Publications

1. Kara E. Garcia, Meghana Bhaskara, Kaylin Taylor, Clemente Velasco-Annis, John Vieth, Jessica Patel, Sha Cao, Ali Gholipour, Caitlin K. Rollins, Cynthia M. Ortinau. Longitudinal magnetic resonance imaging reveals differences in cortical expansion in fetuses with congenital heart defects. Cerebral Cortex. 2025.

2. Tao Yu, Kevin Van der Jeught, Haiqi Zhu, Zhuolong Zhou, Samantha Sharma, Sheng Liu, Ka Man So, Haniyeh Eyvani, George Earl Sandusky, Yunlong Liu, Mateusz Opyrchal, Sha Cao, Jun Wan, Chi Zhang, Xinna Zhang. Targeting Glutamate-to-Glutathione Flux Potentiates Antigen Presentation in Colorectal Cancer. Advanced Science. 2025. In press.

3. Servati M, Vaccaro CN, Diller EE, Pellegrino Da Silva R, Mafra F, Cao S, Stanley KB, Cohen-Gadol AA, Parker JG. Metabolic Insight into Glioma Heterogeneity: Mapping Whole Exome Sequencing to In Vivo Imaging with Stereotactic Localization and Deep Learning. Metabolites. 2024 Jun 16;14(6):337. doi:10.3390/metabo14060337. PMID: 38921472; PMCID: PMC11205750.

4. Chaudhuri S, Dempsey DA, Huang YN, Cao S, Chumin EJ, Craft H, Crane PK, Mukherjee S, Choi SE, Lee ML, Scollard P. Associations between Amyloid, Cardiovascular Risk, and Cognitive Function in Korean Older Adults: Insights from the KBASE Cohort. In Alzheimer's Association International Conference 2024 Jul 31. ALZ.

5. Brothwell JA, Wei YH, Wang J, Guo T, Zhang C, Fortney KR, Duplantier R, Chen L, Batteiger TA, Kaplan MH, Spinola SM, Cao S. Single cell and spatial transcriptomic profiling of H. ducreyi infection in human volunteers. mBio. 2025.

6. Wang X, Wang J, Zhao T, Wang Y, Zhang N, Zang Y, Cao S†, Zhang C†. Bias-aware Boolean Matrix Factorization Using Disentangled Representation Learning. In The 40th Conference on Uncertainty in Artificial Intelligence. 2024

7. Wan, C., Zhang, M., Dang, P., Hao W., Cao S., Li P., Zhang C. Ambiguities in neural-network-based hyperedge prediction. J Appl. and Comput. Topology (2024). https://doi.org/10.1007/s41468-024-00172-x

1. Pengtao Dang, Haiqi Zhu, Changlin Wan, Tong Zhao, Tingbo Guo, Paul Salama, Sha Cao, and Chi Zhang. Generalized matrix local low rank representation by random projection and submatrix propagation. 2023. KDD 2023 Research Track.

2. Zixuan Zhang, Haiqi Zhu, Pengtao Dang, Jia Wang, Wennan Chang, Xiao Wang, Norah Alghamdi, Alex Lu, Yong Zang, Wenzhuo Wu, Yijie Wang, Yu Zhang, Sha Cao, and Chi Zhang. Fluxestimator: a webserver for predicting metabolic flux and variations using transcriptomics data. 2023. Nucleic Acids Research 2023 Web server issue

3. Sha Cao, Wennan Chang, Changlin Wan, Xiaoyu Lu, Pengtao Dang, Xinyu Zhou, Haiqi Zhu, Jian Chen, Bo Li, Yong Zang, Yijie Wang, Chi Zhang. Pipeline for characterizing alternative mechanisms (PCAM) based on bi-clustering to study colorectal cancer heterogeneity. Computational and Structural Biotechnology Journal

4. Santhosh Kumar Pasupuleti, Baskar Ramdas, Sarah S Burns, Lakshmi Reddy Palam, Rahul Kanumuri, Ramesh Kumar, Taruni R Pandhiri, Utpal Dave, Nanda Kumar Yellapu, Xinyu Zhou, Chi Zhang, George E Sandusky, Zhi Yu, Michael C Honigberg, Alexander G Bick, Gabriel K Griffin, Abhishek Niroula, Benjamin L Ebert, Sophie Paczesny, Pradeep Natarajan, Reuben Kapur. The Journal of Clinical Investigation

5. Mahmut Mijit, Megan Boner, Ricardo A Cordova, Silpa Gampala, Eyram Kpenu, Angela J Klunk, Chi Zhang, MarK R Kelley, Kirk A Staschke, Melissa L Fishel. Activation of the integrated stress response (ISR) pathways in response to Ref-1 inhibition in human pancreatic cancer and its tumor microenvironment. Frontiers in Medicine

