Academic Publications

Papers:

2021

  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. 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]

  3. 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

  4. 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

  5. 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]

  6. 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

  7. 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

  8. 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.

2020

  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, Changlin Wan, Yong Zang, Chi Zhang^, Sha Cao^. Supervised clustering of high dimensional data using regularized mixture modeling, 2020. arXiv:2007.09720 [abstract] [paper]

  6. 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]

  7. 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

  8. 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]

  9. 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

  10. 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].

  11. 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

  12. 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]

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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]

  18. 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

  19. 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

  20. 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]

  21. 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

  22. 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

  23. 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

  24. 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]

  25. 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.

  26. 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

  27. 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

  28. 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

2018

  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

2017

  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

2016

  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

Abstracts:

2019

  1. Changlin Wan, Wennan Chang, Xiaoyu Lu, Yifan Sun, Xiongbin Lu, Sha Cao and Chi Zhang. A statistical model to reveal transcriptional regulatory state in tumor single-cell RNA-seq data. April 2019 AACR.

  2. Xiaoyu Lu, Szu-wei Tu, Wennan Chang, Yan Huo, Pengcheng Wang, Yu Zhang, Chi Zhang, Sha Cao. A new deconvolution algorithm for accurate assessing immune and stromal cell populations in mouse transcriptomic data. April 2019 AACR

  3. Wennan Chang, Changlin Wan, Yifan Sun, Yan Han, Siyuan Qi, Xiongbin Lu, Sha Cao, Chi Zhang. A semi-supervised deconvolution method for quantifying the composition and activity of tumor-infiltrating cell types. April 2019 AACR.

2017

  1. Tao Sheng, Sha Cao, Chi Zhang, Ying Xu. A computational approach to predict tissue level cell cycle regulatory network for normal proliferating and cancer cells. July 2017. Cancer Research 77 (13 Supplement): 5547-5547 DOI: https://doi.org/10.1158/1538-7445.AM2017-5547

  2. Sha Cao, Chi Zhang, Ying Xu. Development of a deconvolution algorithm for tissue-based gene expression data. July 2017. Cancer Research. 77 (13 Supplement): 1554-1554 DOI: https://doi.org/10.1158/1538-7445.AM2017-1554

  3. Chi Zhang, Fang Yao, Sha Cao, Ying Xu. A pan-inflammatory and precancerous disease analysis reveals key biological characteristics in chronic inflammatory diseases with high oncogenic risk July 2017. Cancer Research 77 (13 Supplement):560-560 DOI: https://doi.org/10.1158/1538-7445.AM2017-560

  4. Chi Zhang, Sen Liang. A bi-clustering based computational approach to identify molecular markers for Neoadjuvant chemotherapy outcome prediction in complement to cancer subtype classifications July 2017. Cancer Research 77 (13 Supplement): 404-404 DOI: https://doi.org/10.1158/1538-7445.AM2017