Zhi Wei
Distinguished Professor, Computer Science
3801 Guttenberg Information Technologies Center (GITC)
Education
Ph.D.
; University of Pennsylvania
; Bioinformatics
; 2008
M.S. ; Rutgers University-New Brunswick ; Computer Science ; 2004
B.S. ; Wuhan University ; Computer Science ; 2000
M.S. ; Rutgers University-New Brunswick ; Computer Science ; 2004
B.S. ; Wuhan University ; Computer Science ; 2000
Website
2025 Fall Courses
CS 725 - INDEPENDENT STUDY I
CS 790A - DOCT DISSERTATION & RES
DS 701C - MASTER'S THESIS
CS 700B - MASTER'S PROJECT
DS 725 - INDEPENDENT STUDY I
CS 792 - PRE-DOCTORAL RESEARCH
DS 488 - INDEPENDENT STUDY IN DS
CS 726 - INDEPENDENT STUDY II
DS 700B - MASTER'S PROJECT
CS 489 - COMPUTER SCIENCE RESEARCH PROJ
DS 701B - MASTER'S THESIS
DS 726 - INDEPENDENT STUDY II
CS 488 - INDEPENDENT STUDY IN CS
DS 792B - PRE-DOCTORAL RESEARCH
CS 701B - MASTER'S THESIS
DS 790A - DOCT DISSERTATION & RES
CS 790A - DOCT DISSERTATION & RES
DS 701C - MASTER'S THESIS
CS 700B - MASTER'S PROJECT
DS 725 - INDEPENDENT STUDY I
CS 792 - PRE-DOCTORAL RESEARCH
DS 488 - INDEPENDENT STUDY IN DS
CS 726 - INDEPENDENT STUDY II
DS 700B - MASTER'S PROJECT
CS 489 - COMPUTER SCIENCE RESEARCH PROJ
DS 701B - MASTER'S THESIS
DS 726 - INDEPENDENT STUDY II
CS 488 - INDEPENDENT STUDY IN CS
DS 792B - PRE-DOCTORAL RESEARCH
CS 701B - MASTER'S THESIS
DS 790A - DOCT DISSERTATION & RES
Past Courses
BNFO 135: PROGRAMMING FOR BIOINFORMATICS
BNFO 615: BIOINFORMATICS-CENTRIC DATA STR
BNFO 615: BIOINFRMTCS CENTRC DATA STRUC
BNFO 620: GENOMIC DATA ANALYSIS
CS 103: COMPUT SCI-BUSINESS PROB
CS 636: DATA ANALYTICS WITH R PROGRAM
CS 698: ST:
CS 698: ST: R PROGRAMMING AND DATA ANALYTICS
CS 698: ST:HIGH DIMENSIONAL DATA ANALY
CS 732: ADVANCED MACHINE LEARNING
CS 786: SEL TOP IN COM INF SCI II
DS 636: DATA ANALYTICS WITH R PROGRAM
BNFO 615: BIOINFORMATICS-CENTRIC DATA STR
BNFO 615: BIOINFRMTCS CENTRC DATA STRUC
BNFO 620: GENOMIC DATA ANALYSIS
CS 103: COMPUT SCI-BUSINESS PROB
CS 636: DATA ANALYTICS WITH R PROGRAM
CS 698: ST:
CS 698: ST: R PROGRAMMING AND DATA ANALYTICS
CS 698: ST:HIGH DIMENSIONAL DATA ANALY
CS 732: ADVANCED MACHINE LEARNING
CS 786: SEL TOP IN COM INF SCI II
DS 636: DATA ANALYTICS WITH R PROGRAM
Conference Proceeding
"Poster: Identifying SMILES from Molecular Structure Images"
June, 2025.
"The Network of Mutual Funds: A Dynamic Heterogeneous Graph Neural Network for Estimating Mutual Funds Performance"
ACM, November, 2023.
"RM-NET: Rasterizing Markov Signals to Images for Deep Learning"
November, 2023.
"Conformal Risk Control for Ordinal Classification"
July (3rd Quarter/Summer), 2023.
"Cox-ResNet: A Survival Analysis Model Based on Residual Neural Networks for Gene Expression Data"
January (1st Quarter/Winter), 2023.
June, 2025.
"The Network of Mutual Funds: A Dynamic Heterogeneous Graph Neural Network for Estimating Mutual Funds Performance"
ACM, November, 2023.
"RM-NET: Rasterizing Markov Signals to Images for Deep Learning"
November, 2023.
"Conformal Risk Control for Ordinal Classification"
July (3rd Quarter/Summer), 2023.
"Cox-ResNet: A Survival Analysis Model Based on Residual Neural Networks for Gene Expression Data"
January (1st Quarter/Winter), 2023.
SHOW MORE
"Identification of Electrical Equipment Based on Faster LSTM-CNN Network"
October (4th Quarter/Autumn), 2020.
"User Profiling and Behavior Evaluation Based on Improved Logistics Algorithm"
October (4th Quarter/Autumn), 2020.
"AirNet: A Calibration Model for Low-Cost Air Monitoring Sensors Using Dual Sequence Encoder Networks"
April (2nd Quarter/Spring), 2020.
"DeepVar: An End-to-End Deep Learning Approach for Genomic Variant Recognition in Biomedical Literature"
April (2nd Quarter/Spring), 2020.
"User response driven content understanding with causal inference"
November, 2019.
"Success Prediction on Crowdfunding with Multimodal Deep Learning"
IJCAI'19 Proceedings of the 28th International Joint Conference on Artificial Intelligence , August, 2019.
"A Blended Deep Learning Approach for Predicting User Intended Actions"
Proceedings of IEEE International Conference on Data Mining, December, 2018.
"A Novel Risk Assessment Scheme and Practice for Peer-to-Peer Lending"
SIGKDD Workshop Data Science in Fintech, October (4th Quarter/Autumn), 2018.
"Modeling Item-specific Effects for Video Click"
the 2018 SIAM International Conference on Data Mining, May, 2018.
"Network Inference from Contrastive Groups Using Discriminative Structural Regularization"
the 2018 SIAM International Conference on Data Mining, May, 2018.
"Deep learning for sequence pattern recognition"
2018 IEEE 15th International Conference on Networking, Sensing and Control (ICNSC), March, 2018.
"Time-Aware Latent Hierarchical Model for Predicting House Prices"
the 2017 IEEE International Conference on Data Mining (ICDM), November, 2017.
"A Feature Sampling Strategy for Analysis of High Dimensional Genomic Data"
The Fifteenth Asia Paci c Bioinformatics Conference (APBC 2017), January (1st Quarter/Winter), 2017.
"Modeling Real Estate for School District Identification"
2016 IEEE 16th International Conference on Data Mining (ICDM), December, 2016.
"Reliable Gender Prediction Based on Users' Video Viewing Behavior"
2016 IEEE 16th International Conference on Data Mining (ICDM), December, 2016.
"A Link Prediction Approach to Cancer Drug Sensitivity Prediction"
International Conference on Intelligent Biology and Medicine (ICIBM), December, 2016.
"A Noise-Filtering Approach for Cancer Drug Sensitivity Prediction"
NIPS 2016 Workshop on Machine Learning for Health, December, 2016.
"A novel under-sampling algorithm based on Iterative-Partitioning Filters for imbalanced classification"
2016 IEEE International Conference on Automation Science and Engineering (CASE), November, 2016.
"Learning approaches to improve prediction of drug sensitivity in breast cancer patients"
38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), October (4th Quarter/Autumn), 2016.
"Annealed Sparsity via Adaptive and Dynamic Shrinking"
Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, August, 2016.
"Structural features of novel dimeric quinacrines that have single-agent antitumor activity determine the mechanism of action: destabilization of mTORC1/lysosomal interaction versus DNA damage"
American Association for Cancer Research 107th Annual Meeting 2016, July (3rd Quarter/Summer), 2016.
"A greedy-based oversampling approach to improve the prediction of mortality in MERS patients"
2016 Annual IEEE Systems Conference (SysCon), April (2nd Quarter/Spring), 2016.
"Use of a novel orthotopic ovarian cancer transplant patient derived xenograft model as a preclinical platform for bench to bedside research."
AACR Special Conference: Advances in Ovarian Cancer, January (1st Quarter/Winter), 2016.
"Collaborated Online Change-point Detection in Sparse Time Series for Online Advertising"
Proceedings of IEEE International Conference on Data Mining (ICDM), November, 2015.
" MSX1-induced neural crest-like reprograming promotes melanoma progression"
Proceedings of the AACR Special Conference on Advances in Melanoma, July (3rd Quarter/Summer), 2015.
"Top-k parametrized boost"
December, 2014.
"Scoring of ChIP-seq experiments by modeling large-scale correlated tests"
Critical Assessment of Massive Data Analysis (CAMDA) 2009 Conference, October (4th Quarter/Autumn), 2009.
"A Spatially Varying Two-sample Recombinant Coalescent, with Applications to HIV Escape Response"
Advances in Neural Information Processing Systems 21(NIPS), June, 2009.
"Exploiting the Marginal Profits of Constraints with Evolutionary Multi-objective Optimization Techniques"
Proceedings of the International Conference on Artificial Intelligence, 2003.
October (4th Quarter/Autumn), 2020.
"User Profiling and Behavior Evaluation Based on Improved Logistics Algorithm"
October (4th Quarter/Autumn), 2020.
"AirNet: A Calibration Model for Low-Cost Air Monitoring Sensors Using Dual Sequence Encoder Networks"
April (2nd Quarter/Spring), 2020.
"DeepVar: An End-to-End Deep Learning Approach for Genomic Variant Recognition in Biomedical Literature"
April (2nd Quarter/Spring), 2020.
"User response driven content understanding with causal inference"
November, 2019.
"Success Prediction on Crowdfunding with Multimodal Deep Learning"
IJCAI'19 Proceedings of the 28th International Joint Conference on Artificial Intelligence , August, 2019.
"A Blended Deep Learning Approach for Predicting User Intended Actions"
Proceedings of IEEE International Conference on Data Mining, December, 2018.
"A Novel Risk Assessment Scheme and Practice for Peer-to-Peer Lending"
SIGKDD Workshop Data Science in Fintech, October (4th Quarter/Autumn), 2018.
"Modeling Item-specific Effects for Video Click"
the 2018 SIAM International Conference on Data Mining, May, 2018.
"Network Inference from Contrastive Groups Using Discriminative Structural Regularization"
the 2018 SIAM International Conference on Data Mining, May, 2018.
"Deep learning for sequence pattern recognition"
2018 IEEE 15th International Conference on Networking, Sensing and Control (ICNSC), March, 2018.
"Time-Aware Latent Hierarchical Model for Predicting House Prices"
the 2017 IEEE International Conference on Data Mining (ICDM), November, 2017.
"A Feature Sampling Strategy for Analysis of High Dimensional Genomic Data"
The Fifteenth Asia Paci c Bioinformatics Conference (APBC 2017), January (1st Quarter/Winter), 2017.
"Modeling Real Estate for School District Identification"
2016 IEEE 16th International Conference on Data Mining (ICDM), December, 2016.
"Reliable Gender Prediction Based on Users' Video Viewing Behavior"
2016 IEEE 16th International Conference on Data Mining (ICDM), December, 2016.
"A Link Prediction Approach to Cancer Drug Sensitivity Prediction"
International Conference on Intelligent Biology and Medicine (ICIBM), December, 2016.
"A Noise-Filtering Approach for Cancer Drug Sensitivity Prediction"
NIPS 2016 Workshop on Machine Learning for Health, December, 2016.
"A novel under-sampling algorithm based on Iterative-Partitioning Filters for imbalanced classification"
2016 IEEE International Conference on Automation Science and Engineering (CASE), November, 2016.
"Learning approaches to improve prediction of drug sensitivity in breast cancer patients"
38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), October (4th Quarter/Autumn), 2016.
"Annealed Sparsity via Adaptive and Dynamic Shrinking"
Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, August, 2016.
"Structural features of novel dimeric quinacrines that have single-agent antitumor activity determine the mechanism of action: destabilization of mTORC1/lysosomal interaction versus DNA damage"
American Association for Cancer Research 107th Annual Meeting 2016, July (3rd Quarter/Summer), 2016.
"A greedy-based oversampling approach to improve the prediction of mortality in MERS patients"
2016 Annual IEEE Systems Conference (SysCon), April (2nd Quarter/Spring), 2016.
"Use of a novel orthotopic ovarian cancer transplant patient derived xenograft model as a preclinical platform for bench to bedside research."
AACR Special Conference: Advances in Ovarian Cancer, January (1st Quarter/Winter), 2016.
"Collaborated Online Change-point Detection in Sparse Time Series for Online Advertising"
Proceedings of IEEE International Conference on Data Mining (ICDM), November, 2015.
" MSX1-induced neural crest-like reprograming promotes melanoma progression"
Proceedings of the AACR Special Conference on Advances in Melanoma, July (3rd Quarter/Summer), 2015.
"Top-k parametrized boost"
December, 2014.
"Scoring of ChIP-seq experiments by modeling large-scale correlated tests"
Critical Assessment of Massive Data Analysis (CAMDA) 2009 Conference, October (4th Quarter/Autumn), 2009.
"A Spatially Varying Two-sample Recombinant Coalescent, with Applications to HIV Escape Response"
Advances in Neural Information Processing Systems 21(NIPS), June, 2009.
"Exploiting the Marginal Profits of Constraints with Evolutionary Multi-objective Optimization Techniques"
Proceedings of the International Conference on Artificial Intelligence, 2003.
COLLAPSE
Journal Article
Y Li , Z Cui, X Song, Y Chen, C Li , J Shi, W Qian, G Ren, J Zhou, C Li , X Ma, Y Chen, D Jia, Y Zhang, Z Zhang, R Zhang, Z Zhang, Y Chen, Z Xu, W Chen, X Miao, H Yu, J Chen, K Wang, C R Goding, Zhi Wei, T Li , R Cui.
2025. "Single-Cell Transcriptomic Landscape Deciphers Intratumoral Heterogeneity and Subtypes of Acral and Mucosal Melanomas.."
Clinical cancer research : an official journal of the American Association for Cancer Research , vol. 31 , no. 12 , pp. 2495-2514.
Yeqing Chen, Wen-Zhe Ho, Zhi Wei. 2025. "Dissecting Opioid Effects in Cell-Cell Communication Within the Ventral Tegmental Area." bioRxiv .
Jianlan Ren, Yeqing Chen, Wen-Zhe Ho, Zhi Wei. 2025. "Dysregulated Gene Regulatory Networks in Substance Use Disorder and HIV Infection: Insights from Single-Cell Genomics." bioRxiv .
E C MacDuffie, L Cocka, X Lin, M Bvochora-Nsingo, S Chiyapo, D Balang, B Maswabi, K Ngoni, D Ramogola-Masire, N M Zetola, Zhi Wei, H Shen, S Bassa, S Grover, E S Robertson. 2025. "Patients with Cervical Cancer with and without HIV Infection Have Unique T-cell Activation Profiles despite Similar Survival Outcomes after Chemoradiation.." Cancer research communications , vol. 5 , no. 4 , pp. 610-620.
