Jin Xu, Ph.D.
Professor, School of Life Sciences, Sun Yat-sen University
Principal Investigator, State Key Laboratory of Biocontrol | Innovation Center for Evolutionary Synthetic Biology
Guangzhou, China
Email: xujin7@mail.sysu.edu.cn
ORCID · Google Scholar
Biography
Jin Xu is a Professor in the School of Life Sciences at Sun Yat-sen University. Her research investigates how cells with the same genome acquire distinct identities and functions, how genetic and epigenetic variation shapes cellular phenotypes, and how cellular diversity contributes to adaptation, aging, and disease. Her laboratory integrates single-cell multi-omics, mitochondrial genetics, functional and comparative genomics, molecular genetics, and computational modeling.
Professor Xu received her Ph.D. in Bioinformatics from the Beijing Institute of Genomics, Chinese Academy of Sciences, under the supervision of Chung-I Wu. She subsequently conducted postdoctoral research with Howard Y. Chang at Stanford University School of Medicine. During this period, she contributed to studies of three-dimensional genome organization, enhancer–promoter interactions, long noncoding RNA regulation, and subcellular RNA localization. She joined Sun Yat-sen University as a principal investigator in 2019.
Her work has been published in Cell, Nature, Nature Genetics, Nature Communications, Genome Biology, Molecular Biology and Evolution, Communications Biology, and Cell Reports. She serves on the Youth Editorial Board of National Science Review and the Chemical Senses Committee of the Chinese Society for Cognitive Science.
Research
The Xu laboratory studies the regulatory and evolutionary principles underlying cellular heterogeneity. Its long-term goal is to move from descriptive cell atlases toward predictive models of cellular identity, adaptation, and resilience.
Cell identity and neuronal diversification
Olfactory sensory neurons provide a powerful model for understanding how closely related cells acquire distinct receptor identities, spatial distributions, and axonal projection patterns. The laboratory combines allele-resolved single-cell transcriptomics and chromatin accessibility, long-read sequencing, spatial assays, and genetic perturbation to investigate random monoallelic expression, chromatin-state variation, transcript-isoform remodeling, and the coupling of neuronal identity to circuit organization. This work has identified regulatory programs controlling the divergence of Cd36-positive olfactory sensory neurons and has revealed extensive isoform remodeling during neuronal differentiation.
Mitochondrial genetics and cell-state adaptation
The laboratory studies how variation in mitochondrial mutation load, heteroplasmy, copy number, and clonal history influences cellular fitness. Its work identified a stringent mitochondrial genetic bottleneck during human lymphocyte development and demonstrated that the reliability of mtDNA-based lineage tracing depends strongly on biological context and the extent of clonal expansion. Current research examines how mitochondrial genotype interacts with changing bioenergetic demand during immune activation, differentiation, and aging. This demand–capacity framework helps explain why pathogenic mitochondrial variants may be tolerated at baseline yet become functionally limiting during cell-state transitions.
Evolution of sensory systems and cellular diversity
Using comparative single-cell genomics, the laboratory investigates how gene-family expansion, genome architecture, and regulatory innovation generate new cell types and adaptive functions. A single-cell multi-omic atlas of the honeybee antenna revealed a close relationship between olfactory-receptor expansion and sensory-neuron diversification. The work further identified distinct modes of receptor co-expression involving polycistronic transcription, tandem-gene organization, and promoter-level regulation. These studies connect molecular evolution with the emergence of species-specific cellular phenotypes.
Single-cell technologies and regulatory design
The laboratory develops experimental and computational approaches that improve the accuracy, scalability, and interpretation of single-cell studies. These include MitoSort, which uses endogenous mitochondrial variants to demultiplex pooled single-cell genomic data; computational frameworks for evaluating lineage-informative mtDNA variants; systematic benchmarking of ambient-RNA correction methods; and single-cell long-read transcriptomics. An emerging direction uses predictive and generative models to design cell-type- and state-specific cis-regulatory elements, translating principles learned from natural regulatory evolution into programmable systems for precise gene control.
