52 Publications (Page 1 of 3)
2023
Asparagine starvation suppresses histone demethylation through iron depletion.
Jiang, Jie⋅Srivastava, Sankalp⋅Liu, Sheng⋅Seim, Gretchen⋅Claude, Rodney⋅Zhong, Minghua⋅Cao, Sha⋅Davé, Utpal⋅Kapur, Reuben⋅Mosley, Amber L⋅Zhang, Chi⋅Wan, Jun⋅Fan, Jing and Zhang, Ji
iScience, vol. 26, (no. 4), pp. 106425, April 21, 2023. | Journal Article
 
Pipeline for characterizing alternative mechanisms (PCAM) based on bi-clustering to study colorectal cancer heterogeneity.
Cao, Sha⋅Chang, Wennan⋅Wan, Changlin⋅Lu, Xiaoyu⋅Dang, Pengtao⋅Zhou, Xinyu⋅Zhu, Haiqi⋅Chen, Jian⋅Li, Bo⋅Zang, Yong⋅Wang, Yijie and Zhang, Chi
Computational and structural biotechnology journal, vol. 21, pp. 2160-2171, 2023. | Journal Article
2022
Aberrant epigenetic and transcriptional events associated with breast cancer risk.
N, Marino⋅R, German⋅R, Podicheti⋅DB, Rusch⋅P, Rockey⋅J, Huang⋅GE, Sandusky⋅CJ, Temm⋅S, Althouse⋅KP, Nephew⋅H, Nakshatri⋅J, Liu⋅A, Vode⋅S, Cao and AMV, Storniolo
Clinical epigenetics. | Journal Article
 
A Feasibility Study: Testing Whether a Sleep Application Providing Objective Sleep Data to Physicians Improves Patient-Physician Communication Regarding Sleep Experiences, Habits, and Behaviors.
S, Durrani⋅S, Cao⋅N, Bo⋅JK, Pai⋅J, Baker⋅L, Rawlings⋅ZP, Qureshi⋅NL, Sigua⋅S, Manchanda and B, Khan
Advances in therapy. | Journal Article
 
Bias Aware Probabilistic Boolean Matrix Factorization.
Wan, Changlin⋅Dang, Pengtao⋅Zhao, Tong⋅Zang, Yong⋅Zhang, Chi and Cao, Sha
Proceedings of machine learning research, vol. 180, pp. 2035-2044, August 2022. | Journal Article
 
Genetically programmed alternative splicing of NEMO mediates an autoinflammatory disease phenotype.
Lee, Younglang⋅Y, Lee⋅Wessel, Alex W⋅AW, Wessel⋅J, Xu⋅Xu, Jiazhi⋅Reinke, Julia G⋅JG, Reinke⋅Lee, Eries⋅E, Lee⋅SM, Kim⋅Kim, Somin M⋅AP, Hsu⋅Hsu, Amy P⋅Zilberman-Rudenko, Jevgenia⋅J, Zilberman-Rudenko⋅S, Cao⋅Cao, Sha⋅Enos, Clinton⋅C, Enos⋅Brooks, Stephen R⋅SR, Brooks⋅Deng, Zuoming⋅Z, Deng⋅Lin, Bin⋅B, Lin⋅Jesus AA⋅de Jesus, Adriana A⋅DN, Hupalo⋅Hupalo, Daniel N⋅Piotto, Daniela Gp⋅EP, Hanson⋅Terreri, Maria T⋅Dimitriades, Victoria R⋅Dalgard, Clifton L⋅Holland, Steven M⋅Goldbach-Mansky, Raphaela⋅Siegel, Richard M and Hanson, Eric P
The Journal of clinical investigation. | Journal Article
 
PLUS: Predicting cancer metastasis potential based on positive and unlabeled learning
Zhou, Junyi⋅Lu, Xiaoyu⋅Chang, Wennan⋅Wan, Changlin⋅Lu, Xiongbin⋅Zhang, Chi and Cao, Sha
PLOS Computational Biology, vol. 18, pp. e1009956. | Journal Article
 
