Publications
Ziyi’s Google Scholar
Methodology Works
[1] Ziyi Li, Sandra Safo, Qi Long. “Incorporating Biological Information in Sparse Principal Component Analysis with Application to Genomic Data.” BMC Bioinformatics 18.1 (2017): 332.
[2] Ziyi Li†, Changgee Chang†, Suprateek Kundu, Qi Long. “Bayesian Biclustering Analysis via Adaptive Structured Shrinkage.” Biostatistics (2018) 00, pp. 1-15.
[3] Ziyi Li, Xiaoqian Jiang and Qi Long. “Distributed Learning from Multiple EHR Databases: Contextual Embedding Models for Medical Events.” Journal of Biomedical Informatics (2019): 103138.
[4] Ziyi Li, Zhijin Wu, Peng Jin, Hao Wu. “Dissecting differential signals in high-throughput data from complex tissues.” Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 3898–3905, https://doi.org/10.1093/bioinformatics/btz196.
[5] Ziyi Li, Hao Wu. “Improving reference-free cell composition estimation by cross-cell type differential analysis.” Genome Biology 20.1 (2019): 1-17
[6] Weiwei Zhang†, Ziyi Li†, Nana Wei, Hao Wu, Xiaoqi Zheng. “Detection of differentially methylated CpG sites between tumor samples with uneven tumor purities.” Bioinformatics, Volume 36, Issue 7, 1 April 2020, Pages 2017–2024, https://doi.org/10.1093/bioinformatics/btz885.
[7] Ziyi Li#;, Zhenxing Guo, Ying Cheng, Peng Jin, Hao Wu#;. “Robust partial reference-free cell composition estimation from tissue expression.” Bioinformatics, Volume 36, Issue 11, June 2020, Pages 3431–3438, https://doi.org/10.1093/bioinformatics/btaa184.
[8] Weiwei Zhang, Hao Wu#;, Ziyi Li#;. “Complete deconvolution of DNA methylation signals from complex tissues: a geometric approach.” Bioinformatics, 37, no. 8 (2021): 1052-1059.
[9] Ziyi Li, Yijian Huang, Datta Patil, Martin G. Sanda. “Covariate adjustment in continuous biomarker assessment.” Biometrics, in press.
[10] Ziyi Li#;, Hao Feng#;. “A neural network based exhaustive cell annotation method for single cell RNA-seq transcripts.” Scientific Reports, in press.
[11] Ziyi Li, Xiaoqian Jiang, Yizhuo Wang, Yejin Kim; Applied machine learning in Alzheimer’s disease research: omics, imaging, and clinical data. Emerg Top Life Sci 2021; ETLS20210249. doi: https://doi.org/10.1042/ETLS20210249
[12] Yizhuo Wang, Bing Z. Carter, Ziyi Li#;, Xuelin Huang#;. “Application of machine learning methods in clinical trials with response-adaptive randomization.” JAMIA, in press.
[13] Xin Wei†, Ziyi Li†, Hao Wu. “EDClust: An EM-MM hybrid method for cell clustering in multiple-subject single-cell RNA sequencing.” Accepted for Bioinformatics.
[14] Xiaobo Sun, Xiaochu Lin, Ziyi Li, Hao Wu. “A comprehensive comparison of supervised and unsupervised methods for cell type identification in single cell RNA-seq.” Accepted for Briefs in Bioinformatics.
[15] Duan, Daoyu, Sijia He, Emina Huang, Ziyi Li, and Hao Feng. “NeuCA web server: a neural network-based cell annotation tool with web-app and GUI.” Bioinformatics. 2022 Feb 17;38(8):2361–3.
[16] Yizhuo Wang, Christopher Flowers, Ziyi Li#;, Xuelin Huang#;. “A conditional survival distribution-based method for censored data imputation: overcoming the hurdle in machine learning-based survival analysis”. Journal of Biomedical Informatics 2022 Jul;131:104117.
[17] Yizhuo Wang, Christopher Flowers, Ziyi Li#;, Xuelin Huang#;. “CondiS Web App: Imputation of censored lifetimes for machine learning-based survival analysis.” Bioinformatics. 2022 Jul 8:btac461.
[18] Ziyi Li#;, Yizhuo Wang, Irene Ganan-Gomez, Simona Colla, Kim-Anh Do#;. “A machine learning-based method for automatically identifying novel cells in annotating single cell RNA-seq data.” Bioinformatics 38.21 (2022): 4885-4892.