Xiang Lin, Jianlan Ren, Le Gao, Junwen Wang, Zhi Wei. 2025. "scDILT: A Model-Based and Constrained Deep Learning Framework for Single-Cell Data Integration, Label Transferring, and Clustering." IEEE Transactions on Computational Biology and Bioinformatics , vol. 22 , no. 3 , pp. 1086-1094.
Yeqing Chen, Wen-Zhe Ho, Zhi Wei. 2025. "Dissecting Opioid Effects in Cell-Cell Communication Within the Ventral Tegmental Area." bioRxiv .
Jianlan Ren, Yeqing Chen, Wen-Zhe Ho, Zhi Wei. 2025. "Dysregulated Gene Regulatory Networks in Substance Use Disorder and HIV Infection: Insights from Single-Cell Genomics." bioRxiv .
E C MacDuffie, L Cocka, X Lin, M Bvochora-Nsingo, S Chiyapo, D Balang, B Maswabi, K Ngoni, D Ramogola-Masire, N M Zetola, Zhi Wei, H Shen, S Bassa, S Grover, E S Robertson. 2025. "Patients with Cervical Cancer with and without HIV Infection Have Unique T-cell Activation Profiles despite Similar Survival Outcomes after Chemoradiation.." Cancer research communications , vol. 5 , no. 4 , pp. 610-620.
Xiang Lin, Jianlan Ren, Le Gao, Junwen Wang, Zhi Wei. 2025. "scDILT: A Model-Based and Constrained Deep Learning Framework for Single-Cell Data Integration, Label Transferring, and Clustering." IEEE Transactions on Computational Biology and Bioinformatics , vol. 22 , no. 3 , pp. 1086-1094.
SHOW MORE
J Ren, N Ma, T Seckar, S Bassa, N Zetola, S Grover, Zhi Wei, E Robertson.
2025. "Characterization of the Genomic Landscape in HPV-positive Cervical and Head and Neck Squamous Cell Carcinomas by Whole Genome Next Generation Sequencing.."
Cancer genomics & proteomics , vol. 22 , no. 2 , pp. 188-207.
Haoran Liu, Xiang Lin, Zhi Wei. 2025. "Marker Gene-Guided Graph Neural Networks for Enhanced Spatial Transcriptomics Clustering." AI Medicine , vol. 2 , no. 1 , pp. 1.
H Wang, Y Wang, J Zhou, B Song, G Tu, A Nguyen, J Su, F Coenen, Zhi Wei, D J Rigden, J Meng. 2025. "Statistical modeling of single-cell epitranscriptomics enabled trajectory and regulatory inference of RNA methylation.." Cell genomics , vol. 5 , no. 1 , pp. 100702.
H Duan, J Ren, S Wei, Z Yang, C Li , Z Wang, M Li , Zhi Wei, Y Liu, X Wang, H Lan, Z Zeng, M Xie, Y Xie, S Wu, W Hu, C Guo, X Zhang, L Liang, C Yu, Y Mou, Y Jiang, H Li , E Sugarman, R A Deek, Z Chen, T Li , Y Chen, M Yao, L Chen, L Liu, G Zhang, Y Mou. 2024. "Integrated analyses of multi-omic data derived from paired primary lung cancer and brain metastasis reveal the metabolic vulnerability as a novel therapeutic target.." Genome medicine , vol. 16 , no. 1 , pp. 138.
Kuang Du, Jing Du, Zhi Wei. 2024. "Self-Supervised Based Multi-View Graph Presentation Learning for Drug-Drug Interaction Prediction." Transactions on Artificial Intelligence , vol. 1 , no. 1 , pp. 1.
X Lin, S Jiang, L Gao, Zhi Wei, J Wang. 2024. "MultiSC: a deep learning pipeline for analyzing multiomics single-cell data.." Briefings in bioinformatics , vol. 25 , no. 6 .
T Tian, J Zhang, X Lin, Zhi Wei, H Hakonarson. 2024. "Dependency-aware deep generative models for multitasking analysis of spatial omics data.." Nature methods , vol. 21 , no. 8 , pp. 1501-1513.
S R Bonam, N C Hazell, M J Mathew, Y Liang, X Zhang, Zhi Wei, M G Alameh, D Weissman, H Hu. 2024. "Innate and Adaptive Immune Parameters following mRNA Vaccination in Mice.." Vaccines , vol. 12 , no. 5 .
Zhi Wei. 2024. "Discrete latent embeddings illuminate cellular diversity in single-cell epigenomics.." Nature computational science , vol. 4 , no. 5 , pp. 316-317.
Hao Chen, Fengzhu Jia, Xiaoying Pan, Zhi Wei. 2023. "Theta-Mechanism based Cluster Search Algorithm for Global Constrained Optimization." Applied Soft Computing , pp. 110963.
C Zhong, T Tian, Zhi Wei. 2023. "Hidden Markov random field models for cell-type assignment of spatially resolved transcriptomics.." Bioinformatics (Oxford, England) , vol. 39 , no. 11 .
Iyshwarya Balasubramanian, Sheila Bandyopadhyay, Juan Flores, Jared Bianchi-Smak, Xiang Lin, Haoran Liu, Shengxiang Sun, Natasha B Golovchenko, Yue Liu, Dahui Wang, Radha Patel, Ivor Joseph, Panan Suntornsaratoon, Justin Vargas, Peter HR Green, Govind Bhagat, Stephen M Lagana, Wang Ying, Yi Zhang, Zhihan Wang, Wei Vivian Li, Sukhwinder Singh, Zhongren Zhou, George Kollias, Laura A Farr, Shannon N Moonah, Shiyan Yu, Zhi Wei, Edward M Bonder, Lanjing Zhang, Pawel R Kiela, Karen L Edelblum, Ronaldo Ferraris, Ta-Chiang Liu, Nan Gao. 2023. "Infection and inflammation stimulate expansion of a CD74+ Paneth cell subset to regulate disease progression." The EMBO Journal , vol. 42 , no. 21 , pp. e113975.
Ivor Joseph, Juan Flores, Victoria Farrell, Justin Davis, Jared Bianchi-Smak, Qiang Feng, Sayantani Goswami, Xiang Lin, Zhi Wei, Kevin Tong, others. 2023. "RAB11A and RAB11B control mitotic spindle function in intestinal epithelial progenitor cells." EMBO reports , pp. e56240.
Charles C. L. Tong, Xiang Lin, Tyler Seckar, Mateusz Koptyra, Michael A. Kohanski, Noam A. Cohen, David W. Kennedy, Nithin D. Adappa, Peter Papagiannopoulos, Edward C. Kuan, Esther Baranov, Jalal B. Jalaly, Michael D. Feldman, Phillip B. Storm, Adam C. Resnick, James N. Palmer, Zhi Wei, Erle S. Robertson. 2023. "A metagenomic analysis of the virome of inverted papilloma and squamous cell carcinoma." International Forum of Allergy \& Rhinology , vol. 13 , no. 11 , pp. 2055-2062.
Dipayan Bose, Xiang Lin, Le Gao, Zhi Wei, Yonggang Pei, Erle S Robertson. 2023. "Attenuation of IFN signaling due to m6A modification of the host epitranscriptome promotes EBV lytic reactivation." Journal of Biomedical Science , vol. 30 , no. 1 , pp. 18.
Tian Tian, Cheng Zhong, Xiang Lin, Zhi Wei, Hakon Hakonarson. 2023. "Complex hierarchical structures in single-cell genomics data unveiled by deep hyperbolic manifold learning." Genome Research , vol. 33 , no. 2 , pp. 232--246.
Christopher J Cardinale, Xiao Chang, Zhi Wei, Hui-Qi Qu, Jonathan P Bradfield, Constantin Polychronakos, Hakon Hakonarson. 2023. "Genome-wide association study of the age of onset of type 1 diabetes reveals HTATIP2 as a novel T cell regulator." Frontiers in Immunology , vol. 14 , pp. 1101488.
Ronald Benjamin, Christopher J Giacoletto, Zachary T FitzHugh, Danielle Eames, Lindsay Buczek, Xiaogang Wu, Jacklyn Newsome, Mira V Han, Tony Pearson, Zhi Wei, Atoshi Banerjee, Lancer Brown, Liz J. Valente, Shirley Shen, Hong-Wen Deng, Martin R. Schiller. 2022. "Data supporting a saturation mutagenesis assay for Tat-driven transcription with the GigaAssay." Data in Brief , vol. 45 , pp. 108641.
Xiang Lin, Tian Tian, Zhi Wei, Hakon Hakonarson. 2022. "Clustering of single-cell multi-omics data with a multimodal deep learning method." Nature Communications , vol. 13 , no. 1 , pp. 7705.
X Lin, L Gao, N Whitener, A Ahmed, Zhi Wei. 2022. "A model-based constrained deep learning clustering approach for spatially resolved single-cell data.." Genome research .
Q Yin, W Chen, C Zhang, Zhi Wei. 2022. "A convolutional neural network model for survival prediction based on prognosis-related cascaded Wx feature selection.." Laboratory investigation; a journal of technical methods and pathology , vol. 102 , no. 10 , pp. 1064-1074.
J Li , Y R Li , J T Glessner, J Yang, M E March, C Kao, C N Vaccaro, J P Bradfield, J Li , F D Mentch, H Q Qu, X Qi, X Chang, C Hou, D J Abrams, H Qiu, Zhi Wei, J J Connolly, F Wang, J Snyder, B Flatø, S D Thompson, C D Langefeld, B A Lie, J E Munro, C Wise, Sleiman PMA, H Hakonarson. 2022. "Identification of Novel Loci Shared by Juvenile Idiopathic Arthritis Subtypes Through Integrative Genetic Analysis.." Arthritis & rheumatology (Hoboken, N.J.) , vol. 74 , no. 8 , pp. 1420-1429.
Yang Jia, Xinmeng Zhang, Hanrong Du, Weiguang Chen, Xiaohui Jin, Wei Qi, Bin Yang, Qiujuan Zhang, Zhi Wei. 2022. "Fine-grained precise-bone age assessment by integrating prior knowledge and recursive feature pyramid network." EURASIP Journal on Image and Video Processing , vol. 2022 , no. 1 , pp. 12.
Liulin Yang, Yu Li, Zhi Wei. 2022. "Fa-Mb-ResNet for Grounding Fault Identification and Line Selection in the Distribution Networks." IEEE Internet of Things Journal .
R Benjamin, C J Giacoletto, Z T FitzHugh, D Eames, L Buczek, X Wu, J Newsome, M V Han, T Pearson, Zhi Wei, A Banerjee, L Brown, L J Valente, S Shen, H W Deng, M R Schiller. 2022. "GigaAssay - An adaptable high-throughput saturation mutagenesis assay platform.." Genomics , vol. 114 , no. 4 , pp. 110439.
D M Hristova, T Fukumoto, C Takemori, L Gao, X Hua, J X Wang, L Li , M Beqiri, A Watters, A Vultur, Y Gimie, V Rebecca, A Samarkina, H Jimbo, C Nishigori, J Zhang, C Cheng, Zhi Wei, R Somasundaram, M Fukunaga-Kalabis, M Herlyn. 2022. "NUMB as a Therapeutic Target for Melanoma.." The Journal of investigative dermatology , vol. 142 , no. 7 , pp. 1882-1892.e5.
S Wei, D Yin, S Yu, X Lin, M R Savani, K Du , Y Ku, D Wu, S Li , H Liu, M Tian, Y Chen, M Bowie, S Hariharan, M Waitkus, S T Keir, E T Sugarman, R A Deek, M Labrie, M Khasraw, Y Lu, G B Mills, M Herlyn, K Wu, L Liu, Zhi Wei, K T Flaherty, K Abdullah, G Zhang, D M Ashley. 2022. "Antitumor Activity of a Mitochondrial-Targeted HSP90 Inhibitor in Gliomas.." Clinical cancer research : an official journal of the American Association for Cancer Research , vol. 28 , no. 10 , pp. 2180-2195.
Turki Turki, Zhi Wei. 2022. "Improved Deep Convolutional Neural Networks via Boosting for Predicting the Quality of In Vitro Bovine Embryos." Electronics , vol. 11 , no. 9 , pp. 1363.
F Tan, C Hu, Y Hu, K Yen, Zhi Wei, A Pappu, S Park, K Li . 2022. "MGEL: Multigrained Representation Analysis and Ensemble Learning for Text Moderation.." IEEE transactions on neural networks and learning systems , vol. PP .
Tong CCL, M Koptyra, P Raman, K S Rathi, N Choudhari, X Lin, T Seckar, Zhi Wei, M A Kohanski, B W O'Malley, N A Cohen, D W Kennedy, N D Adappa, E S Robertson, E Baranov, E C Kuan, P Papagiannopoulos, J B Jalaly, M D Feldman, P B Storm, A C Resnick, J N Palmer. 2022. "Targeted gene expression profiling of inverted papilloma and squamous cell carcinoma.." International forum of allergy & rhinology , vol. 12 , no. 2 , pp. 200-209.
S Das, Q Feng, I Balasubramanian, X Lin, H Liu, O Pellón-Cardenas, S Yu, X Zhang, Y Liu, Zhi Wei, E M Bonder, M P Verzi, W Hsu, L Zhang, T C Wang, N Gao. 2022. "Colonic healing requires Wnt produced by epithelium as well as Tagln+ and Acta2+ stromal cells.." Development (Cambridge, England) , vol. 149 , no. 1 .
Xiang Lin, Haoran Liu, Zhi Wei, Senjuti Basu Roy, Nan Gao. 2021. "An active learning approach for clustering single-cell RNA-seq data." Laboratory Investigation , pp. 1--9.
S Yu, S Wei, M Savani, X Lin, K Du , I Mender, S Siteni, T Vasilopoulos, Z J Reitman, Y Ku, D Wu, H Liu, M Tian, Y Chen, M Labrie, C M Charbonneau, E Sugarman, M Bowie, S Hariharan, M Waitkus, W Jiang, R E McLendon, E Pan, M Khasraw, K M Walsh, Y Lu, M Herlyn, G Mills, U Herbig, Zhi Wei, S T Keir, K Flaherty, L Liu, K Wu, J W Shay, K Abdullah, G Zhang, D M Ashley. 2021. "A Modified Nucleoside 6-Thio-2'-Deoxyguanosine Exhibits Antitumor Activity in Gliomas.." Clinical cancer research : an official journal of the American Association for Cancer Research , vol. 27 , no. 24 , pp. 6800-6814.