SCI: A Bayesian adaptive phase I/II dose-finding design accounting for semi-competing risks outcomes for immunotherapy trials.
Y, Zhang⋅Zhang, Yifei⋅B, Guo⋅Guo, Beibei⋅S, Cao⋅Cao, Sha⋅Zhang, Chi⋅C, Zhang⋅Y, Zang and Zang, Yong
Pharmaceutical statistics. | Journal Article
2021
A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data.
Alghamdi, Norah⋅Alghamdi, Norah⋅N, Alghamdi⋅Alghamdi, Norah⋅W, Chang⋅Chang, Wennan⋅Chang, Wennan⋅Chang, Wennan⋅Dang, Pengtao⋅Dang, Pengtao⋅Dang, Pengtao⋅P, Dang⋅Lu, Xiaoyu⋅Lu, Xiaoyu⋅Lu, Xiaoyu⋅X, Lu⋅Wan, Changlin⋅Wan, Changlin⋅Wan, Changlin⋅C, Wan⋅S, Gampala⋅Gampala, Silpa⋅Gampala, Silpa⋅Gampala, Silpa⋅Huang, Zhi⋅Huang, Zhi⋅Huang, Zhi⋅Z, Huang⋅Wang, Jiashi⋅J, Wang⋅Wang, Jiashi⋅Wang, Jiashi⋅Q, Ma⋅Ma, Qin⋅Ma, Qin⋅Ma, Qin⋅Y, Zang⋅Zang, Yong⋅Zang, Yong⋅Zang, Yong⋅Fishel, Melissa L⋅Fishel, Melissa L⋅Fishel, Melissa⋅M, Fishel⋅Cao, Sha⋅Cao, Sha⋅S, Cao⋅Cao, Sha⋅Zhang, Chi⋅C, Zhang⋅Zhang, Chi and Zhang, Chi
Genome research. | Journal Article
 
MAL2 drives immune evasion in breast cancer by suppressing tumor antigen presentation.
Fang, Yuanzhang⋅Fang, Yuanzhang⋅Fang, Yuanzhang⋅Y, Fang⋅Fang, Yuanzhang⋅Wang, Lifei⋅L, Wang⋅Wang, Lifei⋅Wang, Lifei⋅Wang, Lifei⋅C, Wan⋅Wan, Changlin⋅Wan, Changlin⋅Wan, Changlin⋅Wan, Changlin⋅Sun, Yifan⋅Sun, Yifan⋅Y, Sun⋅Sun, Yifan⋅Sun, Yifan⋅Jeught K, Van⋅VAn der Jeught, Kevin⋅VAn der Jeught, Kevin⋅VAn der Jeught, Kevin⋅VAn der Jeught, Kevin⋅Zhou, Zhuolong⋅Z, Zhou⋅Zhou, Zhuolong⋅Zhou, Zhuolong⋅Zhou, Zhuolong⋅Dong, Tianhan⋅T, Dong⋅Dong, Tianhan⋅Dong, Tianhan⋅Dong, Tianhan⋅So, Ka M⋅KM, So⋅So, Ka M⋅So, Ka M⋅So, Ka M⋅Yu, Tao⋅Yu, Tao⋅Yu, Tao⋅T, Yu⋅Yu, Tao⋅Li, Yujing⋅Y, Li⋅Li, Yujing⋅Li, Yujing⋅Li, Yujing⋅Eyvani, Haniyeh⋅Eyvani, Haniyeh⋅Eyvani, Haniyeh⋅H, Eyvani⋅Eyvani, Haniyeh⋅AB, Colter⋅Colter, Austyn B⋅Colter, Austyn B⋅Colter, Austyn B⋅Colter, Austyn B⋅Dong, Edward⋅E, Dong⋅Dong, Edward⋅Dong, Edward⋅Dong, Edward⋅Cao, Sha⋅S, Cao⋅Cao, Sha⋅Cao, Sha⋅Cao, Sha⋅Wang, Jin⋅J, Wang⋅Wang, Jin⋅Wang, Jin⋅Wang, Jin⋅Schneider, Bryan P⋅Schneider, Bryan P⋅BP, Schneider⋅Schneider, Bryan P⋅Schneider, Bryan P⋅Sandusky, George E⋅Sandusky, George E⋅X, Zhang⋅Sandusky, George E⋅Sandusky, George E⋅Liu, Yunlong⋅Liu, Yunlong⋅Liu, Yunlong⋅Liu, Yunlong⋅Zhang, Chi⋅Zhang, Chi⋅Zhang, Chi⋅Zhang, Chi⋅Lu, Xiongbin⋅Lu, Xiongbin⋅Lu, Xiongbin⋅Lu, Xiongbin⋅Zhang, Xinna⋅Zhang, Xinna⋅Zhang, Xinna and Zhang, Xinna
The Journal of clinical investigation. | Journal Article
 
