Ruoyan Li, PHD
Department of Systems Biology, Division of Division of Discovery Science
Present Title & Affiliation
Primary Appointment
Assistant Professor, Department of Systems Biology, Division of Discovery Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
Dual/Joint/Adjunct Appointment
Assistant Professor, Department of Systems Biology, The University of Texas MD Anderson Cancer Center
Research Interests
My research focuses on understanding somatic mutations and mutant clonal evolution in normal and precancerous tissues and their impact on cancer development. From the moment of the first cell division, every cell in our bodies begins to inevitably accumulate somatic mutations over time. These mutations mainly arise from DNA damage that is unrepaired or incorrectly repaired in the genome. Although most somatic mutations are believed to have no phenotypic consequence, some can confer a selective advantage to mutant cells and lead to the expansion of somatic mutant clones under positive selection. Over time, these mutant clones can progressively colonize tissues, making our bodies a mosaic of genetically distinct clones. Some mutant clones carry driver mutations and expand in normal and precancerous tissues, representing the earliest steps towards cancer. Despite their significance, our understanding of these early somatic mutant clones and their impact on cancer development is still limited, largely due to technical challenges in detecting low-frequency somatic mutations and small mutant clones in normal and precancerous tissues. My research applies and develops cutting-edge genomics, single-cell multi-omics, and spatial genomics technologies to study somatic mutation accumulation and mutant clonal evolution in normal and precancerous tissues. The overarching goal is to use the new knowledge from my research to facilitate the development of strategies for the prevention, detection, and interception of cancer before it progresses to an intractable stage.
Education & Training
Degree-Granting Education
| 2017 | Peking University, Beijing, CN, Biophysics, PhD |
| 2012 | University of Electronic Science and Technology of China, Chengdu, CN, Biotechnology, BS |
Postgraduate Training
| 2020-2023 | Postgraduate Fellow, Single-cell genomics, Wellcome Sanger Institute, Cambridge |
| 2017-2019 | Postgraduate Fellow, Cancer genomics, Peking University, Beijing |
Honors & Awards
| 2025 - Present | Andrew Sabin Fellowship Award |
| 2024 - Present | The University of Texas Rising Star Award |
| 2020 | Outstanding Research Award in Urology, Chinese Research Hospital Association |
| 2017 - 2019 | Boya Postdoctoral Fellowship, Peking University |
Selected Presentations & Talks
Local Presentations
- 2025. Somatic mosaicism in normal and premalignant tissues. Invited. Research Town Hall. Houston, Texas, US.
- 2025. Somatic mutations and clonal expansion in normal human tissues. Invited. MCO Distinguished Scientist Seminar Series. Houston, Texas, US.
- 2024. Exploring cancer development and heterogeneity. Invited. The Department of Systems Biology Seminar Series. Houston, Texas, US.
Selected Publications
Peer-Reviewed Articles
- Guo, XL, Wang, YD, Liu, YJ, Chu, L, Zhu, H, Hu, Y, Wu, RY, Xie, HY, Yu, J, Li, SP, Xiong, ZY, Li, R, Ke, F, Chen, L, Chen, GQ, Chen, L, Bai, F, Enver, T, Li, GH, Li, HF, Hong, DL. Fetal hepatocytes protect the HSPC genome via fetuin-A. Nature 637(8045):402-411, 2025. e-Pub 2025. PMID: 39633051.
- Li, R, Strobl, J, Poyner, EF, Balbaa, A, Torabi, F, Mazin, PV, Chipampe, NJ, Stephenson, E, Ramírez-Suástegi, C, Shanmugiah, VM, Gardner, L, Olabi, B, Coulthard, R, Botting, RA, Zila, N, Prigmore, E, Gopee, NH, Chroscik, MA, Kritikaki, E, Engelbert, J, Goh, I, Chan, HM, Johnson, HF, Ellis, J, Rowe, V, Tun, W, Reynolds, G, Yang, D, Foster, AR, Gambardella, L, Winheim, E, Admane, C, Rumney, B, Steele, L, Jardine, L, Nenonen, J, Pickard, K, Lumley, J, Hampton, P, Hu, S, Liu, F, Liu, X, Horsfall, D, Basurto-Lozada, D, Grimble, L, Bacon, CM, Weatherhead, SC, Brauner, H, Wang, Y, Bai, F, Reynolds, NJ, Allen, JE, Jonak, C, Brunner, PM, Teichmann, SA, Haniffa, M. Cutaneous T cell lymphoma atlas reveals malignant TH2 cells supported by a B cell-rich tumor microenvironment. Nature Immunology 25(12):2320-2330, 2024. e-Pub 2024. PMID: 39558094.