6. Grace Yang, Shaoyang Huang, Kevin Hu, Alex Lu, Jonathan Yang, Noah Meroueh, Pengtao Dang, Haiqi Zhu*, Sha Cao*, and Chi Zhang*. Flux estimation analysis systematically characterizes the metabolic shifts of the central metabolism pathway in human cancer. Frontiers in Oncology, Rising Star of Cancer Research 2023 special issue, 2023

7. Qiu Y, Zhao Y, Liu H, Cao S, Zhang C, Zang Y. Modified isotonic regression based phase I/II clinical trial design identifying optimal biological dose. Contemporary Clinical Trials. 2023 Mar 2:107139.

1. Baskar Ramdas, Palam Lakshmi Reddy, Raghuveer Singh Mali, Santhosh Kumar Pasupuleti, Ji Zhang, Mark R Kelley, Sophie Paczesny, Chi Zhang, Reuben Kapur. Combined heterozygosity of FLT3 ITD, TET2, and DNMT3A results in aggressive leukemia. JCI insight. 2022.

2. Wennan Chang, Chi Zhang, Sha Cao. Response to ‘Letter to the Editor: on the stability and internal consistency of component-wise sparse mixture regression based clustering’. Briefings in Bioinformatics. 2022.

3. Arafat Aljoufi+, Chi Zhang+, James Ropa, Wennan Chang, Lakshmi Reddy Palam, Scott Cooper, Baskar Ramdas, Maegan L Capitano, Hal E Broxmeyer, Reuben Kapur. Physioxia induced Downregulation of Tet2 in Hematopoietic Stem Cells contributes to Enhanced Self-renewal. Blood. 2022.

4. Cátia Gomes, Kirstin B VanderWall, Yanling Pan, Xiaoyu Lu, Sailee S Lavekar, Kang-Chieh Huang, Clarisse M Fligor, Jade Harkin, Chi Zhang, Theodore R Cummins, Jason S Meyer. Astrocytes modulate neurodegenerative phenotypes associated with glaucoma in OPTN (E50K) human stem cell-derived retinal ganglion cells. Stem cell reports. 2022

5. Yuetian Luo, Qin Ma, Chi Zhang, Anru R Zhang. Provable Second-Order Riemannian Gauss-Newton Method for Low-Rank Tensor Estimation. IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) 2022.

6. Baskar Ramdas, Lisa Deng Yuen, Lakshmi Reddy Palam, Roshini Patel, Santhosh Kumar Pasupuleti, Victoria Jideonwo, Ji Zhang, Callista Maguire, Eric Wong, Rahul Kanumuri, Chujing Zhang, George Sandusky, Rebecca J Chan, Chi Zhang, Elliot Stieglitz, Laura Haneline, Reuben Kapur. Inhibition of BTK and PI3Kδ impairs the development of human JMML stem and progenitor cells. Molecular Therapy. 2022

7. Junyi Zhou, Xiaoyu Lu, Wennan Chang, Changlin Wan, Xiongbin Lu, Chi Zhang, Sha Cao. PLUS: Predicting cancer metastasis potential based on positive and unlabeled learning. PloS Computational Biology. 2022

8. Changlin Wan, Pengtao Dang, Tong Zhao, Yong Zang, Chi Zhang, Sha Cao. Bias Aware Probabilistic Boolean Matrix Factorization. The 38th Conference on Uncertainty in Artificial Intelligence (UAI) 2022.

9. Yifei Zhang, Beibei Guo, Sha Cao, Chi Zhang, Yong Zang. SCI: A Bayesian adaptive phase I/II dose‐finding design accounting for semi‐competing risks outcomes for immunotherapy trials. Pharmaceutical Statistics. 2022

10. Mahmut Mijit, Randall Wireman, Lee Armstrong, Silpa Gampala, Zonera Hassan, Christian Schneeweis, Guenter Schneider, Chi Zhang, Melissa L Fishel, Mark R Kelley. RelA Is an Essential Target for Enhancing Cellular Responses to the DNA Repair/Ref-1 Redox Signaling Protein and Restoring Perturbated Cellular Redox Homeostasis in Mouse PDAC Cells. Frontiers in oncology. 2022. DOI: 10.3389/fonc.2022.826617 

11. Yi Zhou, Wennan Chang, Xiaoyu Lu, Jin Wang, Chi Zhang, Ying Xu. Acid-Base Homeostasis and Implications to the Phenotypic Behaviors of Cancer. Genomics, Proteomics, Bioinformatics. 2022 DOI: 10.1016/j.gpb.2022.06.003