Jianglan Liu, Vito W. Rebecca, Andrew V. Kossenkov, Thomas Connelly, Qin Liu, Alexis Gutierrez, Min Xiao, Ling Li, Gao Zhang, Anastasia Samarkina, Delaine Zayasbazan, Jie Zhang, Chaoran Cheng, Zhi Wei, Gretchen M. Alicea, Mizuho Fukunaga-Kalabis, Clemens Krepler, Pedro Aza-Blanc, Chih-Cheng Yang, Bela Delvadia, Cynthia Tong, Ye Huang, Maya Delvadia, Alice S. Morias, Katrin Sproesser, Patricia Brafford, Joshua X. Wang, Marilda Beqiri, Rajasekharan Somasundaram, Adina Vultur, Denitsa M. Hristova, Lawrence W. Wu, Yiling Lu, Gordon B. Mills, Wei Xu, Giorgos C. Karakousis, Xiaowei Xu, Lynn M. Schuchter, Tara C. Mitchell, Ravi K. Amaravadi, Lawrence N. Kwong, Dennie T. Frederick, Genevieve M. Boland, Joseph M. Salvino, David W. Speicher, Keith T. Flaherty, Ronai, Ze'ev A., Meenhard Herlyn. 2021. "Neural Crest-Like Stem Cell Transcriptome Analysis Identifies LPAR1 in Melanoma Progression and Therapy Resistance." Cancer Research , vol. 81 , no. 20 , pp. 5230--5241.
Kuang Du, Shiyou Wei, Zhi Wei, Dennie T. Frederick, Benchun Miao, Tabea Moll, Tian Tian, Eric Sugarman, Dmitry I. Gabrilovich, Ryan J. Sullivan, Lunxu Liu, Keith T. Flaherty, Genevieve M. Boland, Meenhard Herlyn, Gao Zhang. 2021. "Pathway signatures derived from on-treatment tumor specimens predict response to anti-PD1 blockade in metastatic melanoma." Nature Communications , vol. 12 , no. 1 .
Sagarika Banerjee, Zhi Wei, Tian Tian, Dipayan Bose, Natalie NC Shih, Michael D Feldman, Thaer Khoury, Angela De Michele, Erle S Robertson. 2021. "Prognostic correlations with the microbiome of breast cancer subtypes." Cell Death & Disease , vol. 12 , no. 9 , pp. 1--14.
Russell J. Buono, Jonathan P. Bradfield, Zhi Wei, Michael R. Sperling, Dennis J. Dlugos, Michael D. Privitera, Jacqueline A. French, Warren Lo, Patrick Cossette, Steven C. Schachter, Heather Basehore, Falk W. Lohoff, Struan F.A. Grant, Thomas N. Ferraro, Hakon Hakonarson. 2021. "Genetic variation in PADI6-PADI4 on 1p36.13 is associated with common forms of human generalized epilepsy." Genes , vol. 12 , no. 9 .
Tian Tian, Martin Renqiang Min, Zhi Wei. 2021. "Model-based autoencoders for imputing discrete single-cell RNA-seq data." Methods , vol. 192 , pp. 112-119.
Beike Wang, Wei Zhang, Gao Zhang, Lawrence Kwong, Hezhe Lu, Jiufeng Tan, Norah Sadek, Min Xiao, Jie Zhang, Marilyne Labrie, Sergio Randell, Aurelie Beroard, Eric Sugarman, Vito W. Rebecca, Zhi Wei, Yiling Lu, Gordon B. Mills, Jeffrey Field, Jessie Villanueva, Xiaowei Xu, Meenhard Herlyn, Wei Guo. 2021. "Targeting mTOR signaling overcomes acquired resistance to combined BRAF and MEK inhibition in BRAF-mutant melanoma." Oncogene , vol. 40 , no. 37 , pp. 5590-5599.
Xiang Lin, Jie Zhang, Zhi Wei, Turki Turki. 2021. "An Omnibus Test for Differential Distribution Analysis of Continuous Microbiome Data." IEEE Access , vol. 9 , pp. 100029-100039.
Karthik Rajasekaran, Ryan M. Carey, Xiang Lin, Tyler D. Seckar, Zhi Wei, Kevin Chorath, Jason G. Newman, Bert W. O'Malley, Gregory S. Weinstein, Michael D. Feldman, Erle Robertson. 2021. "The microbiome of HPV-positive tonsil squamous cell carcinoma and neck metastasis." Oral Oncology , vol. 117 .
Xiurui Hou, Kai Wang, Cheng Zhong, Zhi Wei. 2021. "ST-Trader: A Spatial-Temporal Deep Neural Network for Modeling Stock Market Movement." IEEE/CAA Journal of Automatica Sinica , vol. 8 , no. 5 , pp. 1015-1024.
Tian Tian, Jie Zhang, Xiang Lin, Zhi Wei, Hakon Hakonarson. 2021. "Model-based deep embedding for constrained clustering analysis of single cell RNA-seq data." Nature Communications , vol. 12 , no. 1 .
Tyler Seckar, Xiang Lin, Dipayan Bose, Zhi Wei, Joseph Rohrbaugh, Ronald G. Collman, Erle S. Robertson. 2021. "Detection of Microbial Agents in Oropharyngeal and Nasopharyngeal Samples of SARS-CoV-2 Patients." Frontiers in Microbiology , vol. 12 .
Joseph T. Glessner, Xiao Chang, Yichuan Liu, Jin Li, Munir Khan, Zhi Wei, Patrick M.A. Sleiman, Hakon Hakonarson. 2021. "MONTAGE: a new tool for high-throughput detection of mosaic copy number variation." BMC Genomics , vol. 22 , no. 1 .
Fentaw Abegaz, François Van Lishout, Jestinah M. Mahachie John, Kridsadakorn Chiachoompu, Archana Bhardwaj, Diane Duroux, Elena S. Gusareva, Zhi Wei, Hakon Hakonarson, Kristel Van Steen. 2021. "Performance of model-based multifactor dimensionality reduction methods for epistasis detection by controlling population structure." BioData Mining , vol. 14 , no. 1 .
Matthias Gromeier, Michael C. Brown, Gao Zhang, Xiang Lin, Yeqing Chen, Zhi Wei, Nike Beaubier, Hai Yan, Yiping He, Annick Desjardins, James E. Herndon, Frederick S. Varn, Roel G. Verhaak, Junfei Zhao, Dani P. Bolognesi, Allan H. Friedman, Henry S. Friedman, Frances McSherry, Andrea M. Muscat, Eric S. Lipp, Smita K. Nair, Mustafa Khasraw, Katherine B. Peters, Dina Randazzo, John H. Sampson, Roger E. McLendon, Darell D. Bigner, David M. Ashley. 2021. "Very low mutation burden is a feature of inflamed recurrent glioblastomas responsive to cancer immunotherapy." Nature Communications , vol. 12 , no. 1 .
Joseph T Glessner, Xiurui Hou, Cheng Zhong, Jie Zhang, Munir Khan, Fabian Brand, Peter Krawitz, Patrick M A Sleiman, Hakon Hakonarson, Zhi Wei. 2021. "DeepCNV: a deep learning approach for authenticating copy number variations." Briefings in Bioinformatics , vol. 22 , no. 5 .
Tian Tian, Ruihua Cheng, Zhi Wei. 2021. "An empirical bayes change-point model for transcriptome time-course data." Annals of Applied Statistics , vol. 15 , no. 1 , pp. 509-526.
Yun Rose Li, Joseph T. Glessner, Bradley P. Coe, Jin Li, Maede Mohebnasab, Xiao Chang, John Connolly, Charlly Kao, Zhi Wei, Jonathan Bradfield, Cecilia Kim, Cuiping Hou, Munir Khan, Frank Mentch, Haijun Qiu, Marina Bakay, Christopher Cardinale, Maria Lemma, Debra Abrams, Andrew Bridglall-Jhingoor, Meckenzie Behr, Shanell Harrison, George Otieno, Alexandria Thomas, Fengxiang Wang, Rosetta Chiavacci, Lawrence Wu, Dexter Hadley, Elizabeth Goldmuntz, Josephine Elia, John Maris, Robert Grundmeier, Marcella Devoto, Brendan Keating, Michael March, Renata Pellagrino, Struan F.A. Grant, Patrick M.A. Sleiman, Mingyao Li, Evan E. Eichler, Hakon Hakonarson. 2020. "Rare copy number variants in over 100,000 European ancestry subjects reveal multiple disease associations." Nature Communications , vol. 11 , no. 1 .
Yonggang Pei, Josiah Hiu-yuen Wong, Hem Chandra Jha, Tian Tian, Zhi Wei, Erle S Robertson. 2020. "Epstein-Barr Virus Facilitates Expression of KLF14 by Regulating the Cooperative Binding of the E2F-Rb-HDAC Complex in Latent Infection." Journal of Virology , vol. 94 , no. 22 .
Liangliang Wang, Yan Gao, Gao Zhang, Dan Li, Zhenda Wang, Jie Zhang, Leandro C. Hermida, Lei He, Zhisong Wang, Jingwen Si, Shuang Geng, Rizi Ai, Fei Ning, Chaoran Cheng, Haiteng Deng, Dimiter S. Dimitrov, Yan Sun, Yanyi Huang, Dong Wang, Xiaoyu Hu, Zhi Wei, Wei Wang, Xuebin Liao. 2020. "Enhancing KDM5A and TLR activity improves the response to immune checkpoint blockade." Science translational medicine , vol. 12 , no. 560 .
Shiyan Yu, Iyshwarya Balasubramanian, Daniel Laubitz, Kevin Tong, Sheila Bandyopadhyay, Xiang Lin, Juan Flores, Rajbir Singh, Yue Liu, Carlos Macazana, Yanlin Zhao, Fabienne Béguet-Crespel, Karuna Patil, Monica T. Midura-Kiela, Daniel Wang, George S. Yap, Ronaldo P. Ferraris, Zhi Wei, Edward M. Bonder, Max M. Häggblom, Lanjing Zhang, Veronique Douard, Michael P. Verzi, Ken Cadwell, Pawel R. Kiela, Nan Gao. 2020. "Paneth Cell-Derived Lysozyme Defines the Composition of Mucolytic Microbiota and the Inflammatory Tone of the Intestine." Immunity , vol. 53 , no. 2 , pp. 398-416.e8.
Fei Tan, Tian Tian, Xiurui Hou, Xiang Yu, Lei Gu, Fernanda Mafra, Brian D. Gregory, Zhi Wei, Hakon Hakonarson. 2020. "Elucidation of DNA methylation on N <sup>6</sup>-adenine with deep learning." Nature Machine Intelligence , vol. 2 , no. 8 , pp. 466-475.
Christopher J. Cardinale, Michael E. March, Xiang Lin, Yichuan Liu, Lynn A. Spruce, Jonathan P. Bradfield, Zhi Wei, Steven H. Seeholzer, Struan F.A. Grant, Hakon Hakonarson. 2020. "Regulation of Janus Kinase 2 by an Inflammatory Bowel Disease Causal Non-coding Single Nucleotide Polymorphism." Journal of Crohn's and Colitis , vol. 14 , no. 5 , pp. 646-653.
Hongyun Yue, Zhi Wei, Qingjiang Chen, Xiaoyan Zhang. 2020. "Dynamic surface control for a class of nonlinearly parameterized systems with input time delay using neural network." Journal of the Franklin Institute , vol. 357 , no. 4 , pp. 1961-1986.
Ryan M. Carey, Karthik Rajasekaran, Tyler Seckar, Xiang Lin, Zhi Wei, Charles C.L. Tong, Viran J. Ranasinghe, Jason G. Newman, Bert W. O'Malley, Gregory S. Weinstein, Michael D. Feldman, Erle S. Robertson. 2020. "The virome of HPV-positive tonsil squamous cell carcinoma and neck metastasis." Oncotarget , vol. 11 , no. 3 , pp. 282-293.
Xiurui Hou, Kai Wang, Jie Zhang, Zhi Wei. 2020. "An Enriched Time-Series Forecasting Framework for Long-Short Portfolio Strategy." IEEE Access , vol. 8 , pp. 31992-32002.
Xiaoying Pan, Yizhe Zhao, Hao Chen, De Wei, Chen Zhao, Zhi Wei. 2020. "Fully Automated Bone Age Assessment on Large-Scale Hand X-Ray Dataset." International Journal of Biomedical Imaging , vol. 2020 .
Jin Li, Zhi Wei, Jie Zhang, Hakon Hakonarson, Scott D. Cook-Sather. 2019. "Candidate gene analyses for acute pain and morphine analgesia after pediatric day surgery: African American versus European Caucasian ancestry and dose prediction limits." Pharmacogenomics Journal , vol. 19 , no. 6 , pp. 570-581.
Andrea Aloia, Daniela Müllhaupt, Christophe D. Chabbert, Tanja Eberhart, Stefanie Flückiger-Mangual, Ana Vukolic, Ossia Eichhoff, Anja Irmisch, Leila T. Alexander, Ernesto Scibona, Dennie T. Frederick, Benchun Miao, Tian Tian, Chaoran Cheng, Lawrence N. Kwong, Zhi Wei, Ryan J. Sullivan, Genevieve M. Boland, Meenhard Herlyn, Keith T. Flaherty, Nicola Zamboni, Reinhard Dummer, Gao Zhang, Mitchell P. Levesque, Wilhelm Krek, Werner J. Kovacs. 2019. "A Fatty Acid Oxidation-dependent Metabolic Shift Regulates the Adaptation of BRAF-mutated Melanoma to MAPK Inhibitors." Clinical Cancer Research , vol. 25 , no. 22 , pp. 6852-6867.
Fentaw Abegaz, François Van Lishout, Jestinah M. Mahachie John, Kridsadakorn Chiachoompu, Archana Bhardwaj, Elena S. Gusareva, Zhi Wei, Hakon Hakonarson, Kristel Van Steen. 2019. "Epistasis Detection in Genome-Wide Screening for Complex Human Diseases in Structured Populations." Systems Medicine , vol. 2 , no. 1 , pp. 19-27.
Xiali Li, Shuai He, Zhi Wei, Licheng Wu. 2019. "Improved Online Sequential Extreme Learning Machine: A New Intelligent Evaluation Method for AZ-Style Algorithms." IEEE Access , vol. 7 , pp. 124891-124901.
Xiali Li, Zhengyu Lv, Song Wang, Zhi Wei, Licheng Wu. 2019. "A Reinforcement Learning Model Based on Temporal Difference Algorithm." IEEE Access , vol. 7 , pp. 121922--121930.
Xiali Li, Zhengyu Lv, Song Wang, Zhi Wei, Xiaochuan Zhang, Licheng Wu. 2019. "A Middle Game Search Algorithm Applicable to Low-Cost Personal Computer for Go." IEEE Access , vol. 7 , pp. 121719--121727.
Sagarika Banerjee, James C. Alwine, Zhi Wei, Tian Tian, Natalie Shih, Colin Sperling, Thomas Guzzo, Michael D. Feldman, Erle S. Robertson. 2019. "Microbiome signatures in prostate cancer." Carcinogenesis , vol. 40 , no. 6 , pp. 749-764.
Jie Zhang, Zhi Wei, Zhenyu Yan, Mengchu Zhou, Abhishek Pani. 2019. "Online Change-Point Detection in Sparse Time Series with Application to Online Advertising." IEEE Transactions on Systems, Man, and Cybernetics: Systems , vol. 49 , no. 6 , pp. 1141-1151.