- To, K, Fei, L, Pett, JP, Roberts, K, Blain, R, Polański, K, Li, T, Yayon, N, He, P, Xu, C, Cranley, J, Moy, M, Li, R, Kanemaru, K, Huang, N, Megas, S, Richardson, L, Kapuge, R, Perera, S, Tuck, E, Wilbrey-Clark, A, Mulas, I, Memi, F, Cakir, B, Predeus, AV, Horsfall, D, Murray, S, Prete, M, Mazin, PV, He, X, Meyer, KB, Haniffa, M, Barker, RA, Bayraktar, OA, Chedotal, A, Buckley, CD, Teichmann, SA. A multi-omic atlas of human embryonic skeletal development. Nature 635(8039):657-667, 2024. e-Pub 2024. PMID: 39567793.
- Oliver, AJ, Huang, N, Bartolome-Casado, R, Li, R, Koplev, S, Nilsen, HR, Moy, M, Cakir, B, Polański, K, Gudiño, V, Melón-Ardanaz, E, Sumanaweera, D, Dimitrov, D, Milchsack, LM, FitzPatrick, ME, Provine, NM, Boccacino, JM, Dann, E, Predeus, AV, To, K, Prete, M, Chapman, JA, Masi, AC, Stephenson, E, Engelbert, J, Lobentanzer, S, Perera, S, Richardson, L, Kapuge, R, Wilbrey-Clark, A, Semprich, CI, Ellams, S, Tudor, C, Joseph, P, Garrido-Trigo, A, Corraliza, AM, Oliver, TR, Hook, CE, James, KR, Mahbubani, KT, Saeb-Parsy, K, Zilbauer, M, Saez-Rodriguez, J, Lie Høivik, M, Baekkevold, ES, Stewart, CJ, Berrington, JE, Meyer, KB, Klenerman, P, Salas, A, Haniffa, M, Jahnsen, FL, Elmentaite, R, Teichmann, SA. Single-cell integration reveals metaplasia in inflammatory gut diseases. Nature 635(8039):699-707, 2024. e-Pub 2024. PMID: 39567783.
- Pacyna, CN, Anandapadamanaban, M, Loudon, KW, Hay, IM, Perisic, O, Li, R, Byrne, M, Allen, L, Roberts, K, Hooks, Y, Warren, AY, Stewart, GD, Clatworthy, M, Teichmann, SA, Behjati, S, Campbell, PJ, Williams, RL, Mitchell, T. Multifocal, multiphenotypic tumours arising from an MTOR mutation acquired in early embryogenesis. Oncogene 43(44):3268-3276, 2024. e-Pub 2024. PMID: 39271965.
- Xiao R, Xu D, Zhang M, Chen Z, Cheng L, Du S, Lu M, Zhou T, Li R, Bai F, Huang Y. Aneuploid embryonic stem cells drive teratoma metastasis. Nature Communications, 2024. e-Pub 2024. PMID: 38316790.
- Muyas F, Sauer CM, Valle-Inclán JE, Li R, Rahbari R, Mitchell TJ, Hormoz S, Cortés-Ciriano I. De novo detection of somatic mutations in high-throughput single-cell profiling data sets. Nature Biotechnology 42(5):758-767, 2023. e-Pub 2023. PMID: 37414936.
- Gao, Y, Hu, S, Li, R, Jin, SZ, Liu, F, Liu, X, Li, Y, Yan, Y, Liu, W, Gong, J, Yang, S, Tu, P, Shen, L, Bai, F, Wang, Y. Hyperprogression of cutaneous T cell lymphoma after anti-PD-1 treatment. JCI Insight 8(4), 2023. e-Pub 2023. PMID: 36649072.