1. Norah Alghamdi+, Wennan Chang+, Pengtao Dang, Xiaoyu Lu, Changlin Wan, Silpa Gampala, Zhi Huang, Jiashi Wang, Qin Ma, Yong Zang, Melissa Fishel, Sha Cao^, Chi Zhang^. A graph neural network model to estimate cell-wise metabolic flux using single cell RNA-seq data. Genome Research. [paper] [github]

2. Wennan Chang, Pengtao Dang, Xiaoyu Lu, Yue Fang, Tong Zhao, Bo Li, Chi Zhang, and Sha Cao. Spatially and Robustly Hybrid Mixture Regression Model for Inference of Spatial Dependence. 2021 IEEE International Conference on Data Mining (ICDM), 2021, pp. 31-40, doi: 10.1109/ICDM51629.2021.00013.

3. Changlin Wan, Muhan Zhang, Wei Hao, Sha Cao^, Pan Li^, Chi Zhang^. Principled Hyperedge Prediction with Structural Spectral Features and Neural Networks (submitted to NeurIPS 2021). [abstract] [paper]

4. Wennan Chang, Changlin Wan, Yong Zang, Chi Zhang†, and Sha Cao†. Supervised clustering of high dimensional data using regularized mixture modeling. Briefings in Bioinformatics. 2021 Jul;22(4):bbaa291.

5. Ricardo Melo Ferreira, Angela R Sabo, Seth Winfree, Kimberly S Collins, Danielle Janosevic, Connor J Gulbronson, Ying-Hua Cheng, Lauren Casbon, Daria Barwinska, Michael J Ferkowicz, Xiaoling Xuei, Chi Zhang, Kenneth W Dunn, Katherine J Kelly, Timothy A Sutton, Takashi Hato, Pierre C Dagher, Tarek M El-Achkar, Michael T Eadon. Integration of spatial and single cell transcriptomics localizes epithelial-immune cross-talk in kidney injury. JCI insight. https://insight.jci.org/articles/view/147703

6. Hanchen Xu, Kevin Van der Jeught, Zhuolong Zhou, Lu Zhang, Tao Yu, Yifan Sun, Yujing Li, Changlin Wan, Ka Man So, Degang Liu, Michael Frieden, Yuanzhang Fang, Amber L Mosley, Xiaoming He, Xinna Zhang, George E Sandusky, Yunlong Liu, Samy O Meroueh, Chi Zhang, Aruna B Wijeratne, Cheng Huang, Guang Ji, Xiongbin Lu. Atractylenolide I enhances responsiveness to immune checkpoint blockade therapy by activating tumor antigen presentation. The Journal of Clinical Investigation. https://www.jci.org/articles/view/146832?elqTrackId=2adea9e04a254b66be1b83c938370c73

7. Yan Han, Hao Liu, Sha Cao, Chi Zhang, Yong Zang. TSNP: A two‐stage nonparametric phase I/II clinical trial design for immunotherapy. Pharmaceutical Statistics, 20(1), p.282-296. [paper]

8. Zhigang Cai, Xiaoyu Lu, Chi Zhang, Sai Nelanuthala, Fabiola Aguilera, Abigail Hadley, Baskar Ramdas, Fang Fang, Kenneth Nephew, Jonathan J Kotzin, Adam Williams, Jorge Henao-Mejia, Laura Haneline, Reuben Kapu. Hyperglycemia cooperates with Tet2 heterozygosity to induce leukemia driven by proinflammatory cytokine–induced lncRNA Morrbid. The Journal of clinical investigation. https://www.jci.org/articles/view/140707

9. Michael J Fisher, Chie-Schin Shih, Steven D Rhodes, Amy E Armstrong, Pamela L Wolters, Eva Dombi, Chi Zhang, Steven P Angus, Gary L Johnson, Roger J Packer, Jeffrey C Allen, Nicole J Ullrich, Stewart Goldman, David H Gutmann, Scott R Plotkin, Tena Rosser, Kent A Robertson, Brigitte C Widemann, Abbi E Smith, Waylan K Bessler, Yongzheng He, Su-Jung Park, Julie A Mund, Li Jiang, Khadijeh Bijangi-Vishehsaraei, Coretta Thomas Robinson, Gary R Cutter, Bruce R Korf, Jaishri O Blakeley, D Wade Clapp. Cabozantinib for neurofibromatosis type 1–related plexiform neurofibromas: a phase 2 trial. Nature medicine, 27(1), p.165-173. https://pesquisa.bvsalud.org/controlecancer/resource/pt/mdl-33442015?src=similardocs

10. Apoorva Tangri, Kinzie Lighty, Jagadish Loganathan, Fahmi Mesmar, Ram Podicheti, Chi Zhang, Marcin Iwanicki, Ronny Drapkin, Harikrishna Nakshatri, Sumegha Mitra. Deubiquitinase UCHL1 Maintains Protein Homeostasis through the PSMA7-APEH-Proteasome Axis in High-Grade Serous Ovarian Carcinoma. Molecular Cancer Research.