[19] Guanqun Meng, Wen Tang, Emina Huang, Ziyi Li, Hao Feng. “A Comprehensive Assessment of Cell Type-specific Differential Expression Methods in RNA-seq Data.” Briefings in Bioinformatics. 2022 Dec 6.
[20] Ziyi Li, Yijian Huang, Datta Patil, Mark Rubin, Martin G. Sanda. “Covariate-specific evaluation of continuous biomarkers.” Statistics in Medicine 42.7 (2023): 953-969.
[21] Luxiao Chen, Ziyi Li, Hao Wu. “Incorporating cell type hierarchy improves cell type specific differential analyses in bulk omics data.” Genome Biology 24.1 (2023): 1-26.
[22] Ziyi Li, Yu Shen, Jing Ning. “Accommodating time-varying heterogeneity in risk estimation under the Cox model: a transfer learning approach.” Journal of the American Statistical Association (2023): 1-19.
[23] Ruoxing Li, Jianjun Zhang, Ziyi Li#. “EasyCellType: Marker based cell type annotation by automatically querying multiple databases.” Bioinformatics Advances 3.1 (2023): vbad029.
[24] Ruoxing Li, Mehmet Altan, Alexandre Reuben, Ruitao Lin, John V. Heymach, Hai Tran, Runzhe Chen, Latasha Little, Shawna Hubert, Jianjun Zhang#, Ziyi Li#. “A novel statistical method for decontaminating T-cell receptor sequencing data.” Briefings in Bioinformatics (2023): bbad230.
[25] Hao Feng, Guanqun Meng, Tong Lin, Hemang Parikh, Yue Pan, Ziyi Li, Jeffery Krischer, Qian Li. “ISLET: individual-specific reference panel recovery improves cell-type-specific inference.” Genome Biology 24.1 (2023): 174.
[26] Sunyi Chi, Christopher R. Flowers, Ziyi Li, Xuelin Huang, Peng Wei. “MASH: Mediation Analysis of Survival Outcome and High-Dimensional Omics Mediators with Application to Complex Diseases. “ Ann Appl Stat. 2024 Jun;18(2):1360-1377. doi: 10.1214/23-aoas1838. Epub 2024 Apr 5. PMID: 39328363; PMCID: PMC11426188.
[27] Yuanxin Wang, Vakul Mohanty, Jinzhuang Dou, Ziyi Li, Ken Chen. “Identifying and characterizing transition cells in developmental processes from scRNA-seq data.” Under invited revision.
[28] Peng Yang#, Shawna M. Hubert, P. Andrew Futreal, Xingzhi Song, Jianhua Zhang, J. Jack Lee, Ignacio Wistuba, Ying Yuan, Jianjun Zhang, Ziyi Li#. “A novel Bayesian model for assessing intratumor heterogeneity of tumor infiltrating leukocytes with multi-region gene expression sequencing.” Ann. Appl. Stat. 18(3): 1879-1898 (September 2024). DOI: 10.1214/23-AOAS1862. [An earlier version of this work won 2023 ASA SGG student paper award].
[29] Ziyi Li#, Ruoxing Li, Irene Ganan-Gomez, Hussein A. Abbas, Guillermo Garcia-Manero, Wei Sun#. “Accurate identification of locally aneuploid cells by incorporating cytogenetic information in single cell data analysis.” Sci Rep 14.1 (2024): 24152.
[30] Yizhuo Wang, Christopher Flowers, Michael Wang, Xuelin Huang#, Ziyi Li#. “CASi: A multi-timepoint scRNAseq data analysis framework.” Sci Rep 14, 10633 (2024). https://doi.org/10.1038/s41598-024-58566-x.
[31] Yue Lyu, Chong Wu, Wei Sun, Ziyi Li#. “Regional analysis to delineate intrasample heterogeneity with RegionalST.” Bioinformatics. 2024 Apr 1;40(4):btae186.
[32] Ruoxing Li, Jianjun Zhang, Ziyi Li#. “A Systematic Benchmark of Clustering and Antigen-specific Prediction Methods using T Cell Receptor Sequencing Data.” Submitted.
[33] Yue Lyu, Steven H. Lin, Hao Wu, Ziyi Li#. “SCIntRuler: Guiding the integration of multiple single-cell RNA-seq datasets with a novel statistical metric.” Bioinformatics. 2024 Sep 2;40(9):btae537. doi: 10.1093/bioinformatics/btae537. PMID: 39226185; PMCID: PMC11415828.