Academic Appointments and Training
- 2019–present — Professor and Principal Investigator, School of Life Sciences, Sun Yat-sen University, China
- 2014–2019 — Postdoctoral Scholar, Stanford University School of Medicine, USA; advisor: Howard Y. Chang
- 2008–2014 — Ph.D. in Bioinformatics, Beijing Institute of Genomics, Chinese Academy of Sciences, China; advisor: Chung-I Wu
- 2003–2007 — B.Eng. in Software Engineering, Northeast Normal University, China
Selected Honors and Academic Service
- National Young Talents Program
- Pearl River Young Top Talent Program, Guangdong Province
- Sun Yat-sen University Hundred Talents Program
- Youth Editorial Board Member, National Science Review
- Committee Member, Chemical Senses Committee, Chinese Society for Cognitive Science
Publication
2026
Systematic benchmarking of ambient RNA decontamination tools to advance precision in single-cell transcriptomic analysis. Nature Communications (2026). https://doi.org/10.1038/s41467-026-77458-4
Single-cell long-read profiling of olfactory sensory neuron differentiation and diversity. Communications Biology (2026). https://doi.org/10.1038/s42003-026-10544-x
2025
Methanol fixation and tagmentation of RNA/DNA hybrids directly enable single-cell transcriptome sequencing. Frontiers in Genetics (2025). https://doi.org/10.3389/fgene.2025.1629655
Evolutionary process underlying receptor gene expansion and cellular divergence of olfactory sensory neurons in honeybees. Molecular Biology and Evolution (2025). https://doi.org/10.1093/molbev/msaf080
Clonal expansion dictates the efficacy of mitochondrial lineage tracing in single cells. Genome Biology (2025). https://doi.org/10.1186/s13059-025-03540-7
Immunoregulatory programs in anti-N-methyl-D-aspartate receptor encephalitis identified by single-cell multi-omics analysis. Clinical and Translational Medicine (2025). https://doi.org/10.1002/ctm2.70173
2024
MitoSort: Robust demultiplexing of pooled single-cell genomic data using endogenous mitochondrial variants. Genomics, Proteomics & Bioinformatics (2024). https://doi.org/10.1093/gpbjnl/qzae073
Single-cell mitochondrial DNA sequencing: Methodologies and applications. Mitochondrial Communications (2024). https://doi.org/10.1016/j.mitoco.2024.10.001（Review）
Regulatory mechanisms orchestrating cellular diversity of Cd36+ olfactory sensory neurons revealed by scRNA-seq and scATAC-seq analysis. Cell Reports (2024). https://doi.org/10.1016/j.celrep.2024.114671
Soma-germline communication drives sex maintenance in the Drosophila testis. National Science Review (2024). https://doi.org/10.1093/nsr/nwae215
2023
Integrative multi-omic profiling of adult mouse brain endothelial cells and potential implications in Alzheimer's disease. Cell Reports (2023). https://doi.org/10.1016/j.celrep.2023.113392
2022
Fundamental and practical approaches for single-cell ATAC-seq analysis. aBIOTECH (2022). https://doi.org/10.1007/s42994-022-00082-5（Review）
A genetic bottleneck of mitochondrial DNA during human lymphocyte development. Molecular Biology and Evolution (2022). https://doi.org/10.1093/molbev/msac090
Selected Before 2022
Run or die in the evolution of new microRNAs—testing the Red Queen hypothesis on de novo new genes. Molecular Biology and Evolution (2021). https://doi.org/10.1093/molbev/msaa317
Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation. eLife (2020). https://doi.org/10.7554/eLife.54508
Single-cell lineage tracing by endogenous mutations enriched in transposase-accessible mitochondrial DNA. eLife (2019). https://doi.org/10.7554/eLife.45105
Promoter of lncRNA gene PVT1 is a tumor-suppressor DNA boundary element. Cell (2018). https://doi.org/10.1016/j.cell.2018.03.068
Free-living human cells reconfigure their chromosomes in the evolution back to unicellularity. eLife (2017). https://doi.org/10.7554/eLife.28070
Genome-wide temporal profiling of transcriptome and open chromatin of early cardiomyocyte differentiation derived from hiPSCs and hESCs. Circulation Research (2017). https://doi.org/10.1161/CIRCRESAHA.116.310456
Landscape of monoallelic DNA accessibility in mouse embryonic stem cells and neural progenitor cells. Nature Genetics (2017). https://doi.org/10.1038/ng.3769
Molecular and neural functions of Rai1, the causal gene for Smith–Magenis syndrome. Neuron (2016). https://doi.org/10.1016/j.neuron.2016.09.019
Transcriptome sequencing reveals genetic mechanisms underlying the transition between the laying and brooding phases and gene-expression changes associated with divergent reproductive phenotypes in chickens. Molecular Biology Reports (2016). https://doi.org/10.1007/s11033-016-4033-8
Structural organization of the inactive X chromosome in the mouse. Nature (2016). https://doi.org/10.1038/nature18589
The evolution of evolvability in microRNA target sites in vertebrates. Genome Research (2013). https://doi.org/10.1101/gr.148916.112