1. Changlin Wan, Wennan Chang, Tong Zhao, Mengya Li, Sha Cao, Chi Zhang^. MEBF: a fast and efficient Boolean matrix factorization method. (2020) Proceedings of thirty fourth AAAI conference on Artificial Intelligence. https://doi.org/10.1609/aaai.v34i04.6072 [abstract] [paper]

2. Changlin Wan, Wennan Chang, Tong Zhao, Sha Cao, Chi Zhang^. Denoising individual bias for a fairer binary submatrix detection. The Conference on Information and Knowledge Management (CIKM 2020), Doi: 10.1145/3340531.3412156 [abstract] [paper]

3. Changlin Wan, Wennan Chang, Tong Zhao, Sha Cao, Chi Zhang^. Geometric All-Way Boolean Tensor Decomposition (NeurIPS 2020), arXiv:2007.15821 [abstract] [paper]

4. Zhigang Cai, Chi Zhang, Jonathan J Kotzin, Adam Williams, Jorge Henao-Mejia, Reuben Kapur. Role of lncRNA Morrbid in PTPN11(Shp2)E76K-driven juvenile myelomonocytic leukemia. Blood Advances, 2020. https://doi.org/10.1182/bloodadvances.2020002123

5. Wennan Chang, Xinyu Zhou, Yong Zang, Chi Zhang^, Sha Cao^. A New Algorithm using Component-wise Adaptive Trimming for Robust Mixture Regression. arXiv:2005.11599 [abstract] [paper]

6. Wennan Chang, Changlin Wan, Chun Yu, Weixin Yao, Chi Zhang^, Sha Cao^. RobMixReg: an R package for robust, flexible and high dimensional mixture regression. BioRxiv 2020. https://doi.org/10.1101/2020.08.02.233460

7. Daniela Pucciarelli, Steven P Angus, Benjamin Huang, Chi Zhang, Hiroki J Nakaoka, Ganesh Krishnamurthi, Sourav Bandyopadhyay, D Wade Clapp, Kevin Shannon, Gary L Johnson, Jean L Nakamura. Nf1 mutant tumors undergo transcriptome and kinome re-modeling after inhibition of either mTOR or MEK. Molecular Cancer Therapeutics 2020. DOI: 10.1158/1535-7163.MCT-19-1017 [abstract]

8. Wang, Ji and Cheng, Frank HC and Tedrow, Jessica and Chang, Wennan and Zhang, Chi^ and Mitra, Anirban K^. Modulation of immune infiltration of ovarian cancer tumor microenvironment by specific subpopulations of fibroblasts. Cancers, 12(11), p.3184. https://doi.org/10.3390/cancers12113184

9. Pierce, Suresh Marru and Abeysinghe, Eroma and Marlon and Quick, Rob and Zhao, Yi and Cao, Sha and Liu, Xiaowen and Wu, Huanmei and Liu, Jiannan and Chen, Li and others. Alzheimer’s Disease Drug Discovery Center Data Sharing Platform. [Gateway 2020].

10. Cardenas, Horacio and Fang, Fang and Jiang, Guanglong and Perkins, Susan M and Zhang, Chi and Emerson, Robert E and Hutchins, George and Keer, Harold N and Liu, Yunlong and Matei, Daniela and others. Methylomic Signatures of High Grade Serous Ovarian Cancer. Epigenetics, p.1-16. https://doi.org/10.1080/15592294.2020.1853402

11. Wan, Changlin and Jia, Dongya and Zhao, Yue and Chang, Wennan and Cao, Sha^ and Wang, Xiao^ and* **Zhang, Chi^**. A data denoising approach to optimize functional clustering of single cell RNA-sequencing data. 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), p.217-222. [paper]

12. Yifei Zhang, Sha Cao, Chi Zhang, Yong Zang. A Bayesian Adaptive Phase I/II Clinical Trial Design with Late-onset Competing Risk Outcomes. Biometrics (2020). doi: https://doi.org/10.1111/biom.13347

13. John Paul Spence, Dongbing Lai, Jill L Reiter, Sha Cao, Richard L Bell, Kent E Williams, Tiebing Liang.Epigenetic changes on rat chromosome 4 contribute to disparate alcohol drinking behavior in alcohol-preferring and–nonpreferring rats. Alcohol 2020. https://doi.org/10.1016/j.alcohol.2020.08.004

