Hi, I am a postdoc in Xiaowei Zhuang Lab in the Department of Chemistry and Chemical Biology at Harvard University. I was a Ph.D. student in Bruce Aronow Lab at Cincinnati Children’s Hospital, and a visiting student in Shu lab at Massachusetts General Hospital.
As an enthusiastic researcher, I am passionate about harnessing advanced computational techniques to unveil the biological mechanisms hidden within high-content imaging and high-throughput sequencing data, with a specific focus on image-based spatial profiling.
My previous work primarily centered around the development of cutting-edge deep learning models tailored to image-based spatial omics data (Jin*, Zhang* et al., bioRxiv, 2023)
and the analysis of temporal perturbation patterns in single-cell experiments (Jin et al., Briefings in Bioinformatics, 2022).
My commitment extends to active involvement in the experimental design of spatial multi-omics experiments,
and I possess a wealth of experience in exploring single cell data across various biological systems and diseases,
including HLHS (Xu, Jin et al., Cell Stem Cell, 2022),
schizophrenia (Sebastian*, Jin* et al. Nat Communications, 2023), among others.
I am particularly interested in cutting-edge bioengineering innovations, such as image-based spatial transcriptomics and optical molecular recording.
With expertise in computational biology and a strong interest in bioengineering,
my ultimate goal is to advance our understanding of neuroscience and cancer biology by implementing cutting-edge computational methods with emerging new molecular recording technologies.
2023 - Present, Depart of Chemistry and Chemical Biology, Harvard University,
Postdoc
2022 - 2023, Massachusetts General Hospital, Harvard Medical School,
Visiting student
2018 - 2023, Department of Biomedical Informatics, Cincinnati Children's Hospital, University of Cincinnati,
Ph.D. student
2014 - 2018, Department of Life Sciences, Zhejiang University,
Bachelor of Biological Science
Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings
[paper] [code]
Kang Jin*, Zuobai Zhang*, Ke Zhang, Francesca Viggiani, Claire Callahan, Jian Tang, Bruce J. Aronow, Jian Shu
bioRxiv (2023).
CellDrift: Inferring Perturbation Responses in Temporally-Sampled Single Cell Data
[paper] [code]
Kang Jin, Dan Schnell, Guangyuan Li, Nathan Salomonis, Surya Prasath, Rhonda Szczesniak, Bruce J Aronow
Briefings in Bioinformatics (2022).
Single cell transcriptomic profiling of human brain organoids reveals developmental timing- and cell-type-specific vulnerabilities induced by NRXN1 CNVs in schizophrenia
[paper] [code]
Rebecca Sebastian*, Kang Jin*, Narciso Pavon, Ruby Bansal, Andrew Potter, Yoonjae Song, Juliana Babu, Rafael Gabriel, Yubing Sun, Bruce Aronow, ChangHui Pak
Nature Communications (2023).
An interactive single cell web portal identifies gene and cell networks in COVID-19 host responses
[paper] [code]
Kang Jin, Eric E. Bardes, Alexis Mitelpunkt, Jake Y. Wang, Surbhi Bhatnagar, Soma Sengupta, Daniel Pomeranz Krummel, Marc E. Rothenberg, Bruce J. Aronow
iScience (2021).
Uncompensated mitochondrial oxidative stress underlies heart failure in an iPSC-derived model of congenital heart disease
[paper]
Xinxiu Xu, Kang Jin, Abha S Bais, Wenjuan Zhu, Hisato Yagi, Timothy N Feinstein, Phong K Nguyen, Joseph D Criscione, Xiaoqin Liu, Gisela Beutner, Kalyani B Karunakaran, Krithika S Rao, Haoting He, Phillip Adams, Catherine K Kuo, Dennis Kostka, Gloria S Pryhuber, Sruti Shiva, Madhavi K Ganapathiraju, George A Porter Jr, Jiuann-Huey Ivy Lin, Bruce Aronow, Cecilia W Lo
Cell Stem Cell (2022).
