cv

Genomics Scientist at Stanford University — full CV available as PDF.

General Information

Full Name Pin-Chung (Tony) Cheng
Location Palo Alto, CA, United States
Email tonycheng521@gmail.com
GitHub tonypincheng
LinkedIn pin-chung-tony-cheng

Summary

  • Genomics Scientist at Stanford University specializing in epigenomics and brain aging. MD/PhD with a track record of developing high-resolution single-cell multi-omic technologies, including a ~250-fold improvement in lineage tracing resolution. Combines deep wet-lab expertise with scalable bioinformatic pipelines to advance translational research in aging, cancer, and regenerative medicine.

Education

  • 2019 – 2026
    Doctor of Philosophy (Ph.D.), Biological Sciences / Quantitative Biology
    University of California San Diego, San Diego, CA
  • 2017 – 2018
    Master of Science (M.S.), Stem Cell Biology and Regenerative Medicine
    University of Southern California, Los Angeles, CA
  • 2007 – 2014
    Doctor of Medicine (M.D.), Medicine
    Kaohsiung Medical University, Kaohsiung, Taiwan

Professional Experience

  • 2026 – present
    Genomics Scientist, Knight Initiative for Brain Resilience
    Stanford University, Palo Alto, CA
    • Methylation profiling of ~400 human brain samples to investigate epigenetic changes in the aging brain and uncover mechanisms of brain resilience.
  • 2023 – 2026
    Graduate Student Researcher
    Altos Labs, San Diego, CA
    • Developed RETrace2, a dual-omic single-cell lineage tracing and methylation profiling technology, achieving ~250-fold improvement in resolution.
    • Improved probe target capture efficiency 4X, identified 2X more informative targets and expanded probe panel from 11,000 to 92,000 targets, resulting in 21X more targets captured per cell.
    • Built an oligonucleotide model to evaluate microsatellite PCR and sequencing accuracy across polymerases and sequencing platforms (Illumina NextSeq, Element Bio AVITI), reducing overall errors by 30%.
    • Developed a Docker-containerized, dual-omic Nextflow pipeline for single-cell analysis using microsatellite mutations and sparse methylation data, improving process speed by 16x.
    • Generated and analyzed ~4000 single-cell methylomes using ScaleBio's sciMET kit.
  • 2019 – 2023
    Graduate Student Researcher
    University of California San Diego, Kun Zhang Lab, San Diego, CA
    • Analyzed single-nucleus chromatin accessibility and mRNA expression (SNARE-seq2) data in the human fetal heart and glioblastoma samples.
    • Graduate Instructional Apprentice (IA) in Genetics and Bioinformatics.
  • 2017 – 2019
    Research Associate
    University of Southern California, Joseph Rodgers Lab, Los Angeles, CA
    • Pharmacologically targeted metabolic pathways to rejuvenate aged muscle stem cells.
  • 2016 – 2017
    Graduate Research Assistant
    Academia Sinica, Yun-Ru Chen Lab, Taipei, Taiwan
    • Characterized a novel antibody targeting TDP-43 oligomers in an ALS mouse model.

Skills

  • Automation
    • QIAcube HT (96 DNA), QIAcube Connect (cfDNA), KingFisher, SPT Firefly.
  • Computational
    • AI tools (Claude Code/Science, Cursor/Grok, Gemini), Python, R, Linux/Bash, Scanpy, Seurat, variant calling (SNP/CNV), HipSTR, bwa, Bismark, MethylPy, samtools, bcftools, bedtools, Docker, AWS, Nextflow, Git/GitHub, SLURM.
  • Genomics
    • Single nuclei isolation (10X protocol, Singulator), DNA shearing (Covaris), DNA extraction, restriction enzyme digestion, adapter ligation, DNA amplification, Illumina/AVITI sequencing.
  • Methylation Library Preparation
    • Illumina 5-base solution, Zymo Bisulfite Conversion, NEB EM-Seq, single cell methylome (sciMET).
  • Probe-Based Target Enrichment
    • IDT xGEN Hybridization Kit; DNA probe production via in vitro transcription and reverse transcription from DNA oligo pools (Twist Bioscience, up to 169,000 oligos).
  • Molecular Biology
    • PCR, qPCR, PCR clean up, immunohistochemistry, immunofluorescence, microscopy, western-blot, Tapestation, Qubit, Benchling (ELN).
  • Cell Biology
    • Stem cell isolation and culture, FACS (BD/Sony).

Honors and Certificates

  • Featured in Element Biosciences Blog for RETrace2 lineage tracing technology (April 2026)
  • J Yang Scholarship Award, UC San Diego Institute of Engineering in Medicine
  • Excellence in Teaching Award, UC San Diego, Bioinformatics
  • Taiwan Medical License; Australian Medical Council MCQ; USMLE Step 1 & 2 – Passed

Publications

  • Pin-Chung Cheng, Dmitrii Kamenev, Polina Kameneva, Conor Fitzpatrick, Igor Adameyko, Peter V Kharchenko, Kun Zhang (2026). High-resolution retrospective single cell lineage tracing with mutable homopolymers. bioRxiv. doi:10.64898/2026.03.10.709901 (In review at Nature Communications)
  • Manmeet H. Raval, Pin-Chung Cheng, Nicholas Guardino, et al. (2020). PDH mediated mitochondrial respiration controls the speed of muscle stem cell activation in muscle repair and aging. bioRxiv.