14. Kirstin B VanderWall, Kang-Chieh Huang, Yanling Pan, Sailee S Lavekar, Clarisse M Fligor, Anna R Allsop, Kelly A Lentsch, Pengtao Dang, Chi Zhang, Henry C Tseng, Theodore R Cummins, Jason S Meyer. Retinal Ganglion Cells With a Glaucoma OPTN (E50K) Mutation Exhibit Neurodegenerative Phenotypes when Derived from Three-Dimensional Retinal Organoids. Stem Cell Reports 2020. https://doi.org/10.1016/j.stemcr.2020.05.009

15. Zhigang Cai, Fabiola Aguilera, Baskar Ramdas, Swapna Vidhur Daulatabad, Rajneesh Srivastava, Jonathan J Kotzin, Martin Carroll, Gerald Wertheim, Adam Williams, Sarath Chandra Janga, Chi Zhang, Jorge Henao-Mejia, Reuben Kapur. Targeting Bim via a lncRNA Morrbid Regulates the Survival of Preleukemic and Leukemic Cells. Cell reports 2020. https://doi.org/10.1016/j.celrep.2020.107816

16. Julie A Mund, Su-Jung Park, Abbi E Smith, Yongzheng He, Li Jiang, Eric Hawley, Michelle J Roberson, Dana K Mitchell, Mohannad Abu-Sultanah, Jin Yuan, Waylan K Bessler, George Sandusky, Shi Chen, Chi Zhang, Steven D Rhodes, D Wade Clapp. Genetic disruption of the small GTPase RAC1 prevents plexiform neurofibroma formation in mice with neurofibromatosis type 1. Journal of Biological Chemistry. 2020. doi: 10.1074/jbc.RA119.010981 [abstract] [paper]

17. Liang Dong, Joshua Watson, Sha Cao, Samuel Arregui, Vijay Saxena, John Ketz, Abduselam K Awol, Daniel M Cohen, Jeffrey M Caterino, David S Hains, Andrew L Schwaderer. Aptamer based proteomic pilot study reveals a urine signature indicative of pediatric urinary tract infections. PloS one, 2020. https://doi.org/10.1371/journal.pone.0235328

18. Yurika Upadhyaya, Linhui Xie, Paul Salama, Sha Cao, Kwangsik Nho, Andrew J Saykin, Jingwen Yan. Differential co-expression analysis reveals early stage transcriptomic decoupling in alzheimer’s disease. BMC Medical Genomics 2020. https://doi.org/10.1186/s12920-020-0689-y

19. Samuel A Miller, Robert A Policastro, Sudha S Savant, Shruthi Sriramkumar, Ning Ding, Xiaoyu Lu, Helai P Mohammad, Sha Cao, Jay H Kalin, Philip A Cole, Gabriel E Zentner, Heather M O’Hagan. Lysine-Specific Demethylase 1 Mediates AKT Activity and Promotes Epithelial-to-Mesenchymal Transition in PIK3CA-Mutant Colorectal Cancer. Molecular Cancer Research 2020. DOI: 10.1158/1541-7786.MCR-19-0748 [abstract]

20. Xiangchun Yu, Sha Cao, Yi Zhou, Zhezhou Yu, Ying Xu. Co-expression based cancer staging and application. Scientific reports 2020. https://doi.org/10.1038/s41598-020-67476-7

21. Jian Chen, Yun Tan, Fenghuan Sun, Likun Hou, Chi Zhang, Tao Ge, Huansha Yu, Chunxiao Wu, Yuming Zhu, Liang Duan, Liang Wu, Nan Song, Liping Zhang, Wei Zhang, Di Wang, Chang Chen, Chunyan Wu, Gening Jiang, Peng Zhang. Single-cell transcriptome and antigen-immunoglobin analysis reveals the diversity of B cells in non-small cell lung cancer. Genome Biology 2020. https://doi.org/10.1186/s13059-020-02064-6

22. Zhi Huang, Travis S Johnson, Zhi Han, Bryan Helm, Sha Cao, Chi Zhang, Paul Salama, Maher Rizkalla, Christina Y Yu, Jun Cheng, Shunian Xiang, Xiaohui Zhan, Jie Zhang, Kun Huang. Deep learning-based cancer survival prognosis from RNA-seq data: approaches and evaluations. BMC medical genomics 2020. https://doi.org/10.1186/s12920-020-0686-1