[34] Zhining Sui, Ziyi Li, Wei Sun. “Exploit Spatially Resolved Transcriptomic Data to Infer Cellular Features from Pathology Imaging Data.” Under review.
[35] Chenxuan Zang, Charles C. Guo, Peng Wei#, Ziyi Li#. “TUSCAN: Tumor segmentation and classification analysis in spatial transcriptomics.” Under review.
[36] Lan Shui, Anirban Maitra, Ying Yuan, Ken Lau, Harsimran Kaur, Liang Li#, Ziyi Li#, and for the Translational and Basic Science Research in Early Lesions (TBEL) Program. “PoweREST: Statistical Power Estimation for Spatial Transcriptomics Experiments to Detect Differentially Expressed Genes Between Two Conditions.” Submitted.
[37] Eric Li, Liang Li#, Ziyi Li#. “Delineating the Spatial Patterns of Cell Type-Specific Stemness Using a Statistical Deconvolution Model.” Submitted.
† = co-first authorship; these authors contributed equally
#; = corresponding authorship
Collaboration works
[1] Lal, Brajesh K., Wei Zhou, Ziyi Li, Tassos Kyriakides, Jon Matsumura, Frank A. Lederle, Julie Freischlag, and OVER Veterans Aairs Cooperative Study Group. “Predictors and outcomes of endoleaks in the Veterans Aairs Open Versus Endovascular Repair (OVER) Trial of Abdominal Aortic Aneurysms.” Journal of vascular surgery 62, no. 6 (2015): 1394-1404.
[2] Yi-Juan Hu, Amand F Schmidtb, Frank Dudbridge, Michael V Holmes, James M Brophy, Vinicius Tragante, Ziyi Li, Peizhou Liao, Ray McCubrey, Benjamin Horne, Aroon Hingorani, Folkert Asselbergs, Riyaz Patel, Qi Long on behalf of the GENIUS-CHD Consortium. “Impact of Selection Bias on Estimation of Subsequent Event RiskCLINICAL PERSPECTIVE.” Circulation: Cardiovascular Genetics. 2017 Oct 1;10(5):e001616.
[3] Liping Li, Liqun Zang, Feiran Zhang, Junchen Chen, Hui Shen, Liqi Shu, Feng Liang, Chunyue Feng, Deng Chen, Huikang Tao, Tianlei Xu, Ziyi Li, Yunhee Kang, Hao Wu, Lichun Tang, Pumin Zhang, Peng Jin, Qiang Shu, Xuekun Li. “Fat mass and obesity-associated (FTO) protein regulates adult neurogenesis.” Human Molecular Genetics, Volume 26, Issue 13, 1 July 2017, Pages 23982411
[4] Elizabeth P. Parks, Renee H. Moore, Ziyi Li, Chanelle T. Bishop-Gilyard, David B. Sarwer. “Assessing the Feasibility of a Social Media to Promote Weight Management Engagement in Adolescents with Severe Obesity: Pilot Study.” JMIR research protocols 7.3 (2018).
[5] Ying Cheng, Ziyi Li, Sasicha Manupipatpong, Li Lin, Xuekun Li, Tianlei Xu, Yong-hui Jiang, Qiang Shu, Hao Wu, and Peng Jin. “5-hydroxymethylcytosine alterations in the human postmortem brains of autism spectrum disorder.” Human molecular genetics (2018).
[6] Ying Cheng , Miao Sun, Li Chen, Yujing Li, Li Lin, Bing Yao, Ziyi Li, Zhiqin Wang, Jack Chen, Zhigang Miao, Ning Xin, Luoxiu Huang, Emily Allen, Hao Wu, Xingshun Xu, Peng Jin. “Ten-Eleven Translocation Proteins Modulate the Response to Environmental Stress in Mice.” Cell Reports. 2018 Dec 11;25(11):3194-203.
[7] Lixia Qin, Qian Xu, Ziyi Li, Li Chen, Yujing Li, Nannan Yang, Zhenhua Liu, Jifeng Guo, Lu Shen, Chao Shen, Chao Ma, Hao Wu, Peng Jin, Xiongwei Zhu, Beisha Tang. “Identification of aberrant DNA hydroxymethylation in the human frontal cortex of Alzheimer’s disease patients of Chinese origin.” Human Molecular Genetics 29.1 (2020): 149-158.