Spatially and Robustly Hybrid Mixture Regression Model for Inference of Spatial Dependence
Chang, Wennan⋅Dang, Pengdao⋅Wan, Changlin⋅Lu, Xiaoyu⋅Fang, Yue⋅Zhao, Tong⋅Zang, Yong⋅Li, Bo⋅Zhang, Chi and Cao, Sha
IEEE. | Conference Proceeding
 
SSMD: a semi-supervised approach for a robust cell type identification and deconvolution of mouse transcriptomics data.
Lu, Xiaoyu⋅Lu, Xiaoyu⋅X, Lu⋅SW, Tu⋅Tu, Szu-Wei⋅Tu, Szu-Wei⋅Chang, Wennan⋅W, Chang⋅Chang, Wennan⋅C, Wan⋅Wan, Changlin⋅Wan, Changlin⋅Wang, Jiashi⋅Wang, Jiashi⋅J, Wang⋅Zang, Yong⋅Y, Zang⋅Zang, Yong⋅Ramdas, Baskar⋅B, Ramdas⋅Ramdas, Baskar⋅Kapur, Reuben⋅Kapur, Reuben⋅R, Kapur⋅Lu, Xiongbin⋅Lu, Xiongbin⋅X, Lu⋅S, Cao⋅Cao, Sha⋅Cao, Sha⋅Zhang, Chi⋅C, Zhang and Zhang, Chi
Briefings in bioinformatics. | Journal Article
 
Supervised clustering of high-dimensional data using regularized mixture modeling.
Chang, Wennan⋅W, Chang⋅Chang, Wennan⋅C, Wan⋅Wan, Changlin⋅Wan, Changlin⋅Y, Zang⋅Zang, Yong⋅Zang, Yong⋅Zhang, Chi⋅C, Zhang⋅Zhang, Chi⋅Cao, Sha⋅Cao, Sha and S, Cao
Briefings in bioinformatics. | Journal Article
 
TSNP: A two-stage nonparametric phase I/II clinical trial design for immunotherapy.
Han, Yan⋅Han, Yan⋅Liu, Hao⋅Liu, Hao⋅Cao, Sha⋅Cao, Sha⋅Zhang, Chi⋅Zhang, Chi⋅Zang, Yong and Zang, Yong
Pharmaceutical statistics, vol. 20, (no. 2), pp. 282-296, March 2021. | Journal Article
 
Tumor-derived IL-6 and trans-signaling among tumor, fat, and muscle mediate pancreatic cancer cachexia.
Rupert, Joseph E⋅Rupert, Joseph E⋅JE, Rupert⋅A, Narasimhan⋅Narasimhan, Ashok⋅Narasimhan, Ashok⋅Jengelley, Daenique H A⋅DHA, Jengelley⋅Jengelley, Daenique H A⋅Jiang, Yanlin⋅Jiang, Yanlin⋅Y, Jiang⋅Liu, Jianguo⋅J, Liu⋅Liu, Jianguo⋅Au, Ernie⋅E, Au⋅Au, Ernie⋅LM, Silverman⋅Silverman, Libbie M⋅Silverman, Libbie M⋅G, Sandusky⋅Sandusky, George⋅Sandusky, George⋅Bonetto, Andrea⋅A, Bonetto⋅Bonetto, Andrea⋅S, Cao⋅Cao, Sha⋅Cao, Sha⋅X, Lu⋅Lu, Xiaoyu⋅Lu, Xiaoyu⋅TM, O’Connell⋅O'Connell, Thomas M⋅O'Connell, Thomas M⋅Liu, Yunlong⋅Y, Liu⋅Liu, Yunlong⋅LG, Koniaris⋅Koniaris, Leonidas G⋅Koniaris, Leonidas G⋅TA, Zimmers⋅Zimmers, Teresa A and Zimmers, Teresa A
The Journal of experimental medicine. | Journal Article
2020
A Bayesian adaptive phase I/II clinical trial design with late-onset competing risk outcomes.
Y, Zhang⋅S, Cao⋅C, Zhang⋅IH, Jin and Y, Zang
Biometrics. | Journal Article
 