23. Kevin Van der Jeught, Yifan Sun, Yuanzhang Fang, Zhuolong Zhou, Hua Jiang, Tao Yu, Jinfeng Yang, Malgorzata M Kamocka, Ka Man So, Yujing Li, Haniyeh Eyvani, George E Sandusky, Michael Frieden, Harald Braun, Rudi Beyaert, Xiaoming He, Xinna Zhang, Chi Zhang, Sophie Paczesny, Xiongbin Lu. ST2 as checkpoint target for colorectal cancer immunotherapy. JCI Insight. DOI: 10.1172/jci.insight.136073 [paper]

24. Yuanzhang Fang, Lifei Wang, Changlin Wan, Yifan Sun, Kevin Van der Jeught, Zhuolong Zhou, Tianhan Dong, Kaman So1, Tao Yu1, Yujing Li, Yunlong Liu, Chi Zhang, Xiongbin Lu^, Xinna Zhang^. Mal2 drives immune evasion by reducing antigen presentation on tumor cells. (2020) Journal of Clinical Investigation.

25. Andrea M Gross, Pamela L Wolters, Eva Dombi, Andrea Baldwin, Patricia Whitcomb, Michael J Fisher, Brian Weiss, AeRang Kim, Miriam Bornhorst, Amish C Shah, Staci Martin, Marie C Roderick, Dominique C Pichard, Amanda Carbonell, Scott M Paul, Janet Therrien, Oxana Kapustina, Kara Heisey, D Wade Clapp, Chi Zhang, Cody J Peer, William D Figg, Malcolm Smith, John Glod, Jaishri O Blakeley, Seth M Steinberg, David J Venzon, L Austin Doyle, Brigitte C Widemann. Selumetinib in children with inoperable plexiform neurofibromas. New England Journal of Medicine (2020). DOI: 10.1056/NEJMoa1912735

26. Yan Guo, Xia Ning, Ewy Mathé, Kai Wang, Lang Li, Chi Zhang, Zhongming Zhao. Innovating Computational Biology and Intelligent Medicine: ICIBM 2019 Special Issue. Gene 2020. https://doi.org/10.3390/genes11040437

27. Yan Han, Ying Yuan, Sha Cao, Muyi Li, Yong Zang. On the Use of Marker Strategy Design to Detect Predictive Marker Effect in Cancer Immunotherapy and Targeted Therapy. Statistics in Biosciences, 2020. https://doi.org/10.1007/s12561-019-09255-1

2019

1. Z Zhao, Y Dai, C Zhang, E Mathé, L Wei, K Wang. The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: bioinformatics methods and applications for human diseases, 2019, BMC bioinformatics 20 (24), 1-5. https://doi.org/10.1186/s12859-019-3272-9

2. Changlin Wan, Wennan Chang, Yu Zhang, Fenil Shah, Xiaoyu Lu, Yong Zang, Anru Zhang, Sha Cao, Melissa L Fishel, Qin Ma, Chi Zhang^, LTMG: a novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data, Nucleic Acids Research, Volume 47, Issue 18, 10 October 2019, Page e111, https://doi.org/10.1093/nar/gkz655

3. Jin Zhao, Haodi Feng, Daming Zhu, Chi Zhang & Ying Xu. DTA-SiST: de novo transcriptome assembly by using simplified suffix trees. BMC Bioinformatics 2019. https://doi.org/10.1186/s12859-019-3272-9

4. Fenil Shah, Olivia Babb, Chi Zhang, Silpa Gampala, Emily Zhang, Steven D Rhodes, Andrew R Tee, Brian Calver, Ellie Rad, Verena Staedtke, Karen E Pollok, D Wade Clapp, Mark R Kelley, Melissa L Fishel. Signaling through Ref-1 and STAT3 in soft tissue sarcoma (MPNST) and the effects of perturbing this pathway on tumor cell survival and gene expression. MOLECULAR CANCER THERAPEUTICS, 2019. DOI: 10.1158/1535-7163

5. Juan Xie, Anjun Ma, Yu Zhang, Bingqiang Liu, Sha Cao, Cankun Wang, Jennifer Xu, Chi Zhang^, Qin Ma^, QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data, Bioinformatics, btz692, https://doi.org/10.1093/bioinformatics/btz692

6. Yu Zhang, Changlin Wan, Pengcheng Wang, Wennan Chang, Yan Huo, Jian Chen, Qin Ma, Sha Cao, Chi Zhang^. M3S: A comprehensive model selection for multi-modal single-cell RNA sequencing data. BMC Bioinformatics (2019), ICIBM2019 special issue. BMC bioinformatics 20 (24), 1-5

7. Hai Lin, Katherine A Hargreaves, Rudong Li, Jill L Reiter, Yue Wang, Matthew Mort, David N Cooper, Yaoqi Zhou, Chi Zhang, Michael T Eadon, M Eileen Dolan, Joseph Ipe, Todd C Skaar, Yunlong Liu. RegSNPs-intron: a computational framework for predicting pathogenic impact of intronic single nucleotide variants. Genome Biology, 2019. https://doi.org/10.1186/s13059-019-1847-4

8. Ruchi Pandey, Baskar Ramdas, Changlin Wan, George Sandusky, Morvarid Mohseni, Chi Zhang, and Reuben Kapur. SHP2 inhibition reduces leukemogenesis in models of combined genetic and epigenetic mutations. The Journal of Clinical Investigation. 2019 10.1172/JCI130520.