[8] Janise N. Kuehner, Junyu Chen, Emily C. Bruggeman, Chongchong Xu, Feng Wang, Yangping Li, Chadwick M. Hales, Ziyi Li, Li Chen, Zhexing Wen, Jingjing Yang, and Bing Yao. “5-hydroxymethylcytosine is Dynamically Regulated During Forebrain Organoid Development and Prematurely Altered in Forebrain Organoids of Alzheimer’s Disease.” Cell Reports 35.4 (2021): 109042.
[9] Katharine E Shelly, Nicholes R Candelaria, Ziyi Li, Emily G Allen, Peng Jin, David L Nelson. “Ectopic expression of CGG-repeats alters ovarian response to gonadotropins and leads to infertility in a murine FMR1 premutation model.” Human molecular Genetics 30.10 (2021): 923-938.
[10] Jacob J. Mandela, Michael Youssefg, Shlomit Yust-Katz, Akash J. Patel, Ali Jalali, Ziyi Li, Jimin Wu, Ethan B. Ludmir, John F. de Groot. “IDH mutation status and the development of venous thromboembolism in astrocytoma patients.” Journal of the Neurological Sciences (2021).
[11] Yunhee Kang, Ying Zhou, Yujing Li, Yanfei Han, Jie Xu, Weibo Niu, Ziyi Li, Shiying Liu, Hao Feng, Wen Huang, Ranhui Duan, Tianmin Xu, Nisha Raj, Hao Wu, Gary J Bassell, Stephen T Warren, Emily G Allen, Peng Jin, and Zhexing Wen. “Fragile X mental retardation protein regulates neurogenesis and neuronal differentiation in a human organoid model of fragile X syndrome.” Nature Neuroscience (2021).
[12] Aiham Qdaisat, Sai-Ching Jim Yeung, Cristhiam M Rojas Hernandez, Pavani Samudrala, Mona Kamal, Ziyi Li, Adriana H. Wechsler. “Characteristics and outcomes of intracranial hemorrhage in cancer patients visiting the emergency department.” Journal of Clinical Medicine 11.3 (2022): 643.
[13] Qian Zhang, Qicheng Hu, Junjie Wang, Zhigang Miao, Ziyi Li, Yuwen Zhao, Bo Wan, Emily G Allen, Miao Sun, Peng Jin, Xingshun Xu. “Stress modulates Ahi1-dependent nuclear localization of Ten-Eleven Translocation Protein 2.” Human molecular genetics 30.22 (2021): 2149-2160.
[14] Cuida Meng, Lei Gu, Yujing Li, Ronghua Li, Yiqu Cao, Ziyi Li, Emily G Allen, Dongdong Zhu, Peng Jin. “Ten-Eleven Translocation 2 Modulates allergic inflammation by 5-hydroxymethylcytosine remodeling of immunologic pathways.” Human molecular genetics 30.21 (2021): 1985-1995.
[15] Xu, Weize, Xicheng Zhang, Feng Liang, Yuhang Cao, Ziyi Li, Wenzheng Qu, Jinyu Zhang, Bingui Sun, Qiang Shu, Xuekun Li. Tet1 Regulates Astrocyte Development and Cognition of Mice Through Modulating GluA1. Front Cell Dev Biol. 2021 Oct 28;9:644375. doi: 10.3389/fcell.2021.644375. PMID: 34778243; PMCID: PMC8581465.
[16] Irene Ganan-Gomez, Hui Yang, Feiyang Ma, Natthakan Thongon, Ms Valentina Marchica, Guillaume Richard-Carpentier, Guillermo Montalban-Bravo, Ganiraju Manyam, Feng Wang, Ana Alfonso, Andrea Santoni, Mr Shuaitong Chen, Caleb Class, Kelly Chien, Rashmi Kanagal Shamanna, Justin Ingram, Yamini Ogoti, Ashley Rose, Sanam Loghavi, Pamela Lockyer, Benedetta Cambò, Ms Sarah Schneider, Vera Adema, Mr Michael McLellan, John Garza, Matteo Marchesini, Professor Nicola Giuliani, Matteo Pellegrini, Jing Wang, Jason Walker, Ziyi Li, Koichi Takahashi, Stephanie Halene, Joel Leverson, Carlos Bueso-Ramos, Karen Clise-Dwyer, Guillermo Garcia-Manero “Stem cell-specific survival pathways drive the progression of myelodysplastic syndromes.” Nature Medicine, 2022 Mar 3:1-1.
[17] Wang, Sheng, Yang Yang, Andrew Suen, Jing Zhu, Brittney Williams, Jiang Hu, Fengqian Chen, Rosemary Kozar, Shiqian Shen, Ziyi Li, Anjana Jeyaram, Steven M.Jay, Lin Zou, Wei Chao. “Role of Extracellular MicroRNA-146a-5p in Host Innate Immunity and Bacterial Sepsis.” iScience 24.12 (2021).