A data denoising approach to optimize functional clustering of single cell RNA-sequencing data
Wan, Changlin⋅Jia, Dongya⋅Zhao, Yue⋅Chang, Wennan⋅Cao, Sha⋅Wang, Xiao and Zhang, Chi
IEEE. | Conference Proceeding
 
Aptamer based proteomic pilot study reveals a urine signature indicative of pediatric urinary tract infections.
L, Dong⋅J, Watson⋅S, Cao⋅S, Arregui⋅V, Saxena⋅J, Ketz⋅AK, Awol⋅DM, Cohen⋅JM, Caterino⋅DS, Hains and AL, Schwaderer
PloS one. | Journal Article
 
Co-expression based cancer staging and application.
Yu, Xiangchun⋅X, Yu⋅S, Cao⋅Cao, Sha⋅Zhou, Yi⋅Y, Zhou⋅Yu, Zhezhou⋅Z, Yu⋅Y, Xu and Xu, Ying
Scientific reports. | Journal Article
 
Deep learning-based cancer survival prognosis from RNA-seq data: approaches and evaluations.
Huang, Zhi⋅Huang, Zhi⋅Huang, Zhi⋅Z, Huang⋅Huang, Zhi⋅Huang, Zhi⋅Huang, Zhi⋅Huang, Zhi⋅Johnson, Travis S⋅Johnson, Travis S⋅Johnson, Travis S⋅Johnson, Travis S⋅Johnson, Travis S⋅TS, Johnson⋅Johnson, Travis S⋅Johnson, Travis S⋅Han, Zhi⋅Han, Zhi⋅Han, Zhi⋅Han, Zhi⋅Han, Zhi⋅Z, Han⋅Han, Zhi⋅Han, Zhi⋅Helm, Bryan⋅Helm, Bryan⋅Helm, Bryan⋅Helm, Bryan⋅Helm, Bryan⋅B, Helm⋅Helm, Bryan⋅Helm, Bryan⋅Cao, Sha⋅Cao, Sha⋅Cao, Sha⋅Cao, Sha⋅Cao, Sha⋅S, Cao⋅Cao, Sha⋅Cao, Sha⋅C, Zhang⋅Zhang, Chi⋅Zhang, Chi⋅Zhang, Chi⋅Zhang, Chi⋅Zhang, Chi⋅Zhang, Chi⋅Zhang, Chi⋅Salama, Paul⋅Salama, Paul⋅Salama, Paul⋅Salama, Paul⋅Salama, Paul⋅Salama, Paul⋅P, Salama⋅Salama, Paul⋅Rizkalla, Maher⋅Rizkalla, Maher⋅Rizkalla, Maher⋅M, Rizkalla⋅Rizkalla, Maher⋅Rizkalla, Maher⋅Rizkalla, Maher⋅Rizkalla, Maher⋅Yu, Christina Y⋅Yu, Christina Y⋅Yu, Christina Y⋅Yu, Christina Y⋅CY, Yu⋅Yu, Christina Y⋅Yu, Christina Y⋅Yu, Christina Y⋅Cheng, Jun⋅Cheng, Jun⋅Cheng, Jun⋅J, Cheng⋅Cheng, Jun⋅Cheng, Jun⋅Cheng, Jun⋅Cheng, Jun⋅Xiang, Shunian⋅Xiang, Shunian⋅Xiang, Shunian⋅Xiang, Shunian⋅Xiang, Shunian⋅S, Xiang⋅Xiang, Shunian⋅Xiang, Shunian⋅X, Zhan⋅Zhan, Xiaohui⋅Zhan, Xiaohui⋅Zhan, Xiaohui⋅Zhan, Xiaohui⋅Zhan, Xiaohui⋅Zhan, Xiaohui⋅Zhan, Xiaohui⋅Zhang, Jie⋅Zhang, Jie⋅Zhang, Jie⋅J, Zhang⋅Zhang, Jie⋅Zhang, Jie⋅Zhang, Jie⋅Zhang, Jie⋅Huang, Kun⋅K, Huang⋅Huang, Kun⋅Huang, Kun⋅Huang, Kun⋅Huang, Kun⋅Huang, Kun and Huang, Kun
BMC medical genomics. | Journal Article
 
