Department of Oral Medicine
The University of Pennsylvania School of Dental Medicine

Research Interests

Research in Dr. Su’s laboratory focuses on elucidating the molecular mechanisms that regulate gene expression in a cell type-, brain region-, tissue-, and species-specific manner under both physiological and pathological conditions.

Key words

epigenetics, epitranscriptomics, neuroscience

Description of research

Her lab integrates bulk and sc/snRNA sequencing, ATAC-seq, ChIP-seq, and emerging epitranscriptomic profiling approaches to dissect gene regulatory programs across diverse biological contexts. Dr. Su has extensive expertise in computational and statistical modeling of high-dimensional genomic data, including pseudocell-based modeling, cross-group validation strategies, and analyses of age-associated gene expression dynamics across cell types. Her work bridges experimental neuroscience and quantitative genomics, with the goal of uncovering fundamental regulatory principles that govern brain plasticity, resilience, and vulnerability to disease.

Selected publications

https://www.ncbi.nlm.nih.gov/myncbi/1j7xeS4Ptczsf3/bibliography/public/

https://scholar.google.com/citations?user=9ZHH9cwAAAAJ&hl=en

• Zhou Y*, Su Y*, Yang Q*, Li J*, Hong Y, Gao T, Zhong Y, Ma X, Jin M, Liu X, Yuan N, Kennedy BC, Wang L, Yan L, Viaene AN, Helbig I, Kessler SK, Kleinman JE, Hyde TM, Nauen DW, Liu C, Liu Z, Shen Z, Li C, Xu S, He J, Weinberger DR, Ming GL, Song H. Cross-species analysis of adult hippocampal neurogenesis reveals human-specific gene expression but convergent biological processes. Nat Neurosci. 2025 Sep;28(9):1820-1829. doi: 10.1038/s41593-025-02027-9. Epub 2025 Aug 11. PubMed PMID: 40790267.
• Gao T, Fujita Y, Chen Y, Wang Z, Lu Y, Huang D, Shen J, Yan L, Zhang S, Wang Y, Li P, Fang X, Hrabovszky E, Xu C, Su Y^#, Li Y^#, Zhang L^#, Zhou Y^#. From seq-ing to modeling: towards a molecular understanding of special properties of immature neurons in the human hippocampus. Life Med. 2025 Dec;4(6):lnaf031. doi: 10.1093/lifemedi/lnaf031. eCollection 2025 Dec. PubMed PMID: 41446024; PubMed Central PMCID: PMC12726914.

• Dunn J*, Moore C*, Kim NK*, Gao T, Cheng Z, Jin P, Ming GL, Qian J^#, Su Y^#, Song H^#, Zhu H^#. Transcription Factor-Wide Association Studies (TF-WAS) to Identify Functional SNPs in Alzheimer’s Disease. Journal of Neuroscience. 2024 Dec 2: 2024 Dec 2:e1800242024

• Su Y*^#, Zhou Y*, Bennett ML, Li S, Carceles-Cordon M, Lu L, Huh S, Jimenez-Cyrus D, Kennedy BC, Kessler SK, Viaene AN, Helbig I, Gu X, Kleinman JE, Hyde TM, Weinberger DR, Nauen DW, Song H^#, Ming GL^#. A Single-Cell Transcriptome Atlas of Glia Diversity in the Human Hippocampus across the Postnatal Lifespan. Cell Stem Cell.2022 Nov 3;29(11):1594-1610.e8

• Zhou Y*, Su Y*, Li S*, Kennedy BC, Zhang DY, Bond AM, Sun Y, Jacob F, Lu L, Hu P, Viaene AN, Helbig I, Kessler SK, Lucas T, Salinas RD, Gu X, Chen HI, Wu H, Kleinman JE, Hyde TM, Nauen DW, Weinberger DR, Ming GL, Song H.: Molecular landscapes of human hippocampal immature neurons across lifespan. Nature. 2022 Jul;607(7919):527-533.

• Su Y, Shin J, Zhong C, Wang S, Roychowdhury P, Lim J, Kim D, Ming GL, Song H. Neuronal activity modifies the chromatin accessibility landscape in the adult brain. Nat Neurosci. 2017 Mar;20(3):476-483)

• Su Y, Ming GL, Song H. DNA damage and repair regulate neuronal gene expression. Cell Res. 2015 Sep;25(9):993-4.

• Guo JU*, Su Y*, Shin JH, Shin J, Li H, Xie B, Zhong C, Hu S, Le T, Fan G, Zhu H, Chang Q, Gao Y, Ming GL, Song H. Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain. Nat Neurosci. 2014 Feb;17(2):215-22.

• Hu S*, Wan J*, Su Y*, Song Q, Zeng Y, Nguyen HN, Shin J, Cox E, Rho HS, Woodard C, Xia S, Liu S, Lyu H, Ming GL, Wade H, Song H, Qian J, Zhu H. DNA methylation presents distinct binding sites for human transcription factors. Elife. 2013 Sep 3;2:e00726.

• Su Y, Zhang J, Tang Y, Bi F, Liu JN. The novel function of nesfatin-1: anti-hyperglycemia. Biochem Biophys Res Commun. 2010 Jan 1;391(1):1039-42.