[18] Wilfred Leung,Matthew R. Teater,Ceyda Durmaz,Cem Meydan,Ms. Alexandra G. Chivu,Edward J. Rice,Ashlesha Muley,Jeannie M. Camarillo,Jaison Arivalagan,Amy Chadburn,Neil L. Kelleher,Charles G. Danko,Marcin Imielinski,Sandeep S. Dave,Scott A. Armstrong ,Christopher E. Mason,Ziyi Li,Christopher R. Flowers “SETD2 haploinsufficiency enhances germinal center-associated AICDA somatic hypermutation to drive B cell lymphomagenesis” Cancer discovery 12.7 (2022): 1782-1803.
[19] Hussein A. Abbas, Edward Ayoub, Rashmi Kanagal, Hanxiao Sun, Nicholas Short, Musa Yilmaz, Sherry Pierce, Brent Cham, Shane Wing, Ziyi Li, Danielle Hammond, Elias Jabbour, Guillermo Garcia-Manero, Michael Andreeff, Naval Daver, Tapan Kadia, Marina Konopleva, Courtney DiNardo, Farhad Ravandi “Validation of Acute Leukemia French Association ALFA1200 Model in Older AML Treated with Intensive Chemotherapy.” Blood advances (2022): bloodadvances-2022007172.
[20] Qiong Liu, Kailin Zhang, Yunhee Kang, Penghui Deng, Yujing Li, Yangping Li, Yun Tian, Qiying Sun, Yu Tang, Keqin Xu, Jun-Ling Wang, Jifeng Guo, Jia-Da Li, Kun Xia, Qingtuan Meng, Emily Allen, Zhexing Wen, Ziyi Li, Hong Jiang, Lu Shen, Ranhui Duan, Bing Yao, Beisha Tang, Yongcheng Pan. “GGC repeat expansion within NOTCH2NLC causes behavioral deficits and neurodegeneration through altering splicing and context-dependent gene expression.” Science Advances 8(47): eadd6391.
[21] Weihua Ding, Lukas Fischer, Qian Chen, Ziyi Li, Liuyue Yang, Zerong You, Kun Hu, Lucy Chen, Peter Hu, Wei Chao, Peng Jin, Jianren Mao, Guoping Feng, Mark T. Harnett, and Shiqian Shen. “Highly synchronized cortical neuronal activity in response to neuropathic pain.” J Clin Invest. 2023;133(5):e166408. https://doi.org/10.1172/JCI166408.
[22] Ashley Aaroe, Razelle Kurzrock, Gaurav Goyal, Aaron Goodman, Harsh Patel, Gordon Ruan, Gary Ulaner, Jason Young, Ziyi Li, Derek Dustin, Ronald Go, Eli Diamond, and Filip Janku. “Successful Treatment of Non-Langerhans Cell Histiocytosis with the MEK Inhibitor Trametinib.” Clinical, Cosmetic and Investigational Dermatology (2022): 1575-1582.
[23] Aiham Qdaisat; Adriana H Wechsler; Cristhiam M Rojas Hernandez; Pavani Samudrala; Mona Kamal; Ziyi Li; Sai-Ching Jim Yeung. “Characteristics and outcomes of intracranial hemorrhage in cancer patients visiting the emergency department.”Journal of Clinical Medicine 11.3 (2022): 643.
[24] Lixia Qin, Qian Xu, Shishi Min, Yujing Li, Ziyi Li, Chao Chen, Hao Wu, Junhai Han, Xiongwei Zhu, Peng Jin, Beisha Tang. “Altered Hydroxymethylome in the Substantia Nigra of Parkinson’s Disease.” Human Molecular Genetics 31.20 (2022): 3494-3503.
[25] Hong Zheng; Pamela Pennington Lockyer; Naran Bao; Faezeh Darbaniyan; Ziyi Li; Rashmi Kanagal-Shamanna; Kelly A. Soltysiak; Hui Yang; Irene Ganan-Gomez; Guillermo Montalban-Bravo; Kelly S. Chien; Kim-Anh Do; Naval Daver; Guillermo Garcia-Manero; Yue Wei. “MDM2 antagonist improves the therapeutic activity of azacitidine in myelodysplastic syndromes and chronic myelomonocytic leukemia. “ Leukemia & Lymphoma (2022): 1-11.