Fei Tan, Chaoran Cheng, Zhi Wei. 2019. "Modeling and elucidation of housing price." Data Mining and Knowledge Discovery , vol. 33 , no. 3 , pp. 636-662.
Fei Tan, Xiurui Hou, Jie Zhang, Zhi Wei, Zhenyu Yan. 2019. "A Deep Learning Approach to Competing Risks Representation in Peer-to-Peer Lending." IEEE Transactions on Neural Networks and Learning Systems , vol. 30 , no. 5 , pp. 1565-1574.
Tian Tian, Ji Wan, Qi Song, Zhi Wei. 2019. "Clustering single-cell RNA-seq data with a model-based deep learning approach." Nature Machine Intelligence , vol. 1 , no. 4 , pp. 191.
Jie Zhang, Zhigen Zhao, Kai Zhang, Zhi Wei. 2019. "A feature sampling strategy for analysis of high dimensional genomic data." IEEE/ACM Transactions on Computational Biology and Bioinformatics , vol. 16 , no. 2 , pp. 434-441.
Rani Ojha, Nektaria M. Leli, Angelique Onorati, Shengfu Piao, Ioannis I. Verginadis, Feven Tameire, Vito W. Rebecca, Cynthia I. Chude, Sengottuvelan Murugan, Colin Fennelly, Estela Noguera-Ortega, Shujing Liu, Xiaowei Xu, Clemens Krepler, Min Xiao, Wei Xu, Zhi Wei, Dennie T. Frederick, Genevieve Boland, Tara C. Mitchell, Giorgos C. Karakousis, Lynn M. Schuchter, Keith T. Flaherty, Gao Zhang, Meenhard Herlyn, Constantinos Koumenis, Ravi K. Amaravadi. 2019. "Er translocation of the mapk pathway drives therapy resistance in BRAF-mutant melanoma." Cancer Discovery , vol. 9 , no. 3 , pp. 396-415.
Avinash Das Sahu, Joo S Lee, Zhiyong Wang, Gao Zhang, Ramiro Iglesias-Bartolome, Tian Tian, Zhi Wei, Benchun Miao, Nishanth Ulhas Nair, Olga Ponomarova, Adam A. Friedman, Arnaud Amzallag, Tabea Moll, Gyulnara Kasumova, Patricia Greninger, Regina K. Egan, Leah J. Damon, Dennie T. Frederick, Livnat Jerby-Arnon, Allon Wagner, Kuoyuan Cheng, Seung Gu Park, Welles Robinson, Kevin Gardner, Genevieve Boland, Sridhar Hannenhalli, Meenhard Herlyn, Cyril Benes, Keith Flaherty, Ji Luo, J. Silvio Gutkind, Eytan Ruppin. 2019. "Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy." Molecular Systems Biology , vol. 15 , no. 3 .
Chengqian Yin, Bo Zhu, Ting Zhang, Tongzheng Liu, Shuyang Chen, Yu Liu, Xin Li, Xiao Miao, Shanshan Li, Xia Mi, Jie Zhang, Li Li, Guo Wei, Zhi xiang Xu, Xiumei Gao, Canhua Huang, Zhi Wei, Colin R. Goding, Peng Wang, Xianming Deng, Rutao Cui. 2019. "Pharmacological Targeting of STK19 Inhibits Oncogenic NRAS-Driven Melanomagenesis." Cell , vol. 176 , no. 5 , pp. 1113-1127.e16.
Xin Gao, Zhi Wei, Hakon Hakonarson. 2019. "TRNA-DL: A Deep Learning Approach to Improve tRNAscan-SE Prediction Results." Human Heredity , vol. 83 , no. 3 , pp. 163-172.
Jie Zhang, Zhi Wei, Christopher J. Cardinale, Elena S. Gusareva, Kristel Van Steen, Patrick Sleiman, Hakon Hakonarson. 2019. "Multiple epistasis interactions within MHC are associated with ulcerative colitis." Frontiers in Genetics , vol. 10 .
Xiaoping Xiong, Wenliang Wu, Ning Li, Lu Yang, Jie Zhang, Zhi Wei. 2019. "Risk-based multi-objective optimization of distributed generation based on GPSO-BFA algorithm." IEEE Access , vol. 7 , pp. 30563-30572.
Yan Sun, Xueming Yao, Michael E. March, Xinyi Meng, Junyi Li, Zhi Wei, Patrick M.A. Sleiman, Hakon Hakonarson, Qianghua Xia, Jin Li. 2019. "Target genes of autism risk loci in brain frontal cortex." Frontiers in Genetics , vol. 10 , no. JUL .
Q. Kang, L. Shi, Mengchu Zhou, Xianqin Wang, Q. Wu, Zhi Wei. 2018. "A Distance-Based Weighted Undersampling Scheme for Support Vector Machines and its Application to Imbalanced Classification." IEEE Transactions on Neural Networks and Learning Systems , vol. 29 , no. 9 , pp. 4152-4165.
The International League Against Epilepsy Consortium on Complex Epilepsies, Zhi Wei. 2018. "Genome-wide mega-analysis identifies 16 loci and highlights diverse biological mechanisms in the common epilepsies." Nature Communications , vol. 9 , pp. 5269.
Yukihide Momozawa, Julia Dmitrieva, Emilie Theatre, Valerie Deffontaine, Souad Rahmouni, Benoit Charloteaux, Francois Crins, Elisa Docampo, Mahmoud Elansary, Ann-Stephan Gori, Christelle Lecut, Rob Mariman, Myriam Mni, Cecile Oury, Ilya Altukhov, Dmitry Alexeev, Yuri Aulchenko, Leila Amininejad, Gerd Bouma, Frank Hoentjen, Mark Lowenberg, Bas Oldenburg, Marieke J Pierik, vander Meulen-de Jong, Andrea E, van der Woude, C Janneke, Marijn C Visschedijk, Consortium IBD Genetics, Zhi Wei, Mark Lathrop, Jean-Pierre Hugot, Rinse K Weersma, Martine De Vos, Denis Franchimont, Severine Vermeire, Michiaki Kubo, Edouard Louis, Michel Georges. 2018. "IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes." NATURE COMMUNICATIONS , vol. 9 , pp. 2427.
Shujing Liu, Gao Zhang, Jianping Guo, Xiang Chen, Jingce Lei, Kan Ze, Liyun Dong, Xiangpeng Dai, Yang Gao, Daisheng Song, Brett Ecker, Ruifeng Yang, Caitlin Feltcher, Kai Peng, Cheng Feng, Hui Chen, Rebecca X. Lee, Heddy Kerestes, Jingwen Niu, Suresh Kumar, Weiting Xu, Jie Zhang, Zhi Wei, James S. Martin, Xiaoming Liu, Gordon Mills, Yiling Lu, Wei Guo, Lunquan Sun, Lin Zhang, Ashani Weeraratna, Meenhard Herlyn, Wenyi Wei, Frank S. Lee, Xiaowei Xu. 2018. "Loss of Phd2 cooperates with BRAF <sup>V600E</sup> to drive melanomagenesis." Nature Communications , vol. 9 , no. 1 .
Jane F. Ferguson, Chenyi Xue, Yuanfeng Gao, Tian Tian, Jianting Shi, Xuan Zhang, Ying Wang, Yuhuang D. Li, Zhi Wei, Mingyao Li, Hanrui Zhang, Muredach P. Reilly. 2018. "Tissue-Specific Differential Expression of Novel Genes and Long Intergenic Noncoding RNAs in Humans With Extreme Response to Evoked Endotoxemia." Circulation. Genomic and precision medicine , vol. 11 , no. 11 , pp. e001907.
Turki Turki, Zhi Wei. 2018. "Boosting support vector machines for cancer discrimination tasks." Computers in Biology and Medicine , vol. 101 , pp. 236-249.
Fiona Simpkins, Kibeom Jang, Hyunho Yoon, Karina E. Hew, Minsoon Kim, Diana J. Azzam, Jun Sun, Dekuang Zhao, Tan A. Ince, Wenbin Liu, Wei Guo, Zhi Wei, Gao Zhang, Gordon B. Mills, Joyce M. Slingerland. 2018. "Dual Src and MEK inhibition decreases ovarian cancer growth and targets tumor initiating stem-like cells." Clinical Cancer Research , vol. 24 , no. 19 , pp. 4874-4886.
Gao Zhang, Lawrence W. Wu, Ilgen Mender, Michal Barzily-Rokni, Marc R. Hammond, Omotayo Ope, Chaoran Cheng, Themistoklis Vasilopoulos, Sergio Randell, Norah Sadek, Aurelie Beroard, Min Xiao, Tian Tian, Jiufeng Tan, Umar Saeed, Eric Sugarman, Clemens Krepler, Patricia Brafford, Katrin Sproesser, Sengottuvelan Murugan, Rajasekharan Somasundaram, Bradley Garman, Bradley Wubbenhorst, Jonathan Woo, Xiangfan Yin, Qin Liu, Dennie T. Frederick, Benchun Miao, Wei Xu, Giorgos C. Karakousis, Xiaowei Xu, Lynn M. Schuchter, Tara C. Mitchell, Lawrence N. Kwong, Ravi K. Amaravadi, Yiling Lu, Genevieve M. Boland, Zhi Wei, Katherine Nathanson, Utz Herbig, Gordon B. Mills, Keith T. Flaherty, Meenhard Herlyn, Jerry W. Shay. 2018. "Induction of telomere dysfunction prolongs disease control of therapy-resistant melanoma." Clinical Cancer Research , vol. 24 , no. 19 , pp. 4771-4784.
Q. Kang, L. Shi, Mengchu Zhou, X. Wang, Q. Wu, Zhi Wei. 2018. "A Distance-Based Weighted Undersampling Scheme for Support Vector Machines and its Application to Imbalanced Classification." IEEE Transactions on Neural Networks and Learning Systems , vol. 29 , no. 9 , pp. 4152-4165.
Tian Tian, Ji Wan, Yan Han, Haoran Liu, Feng Gao, Youdong Pan, Qi Song, Zhi Wei. 2018. "A comprehensive survey of immune cytolytic activity-associated gene co-expression networks across 17 tumor and normal tissue types." Cancers , vol. 10 , no. 9 .
Tian Tian, Zhi Wei, Xiao Chang, Yichuan Liu, Raquel E. Gur, Patrick M. A. Sleiman, Hakon Hakonarson. 2018. "The Long Noncoding RNA Landscape in Amygdala Tissues from Schizophrenia Patients." EBioMedicine , vol. 34 , pp. 171-181.
Noam Auslander, Gao Zhang, Joo Sang Lee, Dennie T. Frederick, Benchun Miao, Tabea Moll, Tian Tian, Zhi Wei, Sanna Madan, Ryan J. Sullivan, Genevieve Boland, Keith Flaherty, Meenhard Herlyn, Eytan Ruppin. 2018. "Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma." Nature Medicine , no. 24 , pp. 1545–1549.
Israel Cañadas, Rohit Thummalapalli, Jong Wook Kim, Shunsuke Kitajima, Russell William Jenkins, Camilla Laulund Christensen, Marco Campisi, Yanan Kuang, Yanxi Zhang, Evisa Gjini, Gao Zhang, Tian Tian, Debattama Rai Sen, Diana Miao, Yu Imamura, Tran Thai, Brandon Piel, Hideki Terai, Amir Reza Aref, Timothy Hagan, Shohei Koyama, Masayuki Watanabe, Hideo Baba, Anika Elise Adeni, Christine Anne Lydon, Pablo Tamayo, Zhi Wei, Meenhard Herlyn, Thanh Uyen Barbie, Ravindra Uppaluri, Lynnette Marie Sholl, Ewa Sicinska, Jacob Sands, Scott Rodig, Kwok Kin Wong, Cloud Peter Paweletz, Hideo Watanabe, David Allen Barbie. 2018. "Tumor innate immunity primed by specific interferon-stimulated endogenous retroviruses." Nature Medicine , vol. 24 , no. 8 , pp. 1143-1150.
Turki Turki, Zhi Wei, Jason T. Wang. 2018. "A transfer learning approach via procrustes analysis and mean shift for cancer drug sensitivity prediction." J Bioinform Comput Biol , vol. 16 , no. 3 , pp. 1840014.
R. Dajani, S. J. Shbailat, A. Arafat, S. A. Sober, H. A. Albitar, R. Tayyem, Zhi Wei, H. Hakonarson. 2018. "Association of genetic variants with macronutrient intake in Circassian and Chechan populations in relation to diabetes." Meta Gene , vol. 16 , pp. 199-207.
L. Yang, Y. Li, Zhi Wei, X. Chang. 2018. "Coexpression network analysis identifies transcriptional modules associated with genomic alterations in neuroblastoma." Biochim Biophys Acta , vol. 1864 , no. 6 Pt B , pp. 2341-2348.
L. Yang, Y. Li, T. Turki, H. Tan, Zhi Wei, X. Chang. 2018. "Weighted Gene Co-Expression Network Analysis Reveals Dysregulation of Mitochondrial Oxidative Phosphorylation in Eating Disorders." Genes , vol. 9 , no. 7 , pp. 325.
Verneri Anttila, Brendan Bulik-Sullivan, Hilary K. Finucane, Raymond K. Walters, Jose Bras, Laramie Duncan, Valentina Escott-Price, Guido J. Falcone, Padhraig Gormley, Rainer Malik, Nikolaos A. Patsopoulos, Stephan Ripke, Zhi Wei, Dongmei Yu, Phil H. Lee, Patrick Turley, Benjamin Grenier-Boley, Vincent Chouraki, Yoichiro Kamatani, Claudine Berr, Luc Letenneur, Didier Hannequin, Philippe Amouyel, Anne Boland, Jean-François Deleuze, Emmanuelle Duron, Badri N. Vardarajan, Christiane Reitz, Alison M. Goate, Matthew J. Huentelman, M. Ilyas Kamboh, Eric B. Larson, Ekaterina Rogaeva, Peter St George-Hyslop, Hakon Hakonarson, Walter A. Kukull, Lindsay A. Farrer, Lisa L. Barnes, Thomas G. Beach, F. Yesim Demirci, Elizabeth Head, Christine M. Hulette, Gregory A. Jicha, John S. K. Kauwe, Jeffrey A. Kaye, James B. Leverenz, Allan I. Levey, Andrew P. Lieberman, Vernon S. Pankratz, Wayne W. Poon, Joseph F. Quinn, Andrew J. Saykin, Lon S. Schneider, Amanda G. Smith, Joshua A. Sonnen, Robert A. Stern, Vivianna M. Van Deerlin, Linda J. Van Eldik, Denise Harold, Giancarlo Russo, David C. Rubinsztein, Anthony Bayer, Magda Tsolaki, Petra Proitsi, Nick C. Fox, Harald Hampel, Michael J. Owen, Simon Mead, Peter Passmore, Kevin Morgan, Markus M. Nöthen, Jonathan M. Schott, Martin Rossor, Michelle K. Lupton, Per Hoffmann, Johannes Kornhuber, Brian Lawlor, Andrew McQuillin, Ammar Al-Chalabi, Joshua C. Bis, Agustin Ruiz, Mercè Boada, Sudha Seshadri, Alexa Beiser, Kenneth Rice, van der Lee, Sven J., Philip L. De Jager, Daniel H. Geschwind, Matthias Riemenschneider, Steffi Riedel-Heller, Jerome I. Rotter, Gerhard Ransmayr, Bradley T. Hyman, Carlos Cruchaga, Montserrat Alegret, Bendik Winsvold, Priit Palta, Kai-How Farh, Ester Cuenca-Leon, Nicholas Furlotte, others. 2018. "Analysis of shared heritability in common disorders of the brain." Science , vol. 360 , no. 6395 , pp. eaap8757.
