▸ Main Studies

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• Feature-weight based measurement of cancerous transcriptome using cohort-wide and sample-specific information, Cellular Oncology, 2023, {code, paper, full-text}, corresponding author

• InferLoop: leveraging single-cell chromatin accessibility for the signal of chromatin loop, Briefings in Bioinformatics, 2023, {code, paper}, first & co-corresponding author

• FitDevo: accurate inference of single-cell developmental potential using sample-specific gene weight, Briefings in Bioinformatics, 2022, {code, paper}, first & co-corresponding author

• scMAGIC: accurately annotating single cells using two rounds of reference-based classification, Nucleic Acids Research, 2022, {code, paper}, co-first author

• Unsupervised Inference of Developmental Directions for Single Cells Using VECTOR, Cell Reports, 2020, {code, paper}, first author

• A novel approach to remove the batch effect of single-cell data, Cell Discovery, 2019, {code, paper}, first author

• PhenoPro: a novel toolkit for assisting in the diagnosis of Mendelian disease, Bioinformatics, 2019, {code, paper}, co-first author

• SPRINT: an SNP-free toolkit for identifying RNA editing sites, Bioinformatics, 2017, {code, paper}, first author

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▸ Collaborations

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• Quantitative analysis of the developmental potential of cells and tissues based on evolutionary conservation of genes and regulatory regions, Journal of Shanghai Jiao Tong University (Medical Science), 2024, paper

• Long-read sequencing reveals alternative splicing-driven, shared immunogenic neoepitopes regardless SF3B1 status in uveal melanoma, Cancer Immunology Research, 2023, paper

• Kinase-independent role of mTOR and on-/off-target effects of an mTOR kinase inhibitor, Leukemia, 2023, paper

• Loss of phosphatase CTDNEP1 potentiates aggressive medulloblastoma by triggering MYC amplification and genomic instability, Nature Communications, 2023, paper

• Inducible lncRNA transgenic mice reveal continual role of HOTAIR in promoting breast cancer metastasis, Elife, 2022, paper

• Human fetal cerebellar cell atlas informs medulloblastoma origin and oncogenesis, Nature, 2022, paper

• Single-cell multiomics identifies clinically relevant mesenchymal stem-like cells and key regulators for MPNST malignancy, Science Advances, 2022, paper

• Conserved and Distinct Functions of the Autism-Related Chromatin Remodeler CHD8 in Embryonic and Adult Forebrain Neurogenesis, Journal of Neuroscience, 2022, paper

• CDC42 controlled apical-basal polarity regulates intestinal stem cell to transit amplifying cell fate transition via YAP-EGF-mTOR signaling, Cell Reports, 2022, paper

• OLIG2 maintenance is not essential for diffuse intrinsic pontine glioma cell line growth but regulates tumor phenotypes, Neuro-Oncology, 2021, paper

• Single-cell transcriptomic analysis reveals a hepatic stellate cell-activation roadmap and myofibroblast origin during liver fibrosis, Hepatology, 2021, paper

• Adaptive responses to mTOR gene targeting in hematopoietic stem cells reveal a proliferative mechanism evasive to mTOR inhibition, Proceedings of the National Academy of Sciences of the United States of America, 2020, paper

• CTCF-mediated chromatin looping in EGR2 regulation and SUZ12 recruitment critical for peripheral myelination and repair, Nature Communications, 2020, paper

• The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens, Genome Biology, 2019, paper

• Single-Cell Transcriptomics in Medulloblastoma Reveals Tumor-Initiating Progenitors and Oncogenic Cascades during Tumorigenesis and Relapse, Cancer Cell, 2019, paper

• Single-cell Transcriptomics Uncovers Glial Progenitor Diversity and Cell Fate Determinants during Development and Gliomagenesis, Cell Stem Cell, 2019, paper

• Dual requirement of CHD8 for chromatin landscape establishment and histone methyltransferase recruitment to promote CNS myelination and repair, Developmental Cell, 2018, paper

• Genome-wide identification of regulatory sequences undergoing accelerated evolution in the human genome, Molecular Biology and Evolution, 2016, paper

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▸ Experience & Education

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• Research Assistant Professor (助理研究员), Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, China, 2020-present

• Graduate Assistant & Visiting Scholar, Cincinnati Children’s Hospital Medical Center, USA, 2018-2020. Collaborator: Prof. Qing Richard Lu and Prof. Yi Zheng

• PhD, Biostatistics, School of Life Sciences, Fudan University, China, 2015-2020. Supervisor: Prof. Weidong Tian

• Summer School, University of California, Los Angeles, USA, 2013. Introduction to Biostatistics. Instructor: Prof. Gjertson, D.W.

• BSc, School of Mathmatics, Shandong University, China, 2011-2015

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▸ Contact

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• No.280 South Chong Qing Road, Shanghai, China, 200025

• fzhang@shsmu.edu.cn