Ziyi Li, Ph.D.
Department of Biostatistics, Division of Discovery Science
About Dr. Ziyi Li
Dr. Li is an Assistant Professor in the Department of Biostatistics. She obtained her bachelor’s degree in statistics from Peking University in 2012 and her master’s degree in biostatistics from Yale University in 2014. She obtained her PhD in Biostatistics in 2018 from Emory University. She stayed at Emory University for two more years and received postdoctoral training in both biostatistics and bioinformatics. She joined MD Anderson Cancer Center in November of 2020. She has been endeavoring to be a statistician and data scientist who develops statistical and machine learning methods and applies them to genomics, epigenetics, and computational biology. Personal website: https://ziyili20.github.io/
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Present Title & Affiliation
Primary Appointment
Assistant Professor, Department of Biostatistics, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center, Houston, TX
Dual/Joint/Adjunct Appointment
Adjunct Assistant Professor, Department of Statistics, Rice University, Houston, TX
Research Interests
My research interest is to develop useful statistical tools for the analyses of genomic, multi-omics and electronic health record data. In addition to methodology research, I am also interested in collaboration projects with Biologist and Physicians. My previous collaboration project involves the study of cancer, Alzheimer's disease, autism, obesity and cardiovascular diseases. Keywords: High-throughput data analysis; Bioinformatics; Biomarker analysis; Multi-omics; Single cell data analysis.
Education & Training
Degree-Granting Education
| 2020 | Emory University, Atlanta, TX, USA, Postdoctoral Fellow, Biostatistics and Bioinformatics |
| 2018 | Emory University, Atlanta, GA, USA, PHD, Biostatistics |
| 2014 | Yale University, New Haven, CT, USA, MPH, Biostatistics |
| 2012 | Peking University, Beijing, CHN, BS, Statistics |
Selected Publications
Peer-Reviewed Articles
- Wei Y, Zheng H, Lockyer PP, Darbaniyan F, Li Z, Kanagal-Shamanna R, Soltysiak KA, Yang H, Ganan-Gomez I, Montalban-Bravo G, Chien KS, Do KA, Daver N, Garcia-Manero G. MDM2 antagonist improves therapeutic activity of azacitidine in myelodysplastic syndromes and chronic myelomonocytic leukemia. Leuk Lymphoma 63(13):1-11, 2022. e-Pub 2022. PMID: 36059252.
- Abbas HA, Ayoub E, Sun H, Kanagal-Shamanna R, Short NJ, Issa G, Yilmaz M, Pierce S, Rivera D, Cham B, Wing S, Li Z, Hammond D, Jabbour E, Borthakur G, Garcia-Manero G, Andreeff M, Daver N, Kadia T, Konopleva M, DiNardo C, Ravandi F. Clinical and molecular profiling of AML patients with chromosome 7 or 7q deletions in the context of TP53 alterations and venetoclax treatment. Leuk Lymphoma 63(13):1-12, 2022. e-Pub 2022. PMID: 36089905.
- Li Z, Wang Y, Ganan-Gomez I, Colla S, Do KA. A machine learning-based method for automatically identifying novel cells in annotating single-cell RNA-seq data. Bioinformatics 38(21):4885-4892, 2022. PMID: 36083008.
- Min S, Xu Q, Qin L, Li Y, Li Z, Chen C, Wu H, Han J, Zhu X, Jin P. Altered hydroxymethylome in the substantia nigra of Parkinson's disease. Human Molecular Genetics 30(20):3494-3503, 2022.
- Wang Y, Flowers CR, Li Z, Huang X. CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis. Bioinformatics 38(17):4252-4254, 2022. PMID: 35801895.
- Wang Y, Flowers CR, Li Z, Huang X. CondiS: A conditional survival distribution-based method for censored data imputation overcoming the hurdle in machine learning-based survival analysis. J Biomed Inform 131:104117. e-Pub 2022. PMID: 35690348.
