Yunlong Ma, Ph.D
Department: Psychiatry
Contact information
3615 Civic Center Blvd, Abramson Pediatric Research Center, 1016A
Philadelphia, PA 19104
Philadelphia, PA 19104
Publications
Permanent link
Description of Other Expertise
Dr. Yunlong Ma is a senior research scientist at the University of Pennsylvania, where his research focuses on developing computational and statistical frameworks for functional genomics and single-cell multi-omics. His overarching goal is to elucidate the molecular mechanisms governing human fetal brain development and to understand how their dysregulation contributes to neurodevelopmental and neuropsychiatric disorders. His work lies at the intersection of bioinformatics, genetics, and systems biology. He specializes in designing integrative computational tools that combine large-scale genetic, transcriptomic, and regulatory data to reconstruct cell-type–specific gene regulatory networks in the human brain. These frameworks enable the identification of key RNA-binding proteins (RBPs) and transcriptional regulators that mediate genetic risk effects on disease-relevant molecular pathways. His recent works and software tools—such as scMORE (Nature Aging, 2025), scBPS (Nature Microbiology, 2025), scDrugHunter (Cell Proliferation, 2024), scPagwas (Cell Genomics, 2023), and others published in Science Translational Medicine (2025), Translational Psychiatry (2025), Molecular Psychiatry (2024), Cancer Cell (2023), and Genome Medicine (2022)—demonstrate the commitment to bridging large-scale data science with mechanistic biology.His long-term career goal is to lead an independent research program focused on developing next-generation computational models that integrate genetic, transcriptomic, and spatial multi-omics data to uncover translational regulatory programs in the human brain. Ultimately, He aims to contribute to a systems-level understanding of how molecular regulation drives brain development and disease.
Description of Research Expertise
Dr. Yunlong Ma collaborates with Dr. Michael Gandal. He is a senior research scientist whose work focuses on developing computational and statistical frameworks for functional genomics and single-cell multi-omics. His research aims to uncover the molecular mechanisms of human fetal brain development and their implications in neuropsychiatric and neurodevelopmental disorders. Dr. Ma specializes in developing bioinformatics tools that integrate large-scale genetic, transcriptomic, and regulatory data to dissect cell-type-specific gene regulatory networks in the human brain. He received his Ph.D. in Human genetics from Zhejiang University, where he focused on integrative genomic analysis and regulatory network modeling.Selected Publications
Ma Yunlong, Su Jianzhong: Linking single-cell multiomics with GWAS to reveal key regulators of disease risk. Nature Aging Jan 2026.Ma Yunlong*, Yao Y, Zhou Y, Dai W, Li J, Gui Y, Sun H, Zhu Z, Jiang D, Chen C, Deng C, Huang Y, Han H, Zhou J, Su J*.: Integrating polygenic signals and single-cell multiomics identifies cell-type-specific regulomes critical for immune- and aging-related diseases. Nature Aging Dec 2025.
Liu H#, Ma Yunlong#, Gao N#, Zhou Y, Li G, Zhu Q, Liu X, Li S, Deng C, Chen C, Yang Y, Ren Q, Hu H, Cai Y, Chen M, Xue Y, Zhang K, Qu J*, Su J*.: Identification and characterization of human retinal stem cells capable of retinal regeneration. Science Translational Medicine 17: eadp6864, Mar 2025.
Li J#, Ma Yunlong#, Cao Y#, Zheng G, Ren Q, Chen C, Zhu Q, Zhou Y, Lu Y, Zhang Y, Deng C, Chen WH*, Su J*.: Integrating microbial GWAS and single-cell transcriptomics reveals associations between host cell populations and the gut microbiome. Nature Microbiology May 2025.
Han H, Yao J, Wu J, Mao S, Pan H, Qv L, Zhu G, Ren J, Yu Y, Xuan F, Zeng L, Ma Yunlong, Yang Z, Zhu Z, Zhu F, Li MD.: Implications of neurogenesis in depression through BDNF: rodent models, regulatory pathways, gut microbiota, and potential therapy. Molecular Psychiatry Sep 2025.