9. Melissa L Fishel, Hanyu Xia, Jack McGeown, David W McIlwain, May Elbanna, Ariel A Craft, Hristos Z Kaimakliotis, George E Sandusky, Chi Zhang, Roberto Pili, Mark R Kelley, Travis J Jerde, Antitumor Activity and Mechanistic Characterization of APE1/Ref-1 Inhibitors in Bladder Cancer，Molecular cancer therapeutics， 2019 DOI: 10.1158/1535-7163.MCT-18-1166

10. Menghao Huang, Hyeong Geug Kim, Xiaolin Zhong, Chuanpeng Dong, Brian Zhang, Zhigang Fang, Yang Zhang, Xiaoyu Lu, Romil Saxena, Yunlong Liu, Chi Zhang, Suthat Liangpunsakul, X Charlie Dong， Sestrin 3 Protects Against Diet-Induced Nonalcoholic Steatohepatitis in Mice Through Suppression of Transforming Growth Factor beta Signal Transduction, Hepatology. 2019 Jun 19. doi: 10.1002/hep.30820

11. Marta Codrich, Marina Comelli, Matilde Clarissa Malfatti, Catia Mio, Dilara Ayyildiz, Chi Zhang, Mark R Kelley, Giovanni Terrosu, Carlo EM Pucillo, Gianluca Tell. Inhibition of APE1-endonuclease activity affects cell metabolism in colon cancer cells via a p53-dependent pathway. 2019, DNA repair 82, 102675

12. Sumegha Mitra, Kartikeya Tiwari, Ram Podicheti, Taruni Pandhiri, Douglas B Rusch, Andrea Bonetto, Chi Zhang, Anirban K Mitra. Transcriptome Profiling Reveals Matrisome Alteration as a Key Feature of Ovarian Cancer Progression. 2019. Cancers 11 (10), 1513

13. Jinyu Yang, Anjun Ma, Adam D Hoppe, Cankun Wang, Yang Li, Chi Zhang, Yan Wang, Bingqiang Liu, Qin Ma. Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework. Nucleic Acids Research, Volume 47, Issue 15, 05 September 2019, Pages 7809–7824, https://doi.org/10.1093/nar/gkz672

14. Jing Zhang, Joydeep Ghosh, Safa F Mohamad, Chi Zhang, Xinxin Huang, Maegan L Capitano, Andrea M Gunawan, Scott Cooper, Bin Guo, Qingchun Cai, Hal E Broxmeyer, Edward F Srour. CD166 engagement augments mouse and human hematopoietic progenitor function via activation of stemness and cell cycle pathways. Stem Cells. 2019 https://doi.org/10.1002/stem.3053

15. Clarisse M. Fligor, Kirstin B. Langer, Akshayalakshmi Sridhar, Yuan Ren, Priya K. Shields, Michael C. Edler, Sarah K. Ohlemacher, Valentin M. Sluch, Donald J. Zack, Chi Zhang, Daniel M. Suter & Jason S. Meyer. Three-Dimensional Retinal Organoids Facilitate the Investigation of Retinal Ganglion Cell Development, Organization and Neurite Outgrowth from Human Pluripotent Stem Cells. Scientific Reports. (2019) https://doi.org/10.1038/s41598-018-32871-8

16. Yong Zang, Beibei Guo, Yan Han, Sha Cao, Chi Zhang. A Bayesian adaptive marker‐stratified design for molecularly targeted agents with customized hierarchical modeling. Statistics in Medicine 2019. https://doi.org/10.1002/sim.8159

1. Wennan Chang, Changlin Wan, Yu Zhang, Kaman So, Brooke Richardson, Yifan Sun, Xinna Zhang, Kun Huang, Anru Zhang, Xiongbin Lu, Sha Cao, Chi Zhang. ICTD: Inference of cell types and deconvolution – a next-generation deconvolution method for accurate assess cell population and activities in tumor microenvironment (version I). BioRxiv (2018) DOI: https://doi.org/10.1101/426593.

2. Juan Xie, Anjun Ma, Yu Zhang, Bingqiang Liu, Changlin Wan, Sha Cao, Chi Zhang, Qin Ma. BRIC: biclustering-based gene regulation inference and cell type prediction for single-cell RNA-Seq data.