- Ganan-Gomez I, Yang H, Ma F, Montalban-Bravo G, Thongon N, Marchica V, Richard-Carpentier G, Chien K, Manyam G, Wang F, Alfonso A, Chen S, Class C, Kanagal-Shamanna R, Ingram JP, Ogoti Y, Rose A, Loghavi S, Lockyer P, Cambo B, Muftuoglu M, Schneider S, Adema V, McLellan M, Garza J, Marchesini M, Giuliani N, Pellegrini M, Wang J, Walker J, Li Z, Takahashi K, Leverson JD, Bueso-Ramos C, Andreeff M, Clise-Dwyer K, Garcia-Manero G, Colla S. Author Correction: Stem cell architecture drives myelodysplastic syndrome progression and predicts response to venetoclax-based therapy. Nat Med 28(5):1097, 2022. PMID: 35484266.
- Wei X, Li Z, Ji H, Wu H. EDClust: an EM-MM hybrid method for cell clustering in multiple-subject single-cell RNA sequencing. Bioinformatics 38(10):2692-2699, 2022. PMID: 35561178.
- Wang Y, Carter BZ, Li Z, Huang X. Application of machine learning methods in clinical trials for precision medicine. JAMIA Open 5(1):ooab107, 2022. e-Pub 2022. PMID: 35178503.
- Abbas HA, Sun H, Pierce SR, Kanagal-Shamanna R, Li Z, Yilmaz M, Borthakur G, DiPippo AJ, Jabbour EJ, Konopleva MY, Short NJ, DiNardo CD, Daver NG, Ravandi F, Kadia TM. Validation of Acute Leukemia French Association ALFA1200 model in older patients with AML treated with intensive chemotherapy. Blood Adv. e-Pub 2022. PMID: 35405739.
- Leung W, Teater M, Durmaz C, Meydan C, Chivu AG, Chadburn A, Rice EJ, Muley A, Camarillo JM, Arivalagan J, Li Z, Flowers CR, Kelleher NL, Danko CG, Imielinski M, Dave SS, Armstrong SA, Mason CE, Melnick AM. SETD2 haploinsufficiency enhances germinal center-associated AICDA somatic hypermutation to drive B cell lymphomagenesis. Cancer Discov. e-Pub 2022. PMID: 35443279.
- Ganan-Gomez I, Yang H, Ma F, Montalban-Bravo G, Thongon N, Marchica V, Richard-Carpentier G, Chien K, Manyam G, Wang F, Alfonso A, Chen S, Class C, Kanagal-Shamanna R, Ingram JP, Ogoti Y, Rose A, Loghavi S, Lockyer P, Cambo B, Muftuoglu M, Schneider S, Adema V, McLellan M, Garza J, Marchesini M, Giuliani N, Pellegrini M, Wang J, Walker J, Li Z, Takahashi K, Leverson JD, Bueso-Ramos C, Andreeff M, Clise-Dwyer K, Garcia-Manero G, Colla S. Stem cell architecture drives myelodysplastic syndrome progression and predicts response to venetoclax-based therapy. Nat Med 28(3):557-567, 2022. e-Pub 2022. PMID: 35241842.
- Sun X, Lin X, Li Z, Wu H. A comprehensive comparison of supervised and unsupervised methods for cell type identification in single-cell RNA-seq. Brief Bioinform 23(2), 2022. PMID: 35021202.
- Duan D, He S, Huang E, Li Z, Feng H. NeuCA web server: a neural network-based cell annotation tool with web-app and GUI. Bioinformatics. e-Pub 2022. PMID: 35176143.
- Li Z, Feng H. A neural network-based method for exhaustive cell label assignment using single cell RNA-seq data. Sci Rep 12(1):910, 2022. e-Pub 2022. PMID: 35042860.
- Qdaisat A, Yeung SJ, Rojas Hernandez CH, Samudrala P, Kamal M, Li Z, Wechsler AH. Characteristics and Outcomes of Intracranial Hemorrhage in Cancer Patients Visiting the Emergency Department. J Clin Med 11(3), 2022. e-Pub 2022. PMID: 35160096.
- Li Z, Jiang X, Wang Y, Kim Y. Applied machine learning in Alzheimer's disease research: omics, imaging, and clinical data. Emerg Top Life Sci 5(6):765-777, 2021. PMID: 34881778.
- Wang S, Yang Y, Suen A, Zhu J, Williams B, Hu J, Chen F, Kozar R, Shen S, Li Z, Jeyaram A, Jay SM, Zou L, Chao W. Role of extracellular microRNA-146a-5p in host innate immunity and bacterial sepsis. iScience 24(12):103441, 2021. e-Pub 2021. PMID: 34877498.