Ma Yunlong*, Jiang D, Li J, Zheng G, Deng Y, Gou X, Gao S, Chen C, Zhou Y, Zhang Y, Deng C, Yao Y, Han H, Su J*.: Systematic dissection of pleiotropic loci and critical regulons in excitatory neurons and microglia relevant to neuropsychiatric and ocular diseases. Translational Psychiatry 15: 24, Jan 2025.
Li MD, Liu Q, Shi X, Wang Y, Zhu Z, Guan Y, He J, Han H, Mao Y, Ma Yunlong, Yuan W, Yao J, Yang Z.: Integrative analysis of genetics, epigenetics and RNA expression data reveal three susceptibility loci for smoking behavior in Chinese Han population. Molecular Psychiatry Nov 2024.
Liu Y#, Chen X#, Ma Yunlong#, Song C, Ma J, Chen C, Su J, Ma L*, Saiyin H*.: Endogenous mutant Huntingtin alters the corticogenesis via lowering Golgi recruiting ARF1 in cortical organoid. Molecular Psychiatry Oct 2024.
Ma Yunlong#, Deng C#, Zhou Y#, Zhang Y, Qiu F, Jiang D, Zheng G, Li J, Shuai J, Zhang Y*, Yang J*, Su J*.: Polygenic regression uncovers trait-relevant cellular contexts through pathway activation transformation of single-cell RNA sequencing data. Cell Genomics 3: 100383, Aug 2023.
Liu Z#, Zhang Y#, Ma N#, Yang Y#, Ma Yunlong#, Wang F, Wang Y, Wei J, Chen H, Tartarone A, Velotta JB, Dayyani F, Gabriel E, Wakefield CJ, Kidane B, Carbonelli C, Long L, Liu Z*, Su J*, Li Z*.: Progenitor-like exhausted SPRY1(+)CD8(+) T cells potentiate responsiveness to neoadjuvant PD-1 blockade in esophageal squamous cell carcinoma. Cancer Cell 41: 1852-1870, Nov 2023.
Su J, Yuan J, Xu L, Xing S, Sun M, Yao Y, Ma Yunlong, Chen F, Jiang L, Li K, Yu X, Xue Z, Zhang Y, Fan D, Zhang J, Liu H, Liu X, Zhang G, Wang H, Zhou M, Lyu F, An G, Yu X; Myopia Associated Genetics and Intervention Consortium; Xue Y, Yang J, Qu J.: Sequencing of 19,219 exomes identifies a low-frequency variant in FKBP5 promoter predisposing to high myopia in a Han Chinese population. Cell Reports 42: 112510, May 2023.
Ma Yunlong#, Qiu F#, Deng C#, Li J, Huang Y, Wu Z, Zhou Y, Zhang Y, Xiong Y, Yao Y, Zhong Y, Qu J*, Su J*.: Integrating single-cell sequencing data with GWAS summary statistics reveals CD16+monocytes and memory CD8+T cells involved in severe COVID-19. Genome Medicine 14: 16, Feb 2022.
Xiang B#, Deng C#, Qiu F, Li J, Li S, Zhang H, Lin X, Huang Y, Zhou Y, Su J, Lu M*, Ma Yunlong*.: Single cell sequencing analysis identifies genetics-modulated ORMDL3(+) cholangiocytes having higher metabolic effects on primary biliary cholangitis. J Nanobiotechnology 19: 406, Dec 2021.
Xu L#, Ma Yunlong#, Yuan J#, Zhang Y#, Wang H, Zhang G, Tu C, Lu X, Li J, Xiong C, Chen K, Liu X, Xue Z, Zhou M, Li W, Wu N, Bao J, Chen H, Lu F*, Su J*, Qu J*.: COVID-19 quarantine reveals that behavioral changes have an effect on myopia progression. Ophthalmology Nov 2021.