensitivity checks.

  • Survival models
  • Multi-modal integration
  • LLM agents · RAG
  • scikit-learn · PyTorch

04Team science

Cancer biology, together

Leading the bioinformatics in multidisciplinary teams, from natural killer cell states and the tumor microenvironment to metastatic dormancy, in work published in Nature Cell Biology, Science Translational Medicine and the JCI.

  • NK cells
  • Tumor microenvironment
  • Metastatic dormancy
  • Bulk & single-cell

02Journey

Four cities. One trajectory.

  1. 27.99°N · 120.70°E

    Wenzhou

    2009 – 2014 · China

    M.D., Wenzhou Medical University

    Clinical medicine, with rotations at the First Affiliated Hospital and community health outreach.

  2. 25.27°N · 110.29°E

    Guilin

    2014 – 2017 · China

    M.Sc. in Urology, Guilin Medical University

    Urology residency alongside research on long non-coding RNAs and FISH-based prognosis in bladder cancer.

  3. 59.33°N · 18.07°E

    Stockholm

    2017 – 2022 · Sweden

    Ph.D., Karolinska Institutet

    Oncology-Pathology: multi-omics of Ewing and synovial sarcoma, then quantitative proteomics at SciLifeLab.

  4. 40.84°N · 73.94°W

    New York

    2022 – now · USA

    Postdoctoral Research Scientist, Columbia University Irving Medical Center

    Chromatin architecture in hematopoietic stem cells and leukemia, in the lab of Dr. Aaron Viny. Edward P. Evans MDS Fellow.

03Publications

Selected & complete.

Full list on NCBI MyBibliography ↗

04Recognition

Funding, talks & honors.

$50,000

Edward P. Evans MDS Fellowship

Edward P. Evans Foundation · 2026–2027

R37 · MERIT

Key Personnel, NIH/NCI R37 CA286857

The role of the cohesin complex in hematopoietic transformation and leukemia maintenance · PI: Aaron D. Viny · 2023–2028

    05Toolkit

    Bench & code.

    I design the experiment, run it, and write the pipeline that analyses it.

    { }Computational

    • Hi-C · 3D genome
    • ATAC-seq
    • CUT&RUN · ChIP-seq
    • WGBS
    • Nanopore 5mC · 5hmC
    • scRNA · scATAC
    • CyTOF · spatial proteomics
    • Multi-omics integration
    • Survival modeling
    • LLM agents · RAG
    • scikit-learn
    • PyTorch
    • TensorFlow
    • Python
    • R
    • SQL
    • MATLAB
    • AWS
    • HPC · Slurm

    ⚗Wet lab

    • CRISPR-Cas9
    • Flow cytometry
    • NGS library prep
    • LC-MS proteomics
    • Confocal microscopy
    • FISH
    • IHC · IF
    • Co-IP
    • Western blot
    • qPCR
    • Mouse models
    • Cloning
    • Transfection & transduction
    • ELISA

    06Service

    Giving back to the field.

    19

    Peer reviewer

    • Nature Communications
    • Genome Medicine
    • Journal for ImmunoTherapy of Cancer
    • Advanced Science
    • Cancer Communications
    • iMeta
    • Frontiers in Immunology
    • Frontiers in Oncology
    • Scientific Reports
    • International Journal of Biological Sciences
    • Medical Oncology
    • BMC Cancer
    • BMC Medical Informatics and Decision Making
    • Discover Oncology
    • Cell Biochemistry and Biophysics
    • Molecular Cytogenetics
    • Magnetic Resonance Imaging
    • Medical Science Monitor
    • Journal of King Saud University – Science

    3

    Editorial roles

    • Associate Editor, Discover Oncology
    • Guest Editor, International Journal of Molecular Sciences, special issue on Epigenetic Dysregulation in Cancer
    • Guest Editor, Frontiers in Pharmacology

    3

    Bioinformatics consultant

    • Harvard Stem Cell Institute
    • University of California San Francisco
    • Karolinska Institutet

    2

    Mentorship

    • Edna M. Stewart, Ph.D. student, Viny Laboratory
    • Jacob Winick, undergraduate student, Viny Laboratory

    Languages MandarinEnglish

    07Contact

    Let’s talk science.

    Columbia University Irving Medical Center · New York, NY