3. Clarisse M. Fligor, Kirstin B. Langer, Akshayalakshmi Sridhar, Yuan Ren, Priya K. Shields, Michael C. Edler, Sarah K. Ohlemacher, Valentin M. Sluch, Donald J. Zack, Chi Zhang, Daniel M. Suter and Jason S. Meyer. Three-Dimensional Retinal Organoids Facilitate the Investigation of Retinal Ganglion Cell Development, Organization and Neurite Outgrowth from Human Pluripotent Stem Cells. Scientific Reports. (2018) DOI: https://doi.org/10.1038/s41598-018-32871-8

4. Yong Zang, Wing Kam Fung, Sha Cao, Hon Keung Tony Ng, Chi Zhang. Robust tests for gene-environment interaction in case-control and case-only designs. (2018) Computational Statistics & Data Analysis. DOI: https://doi.org/10.1016/j.csda.2018.08.014

5. Yunhua Liu, Hanchen Xu, Kevin Van der Jeught, Yujing Li, Sheng Liu, Lu Zhang, Yuanzhang Fang, Xinna Zhang, Milan Radovich, Bryan P. Schneider, Xiaoming He, Cheng Huang, Chi Zhang, Jun Wan, Guang Ji, and Xiongbin Lu. Somatic mutation of the cohesin complex subunit confers therapeutic vulnerabilities in cancer. The Journal of Clinical Investigation. (2018). DOI: https://doi.org/10.1172/JCI98727.

6. Huiyan Sun, Chi Zhang, Sha Cao, Tao Sheng, Ning Dong, Ying Xu. Fenton Reactions Drive Nucleotide and ATP Syntheses in Cancer. Journal of Molecular Cell Biology. (2018) DOI: https://doi.org/10.1093/jmcb/mjy039.

7. Chi Zhang, Xiyin Wang, Yanett Anaya, Luca Parodi, Lijun Cheng, Matthew L. Anderson, Shannon M. Hawkins. Distinct Molecular Pathways in Ovarian Endometrioid Adenocarcinoma with Concurrent Endometriosis. International Journal of Cancer. (2018). DOI: https://doi.org/10.1002/ijc.31768

8. Yigang Kwak, BurairAlsaihati, Chi Zhang, Ying Xu, Sha Cao The interplay of immune components and ECM in oral cancer. (2018). DOI: https://doi.org/10.1101/259622

1. Yu Zhang, Sha Cao, Jing Zhao, Qin Ma, Chi Zhang. MRHCA: A nonparametric statistics-based method for hub and co-expression module identification in large gene co-expression network. Quantitative Biology (2017). DOI: https://doi.org/10.1007/s40484-018-0131-z

2. Fang Fang, Horacio Cardenas, Hao Huang, Guanglong Jiang, Susan M. Perkins, Chi Zhang, Harold N. Keer, Yunlong Liu, Daniela Matei, Kenneth P. Nephew. Genomic and Epigenomic Signatures of Platinum Re-sensitization in Ovarian Cancer. Cancer Research (2017). DOI: https://doi.org/10.1158/0008-5472.CAN-17-1492

3. Sha Cao, Tao Sheng, Xin Chen, Qin Ma, Chi Zhang. A probabilistic model-based biclustering method for single-cell transcriptomic data analysis. BioRxiv (2017). DOI: https://doi.org/10.1101/181362

4. Sha Cao, Zhu X, Chi Zhang, Qian H, Schuttler HB, Gong J, Ying Xu. Competition between DNA Methylation, Nucleotide Synthesis, and Antioxidation in Cancer versus Normal Tissues. Cancer Research (2017);77(15):4185-95. DOI: https://doi.org/10.1158/0008-5472.CAN-17-0262 PubMed PMID: 28611042.

5. Jin Zhao, Haodi Feng, Daming Zhu, Chi Zhang, Ying Xu. IsoTree: De Novo Transcriptome Assembly from RNA-Seq Reads. ISBRA 2017 (2017): 71-83

1. Yu Zhang, Juan Xie, Jingyu Yang, Fennell A, Chi Zhang and Qin Ma, QUBIC: a Bioconductor package for qualitative biclustering analysis of gene co-expression data. Bioinformatics (2017) DOI: https://doi.org/10.1093/bioinformatics/btw635

2. Yan Wang, Wei Du, Yanchun Liang, Xin Chen, Chi Zhang, Wei Pang, Ying Xu, PUEPro: A Computational Pipeline for Prediction of Urine Excretory Proteins. [Book] Advanced Data Mining and Applications. (2016) DOI: https://doi.org/10.1007/978-3-319-49586-6_51