[26] Hussein A. Abbas, Edward Ayoub, Hanxiao Sun, Rashmi Kanagal-Shamanna, Nicholas J. Short, Ghayas Issa, Musa Yilmaz, Sherry Pierce, Daniel Rivera, Brent Cham, Shane Wing, Ziyi Li, Danielle Hammond, Elias Jabbour, Gautam Borthakur, Guillermo Garcia-Manero, Michael Andreeff, Naval Daver, Tapan Kadia, Marina Konopleva, Courtney DiNardo & Farhad Ravandi (2022) “Clinical and molecular profiling of AML patients with chromosome 7 or 7q deletions in the context of TP53 alterations and venetoclax treatment,” Leukemia & Lymphoma, DOI: 10.1080/10428194.2022.2118533
[27] Kevin Liu, Allison Palmiero, Nitish Chopra, Brett Velasquez, Ziyi Li, Sam Beddara, Emil Schüler. “Dual beam-current transformer design for monitoring and reporting of electron ultra-high dose rate (FLASH) beam parameters.” Journal of applied clinical medical physics 24.2 (2023): e13891.
[28] Mihnea P. Dragomir, Enrique Funtes-Mattei, Melanie Winkle, Keishi Okubo, Recep Bayraktar, Erik Knutsen, Aiham Qdaisat, Meng Chen, Yongfeng Li, Masayoshi Shimizu, Lan Pang, Kevin Liu, Xiuping Liu, Simone Anfossi, Huanyu Zhang, Drazen Papić, Ines Koch, Anh M. Tran, Swati Mohapatra, Anh Ton, Mecit Kaplan, Mathew Anderson 6, Spencer Rothfuss, Robert Silasi, Ravi S. Keshari, Manuela Ferracin, Cristina Ivan, Cristian Rodriguez-Aguayo, Gabriel Lopez-Berestein, Constantin Georgescu, Pinaki P. Banjeree, Rafet Basar, Ziyi Li, David Horst, Catalin Vasilescu, Maria Teresa Sabrina Bertilaccio, Katy Rezvani, Florea Lupu, Sai-Ching Jim Yeung, George A. Calin. “Anti-miR-93-5p therapy prolongs sepsis survival by restoring the peripheral immune response.” J Clin Invest. 2023 Jul 17;133(14):e158348. doi: 10.1172/JCI158348. PMID: 37261908; PMCID: PMC10348769.
[29] Samuel Urrutia, Ziyi Li, Emmanuel Almanza, Alex Bataller, Rashmi Kanagal-Shamanna, Jayastu Senapati, Koji Sasaki, Kelly Chien, Guillermo Montalban-Bravo, Courtney DiNardo, Gautham Borthakur, Hagop Kantarjian, Carlos Bueso-Ramos, Sherry Pierce, Guillermo Garcia-Manero. “Characteristics of patients with myelodysplastic syndrome (MDS) and spliceosome mutations (SM).” Leukemia (2023): 1-4.
[30] Kelly S Chien, Faustine Ong, Kunhwa Kim, Ziyi Li, Rashmi Kanagal Sharmanna, Courtney D DiNardo, Koichi Takahashi, Guillermo Montalban Bravo, Danielle Hammond, Koji Sasaki, Sherry A Pierce, Hagop M Kantarjian, Guillermo Garcia-Manero. “Cancer Patients with Clonal Hematopoiesis Die from Primary Malignancy or Comorbidities Despite Higher Rates of Transformation to Myeloid Neoplasms.” Cancer Medicine, 13(5), e7093.
[31] Kelly S. Chien, Ziyi Li, Kunhwa Kim, Rashmi Kanagal Shamanna, Faustine Ong, Guillermo Montalban Bravo, Tapan M. Kadia, Elias J. Jabbour, Naveen Pemmaraju, Danielle E. Hammond, Nicholas J. Short, Farhad Ravandi, Yesid Alvarado, Sherry A. Pierce, Xiao Qin Dong, Hui Yang, Yue Wei, Irene Ganan-Gomez, Simona Colla, Hagop M. Kantarjian, Guillermo Garcia-Manero.”Patterns of Hypomethylating Agent Failure in Patients with Myelodysplastic Syndromes.” Submitted.
[32] Simone Anfossi, Faezeh Darbaniyan, Joseph Quinlan, Steliana Calin, Masa Shimizu, Meng Chen, Paola Rausseo, Michael Winters, Elena Bogatenkova, Kim-Anh Do, Ivan Martinez, Ziyi Li, Ignacio Wistuba, George A. Calin. “microRNAs are frequently located at COVID-19 genomic risk regions and act as plasma prognosis biomarkers of COVID-19 in cancer patients.” Accepted to Molecular Cancer.