- Li Z, Huang Y, Patil D, Sanda MG. Covariate adjustment in continuous biomarker assessment. Biometrics. e-Pub 2021. PMID: 34811731.
- Zhang Q, Hu Q, Wang J, Miao Z, Li Z, Zhao Y, Wan B, Allen EG, Sun M, Jin P, Xu X. Stress modulates Ahi1-dependent nuclear localization of ten-eleven translocation protein 2. Hum Mol Genet 30(22):2149-2160, 2021. PMID: 34218273.
- Kang Y, Zhou Y, Li Y, Han Y, Xu J, Niu W, Li Z, Liu S, Feng H, Huang W, Duan R, Xu T, Raj N, Zhang F, Dou J, Xu C, Wu H, Bassell GJ, Warren ST, Allen EG, Jin P, Wen Z. A human forebrain organoid model of fragile X syndrome exhibits altered neurogenesis and highlights new treatment strategies. Nat Neurosci 24(10):1377-1391, 2021. e-Pub 2021. PMID: 34413513.
- Meng C, Gu L, Li Y, Li R, Cao Y, Li Z, Allen EG, Zhu D, Jin P. Ten-eleven translocation 2 modulates allergic inflammation by 5-hydroxymethylcytosine remodeling of immunologic pathways. Hum Mol Genet 30(21):1985-1995, 2021. PMID: 34165552.
- Mandel JJ, Youssef M, Yust-Katz S, Patel AJ, Jalali A, Li Z, Wu J, Ludmir EB, de Groot JF. IDH mutation status and the development of venous thromboembolism in astrocytoma patients. J Neurol Sci 427:117538, 2021. e-Pub 2021. PMID: 34146775.
- Chaftari P, Qdaisat A, Chaftari AM, Maamari J, Li Z, Lupu F, Raad I, Hachem R, Calin G, Yeung SJ. Prognostic Value of Procalcitonin, C-Reactive Protein, and Lactate Levels in Emergency Evaluation of Cancer Patients with Suspected Infection. Cancers (Basel) 13(16), 2021. e-Pub 2021. PMID: 34439240.
- Zhang W, Wu H, Li Z. Complete deconvolution of DNA methylation signals from complex tissues: a geometric approach. Bioinformatics 37(8):1052-1059, 2021. e-Pub 2020. PMID: 33135072.
- Shelly KE, Candelaria NR, Li Z, Allen EG, Jin P, Nelson DL. Ectopic expression of CGG-repeats alters ovarian response to gonadotropins and leads to infertility in a murine FMR1 premutation model. Hum Mol Genet 30(10):923-938, 2021. PMID: 33856019.
- Kuehner JN, Chen J, Bruggeman EC, Wang F, Li Y, Xu C, McEachin ZT, Li Z, Chen L, Hales CM, Wen Z, Yang J, Yao B. 5-hydroxymethylcytosine is dynamically regulated during forebrain organoid development and aberrantly altered in Alzheimer's disease. Cell Rep 35(4):109042, 2021. PMID: 33910000.
- Xu W, Zhang X, Liang F, Cao Y, Li Z, Qu W, Zhang J, Bi Y, Sun C, Zhang J, Sun B, Shu Q, Li X. Tet1 Regulates Astrocyte Development and Cognition of Mice Through Modulating GluA1. Front Cell Dev Biol 9:644375, 2021. e-Pub 2021. PMID: 34778243.
- Li Z, Chang C, Kundu S, Long Q. Bayesian generalized biclustering analysis via adaptive structured shrinkage. Biostatistics 21(3):610-624, 2020. PMID: 30596887.
- Li Z, Guo Z, Cheng Y, Jin P, Wu H. Robust partial reference-free cell composition estimation from tissue expression. Bioinformatics 36(11):3431-3438, 2020. PMID: 32167531.
- Zhang W, Li Z, Wei N, Wu HJ, Zheng X. Detection of differentially methylated CpG sites between tumor samples with uneven tumor purities. Bioinformatics 36(7):2017-2024, 2020. PMID: 31769783.
- Qin L, Xu Q, Li Z, Chen L, Li Y, Yang N, Liu Z, Guo J, Shen L, Allen EG, Chen C, Ma C, Wu H, Zhu X, Jin P, Tang B. Ethnicity-specific and overlapping alterations of brain hydroxymethylome in Alzheimer's disease. Hum Mol Genet 29(1):149-158, 2020. PMID: 31814020.