Identification of distinct tumor cell populations and key genetic mechanisms through single cell sequencing in hepatoblastoma
[paper] [code]
Alexander Bondoc*, Kathryn Glaser*, Kang Jin*, Charissa Lake, Stefano Cairo, James Geller, Gregory Tiao, Bruce Aronow
Communications Biology (2021).
Guided construction of single cell reference for human and mouse lung
[paper]
Minzhe Guo, Michael P Morley, Yixin Wu, Yina Du, Shuyang Zhao, Andrew Wagner, Michal Kouril, Kang Jin, ..., Yan Xu
Nature Communications (2023).
KAT5 activity regulates G0-like states in human gliomas
[paper]
Anca B. Mihalas, Sonali Arora, Samantha A. O’Connor, Heather M. Feldman, John Bassett, Kelly Mitchell, Kang Jin, ..., Patrick J. Paddisons
bioRxiv (2022).
LungMAP Portal Ecosystem: Systems-Level Exploration of the Lung
[paper]
Nathan Gaddis, Joshua Fortriede, Minzhe Guo, ..., Kang Jin, ..., Nathan Salomonis, NHLBI LungMAP Consortium
American Journal of Respiratory Cell and Molecular Biology (2022).
Loss of Neurodevelopmental Gene CASK Disrupts Neural Connectivity in Human Cortical Excitatory Neurons
[paper]
Danny McSweeney, Rafael Gabriel, Kang Jin, Zhiping P Pang, Bruce J Aronow, ChangHui Pak
iScience (2022).
A census of the lung: CellCards from LungMAP
[paper]
Xin Sun, Anne-Karina Perl, Rongbo Li, ..., Kang Jin, ..., Edward E Morrisey, NHLBI LungMAP Consortium
Developmental Cell (2022).
Cross-platform validation of neurotransmitter release impairments in schizophrenia patient-derived NRXN1-mutant neurons
[paper]
ChangHui Pak, Tamas Danko, Vincent R. Mirabella, Jinzhao Wang, Yingfei Liu, Madhuri Vangipuram, Sarah Grieder, Xianglong Zhang, Thomas Ward, Yu-Wen Alvin Huang, Kang Jin, ..., Thomas C. Südhof
PNAS (2021).
Functional immune deficiency syndrome via intestinal infection in COVID-19
[paper]
Erica T. Prates, Michael R. Garvin, Mirko Pavicic, Piet Jones, Manesh Shah, Christiane Alvarez, David Kainer, Omar Demerdash, B Kirtley Amos, Armin Geiger, John Pestian, Kang Jin, Alexis Mitelpunkt, Eric Bardes, Bruce Aronow, Daniel Jacobson
bioRxiv (2020).
Predicted Arabidopsis interactome resource and gene set linkage analysis: a transcriptomic analysis resource
[paper]
Heng Yao, Xiaoxuan Wang, Pengcheng Chen, Ling Hai, Kang Jin, Lixia Yao, Chuanzao Mao, Xin Chen
Plant Physiology (2018).
Bering: Cell segmentation and annotation in high-resolution spatial transcriptomics data
ToppCell: Single-cell gene module exploratory platform
ToppCellPy: Python package for ToppCell. Tutorial on COVID-19 example.
CellDrift: Inferring Perturbation Responses in Temporally-Sampled Single Cell Data.
Bering: Gene colocalization-aware segmentation of image-based spatial transcriptomics using deep learning models (Wrapping up)
Bering Poster
Poster of Bering on MLCB 2022
CellDrift Poster
Poster of CellDrift on ISMB 2022 (Sysmod).
Second Place, Best Poster Award.
CellDrift Poster
Poster of CellDrift on ProbGen22 conference.
COVID-19 Gene Signature Atlas
Modules of most significant gene signatures for COVID-19, which were derived from more than 10 public datasets. More details can be found here.
Digestion of BICCN Nature Paper Collections
A brift digestion of 16 BICCN papers published on Nature on Oct 2021, which introduced comprensive brain atlases and resources covering transcriptomic, epigenomic, morphogenic, eletrophysiological, spatial and other data.
Journal Club: The specious Art of Single Cell Genomics
Slide for a journal club, which covered an overview of current neighbor embedding methods and discussion about Dr. Lior Pachter's recent preprint on UMAP.