- Li R, Ferdinand JR, Loudon KW, Bowyer GS, Laidlaw S, Muyas F, Mamanova L, Neves JB, Bolt L, Fasouli ES, J Lawson AR, Young MD, Hooks Y, W Oliver TR, Butler TM, Armitage JN, Aho T, P Riddick AC, Gnanapragasam V, Welsh SJ, Meyer KB, Warren AY, B Tran MG, Stewart GD, Cortés-Ciriano I, Behjati S, Clatworthy MR, Campbell PJ, Teichmann SA, Mitchell TJ. Mapping single cell transcriptomes in the intra-tumoral and associated territories of kidney cancer. Cancer Cell 40(12):1583-1599, 2022. e-Pub 2022. PMID: 36423636.
- Reichart D, Lindberg # EL, Maatz H, A Miranda AM, Viveiros A, Shvetsov N, Gärtner A, Nadelmann ER, Lee M, Kanemaru K, Ruiz-Orera J, Strohmenger V, DeLaughter DM, Patone G, Zhang H, Woehler A, Lippert C, Kim Y, Adami E, Gorham JM, Barnett SN, Brown K, Buchan RJ, Chowdhury RA, Constantinou C, Cranley J, Felkin LE, Fox H, Ghauri A, Gummert J, Kanda M, Li R, Mach L, McDonough B, Samari S, Shahriaran F, Yapp C, Stanasiuk C, Theotokis PI, Theis FJ, den Bogaerdt AV, Wakimoto H, Ware JS, Worth CL, R Barton PJ, Lee Y, Teichmann SA, Milting H, Noseda M, Oudit GY, Heinig M, Seidman # JG, Hubner N, Seidman CE. Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies. Science, 2022. e-Pub 2022. PMID: 35926050.
- Zhao Y, Wang T, Liu Z, Ke Y, Li R, Chen H, You Y, Wu G, Cao S, Du Z, Bai F, Yang R. Single-cell transcriptomics of immune cells in lymph nodes reveals their composition and alterations in functional dynamics during the early stages of bubonic plague. Sci China Life Sci, 2022. e-Pub 2022. PMID: 35943690.
- Liu X, Jin S, Hu S, Li R, Pan H, Liu Y, Lai P, Xu D, Sun J, Liu Z, Gao Y, Zhao Y, Liu F, Xiao Y, Li Y, Wen Y, Chen Z, Xu B, Lin Y, Ran M, Li Q, Yang S, Li H, Tu P, Haniffa M, Teichmann SA, Bai F, Wang Y. Single-cell transcriptomics links malignant T cells to the tumor immune landscape in cutaneous T cell lymphoma. Nature Communications 13(1):1158, 2022. e-Pub 2022. PMID: 35241665.
- Li R, Di L, Li J, Fan W, Liu Y, Guo W, Liu W, Liu L, Li Q, Chen L, Chen Y, Miao C, Liu H, Wang Y, Ma Y, Xu D, Lin D, Huang Y, Wang J, Bai F, Wu C. A body map of somatic mutagenesis in morphologically normal human tissues. Nature 597:398–403, 2021. e-Pub 2021. PMID: 34433965.
- Li R, YD, ZC, DX, TL, Jin S, Wang G, Liu Z, Lu M, Chen X, Xu T, Bai F. Macroscopic somatic clonal expansion in morphologically normal human urothelium. Science 370(6512):82-89, 2020. e-Pub 2020. PMID: 33004515.
- Jin S, Li R, Chen M, Yu C, Tang L, Liu Y, Li J, Liu Y, Luo Y, Zhao Y, Zhang Y, Xia T, Liu S, Liu Q, Wang G, You R, Peng J, Li J, Han F, Wang J, Chen Q, Zhang L, Mai H, Gewurz BE, Zhao B, Young LS, Zhong Q, Bai F, Zeng M. Single-cell transcriptomic analysis defines the interplay between tumor cells, viral infection, and the microenvironment in nasopharyngeal carcinoma. Cell Research 30(11):950-965, 2020. e-Pub 2020. PMID: 32901110.
- Li Y, Li X, Li H, Zhao Y, Liu Z, Sun K, Zhu X, Qi Q, An B, Shen D, Li R, Liu T, Mi J, Wang L, Yang F, Bai F, Wang J. Genomic characterisation of pulmonary subsolid nodules: mutational landscape and radiological features. Eur Respir J, 2020. e-Pub 2020. PMID: 31699841.