- Li Z, Wu Z, Jin P, Wu H. Dissecting differential signals in high-throughput data from complex tissues. Bioinformatics 35(20):3898-3905, 2019. PMID: 30903684.
- Li Z, Wu H. TOAST: improving reference-free cell composition estimation by cross-cell type differential analysis. Genome Biol 20(1):190, 2019. e-Pub 2019. PMID: 31484546.
- Li Z, Roberts K, Jiang X, Long Q. Distributed learning from multiple EHR databases: Contextual embedding models for medical events. J Biomed Inform 92:103138, 2019. e-Pub 2019. PMID: 30825539.
- Cheng Y, Sun M, Chen L, Li Y, Lin L, Yao B, Li Z, Wang Z, Chen J, Miao Z, Xin N, Huang L, Allen EG, Wu H, Xu X, Jin P. Ten-Eleven Translocation Proteins Modulate the Response to Environmental Stress in Mice. Cell Rep 25(11):3194-3203.e4, 2018. PMID: 30540950.
- Cheng Y, Li Z, Manupipatpong S, Lin L, Li X, Xu T, Jiang YH, Shu Q, Wu H, Jin P. 5-Hydroxymethylcytosine alterations in the human postmortem brains of autism spectrum disorder. Hum Mol Genet 27(17):2955-2964, 2018. PMID: 29790956.
- Prout Parks E, Moore RH, Li Z, Bishop-Gilyard CT, Garrett AR, Hill DL, Bruton YP, Sarwer DB. Assessing the Feasibility of a Social Media to Promote Weight Management Engagement in Adolescents with Severe Obesity: Pilot Study. JMIR Res Protoc 7(3):e52, 2018. e-Pub 2018. PMID: 29555623.
- Hu YJ, Schmidt AF, Dudbridge F, Holmes MV, Brophy JM, Tragante V, Li Z, Liao P, Quyyumi AA, McCubrey RO, Horne BD, Hingorani AD, Asselbergs FW, Patel RS, Long Q, The GENIUS-CHD Consortium. Impact of Selection Bias on Estimation of Subsequent Event Risk. Circ Cardiovasc Genet 10(5), 2017. PMID: 28986451.
- Li L, Zang L, Zhang F, Chen J, Shen H, Shu L, Liang F, Feng C, Chen D, Tao H, Xu T, Li Z, Kang Y, Wu H, Tang L, Zhang P, Jin P, Shu Q, Li X. Fat mass and obesity-associated (FTO) protein regulates adult neurogenesis. Hum Mol Genet 26(13):2398-2411, 2017. PMID: 28398475.
- Li Z, Safo SE, Long Q. Incorporating biological information in sparse principal component analysis with application to genomic data. BMC Bioinformatics 18(1):332, 2017. e-Pub 2017. PMID: 28697740.
- Lal BK, Zhou W, Li Z, Kyriakides T, Matsumura J, Laderle FA, Freischlag J, OVER Veterans Affairs Cooperative Study Group. Predictors and outcomes of endoleaks in the Veterans Affairs Open Versus Endovascular Repair (OVER) trial of abdominal aortic aneurysms. Journal of vascular surgery 62(6):1394-1404, 2015.
Abstracts
- Chien K, Kim K, Li Z, Shamanna RK, Ong F, Bravo GM, Kadia T, Jabbour E, Pemmaraju N, Hammond D, Short N.. MDS-407 Disease Characteristics and Outcomes of Hypomethylating Agent Failure in Patients With Myelodysplastic Syndromes. Clinical Lymphoma Myeloma and Leukemia(22):311, 2022.
- Kim, K., Ong, F., Li, Z., Shamanna, R.K., Bravo, G.M., Kadia, T., Jabbour, E., Pemmaraju, N., Hammond, D., Short, N. and Ravandi, F.. MDS-431 Outcomes of Transformation to Acute Myeloid Leukemia after Hypomethylating Agent Therapy in Patients With Myelodysplastic Syndromes. Clinical Lymphoma Myeloma and Leukemia(22):S313-S314, 2022.
Patient Reviews
CV information above last modified August 28, 2024