S. Banerjee, T. Tian, Zhi Wei, N. Shih, M. D. Feldman, K. N. Peck, A. M. DeMichele, J. C. Alwine, E. S. Robertson. 2018. "Distinct Microbial Signatures Associated With Different Breast Cancer Types." Front Microbiol , no. 9 , pp. 951.
Jie Zhang, Zhi Wei, Jun Chen. 2018. "A distance-based approach for testing the mediation effect of the human microbiome." Bioinformatics , vol. 34 , no. 11 , pp. 1875-1883.
Ileabett M Echevarría‐Vargas, Patricia I Reyes‐Uribe, Adam N Guterres, Xiangfan Yin, Andrew V Kossenkov, Qin Liu, Gao Zhang, Clemens Krepler, Chaoran Cheng, Zhi Wei, Rajasekharan Somasundaram, Giorgos Karakousis, Wei Xu, Jennifer JD Morrissette, Yiling Lu, Gordon B Mills, Ryan J Sullivan, Miao Benchun, Dennie T Frederick, Genevieve Boland, Keith T Flaherty, Ashani T Weeraratna, Meenhard Herlyn, Ravi Amaravadi, Lynn M Schuchter, Christin E Burd, Andrew E Aplin, Xiaowei Xu, Jessie Villanueva. 2018. "Co‐targeting <scp>BET</scp> and <scp>MEK</scp> as salvage therapy for <scp>MAPK</scp> and checkpoint inhibitor‐resistant melanoma." EMBO Molecular Medicine , vol. 10 , no. 5 .
L. Yang, N. Hang, Zhi Wei. 2018. "Dual M-Convex Variable Subsets Family and Extremum Analysis for the OPF Problem." IEEE Access , vol. 6 , pp. 27018-27027.
I. M. Echevarria-Vargas, P. I. Reyes-Uribe, A. N. Guterres, X. Yin, A. V. Kossenkov, Q. Liu, G. Zhang, C. Krepler, C. Cheng, Zhi Wei, R. Somasundaram, G. Karakousis, W. Xu, J. J. Morrissette, Y. Lu, G. B. Mills, R. J. Sullivan, M. Benchun, D. T. Frederick, G. Boland, K. T. Flaherty, A. T. Weeraratna, M. Herlyn, R. Amaravadi, L. M. Schuchter, C. E. Burd, A. E. Aplin, X. Xu, J. Villanueva. 2018. "Co-targeting BET and MEK as salvage therapy for MAPK and checkpoint inhibitor-resistant melanoma." EMBO Mol Med , vol. 10 , no. 5 , pp. e8446.
X. Gao, J. Zhang, Zhi Wei, H. Hakonarson. 2018. "DeepPolyA: A Convolutional Neural Network Approach for Polyadenylation Site Prediction." IEEE Access , vol. 6 , pp. 24340-24349.
G. Zhang, L. W. Wu, I. Mender, M. Barzily-Rokni, M. R. Hammond, O. Ope, C. Cheng, T. Vasilopoulos, S. Randell, N. Sadek, A. Beroard, M. Xiao, T. Tian, J. Tan, U. Saeed, E. Sugarman, C. Krepler, P. Brafford, K. Sproesser, S. Murugan, R. Somasundaram, B. Garman, B. Wubbenhorst, J. Woo, X. Yin, Q. Liu, D. T. Frederick, B. Miao, W. Xu, G. C. Karakousis, X. Xu, L. M. Schuchter, T. C. Mitchell, L. N. Kwong, R. K. Amaravadi, Y. Lu, G. M. Boland, Zhi Wei, K. Nathanson, U. Herbig, G. B. Mills, K. T. Flaherty, M. Herlyn, J. W. Shay. 2018. "Induction of Telomere Dysfunction Prolongs Disease Control of Therapy-Resistant Melanoma." Clin Cancer Res .
R. W. Jenkins, A. R. Aref, P. H. Lizotte, E. Ivanova, S. Stinson, C. W. Zhou, M. Bowden, J. Deng, H. Liu, D. Miao, M. X. He, W. Walker, G. Zhang, T. Tian, C. Cheng, Zhi Wei, S. Palakurthi, M. Bittinger, H. Vitzthum, J. W. Kim, A. Merlino, M. Quinn, C. Venkataramani, J. A. Kaplan, A. Portell, P. C. Gokhale, B. Phillips, A. Smart, A. Rotem, R. E. Jones, L. Keogh, M. Anguiano, L. Stapleton, Z. Jia, M. Barzily-Rokni, I. Canadas, T. C. Thai, M. R. Hammond, R. Vlahos, E. S. Wang, H. Zhang, S. Li, G. J. Hanna, W. Huang, M. P. Hoang, A. Piris, J. P. Eliane, A. O. Stemmer-Rachamimov, L. Cameron, M. J. Su, P. Shah, B. Izar, M. Thakuria, N. R. LeBoeuf, G. Rabinowits, V. Gunda, S. Parangi, J. M. Cleary, B. C. Miller, S. Kitajima, R. Thummalapalli, B. Miao, T. U. Barbie, V. Sivathanu, J. Wong, W. G. Richards, R. Bueno, C. H. Yoon, J. Miret, M. Herlyn, L. A. Garraway, E. M. Van Allen, G. J. Freeman, P. T. Kirschmeier, J. H. Lorch, P. A. Ott, F. S. Hodi, K. T. Flaherty, R. D. Kamm, G. M. Boland, K. K. Wong, D. Dornan, C. P. Paweletz, D. A. Barbie. 2018. "Ex Vivo Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids." Cancer Discov , vol. 8 , no. 2 , pp. 196-215.
J Chen, E King, R Deek, Zhi Wei, Y Yu, D Grill, K Ballman, O Stegle. 2018. "An omnibus test for differential distribution analysis of microbiome sequencing data.." Bioinformatics (Oxford, England) , vol. 34 , no. 4 , pp. 643-651.
M. V. Heppt, J. X. Wang, D. M. Hristova, Zhi Wei, L. Li, B. Evans, M. Beqiri, S. Zaman, J. Zhang, M. Irmler, C. Berking, R. Besch, J. Beckers, F. J. Rauscher, 3rd, R. A. Sturm, D. E. Fisher, M. Herlyn, M. Fukunaga-Kalabis. 2018. "MSX1-Induced Neural Crest-Like Reprogramming Promotes Melanoma Progression." J Invest Dermatol , vol. 138 , no. 1 , pp. 141-149.
B. Zhu, S. Chen, H. Wang, C. Yin, C. Han, C. Peng, Z. Liu, L. Wan, X. Zhang, J. Zhang, C. G. Lian, P. Ma, Z. X. Xu, S. Prince, T. Wang, X. Gao, Y. Shi, D. Liu, M. Liu, W. Wei, Zhi Wei, J. Pan, Y. Wang, Z. Xuan, J. Hess, N. K. Hayward, C. R. Goding, X. Chen, J. Zhou, R. Cui. 2018. "The protective role of DOT1L in UV-induced melanomagenesis." Nat Commun , vol. 9 , no. 1 , pp. 259.
J. Zhang, Zhi Wei, Zhipeng Yan, Mengchu Zhou, A. Pani. 2017. "Online Change-Point Detection in Sparse Time Series With Application to Online Advertising." IEEE Transactions on Systems, Man, and Cybernetics: Systems .
F. Liu, Q. Niu, X. Fan, C. Liu, J. Zhang, Zhi Wei, W. Hou, T. D. Kanneganti, M. L. Robb, J. H. Kim, N. L. Michael, J. Sun, L. Soong, H. Hu. 2017. "Priming and Activation of Inflammasome by Canarypox Virus Vector ALVAC via the cGAS/IFI16-STING-Type I IFN Pathway and AIM2 Sensor." J Immunol , vol. 199 , no. 9 , pp. 3293-3305.
Vito W. Rebecca, Michael C. Nicastri, Noel McLaughlin, Colin Fennelly, Quentin McAfee, Amruta Ronghe, Michel Nofal, Chun-Yan Lim, Eric Witze, Cynthia I. Chude, Gao Zhang, Gretchen M. Alicea, Shengfu Piao, Sengottuvelan Murugan, Rani Ojha, Samuel M. Levi, Zhi Wei, Julie S. Barber-Rotenberg, Maureen E. Murphy, Gordon B. Mills, Yiling Lu, Joshua Rabinowitz, Ronen Marmorstein, Qin Liu, Shujing Liu, Xiaowei Xu, Meenhard Herlyn, Roberto Zoncu, Donita C. Brady, David W. Speicher, Jeffrey D. Winkler, Ravi K. Amaravadi. 2017. "A Unified Approach to Targeting the Lysosome’s Degradative and Growth Signaling Roles." Cancer Discovery , vol. 7 , no. 11 , pp. 1260-1283.
Turki Turki, Zhi Wei. 2017. "A link prediction approach to cancer drug sensitivity prediction." BMC Systems Biology , vol. 11 , no. Suppl 5 , pp. 94.
H. Lu, S. Liu, G. Zhang, Wu Bin, Y. Zhu, D. T. Frederick, Y. Hu, W. Zhong, S. Randell, N. Sadek, W. Zhang, G. Chen, C. Cheng, J. Zeng, L. W. Wu, J. Zhang, X. Liu, W. Xu, C. Krepler, K. Sproesser, M. Xiao, B. Miao, J. Liu, C. D. Song, J. Y. Liu, G. C. Karakousis, L. M. Schuchter, Y. Lu, G. Mills, Y. Cong, J. Chernoff, J. Guo, G. M. Boland, R. J. Sullivan, Zhi Wei, J. Field, R. K. Amaravadi, K. T. Flaherty, M. Herlyn, X. Xu, W. Guo. 2017. "PAK signalling drives acquired drug resistance to MAPK inhibitors in BRAF-mutant melanomas." Nature , vol. 550 , no. 7674 , pp. 133-136.
R. Somasundaram, G. Zhang, M. Fukunaga-Kalabis, M. Perego, C. Krepler, X. Xu, C. Wagner, D. Hristova, J. Zhang, T. Tian, Zhi Wei, Q. Liu, K. Garg, J. Griss, R. Hards, M. Maurer, C. Hafner, M. Mayerhofer, G. Karanikas, A. Jalili, V. Bauer-Pohl, F. Weihsengruber, K. Rappersberger, J. Koller, R. Lang, C. Hudgens, G. Chen, M. Tetzlaff, L. Wu, D. T. Frederick, R. A. Scolyer, G. V. Long, M. Damle, C. Ellingsworth, L. Grinman, H. Choi, B. J. Gavin, M. Dunagin, A. Raj, N. Scholler, L. Gross, M. Beqiri, K. Bennett, I. Watson, H. Schaider, M. A. Davies, J. Wargo, B. J. Czerniecki, L. Schuchter, D. Herlyn, K. Flaherty, M. Herlyn, S. N. Wagner. 2017. "Tumor-associated B-cells induce tumor heterogeneity and therapy resistance." Nat Commun , vol. 8 , no. 1 , pp. 607.
X. Chang, Y. Zhao, C. Hou, J. Glessner, L. McDaniel, M. A. Diamond, K. Thomas, J. Li, Zhi Wei, Y. Liu, Y. Guo, F. D. Mentch, H. Qiu, C. Kim, P. Evans, Z. Vaksman, S. J. Diskin, E. F. Attiyeh, P. Sleiman, J. M. Maris, H. Hakonarson. 2017. "Common variants in MMP20 at 11q22.2 predispose to 11q deletion and neuroblastoma risk." Nat Commun , vol. 8 , no. 1 , pp. 569.
Rana Dajani, Jin Li, Zhi Wei, Michael E March, Qianghua Xia, Yousef Khader, Nancy Hakooz, Raja Fatahallah, Mohammed El-Khateeb, Ala Arafat, others. 2017. "Genome-wide association study identifies novel type II diabetes risk loci in Jordan subpopulations." PeerJ , vol. 5 , pp. e3618.
JI Leu, Thibaut Barnoud, Gao Zhang, Tian Tian, Zhi Wei, Meenhard Herlyn, Maureen E Murphy, Donna L George. 2017. "Inhibition of stress-inducible HSP70 impairs mitochondrial proteostasis and function.." Oncotarget , vol. 8 , no. 28 , pp. 45656–45669.
Sagarika Banerjee, Tian Tian, Zhi Wei, Kristen N Peck, Natalie Shih, Ara A Chalian, O'Malley, Bert W, Gregory S Weinstein, Michael D Feldman, James Alwine, others. 2017. "Microbial Signatures Associated with Oropharyngeal and Oral Squamous Cell Carcinomas." Scientific Reports , vol. 7 , no. 1 , pp. 4036.
Sagarika Banerjee, Tian Tian, Zhi Wei, Natalie Shih, Michael D Feldman, James C Alwine, George Coukos, Erle S Robertson. 2017. "The ovarian cancer oncobiome." Oncotarget , vol. 8 , no. 22 , pp. 36225.
Dongmei Zhang, Gao Zhang, Xiaowen Hu, Lawrence Wu, Yi Feng, Sidan He, Youyou Zhang, Zhongyi Hu, Lu Yang, Tian Tian, Weiting Xu, Zhi Wei, Yiling Lu, Keith T. Flaherty, Xiaomin Zhong, Gordon B. Mills, Phyllis A. Gimotty, Xiaowei Xu, Meenhard Herlyn, Lin Zhang. 2017. "Oncogenic RAS regulates long non-coding RNA Orilnc1 in human cancer." Cancer Research , vol. 77 , no. 14 , pp. 3745-3757.
Turki Turki, Zhi Wei, Jason T. L. Wang. 2017. "Transfer Learning Approaches to Improve Drug Sensitivity Prediction in Multiple Myeloma Patients." IEEE Access , vol. 5 , pp. 7381-7393.
E. O. Melo, D. M. Cordeiro, R. Pellegrino, Zhi Wei, Z. J. Daye, R. C. Nishimura, M. A. N. Dode. 2017. "Identification of molecular markers for oocyte competence in bovine cumulus cells." Animal Genetics , vol. 48 , no. 1 , pp. 19-29.
J Li , Zhi Wei, Y R Li , S M Maggadottir, X Chang, A Desai, H Hakonarson. 2016. "Understanding the genetic and epigenetic basis of common variable immunodeficiency disorder through omics approaches.." Biochimica et biophysica acta , vol. 1860 , no. 11 Pt B , pp. 2656-63.
