Chen Dong
Palo Alto,CA
Summary
Accomplished Senior Research Associate at Chan Zuckerberg Biohub, specializing in single-cell and spatial transcriptomics. Expert in implementing machine learning algorithms for data analysis and mentoring diverse teams. Proven track record in tissue processing and assay development, enhancing research capabilities and driving innovative solutions in genomic studies.
Overview
10
10
years of professional experience
Work History
Senior Research Associate, Single Cell Platform with Dr.Stephen Quake
Chan Zuckerberg Biohub
Stanford, CA
11.2021 - 05.2024
- Demonstrated expertise in orchestrating large-scale single-cell/nucleus RNA sequencing for the Tabula Sapiens Project, aiming to comprehensively catalog gene expression across various tissues within a single organism.
- Established and maintained a comprehensive human tissue biobank, ensuring proper preservation and documentation of diverse tissue samples for the Tabula Sapiens Project.
- Implemented machine learning algorithms to analyze single-cell RNA sequencing data, enabling identification of novel cell populations and state transitions across human tissues.
- Applied deep learning models for automated cell type annotation and trajectory inference in the Tabula Sapiens Project, improving classification accuracy and processing efficiency.
- Utilized supervised learning approaches to integrate multi-modal single-cell data, including spatial transcriptomics and RNA-seq datasets.
- Conducted Single Cell RNA-Seq experiments utilizing both plate-based and droplet methodologies, overseeing the process from sequence alignment and matrix count generation to differential gene expression analysis with bioinformatics tools.
- Implemented imaging and sequencing-based spatial technologies to develop the single cell human spatial transcriptomics atlas.
- Mentored a diverse group in the application of smart-seq2 and 10X Genomics, enhancing their capacity for independent genomic research.
Life Science Research Professional with Dr. Gary K. Steinberg
Stanford University
Stanford, CA
10.2018 - 11.2021
- Working as a part of a team on two projects with a senior scientist, a research associate, and a medical student.
- Responsible for determining the beneficial role of Matrilin-2 protein during sensorimotor recovery via brain infusion and behavioral tests in rodents.
- Evaluating changes in perineuronal nets (PNN) and parvalbumin (PV) expression in the peri-infarct area of the rodent brain using ImageJ and GraphPad software.
- Troubleshooting a protocol for Oxygen-Glucose Deprivation (OGD) assay with human astrocyte cell line to study the expression change of astrocytes under ischemic condition.
- Presenting research progress and journal articles regularly during lab meeting.
Master’s Thesis Research with Dr. Claude Desplan
New York University
New York, NY
01.2016 - 01.2018
- Project: Role of insulin signaling pathway during the aging process of the ant species, H. saltator.
- Improved amplification and molecular cloning protocols for insulin receptors.
- Identified the opposite function of two insulin-like peptides towards their downstream targeted protein during signal transduction via cell culture and Western blot.
Undergraduate research assistant with Dr. Ashlee Rowe
Michigan State University
East Lansing, MI
01.2015 - 01.2016
- Project: Molecular characterization of the potassium (K+) ion channel in a mouse model with different sensitivity (high, medium, and low) towards scorpion venom.
- Identified 5' untranslated region of the gene Kcna1 from three mouse strains using conventional PCR and molecular cloning to study the mechanism of pain regulation in rodent.
Undergraduate research assistant with Dr. Weiming Li
Michigan State University
East Lansing, MI
01.2014 - 01.2015
- Molecular characterized of ATP-binding cassette (ABC) transporter genes from sea lamprey and Japanese lamprey.
Education
M.S. - General Biology
New York University
New York, NY01.2018
B.S. - Zoology, Ecology, Evolutionary Biology and Behavior program
Michigan State University
East Lansing, MI01.2016
Skills
- Immunocytochemistry and assay development
- Tissue processing and cryosectioning
- Image analysis tools
- Feasibility and validation studies
- Single-cell and spatial transcriptomics
- Digital pathology techniques
Publications Presentations Abstracts
- Quake SR, Tabula Sapiens Consortium. Tabula Sapiens reveals transcription factor expression, senescence effects, and sex-specific features in cell types from 28 human organs and tissues. Cell, 05/12/22, 185, 13, 223–239.e19.
- Azevedo-Pereira RL, Manley NC, Dong C, Zhang Y, Lee AG, Zatulovskaia Y, Gupta V, Vu J, Han S, Berry JE, Bliss TM, Steinberg GK. Decoding the molecular crosstalk between grafted stem cells and the stroke-injured brain. Cell Rep., 04/10/23, 42, 4, 112353.
- Seth S Tigchelaar, Ricardo L Azevedo-Pereira, Chen Dong, xibin liang, Tonya Bliss, Gary Steinberg, Decoding the Cross-Talk Between Grafted Neural Stem Cells and Host Brain to Predict the Molecular Mechanisms of Stem Cell-Induced Functional Recovery After Stroke, International Stroke Conference, Denver, CO, 2021
Honors Awards Achievements
- Phi Sigma Theta, Michigan State University, East Lansing, MI, 08/01/12, 05/01/16
- Dean’s List, Michigan State University, East Lansing, MI, 2013, 2015
Professional Associations
- American Heart Association, 2020
- Society for Neuroscience, 2019, 2022
- Human Rights Campaign, 2017, Present
Leadership Experience
- Michigan State University, East Lansing, MI, Leader, Fish, and Wildlife Service Program, 2015, Recruited students to collect algae samples from local natural habitat.
- Red Cross Society of China, Shaoxing, Zhejiang, Summer camp volunteer teacher, Rural China Education Foundation, 2014, Guided primary school students from low-income families.
Timeline
Senior Research Associate, Single Cell Platform with Dr.Stephen Quake
Chan Zuckerberg Biohub
11.2021 - 05.2024
Life Science Research Professional with Dr. Gary K. Steinberg
Stanford University
10.2018 - 11.2021
Master’s Thesis Research with Dr. Claude Desplan
New York University
01.2016 - 01.2018
Undergraduate research assistant with Dr. Ashlee Rowe
Michigan State University
01.2015 - 01.2016
Undergraduate research assistant with Dr. Weiming Li
Michigan State University
01.2014 - 01.2015
M.S. - General Biology
New York University
B.S. - Zoology, Ecology, Evolutionary Biology and Behavior program
Michigan State University
Similar Profiles
Elizabeth OlowoElizabeth Olowo
Executive Assistant at Chan Zuckerberg InitiativeExecutive Assistant at Chan Zuckerberg Initiative
Daishawn MatthewsDaishawn Matthews
Audio Visual Technician at Apex @ Chan Zuckerberg InitiativeAudio Visual Technician at Apex @ Chan Zuckerberg Initiative
Kate Brousseau, MBAKate Brousseau, MBA
Sr. Director School Development & Partnerships at Chan Zuckerberg Initiative - EducationSr. Director School Development & Partnerships at Chan Zuckerberg Initiative - Education
Aarzoo ChundawatAarzoo Chundawat
Front Desk Associate at Best Western HotelFront Desk Associate at Best Western Hotel
Kevin NguyenKevin Nguyen
Leasing Consultant at Sares-Regis GroupLeasing Consultant at Sares-Regis Group