- Wang X, Lu Y, Song Y, Dong J, Li R, Wang G, Wang X, Zhang S, Dong Z, Lu M, Wang S, Ge L, Luo G, Ma R, Rozen SG, Bai F, Wu D, Ma L. Integrative genomic study of Chinese clear cell renal cell carcinoma reveals features associated with thrombus. Nature Communications, 2020. e-Pub 2020. PMID: 32029730.
- Fujimakia K, Li R, Chen H, Crocea KD, Zhangc HH, Xing J, Fan B, Yao G. Graded regulation of cellular quiescence depth between proliferation and senescence by a lysosomal dimmer switch. PNAS 116, 2019. e-Pub 2019. PMID: 31636214.
- Su Z, Wang Z, Ni X, Duan J, Gao Y, Zhuo M, Li R, Zhao J, Ma Q, Bai H, Chen H, Wang S, Chen X, An T, Wang Y, Tian Y, Yu J, Wang D, Xie XS, Bai F, Wang J. Inferring the Evolution and Progression of Small-Cell Lung Cancer by Single-Cell Sequencing of Circulating Tumor Cells. Clin Cancer Res 25(16):5049-5060, 2019. e-Pub 2019. PMID: 31113842.
- Xue R, Chen L, Zhang C, Fujita M, Li R, Yan SM, Ong CK, Liao X, Gao Q, Sasagawa S, Li Y, Wang J, Guo H, Huang QT, Zhong Q, Tan J, Qi L, Gong W, Hong Z, Li M, Zhao J, Peng T, Lu Y, Lim KHT, Boot A, Ono A, Chayama K, Zhang Z, Rozen SG, Teh BT, Wang XW, Nakagawa H, Zeng MS, Bai F, Zhang N. Genomic and Transcriptomic Profiling of Combined Hepatocellular and Intrahepatic Cholangiocarcinoma Reveals Distinct Molecular Subtypes. Cancer Cell 35(6):932-947.e8, 2019. e-Pub 2019. PMID: 31130341.
- Zhang J, Chen H, Li R, Taft DA, Yao G, Bai F, Xing J. Spatial clustering and common regulatory elements correlate with coordinated gene expression. PLoS Comput Biol 15(3):e1006786, 2019. e-Pub 2019. PMID: 30822341.
- Li Z, Li S, Li R, Zhu H, Liu X, Guo X, Mu L, Cai J, Bai F, Chen G, Hong D. Leukaemic alterations of IKZF1 prime stemness and malignancy programs in human lymphocytes. Cell Death Dis 9(5):526, 2018. e-Pub 2018. PMID: 29743561.
- Li R, Li X, Xue R, Yang F, Wang S, Li Y, Shen D, Sun K, Chen K, Weng W, Bai F, Wang J. Early metastasis detected in patients with multifocal pulmonary ground-glass opacities (GGOs). Thorax 73:290-292, 2017. e-Pub 2017. PMID: 29056599.
- Chen XX, Zhong Q, Liu Y, Yan SM, Chen ZH, Jin SZ, Xia TL, Li RY, Zhou AJ, Su Z, Huang YH, Huang QT, Huang LY, Zhang X, Zhao YN, Yun JP, Wu QL, Lin DX, Bai F, Zeng MS. Genomic comparison of esophageal squamous cell carcinoma and its precursor lesions by multi-region whole-exome sequencing. Nat Commun 8(1):524, 2017. e-Pub 2017. PMID: 28900112.
- Xue R, Li R, Guo H, Guo L, Su Z, Ni X, Qi L, Zhang T, Li Q, Zhang Z, Xie XS, Bai F, Zhang N. Variable extent of intra-tumor heterogeneity revealed by genomic sequencing of multiple lesions in patients with hepatocellular carcinoma. Gastroenterology 150(4):998-1008, 2016. e-Pub 2016. PMID: 26752112.
- Zhang J, Tian XJ, Zhang H, Teng Y, Li R, Bai F, Elankumaran S, Xing J. TGF-beta-induced epithelial-to-mesenchymal transition proceeds through stepwise activation of multiple feedback loops. Sci Signal 7(345):ra91, 2014. e-Pub 2014. PMID: 25270257.
Letters to the Editor
- Du Y, Li R, Chen Z, Wang X, Xu T, Bai F. Mutagenic Factors and Complex Clonal Relationship of Multifocal Urothelial Cell Carcinoma. European Urology 71: 841-843, 2016.
Patient Reviews
CV information above last modified March 26, 2026