Mizuho Fukunaga-Kalabis, Markus V Heppt, Joshua X Wang, Denitsa M Hristova, Zhi Wei, Martin Irmler, Carola Berking, Robert Besch, Johannes Beckers, Frank J Rauscher, others. 2016. "MSX1 promotes melanoma progression via neural crest-like reprogramming." Journal of Dermatological Science , vol. 84 , no. 1 , pp. e87.
G van Ingen, J Li , A Goedegebure, R Pandey, Y R Li , M E March, V W Jaddoe, M Bakay, F D Mentch, K Thomas, Zhi Wei, X Chang, H S Hain, A G Uitterlinden, H A Moll, C M van Duijn, F Rivadeneira, H Raat, R J de Baatenburg Jong, P M Sleiman, M P van der Schroeff, H Hakonarson. 2016. "Genome-wide association study for acute otitis media in children identifies FNDC1 as disease contributing gene.." Nature communications , vol. 7 , pp. 12792.
B Shannan, A Watters, Q Chen, S Mollin, M Dörr, E Meggers, X Xu, P A Gimotty, M Perego, L Li , J Benci, C Krepler, P Brafford, J Zhang, Zhi Wei, G Zhang, Q Liu, X Yin, K L Nathanson, M Herlyn, A Vultur. 2016. "PIM kinases as therapeutic targets against advanced melanoma.." Oncotarget .
J Li , Zhi Wei, X Chang, C J Cardinale, C E Kim, R N Baldassano, H Hakonarson. 2016. "Pathway-based Genome-wide Association Studies Reveal the Association Between Growth Factor Activity and Inflammatory Bowel Disease.." Inflammatory bowel diseases , vol. 22 , no. 7 , pp. 1540-51.
J Zhang, Zhi Wei. 2016. "An empirical Bayes change-point model for identifying 3' and 5' alternative splicing by next-generation RNA sequencing.." Bioinformatics (Oxford, England) , vol. 32 , no. 12 , pp. 1823-31.
D Hristova, X Hua, J Wang, L Li, M Beqiri, A Watters, A Vultur, Zhi Wei, M Herlyn, M Fukunaga-Kalabis. 2016. "Numb is induced by GSK3 inhibition and inhibits melanoma migration, invasion and metastasis." Journal of Investigative Dermatology , vol. 136 , no. 5 , pp. S117.
G Zhang, D T Frederick, L Wu, Zhi Wei, C Krepler, S Srinivasan, Y C Chae, X Xu, H Choi, E Dimwamwa, O Ope, B Shannan, D Basu, D Zhang, M Guha, M Xiao, S Randell, K Sproesser, Weiting Xu, J Liu, G C Karakousis, L M Schuchter, T C Gangadhar, R K Amaravadi, Mengnan Gu, C Xu, A Ghosh, W Xu, Tian Tian, Jie Zhang, S Zha, Q Liu, P Brafford, A Weeraratna, M A Davies, J A Wargo, N G Avadhani, Y Lu, G B Mills, D C Altieri, K T Flaherty, M Herlyn. 2016. "Targeting mitochondrial biogenesis to overcome drug resistance to MAPK inhibitors.." The Journal of clinical investigation , vol. 126 , no. 5 , pp. 1834-56.
T H Finkel, J Li , Zhi Wei, W Wang, H Zhang, E M Behrens, E L Reuschel, S Limou, C Wise, M Punaro, M L Becker, J E Munro, B Flatø, Ø Førre, S D Thompson, C D Langefeld, D N Glass, J T Glessner, C E Kim, E Frackelton, D K Shivers, K A Thomas, R M Chiavacci, C Hou, K Xu, J Snyder, H Qiu, F Mentch, K Wang, C A Winkler, B A Lie, J A Ellis, H Hakonarson. 2016. "Variants in CXCR4 associate with juvenile idiopathic arthritis susceptibility.." BMC medical genetics , vol. 17 , pp. 24.
K Hew, C Miller, D El-Ashry, J Sun, A Besser, T A Ince, M Gu, Zhi Wei, G Zhang, P Brafford, W Guo, Y Lu, G Mills, J Slingerland, F Simpkins. 2016. "MAPK activation predicts poor outcome and the MEK inhibitor, selumetininb, reverses antiestrogen resistance in high grade serous ovarian cancer." Clinical Cancer Research , vol. 22 , no. 4 , pp. 935-947.
J Li , Zhi Wei, H Hakonarson. 2016. "Application of computational methods in genetic study of inflammatory bowel disease.." World journal of gastroenterology , vol. 22 , no. 3 , pp. 949-60.
Y Guo, Zhi Wei, B J Keating, H Hakonarson. 2016. "Machine learning derived risk prediction of anorexia nervosa.." BMC medical genomics , vol. 9 , pp. 4.
Xiang Ji, Soon Ae Chun, Zhi Wei, James Geller. 2015. "Twitter sentiment classification for measuring public health concerns." Social Network Analysis and Mining , vol. 5 , no. 1 , pp. 1–25.
X Chang, J Glessner, A Tin, J Li , Y Guo, Zhi Wei, Y Liu, F D Mentch, C Hou, Y Zhao, T Wang, H Qiu, C Kim, P M Sleiman, H Hakonarson. 2015. "Genome-wide association study reveals two loci for serum magnesium concentrations in European-American children.." Scientific reports , vol. 5 , pp. 18792.
Elena S Gusareva, Zhi Wei, James A Traherne, Jean-Pierre Hugot, Isabelle Cleynen, Judy H Cho, Hakon Hakonarson, Kristel Van Steen. 2015. "Epistasis associated to inflammatory bowel disease (IBD) in humans." GENETIC EPIDEMIOLOGY , vol. 39 , no. 7 , pp. 554–555.
S Banerjee, Zhi Wei, F Tan, K N Peck, N Shih, M Feldman, T R Rebbeck, J C Alwine, E S Robertson. 2015. "Distinct microbiological signatures associated with triple negative breast cancer." Scientific Reports , vol. 5 , no. 15162 .
Y R Li , J Li , S D Zhao, J P Bradfield, F D Mentch, S M Maggadottir, C Hou, D J Abrams, D Chang, F Gao, Y Guo, Zhi Wei, J J Connolly, C J Cardinale, M Bakay, J T Glessner, D Li , C Kao, K A Thomas, H Qiu, R M Chiavacci, C E Kim, F Wang, J Snyder, M D Richie, B Flatø, Ø Førre, L A Denson, S D Thompson, M L Becker, S L Guthery, A Latiano, E Perez, E Resnick, R K Russell, D C Wilson, M S Silverberg, V Annese, B A Lie, M Punaro, M C Dubinsky, D S Monos, C Strisciuglio, A Staiano, E Miele, S Kugathasan, J A Ellis, J E Munro, K E Sullivan, C A Wise, H Chapel, C Cunningham-Rundles, S F Grant, J S Orange, P M Sleiman, E M Behrens, A M Griffiths, J Satsangi, T H Finkel, A Keinan, E T Prak, C Polychronakos, R N Baldassano, H Li , B J Keating, H Hakonarson. 2015. "Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases.." Nature medicine , vol. 21 , no. 9 , pp. 1018-27.
R Dajani, Li, Zhi Wei, J Glessner, X Chang, C Cardinale, R Pellegrino, T Wang, N Hakooz, Y Khader, A Sheshani, D Zandaki, H Hakonarson. 2015. "CNV Analysis Associates AKNAD1 with Type-2 Diabetes in Jordan Subpopulations." Scientific Reports , vol. 5 , pp. 13391.
J Li, I Fung, J Glessner, P Pandey, Zhi Wei, m Bakay, F Mentch, R Pellegrino, T Wang, C E Kim, c Hou, F Wang, Rosetta M Chiavacci, K A Thomas, J M Spergel, H Hakonarson, P MA Sleiman. 2015. "Copy Number Variations in CTNNA3 and RBFOX1 Associate with Pediatric Food Allergy." The Journal of Immunology , vol. 195 , no. 4 , pp. 1599-1607.
S Liu, M Tetzlaff, R Yang, L Xie, G Zhang, C Krepler, M Xiao, M Beqiri, W Xu, G Karakousis, L Schuchter, R Amaravadi, Weiting Xu, Zhi Wei, Y Yao, L Zhang, Y Wang, L Zhang, X Xu. 2015. "miR‐200c/Bmi1 Axis and Epithelial‐Mesenchymal Transition Contribute to Acquired Resistance to BRAF Inhibitor Treatment." Pigment Cell & Melanoma Research , vol. 28 , no. 4 , pp. 431–441.
S Wen, Zhi Wei. 2015. "Hierarchical recognition of sparse patterns in large-scale simultaneous inference." Biometrika , vol. 102 , no. 2 , pp. 267-280.
M Fukunaga-Kalabis, D Hristova, J Wang, L Li, M Heppt, Zhi Wei, A Gyurdieva, M R Webster, A T Weeraratna, M Herlyn. 2015. "UV-Induced Wnt7a in the Human Skin Microenvironment Specifies the Fate of Neural Crest–Like Cells via Suppression of Notch." Journal of Investigative Dermatology , vol. 135 , pp. 1521–1532.
Christopher Ochs, James Geller, Yehoshua Perl, Yan Chen, Julia Xu, Hua Min, James T Case, Zhi Wei. 2015. "Scalable quality assurance for large SNOMED CT hierarchies using subject-based subtaxonomies." J American Medical Informatics Association , vol. 22 , no. 3 , pp. 507-518.
X Chang, J Li, Y Guo, Zhi Wei, F Mentch, C Hou, Y Zhao, H Qiu, C Kim, P Sleiman, H Hakonarson. 2015. "Genome-Wide Association Study of Serum Minerals Levels in Children of Different Ethnic Background." PLOS ONE , vol. 10 , no. 4 , pp. e0123499.
S. Melkorka Maggadottir, Jin Li, Joseph T. Glessner, Yun Rose Li, Zhi Wei, Xiao Chang, Frank D. Mentch, Kelly A. Thomas, Cecilia E. Kim, Yan Zhao, Cuiping Hou, Fengxiang Wang, Silje F. Jørgensen, Elena E. Perez, Kathleen E. Sullivan, Jordan S. Orange, Tom H. Karlsen, Helen Chapel, Charlotte Cunningham-Rundles, Hakon Hakonarson. 2015. "Rare variants at 16p11. 2 are associated with common variable immunodeficiency." Journal of Allergy and Clinical Immunology , vol. 135 , no. 6 , pp. 1569–1577.
Haitao Hu, M Eller, S Zafar, Y Zhou, Mengnan Gu, Zhi Wei, J R, M A Marovich, H N Kibuuka, R T Bailer, R A Koup, M L Robb, N L Michael, J H Kim, S Ratto-Kim. 2014. "Preferential infection of human Ad5-specific CD4 T cells by HIV in Ad5 naturally exposed and recombinant Ad5-HIV vaccinated individuals." Proceedings of the National Academy of Sciences , vol. 111 , no. 37 , pp. 13439-13444.
Ruifeng Yang, Ying Zheng, Ling Li, Shujing Liu, Michelle Burrows, Zhi Wei, Arben Nace, Meenhard Herlyn, Rutao Cui, Wei Guo, George Cotsarelis, Xiaowei Xu. 2014. "Direct conversion of mouse and human fibroblasts to functional melanocytes by defined factors." Nature Communications , vol. 5 , no. 1 .
International League Against Epilepsy Consortium on Complex Epilepsies , Zhi Wei. 2014. "Genetic determinants of common epilepsies: a meta-analysis of genome-wide association studies." Lancet , vol. 13 , no. 9 , pp. 893 - 903.
Wei Wang, Zhi Wei, Hongzhe Li. 2014. "A change-point model for identifying 3'UTR switching by next-generation RNA sequencing." Bioinformatics , vol. 30 , no. 15 , pp. 2162-2170.
Wei Wang, Zhi Wei. 2014. "Collapsing singletons may boost signal for associating rare variants in sequencing study." BMC Proceedings , vol. 8 , pp. S50.
L Shi, Z Zhang, A M Yu, Wei Wang, Zhi Wei, E Akhter, K Maurer, P Costa Reis, L Song, M Petri, K E Sullivan. 2014. "The SLE Transcriptome Exhibits Evidence of Chronic Endotoxin Exposure and Has Widespread Dysregulation of Non-Coding and Coding RNAs." PLOS ONE , vol. 9 , no. 5 , pp. e93846.
C Cardinale, Zhi Wei, J Li, Junfei Zhu, M Gu, R Baldassano, S Grant, H Hakonarson. 2014. "Transcriptome Profiling of Human Ulcerative Colitis Mucosa Reveals Altered Expression of Pathways Enriched in Genetic Susceptibility Loci." PLOS ONE , vol. 9 , no. 5 , pp. e96153.
Ruifeng Yang, Ying Zheng, Michelle Burrows, Shujing Liu, Zhi Wei, Arben Nace, Wei Guo, Suresh Kumar, George Cotsarelis, Xiaowei Xu. 2014. "Generation of folliculogenic human epithelial stem cells from induced pluripotent stem cells." Nature Communications , vol. 5 .
Zhigen Zhao, Wei Wang, Zhi Wei. 2013. "An empirical Bayes testing procedure for detecting variants in analysis of next generation sequencing data." Annals of Applied Statistics , vol. 7 , no. 4 , pp. 2229-2248.
C Cardinale, Zhi Wei, J Li, Junfei Zhu, R Baldassano, S Grant, H Hakonarson. 2013. "Expression of Transcripts in Ulcerative Colitis Biopsies and Genome-wide Association Study Loci Overlap Substantially in Pathway-based Analysis." Inflammatory Bowel Diseases , vol. 19 , pp. S14.
S Fish, Zhi Wei, J Bradfield, K Gupta, G Spengler, A Martin, C Judge, C Escajadillo, L Ghanem, H Hakonarson, R Baldassano, J Kelsen. 2013. "SLC11A1 Polymorphism Increases the Risk of Early Surgery in Pediatric Patients With Inflammatory Bowel Disease." Inflammatory Bowel Diseases , vol. 19 , pp. S111-S112.
Zhang Zhang, Anna Maria Pinto, L Wan, Wei Wang, M G Berg, Isabela Oliva, Larry N Singh, Christopher Dengler, Zhi Wei, G Dreyfuss. 2013. "Dysregulation of synaptogenesis genes antecedes motor neuron pathology in spinal muscular atrophy." Proceedings of the National Academy of Sciences , vol. 110 , no. 48 , pp. 19348-19353.
B G Bitler, F S Fink, Zhi Wei, J R Peterson, R Zhang. 2013. "A High-Content Screening Assay for Small-Molecule Modulators of Oncogene-Induced Senescence." Journal of biomolecular screening , vol. 18 , no. 9 , pp. 1054-61.
B A Bruce, J Li, J M McDonough, Zhi Wei, C Kim, R Chiavacci, F Mentch, J B Caboot, J Spergel, J L Allen, P MA Sleiman, H Hakonarson. 2013. "Gene Network Analysis in a Pediatric Cohort Identifies Novel Lung Function Genes." PLOS ONE , vol. 8 , no. 9 , pp. e72899.