Denoising Individual Bias for Fairer Binary Submatrix Detection
Wan, Changlin⋅Chang, Wennan⋅Zhao, Tong⋅Cao, Sha and Zhang, Chi
ACM. | Conference Proceeding
 
Differential co-expression analysis reveals early stage transcriptomic decoupling in alzheimer’s disease.
Upadhyaya, Yurika⋅Y, Upadhyaya⋅Upadhyaya, Yurika⋅Upadhyaya, Yurika⋅Upadhyaya, Yurika⋅Upadhyaya, Yurika⋅Xie, Linhui⋅Xie, Linhui⋅L, Xie⋅Xie, Linhui⋅Xie, Linhui⋅Xie, Linhui⋅Salama, Paul⋅Salama, Paul⋅P, Salama⋅Salama, Paul⋅Salama, Paul⋅Salama, Paul⋅Cao, Sha⋅Cao, Sha⋅Cao, Sha⋅Cao, Sha⋅Cao, Sha⋅S, Cao⋅Nho, Kwangsik⋅Nho, Kwangsik⋅Nho, Kwangsik⋅K, Nho⋅Nho, Kwangsik⋅Nho, Kwangsik⋅Saykin, Andrew J⋅Saykin, Andrew J⋅Saykin, Andrew J⋅AJ, Saykin⋅Saykin, Andrew J⋅Saykin, Andrew J⋅Yan, Jingwen⋅Yan, Jingwen⋅Yan, Jingwen⋅Yan, Jingwen⋅Yan, Jingwen⋅J, Yan⋅Alzheimer’s Disease Neuroimaging In, for the⋅Alzheimer’s Disease Neuroimaging In, for the⋅Alzheimer’s Disease Neuroimaging In, for the⋅FT, Alzheimer’s Disease Neuroimaging Initiative⋅Alzheimer’s Disease Neuroimaging In, for the and Alzheimer’s Disease Neuroimaging In, for the
BMC medical genomics. | Journal Article
 
Epigenetic changes on rat chromosome 4 contribute to disparate alcohol drinking behavior in alcohol-preferring and -nonpreferring rats.
Spence, John Paul⋅Spence, John Paul⋅Spence, John Paul⋅JP, Spence⋅Spence, John P⋅D, Lai⋅Lai, Dongbing⋅Lai, Dongbing⋅Lai, Dongbing⋅Lai, Dongbing⋅Reiter, Jill L.⋅Reiter, Jill L⋅JL, Reiter⋅Reiter, Jill L.⋅Reiter, Jill L⋅Cao, Sha⋅Cao, Sha⋅S, Cao⋅Cao, Sha⋅Cao, Sha⋅Bell, Richard L⋅Bell, Richard L.⋅Bell, Richard L.⋅RL, Bell⋅Bell, Richard L⋅Williams, Kent E.⋅Williams, Kent E⋅Williams, Kent E.⋅Williams, Kent E⋅KE, Williams⋅T, Liang⋅Liang, Tiebing⋅Liang, Tiebing⋅Liang, Tiebing and Liang, Tiebing
Alcohol (Fayetteville, N.Y.). | Journal Article
 
Fast and Efficient Boolean Matrix Factorization by Geometric Segmentation
Wan, Changlin⋅Chang, Wennan⋅Zhao, Tong⋅Li, Mengya⋅Cao, Sha and Zhang, Chi
Proceedings of the AAAI Conference on Artificial Intelligence, vol. 34, pp. 6086–6093. Association for the Advancement of Artificial Intelligence (AAAI). | Conference Proceeding
 
Geometric All-Way Boolean Tensor Decomposition
Wan, Changlin⋅Chang, Wennan⋅Zhao, Tong⋅Cao, Sha and Zhang, Chi
ArXiv, vol. abs/2007.15821. | Conference Proceeding