[33] Samuel Urrutia, Ziyi Li, Alex Bataller, Emmanuel Almanza, Guillermo Montalban-Bravo, Elias Jabbour, Tapan Kadia, Farhad Ravandi3, Gautham Borthakur, Rashmi Kanagal-Shamanna, Carlos Bueso-Ramos, Sherry Pierce, Hagop Kantarjian, Guillermo Garcia-Manero, Kelly Chien. “Performance of IPSS-M in patients with myelodysplastic syndrome after hypomethylating agent failure.” American journal of hematology 98.10 (2023): E281-E284.
[34] Andrew O. Suen, Fengqian Chen, Sheng Wang, Ziyi Li, Jing Zhu, Olivia Conn, Kerri Lopez, Ping Cui, Laurence Wechsler, Alan Cross, Gary Fiskum, Rosemary Kozar, Peter Hu, Catriona Miller, Lin Zou, Brittney Williams, Wei Chao. “Extracellular RNA Sensing Mediates Innate Inflammation and Organ Injury in A Murine Model of Polytrauma.” The Journal of Immunology 210.12 (2023): 1990-2000.
[35] Hiroki Akiyama, Ran Zhao, Samar Jam Yazdani, Lauren B. Ostermann, Ziyi Li, Natalia Baran, Malcolm L. Pryor, Edward Ayoub, Yuki Nishida, Po Yee Mak, Vivian R. Ruvolo, Bing Z. Carter, Michael Andreeff, and Jo Ishizawa. “Mitochondrial regulation of GPX4-mediated ferroptosis in acute myeloid leukemia.” Leukemia. 2023 Dec 26:1-2.
[36] Guillermo Montalban-Bravo, Rashmi Kanagal-Shamanna, Ziyi Li, Danielle Hammond, Kelly Chien, Juan Jose Rodriguez-Sevilla, Koji Sasaki, Elias Jabbour, Courtney DiNardo, Koichi Takahashi, Nicholas Short, Ghayas C. Issa, Naveen Pemmaraju, Tapan Kadia, Farhad Ravandi, Naval Daver, Gautam Borthakur, Sanam Loghavi, Sherry Pierce, Carlos Bueso-Ramos, Hagop Kantarjian, Guillermo Garcia-Manero. “Phenotypic Subtypes of Leukemic Transformation in Chronic Myelomonocytic Leukemia.” British Journal of Haematology (2023).
[37] Yue Wei, Hong Zheng, Pamela Pennington Lockyer, Faezeh Darbaniyan, Ziyi Li, Rashmi Kanagal-Shamanna, Hui Yang, Vera Adema, Simona Colla, and Guillermo Garcia-Manero. “Downregulation of UBA1 Expression in Myelodysplastic Syndrome.” 2024 Oct;38(10):2284-2288. doi: 10.1038/s41375-024-02364-x. Epub 2024 Aug 23. PMID: 39179668; PMCID: PMC11436355.
[38] Monica K. Wattana, Angela Lindsay, Moira Davenport, Nicholas R. Pettit, Jazmin R. Menendez, Ziyi Li, Demis N. Lipe, Aiham Qdaisat, Jason J. Bischof. “Current Gaps in Emergency Medicine Core Content Education for Oncologic Emergencies: A Targeted Needs Assessment.” AEM Educ Train. 2024 May 16;8(3):e10987. doi: 10.1002/aet2.10987. PMID: 38765712; PMCID: PMC11099727.
[39] Mehmet Altan, Ruoxing Li, Ziyi Li, Runzhe Chen, Joshua Baguley, Sheshadri Ajay, Tran Hai, Latasha D. Little, Natalie Vokes, Saumil Gaudhi, Mara B. Antonoff, Stephen G. Swisher, Greg Lizee, Alexandre Reuben, John Heymach, Jianjun Zhang. “High peripheral T cell diversity is associated with lower risk of toxicity and superior response to dual immune checkpoint inhibitor therapy in patients with metastatic NSCLC.” Under invited revision.