C J Cardinale, Zhi Wei, S Panossian, F Wang, C E Kim, F D Mentch, R M Chiavacci, K E Kachelries, R Pandey, S FA Grant, R N Baldassano, H Hakonarson. 2013. "Targeted resequencing identifies defective variants of decoy receptor 3 in pediatric-onset inflammatory bowel disease." Genes and immunity , vol. 14 , pp. 447–452.
I Younis, K Dittmar, Wei Wang, S W Foley, M G Berg, K Y Hu, Zhi Wei, L Wan, G Dreyfuss. 2013. "Minor introns are embedded molecular switches regulated by highly unstable U6atac snRNA." eLife , vol. 2 , pp. e00780.
Zhi Wei, Wei Wang, J P Bradfield, J Li, C Cardinale, E Frackelton, C Kim, F D Mentch, K Van Steen, P M Visscher, R N Baldassano, H Hakonarson. 2013. "Large Sample Size, Wide Variant Spectrum, and Advanced Machine-Learning Technique Boost Risk Prediction for Inflammatory Bowel Disease." The American Journal of Human Genetics , vol. 92 , no. 6 , pp. 1008–1012.
K M Aird, G Zhang, H Li, Z Tu, B G Bilter, A Garipov, H Wu, Zhi Wei, S N Wagner, M Herlyn, R Zhang. 2013. "Suppression of Nucleotide Metabolism Underlies the Establishment and Maintenance of Oncogene-Induced Senescence." Cell reports , vol. 3 , no. 4 , pp. 1252–1265.
J Li, J T Glessner, H Zhang, Cuiping Hou, Zhi Wei, J P Bradfield, F D Mentch, Y Guo, C Kim, Q Xia, R M Chiavacci, K A Thomas, H Qiu, S FA Grant, S L Furth, H Hakonarson, P MA Sleiman. 2013. "GWAS of blood cell traits identifies novel associated loci and epistatic interactions in Caucasian and African-American children." Human molecular genetics , vol. 22 , no. 7 , pp. 1457-1464.
J O'Rawe, T Jiang, G Sun, Y Wu, Wei Wang, P Bodily, L Tian, H Hakonarson, W E Johnson, Zhi Wei, K Wang, G Lyon. 2013. "Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing." Genome Medicine , vol. 5 , no. 3 , pp. Article 28.
H Hu, M Nau, P Ehrenberg, A Chenine, C Macedo, Y Zhou, Z Daye, Zhi Wei, M Vahey, N Michael, J Kim, M Marovich, S Ratto-Kim. 2013. "Distinct gene-expression profiles associated with the susceptibility of pathogen-specific CD4 T cells to HIV-1 infection." Blood , vol. 121 , no. 7 , pp. 1136-1144.
Wei Wang, Weicheng Hu, Fang Hou, Pingzhao Hu, Zhi Wei. 2012. "SNVerGUI: a desktop tool for variant analysis of next-generation sequencing data." Journal of Medical Genetics , vol. 49 , no. 12 , pp. 753-755.
J Jostins, S K Ripke, R H Duerr, D P McGovern, Ken Y Hui, J C Lee, P Schumm, Y Sharma, C A Anderson, J Essers, M Mitrovic, K Ning, I Cleynen, E Theatre, S L Spain, S Raychaudhuri, P Goyette, Zhi Wei, C Abraham, J Achkar, T Ahmad, L Amininejad, A N Ananthakrishnan, V Andersen, J M Andrews, L Baidoo, T Balschun, P A Bampton, A Bitton, G Boucher, S Brand, C Büning, A Cohain, S Cichon, M D’Amato, D De Jong, K L Devaney, M Dubinsky, C Edwards, D Ellinghaus, l R Ferguson, D Franchimont, K Fransen, R Gearry, M Georges, C Gieger, J Glas, T Haritunians, A Hart, C Hawkey, M Hedl, X Hu, T H Karlsen, L Kupcinskas, S Kugathasan, A Latiano, D Laukens, I C Lawrance, C W Lees, E Louis, G Mahy, J Mansfield, A R Morgan, C Mowat, W Newman, O Palmieri, C Ponsioen, U Potocnik, N J Prescott, M Regueiro, J I Rotter, R K Russell, J D Sanderson, M Sans, J Satsangi, S Schreiber, L A Simms, J Sventoraityte, S T Targan, K D Taylor, M M Tremelling, H W Verspaget, M De Vos, C Wijmenga, D C Wilson, J Winkelmann, R J Xavier, S Zeissig, B Zhang, C K Zhang, H Zhao, M S Silverberg, V Annese, H Hakonarson, S R Brant, G Radford-Smith, C G Mathew, J D Rioux, E E Schadt, M J Daly, A Franke, M Parkes, S Vermeire, J C Barrett, J H Cho. 2012. "Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease." Nature , vol. 491 , no. 7422 , pp. 119-124.
Renata Pellegrino, Daniele Y. Sunaga, Camila Guindalini, Raquel C. S. Martins, Diego Robles Mazzotti, Zhi Wei, Z. John Daye, Monica Levy Andersen, Sergio Tufik. 2012. "Whole-blood genome-wide gene expression profile in males after prolonged wakefulness and sleep recovery." Physiological Genomics , vol. 44 , no. 21 , pp. 1003-1012.
H Hu, M Nau, P Ehrenberg, A Chenine, Z Daye, Zhi Wei, N Michael, M Vahey, J Kim, M Marovich, S Ratto-Kim. 2012. "Distinct gene expression profiles associated with the susceptibility of pathogen-specific CD4+ T cells to HIV-1 infection." Retrovirology , vol. 9 , no. s2 , pp. O46.
Yingbin Ge, Rikka Azuma, Bethsebah Gekonge, Alfonso Lopez-Coral, Min Xiao, Gao Zhang, Xiaowei Xu, Luis J. Montaner, Zhi Wei, Meenhard Herlyn, Tao Wang, Russel E. Kaufman. 2012. "Induction of metallothionein expression during monocyte to melanoma-associated macrophage differentiation." Frontiers in Biology , vol. 7 , no. 4 , pp. 359–367.
Zhi Wei, Tao Wang, Yingbin Ge, Min Xiao, Alfonso Lopez-Coral, Rikka Azuma, Rajasekharan Somasundaram, Gao Zhang, Xiaowei Xu, Frank J. Rauscher III, Meenhard Herlyn, Russel E. Kaufman. 2012. "Melanoma‐Derived Conditioned Media Efficiently Induce the Differentiation of Monocytes to Macrophages that Display a Highly Invasive Gene Signature." Pigment Cell & Melanoma Research , vol. 25 , no. 4 , pp. 493–505.
Z. John Daye, Hongzhe Li, Zhi Wei. 2012. "A powerful test for multiple rare variants association studies that incorporates sequencing qualities ." Nucleic Acids Research , vol. 40 , no. 8 .
Zhi Wei, Wei Wang, Pingzhao Hu, Gholson J. Lyon, Hakon Hakonarson. 2011. "SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data." Nucleic Acids Research , vol. 39 , no. 19 .
Weixin Wang, Zhi Wei, Tak-Wah Lam, Junwen Wang. 2011. "Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions." Scientific Reports , vol. 1 .
Gholson J Lyon, Tao Jiang, Richard Van Wijk, Wei Wang , Paul Mark Bodily, Jinchuan Xing, Lifeng Tian, Redi J Robison, Mark Clement, Lin Yang, Peng Zhang, Ying Liu, Barry Moore, Joseph T Glessner, Josephine Elia, Fred Reimherr, Wouter W. van Solinge, Mark Yankell, Hakon Hakonarson, Jun Wang, William Evan Johnson, Zhi Wei, Kai Wang. 2011. "Exome Sequencing and Unrelated Findings in the Context of Complex Disease Research: Ethical and Clinical Implications." Discovery Medicine , vol. 12 , no. 62 .
Wenguang Sun, Zhi Wei. 2011. "Multiple Testing for Pattern Identification, with Applications to Microarray Time Course Experiments." Journal of the American Statistical Association , vol. 106 , no. 493 , pp. 73–88.
Usman W. Roshan, Satishc Chikkagoudar, Zhi Wei, Kai Wang, Hakon Hakonarson. 2011. "Ranking causal variants and associated regions in genome-wide association studies by the support vector machine and random forest ." Nucleic Acids Research .
Wei Wang, Zhi Wei, Wenguang Sun. 2010. "Simultaneous set-wise testing under dependence, with applications to genome-wide association studies." Statistics and Its Interface , vol. 3 , no. 4 , pp. 501-512.
Satish Chikkagoudar, Zhi Wei, Usman W. Roshan. 2010. "PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences." Nucleic Acids Research , vol. 38 , no. Suppl 2 , pp. W59-W63.
Hongzhe Li, Zhi Wei, John Maris. 2010. "A Hidden Markov Random Field Model for Genome-wide Association Studies." Biostatistics , vol. 11 , no. 1 , pp. 139-150.
Caiyan Li, Zhi Wei, Hongzhe Li. 2010. "Network-based Empirical Bayes Methods for Linear Models with Applications to Genomic Data." Journal of Biopharmaceutical Statistics , vol. 20 , no. 2 , pp. 209-222 .
Zhi Wei, Wenguang Sun, Kai Wang, Hakon Hakonarson. 2009. "Multiple Testing in Genome-Wide Association Studies via Hidden Markov Models." Bioinformatics , vol. 25 , no. 21 , pp. 2802-2808.
Zhi Wei, Kai Wang, Hui-Qi Qu, Haitao Zhang, Jonathan Bradfield, Cecilia Kim, Edward Frackleton, Cuiping Hou, Joseph T. Glessner, Rosetta Chiavacci, Charles Stanley, Dimitri Monos, Struan F. A. Grant, Constantin Polychronakos, Hakon Hakonarson. 2009. "From Disease Association to Risk Assessment: An Optimistic View from Genome-Wide Association Studies on Type 1 Diabetes." PLoS Genetics , vol. 10 , no. 5 , pp. e1000678.
Zhi Wei, Mingyao Li, Timothy Rebbeck, Hongzhe Li. 2008. "U-Statistics-based Tests for Multiple Genes in Genetic Association Studies." Annals of Human Genetics/Blackwell Publishing Ltd/University College London , vol. 72 , no. 6 , pp. 821-833.
Zhi Wei, Hongzhe Li. 2008. "A Hidden Spatial-Temporal Markov Random Field Model For Network-Based Analysis Of Time Course Gene Expression Data." Annals of Applied Statistics , vol. 2 , no. 1 , pp. 408-429.
Zhi Wei, Mingyao Li. 2007. "Genome-wide Association Analysis of Rheumatoid Arthritis in a Canadian Population." BMC Proceedings , vol. 1 , no. S1 , pp. S19.
Zhi Wei, Hongzhe Li. 2007. "A Markov Random Field Model for Network-based Analysis of Genomic Data." Bioinformatics , vol. 23 , no. 12 , pp. 1537-1544.
Zhi Wei, Hongzhe Li. 2007. "Nonparametric Pathway-Based Regression Models for Analysis of Genomic Data." Biostatistics , vol. 8 , no. 2 , pp. 265-284.
Zhi Wei, Shane T Jensen. 2006. "A Markov Random Field Model for Network-based Analysis of Genomic Data." Bioinformatics , vol. 22 , no. 13 , pp. 1577-1584.
Haoran Liu, Xiang Lin, Zhi Wei. 2025. "Marker Gene-Guided Graph Neural Networks for Enhanced Spatial Transcriptomics Clustering." AI Medicine , vol. 2 , no. 1 , pp. 1.
H Wang, Y Wang, J Zhou, B Song, G Tu, A Nguyen, J Su, F Coenen, Zhi Wei, D J Rigden, J Meng. 2025. "Statistical modeling of single-cell epitranscriptomics enabled trajectory and regulatory inference of RNA methylation.." Cell genomics , vol. 5 , no. 1 , pp. 100702.
H Duan, J Ren, S Wei, Z Yang, C Li , Z Wang, M Li , Zhi Wei, Y Liu, X Wang, H Lan, Z Zeng, M Xie, Y Xie, S Wu, W Hu, C Guo, X Zhang, L Liang, C Yu, Y Mou, Y Jiang, H Li , E Sugarman, R A Deek, Z Chen, T Li , Y Chen, M Yao, L Chen, L Liu, G Zhang, Y Mou. 2024. "Integrated analyses of multi-omic data derived from paired primary lung cancer and brain metastasis reveal the metabolic vulnerability as a novel therapeutic target.." Genome medicine , vol. 16 , no. 1 , pp. 138.
Kuang Du, Jing Du, Zhi Wei. 2024. "Self-Supervised Based Multi-View Graph Presentation Learning for Drug-Drug Interaction Prediction." Transactions on Artificial Intelligence , vol. 1 , no. 1 , pp. 1.
X Lin, S Jiang, L Gao, Zhi Wei, J Wang. 2024. "MultiSC: a deep learning pipeline for analyzing multiomics single-cell data.." Briefings in bioinformatics , vol. 25 , no. 6 .
T Tian, J Zhang, X Lin, Zhi Wei, H Hakonarson. 2024. "Dependency-aware deep generative models for multitasking analysis of spatial omics data.." Nature methods , vol. 21 , no. 8 , pp. 1501-1513.
S R Bonam, N C Hazell, M J Mathew, Y Liang, X Zhang, Zhi Wei, M G Alameh, D Weissman, H Hu. 2024. "Innate and Adaptive Immune Parameters following mRNA Vaccination in Mice.." Vaccines , vol. 12 , no. 5 .
Zhi Wei. 2024. "Discrete latent embeddings illuminate cellular diversity in single-cell epigenomics.." Nature computational science , vol. 4 , no. 5 , pp. 316-317.
Hao Chen, Fengzhu Jia, Xiaoying Pan, Zhi Wei. 2023. "Theta-Mechanism based Cluster Search Algorithm for Global Constrained Optimization." Applied Soft Computing , pp. 110963.
C Zhong, T Tian, Zhi Wei. 2023. "Hidden Markov random field models for cell-type assignment of spatially resolved transcriptomics.." Bioinformatics (Oxford, England) , vol. 39 , no. 11 .
Iyshwarya Balasubramanian, Sheila Bandyopadhyay, Juan Flores, Jared Bianchi-Smak, Xiang Lin, Haoran Liu, Shengxiang Sun, Natasha B Golovchenko, Yue Liu, Dahui Wang, Radha Patel, Ivor Joseph, Panan Suntornsaratoon, Justin Vargas, Peter HR Green, Govind Bhagat, Stephen M Lagana, Wang Ying, Yi Zhang, Zhihan Wang, Wei Vivian Li, Sukhwinder Singh, Zhongren Zhou, George Kollias, Laura A Farr, Shannon N Moonah, Shiyan Yu, Zhi Wei, Edward M Bonder, Lanjing Zhang, Pawel R Kiela, Karen L Edelblum, Ronaldo Ferraris, Ta-Chiang Liu, Nan Gao. 2023. "Infection and inflammation stimulate expansion of a CD74+ Paneth cell subset to regulate disease progression." The EMBO Journal , vol. 42 , no. 21 , pp. e113975.