[40] Alexandre Bazinet, Sai Prasad Desikan, Ziyi Li, Juanjo Rodriguez-Sevilla, Sangeetha Venugopal, Samuel Urrutia, Guillermo Montalban-Bravo, Koji Sasaki, Kelly Chien, Danielle Hammond, Rashmi Kanagal-Shamanna, Irene Ganan-Gomez, Tapan Kadia, Gautam Borthakur, Courtney DiNardo, Naval Daver, Elias Jabbour, Farhad Ravandi, Hagop Kantarjian, and Guillermo Garcia-Manero. “Cytogenetic and molecular associations with outcomes in HR-MDS treated with hypomethylating agents plus venetoclax.” Clinical Cancer Research: an Official Journal of the American Association for Cancer Research (2024).
[41] Yohei Saito, Yi Xiao, Jun Yao, Yunhai Li, Wendao Liu, Hongzhong Li, Xiangliang Yuan, Weiya Xia, Ms Ping Li, Qingling Zhang, Akosua Badu-Nkansah, Ziyi Li, Yongkun Wei, Xuedong Yin, Jun Zhao, Mr Seyed Kariminia, Yao-Chung Wu, Jinyang Wang, Jun Yang, Eek-hoon Jho, Paul Chiao, Rosa Hwang, Haoqiang Ying, Huamin Wang, Zhongming Zhao, Anirban Maitra, Mien-Chie Hung, Ronald DePinho, Dihua Yu. “Chemo-induced Yap1 activation and stromal remodeling in therapeutic resistance of pancreatic cancer.” Submitted
[42] Linjie Luo, Peng Yang, Sofia Mastoraki, Xiayu Rao, Yan Wang, Nicole M. Kettner, Akshara Singareeka Raghavendra, Debasish Tripathy, Senthil Damodaran, Kelly K. Hunt, Jing Wang, Ziyi Li, Khandan Keyomarsi. “Single-Cell RNA Sequencing Identifies Molecular Biomarkers Predicting Late Progression to CDK4/6 Inhibition in Metastatic HR+/HER2- Breast Cancer.” Submitted
[42] Kevin Liu, Trey Waldrop, Edgardo Aguilar, Nefetiti Mims, Denae Neill, Abagail Delahoussaye, Ziyi Li, David Swanson, Steven H Lin, Albert C Koong, Cullen M Taniguchi, Billy W Loo, Devarati Mitra, Emil Schüler. Redefining FLASH RT: the impact of mean dose rate and dose per pulse in the gastrointestinal Accepted to the International Journal of Radiation Oncology, Biology, Physics.
[43] Kevin Liu, Uwe Titt, Nolan Esplen, Luke Connell, Elise Konradsson, Ming Yang, Xiaochun Wang, Takeshi Takaoka, Ziyi Li, Albert C. Koong, Devarati Mitra, Radhe Mohan, Billy W. Loo, Steven H. Lin, Emil Schüler. “Discordance in acute gastrointestinal toxicity between synchrotron-based proton and linac-based electron ultra-high dose rate irradiation.” Submitted.
[44] Aiham Qdaisat, Ellie Stroh, Cielito Reyes-Gibby, Monica Wattana, Jayne Viets-Upchurch, Ziyi Li, Valda Page, Huda Fatima, Patrick Chaftari and Ahmed Elsayem. “Severity of symptoms as an independent predictor of poor outcomes in patients with advanced cancer presenting to the emergency department: Secondary analysis of a prospective randomized study.” Submitted.
[45] Elina El-Badry, Luxiao Chen, Khader Ghneim, Ziyi Li, Kelsie Brooks, Jake Rhodes, Rafick-Pierre Sekaly, William Kilembe, Susan Allen, Hao Wu, Eric Hunter. “Heightened expression of type I interferon signaling genes in CD4+ T cells from acutely HIV-1 infected women contributes to lower viral loads.” Submitted.
[46] Ruparoshni Jayabalan, Ricardo Gonzalez-Delgado, Luis Castillo Montanez, Jing Pan, Ruoxing Li, Jinsam Chang, Fernanda G. Kugeratski, Shajedul Islam, Marini Thian, Andreas B. Wild, Alexander Steinkasserer, Ziyi Li, Mauro Di Pilato. “CD83 via CCR7+DC limits intratumoral CD8 responses and promotes tumor growth.” Submitted.
[47] Hao Feng, Ying Cheng, Ziyi Li, Hao Wu, Peng Jin. “5-hydroxymethylcytosine alterations, cell-free DNA, aging, Alzheimer’s disease.” In preparation.
Book chapter
[1] Ziyi Li, Hao Wu. “Cell Type-Specific Analysis for High-throughput Data.” Handbook of Statistical Bioinformatics. Springer 2022. https://link.springer.com/book/10.1007/978-3-662-65902-1.