Ivor Joseph, Juan Flores, Victoria Farrell, Justin Davis, Jared Bianchi-Smak, Qiang Feng, Sayantani Goswami, Xiang Lin, Zhi Wei, Kevin Tong, others. 2023. "RAB11A and RAB11B control mitotic spindle function in intestinal epithelial progenitor cells." EMBO reports , pp. e56240.
Charles C. L. Tong, Xiang Lin, Tyler Seckar, Mateusz Koptyra, Michael A. Kohanski, Noam A. Cohen, David W. Kennedy, Nithin D. Adappa, Peter Papagiannopoulos, Edward C. Kuan, Esther Baranov, Jalal B. Jalaly, Michael D. Feldman, Phillip B. Storm, Adam C. Resnick, James N. Palmer, Zhi Wei, Erle S. Robertson. 2023. "A metagenomic analysis of the virome of inverted papilloma and squamous cell carcinoma." International Forum of Allergy \& Rhinology , vol. 13 , no. 11 , pp. 2055-2062.
Dipayan Bose, Xiang Lin, Le Gao, Zhi Wei, Yonggang Pei, Erle S Robertson. 2023. "Attenuation of IFN signaling due to m6A modification of the host epitranscriptome promotes EBV lytic reactivation." Journal of Biomedical Science , vol. 30 , no. 1 , pp. 18.
Tian Tian, Cheng Zhong, Xiang Lin, Zhi Wei, Hakon Hakonarson. 2023. "Complex hierarchical structures in single-cell genomics data unveiled by deep hyperbolic manifold learning." Genome Research , vol. 33 , no. 2 , pp. 232--246.
Christopher J Cardinale, Xiao Chang, Zhi Wei, Hui-Qi Qu, Jonathan P Bradfield, Constantin Polychronakos, Hakon Hakonarson. 2023. "Genome-wide association study of the age of onset of type 1 diabetes reveals HTATIP2 as a novel T cell regulator." Frontiers in Immunology , vol. 14 , pp. 1101488.
Ronald Benjamin, Christopher J Giacoletto, Zachary T FitzHugh, Danielle Eames, Lindsay Buczek, Xiaogang Wu, Jacklyn Newsome, Mira V Han, Tony Pearson, Zhi Wei, Atoshi Banerjee, Lancer Brown, Liz J. Valente, Shirley Shen, Hong-Wen Deng, Martin R. Schiller. 2022. "Data supporting a saturation mutagenesis assay for Tat-driven transcription with the GigaAssay." Data in Brief , vol. 45 , pp. 108641.
Xiang Lin, Tian Tian, Zhi Wei, Hakon Hakonarson. 2022. "Clustering of single-cell multi-omics data with a multimodal deep learning method." Nature Communications , vol. 13 , no. 1 , pp. 7705.
X Lin, L Gao, N Whitener, A Ahmed, Zhi Wei. 2022. "A model-based constrained deep learning clustering approach for spatially resolved single-cell data.." Genome research .
Q Yin, W Chen, C Zhang, Zhi Wei. 2022. "A convolutional neural network model for survival prediction based on prognosis-related cascaded Wx feature selection.." Laboratory investigation; a journal of technical methods and pathology , vol. 102 , no. 10 , pp. 1064-1074.
J Li , Y R Li , J T Glessner, J Yang, M E March, C Kao, C N Vaccaro, J P Bradfield, J Li , F D Mentch, H Q Qu, X Qi, X Chang, C Hou, D J Abrams, H Qiu, Zhi Wei, J J Connolly, F Wang, J Snyder, B Flatø, S D Thompson, C D Langefeld, B A Lie, J E Munro, C Wise, Sleiman PMA, H Hakonarson. 2022. "Identification of Novel Loci Shared by Juvenile Idiopathic Arthritis Subtypes Through Integrative Genetic Analysis.." Arthritis & rheumatology (Hoboken, N.J.) , vol. 74 , no. 8 , pp. 1420-1429.
Yang Jia, Xinmeng Zhang, Hanrong Du, Weiguang Chen, Xiaohui Jin, Wei Qi, Bin Yang, Qiujuan Zhang, Zhi Wei. 2022. "Fine-grained precise-bone age assessment by integrating prior knowledge and recursive feature pyramid network." EURASIP Journal on Image and Video Processing , vol. 2022 , no. 1 , pp. 12.
Liulin Yang, Yu Li, Zhi Wei. 2022. "Fa-Mb-ResNet for Grounding Fault Identification and Line Selection in the Distribution Networks." IEEE Internet of Things Journal .
R Benjamin, C J Giacoletto, Z T FitzHugh, D Eames, L Buczek, X Wu, J Newsome, M V Han, T Pearson, Zhi Wei, A Banerjee, L Brown, L J Valente, S Shen, H W Deng, M R Schiller. 2022. "GigaAssay - An adaptable high-throughput saturation mutagenesis assay platform.." Genomics , vol. 114 , no. 4 , pp. 110439.
D M Hristova, T Fukumoto, C Takemori, L Gao, X Hua, J X Wang, L Li , M Beqiri, A Watters, A Vultur, Y Gimie, V Rebecca, A Samarkina, H Jimbo, C Nishigori, J Zhang, C Cheng, Zhi Wei, R Somasundaram, M Fukunaga-Kalabis, M Herlyn. 2022. "NUMB as a Therapeutic Target for Melanoma.." The Journal of investigative dermatology , vol. 142 , no. 7 , pp. 1882-1892.e5.
S Wei, D Yin, S Yu, X Lin, M R Savani, K Du , Y Ku, D Wu, S Li , H Liu, M Tian, Y Chen, M Bowie, S Hariharan, M Waitkus, S T Keir, E T Sugarman, R A Deek, M Labrie, M Khasraw, Y Lu, G B Mills, M Herlyn, K Wu, L Liu, Zhi Wei, K T Flaherty, K Abdullah, G Zhang, D M Ashley. 2022. "Antitumor Activity of a Mitochondrial-Targeted HSP90 Inhibitor in Gliomas.." Clinical cancer research : an official journal of the American Association for Cancer Research , vol. 28 , no. 10 , pp. 2180-2195.
Turki Turki, Zhi Wei. 2022. "Improved Deep Convolutional Neural Networks via Boosting for Predicting the Quality of In Vitro Bovine Embryos." Electronics , vol. 11 , no. 9 , pp. 1363.
F Tan, C Hu, Y Hu, K Yen, Zhi Wei, A Pappu, S Park, K Li . 2022. "MGEL: Multigrained Representation Analysis and Ensemble Learning for Text Moderation.." IEEE transactions on neural networks and learning systems , vol. PP .
Tong CCL, M Koptyra, P Raman, K S Rathi, N Choudhari, X Lin, T Seckar, Zhi Wei, M A Kohanski, B W O'Malley, N A Cohen, D W Kennedy, N D Adappa, E S Robertson, E Baranov, E C Kuan, P Papagiannopoulos, J B Jalaly, M D Feldman, P B Storm, A C Resnick, J N Palmer. 2022. "Targeted gene expression profiling of inverted papilloma and squamous cell carcinoma.." International forum of allergy & rhinology , vol. 12 , no. 2 , pp. 200-209.
S Das, Q Feng, I Balasubramanian, X Lin, H Liu, O Pellón-Cardenas, S Yu, X Zhang, Y Liu, Zhi Wei, E M Bonder, M P Verzi, W Hsu, L Zhang, T C Wang, N Gao. 2022. "Colonic healing requires Wnt produced by epithelium as well as Tagln+ and Acta2+ stromal cells.." Development (Cambridge, England) , vol. 149 , no. 1 .
Xiang Lin, Haoran Liu, Zhi Wei, Senjuti Basu Roy, Nan Gao. 2021. "An active learning approach for clustering single-cell RNA-seq data." Laboratory Investigation , pp. 1--9.
S Yu, S Wei, M Savani, X Lin, K Du , I Mender, S Siteni, T Vasilopoulos, Z J Reitman, Y Ku, D Wu, H Liu, M Tian, Y Chen, M Labrie, C M Charbonneau, E Sugarman, M Bowie, S Hariharan, M Waitkus, W Jiang, R E McLendon, E Pan, M Khasraw, K M Walsh, Y Lu, M Herlyn, G Mills, U Herbig, Zhi Wei, S T Keir, K Flaherty, L Liu, K Wu, J W Shay, K Abdullah, G Zhang, D M Ashley. 2021. "A Modified Nucleoside 6-Thio-2'-Deoxyguanosine Exhibits Antitumor Activity in Gliomas.." Clinical cancer research : an official journal of the American Association for Cancer Research , vol. 27 , no. 24 , pp. 6800-6814.
Jianglan Liu, Vito W. Rebecca, Andrew V. Kossenkov, Thomas Connelly, Qin Liu, Alexis Gutierrez, Min Xiao, Ling Li, Gao Zhang, Anastasia Samarkina, Delaine Zayasbazan, Jie Zhang, Chaoran Cheng, Zhi Wei, Gretchen M. Alicea, Mizuho Fukunaga-Kalabis, Clemens Krepler, Pedro Aza-Blanc, Chih-Cheng Yang, Bela Delvadia, Cynthia Tong, Ye Huang, Maya Delvadia, Alice S. Morias, Katrin Sproesser, Patricia Brafford, Joshua X. Wang, Marilda Beqiri, Rajasekharan Somasundaram, Adina Vultur, Denitsa M. Hristova, Lawrence W. Wu, Yiling Lu, Gordon B. Mills, Wei Xu, Giorgos C. Karakousis, Xiaowei Xu, Lynn M. Schuchter, Tara C. Mitchell, Ravi K. Amaravadi, Lawrence N. Kwong, Dennie T. Frederick, Genevieve M. Boland, Joseph M. Salvino, David W. Speicher, Keith T. Flaherty, Ronai, Ze'ev A., Meenhard Herlyn. 2021. "Neural Crest-Like Stem Cell Transcriptome Analysis Identifies LPAR1 in Melanoma Progression and Therapy Resistance." Cancer Research , vol. 81 , no. 20 , pp. 5230--5241.
Kuang Du, Shiyou Wei, Zhi Wei, Dennie T. Frederick, Benchun Miao, Tabea Moll, Tian Tian, Eric Sugarman, Dmitry I. Gabrilovich, Ryan J. Sullivan, Lunxu Liu, Keith T. Flaherty, Genevieve M. Boland, Meenhard Herlyn, Gao Zhang. 2021. "Pathway signatures derived from on-treatment tumor specimens predict response to anti-PD1 blockade in metastatic melanoma." Nature Communications , vol. 12 , no. 1 .
Sagarika Banerjee, Zhi Wei, Tian Tian, Dipayan Bose, Natalie NC Shih, Michael D Feldman, Thaer Khoury, Angela De Michele, Erle S Robertson. 2021. "Prognostic correlations with the microbiome of breast cancer subtypes." Cell Death & Disease , vol. 12 , no. 9 , pp. 1--14.
Russell J. Buono, Jonathan P. Bradfield, Zhi Wei, Michael R. Sperling, Dennis J. Dlugos, Michael D. Privitera, Jacqueline A. French, Warren Lo, Patrick Cossette, Steven C. Schachter, Heather Basehore, Falk W. Lohoff, Struan F.A. Grant, Thomas N. Ferraro, Hakon Hakonarson. 2021. "Genetic variation in PADI6-PADI4 on 1p36.13 is associated with common forms of human generalized epilepsy." Genes , vol. 12 , no. 9 .
Tian Tian, Martin Renqiang Min, Zhi Wei. 2021. "Model-based autoencoders for imputing discrete single-cell RNA-seq data." Methods , vol. 192 , pp. 112-119.
Beike Wang, Wei Zhang, Gao Zhang, Lawrence Kwong, Hezhe Lu, Jiufeng Tan, Norah Sadek, Min Xiao, Jie Zhang, Marilyne Labrie, Sergio Randell, Aurelie Beroard, Eric Sugarman, Vito W. Rebecca, Zhi Wei, Yiling Lu, Gordon B. Mills, Jeffrey Field, Jessie Villanueva, Xiaowei Xu, Meenhard Herlyn, Wei Guo. 2021. "Targeting mTOR signaling overcomes acquired resistance to combined BRAF and MEK inhibition in BRAF-mutant melanoma." Oncogene , vol. 40 , no. 37 , pp. 5590-5599.
Xiang Lin, Jie Zhang, Zhi Wei, Turki Turki. 2021. "An Omnibus Test for Differential Distribution Analysis of Continuous Microbiome Data." IEEE Access , vol. 9 , pp. 100029-100039.
Karthik Rajasekaran, Ryan M. Carey, Xiang Lin, Tyler D. Seckar, Zhi Wei, Kevin Chorath, Jason G. Newman, Bert W. O'Malley, Gregory S. Weinstein, Michael D. Feldman, Erle Robertson. 2021. "The microbiome of HPV-positive tonsil squamous cell carcinoma and neck metastasis." Oral Oncology , vol. 117 .
Xiurui Hou, Kai Wang, Cheng Zhong, Zhi Wei. 2021. "ST-Trader: A Spatial-Temporal Deep Neural Network for Modeling Stock Market Movement." IEEE/CAA Journal of Automatica Sinica , vol. 8 , no. 5 , pp. 1015-1024.
Tian Tian, Jie Zhang, Xiang Lin, Zhi Wei, Hakon Hakonarson. 2021. "Model-based deep embedding for constrained clustering analysis of single cell RNA-seq data." Nature Communications , vol. 12 , no. 1 .
Tyler Seckar, Xiang Lin, Dipayan Bose, Zhi Wei, Joseph Rohrbaugh, Ronald G. Collman, Erle S. Robertson. 2021. "Detection of Microbial Agents in Oropharyngeal and Nasopharyngeal Samples of SARS-CoV-2 Patients." Frontiers in Microbiology , vol. 12 .
Joseph T. Glessner, Xiao Chang, Yichuan Liu, Jin Li, Munir Khan, Zhi Wei, Patrick M.A. Sleiman, Hakon Hakonarson. 2021. "MONTAGE: a new tool for high-throughput detection of mosaic copy number variation." BMC Genomics , vol. 22 , no. 1 .
Fentaw Abegaz, François Van Lishout, Jestinah M. Mahachie John, Kridsadakorn Chiachoompu, Archana Bhardwaj, Diane Duroux, Elena S. Gusareva, Zhi Wei, Hakon Hakonarson, Kristel Van Steen. 2021. "Performance of model-based multifactor dimensionality reduction methods for epistasis detection by controlling population structure." BioData Mining , vol. 14 , no. 1 .
Matthias Gromeier, Michael C. Brown, Gao Zhang, Xiang Lin, Yeqing Chen, Zhi Wei, Nike Beaubier, Hai Yan, Yiping He, Annick Desjardins, James E. Herndon, Frederick S. Varn, Roel G. Verhaak, Junfei Zhao, Dani P. Bolognesi, Allan H. Friedman, Henry S. Friedman, Frances McSherry, Andrea M. Muscat, Eric S. Lipp, Smita K. Nair, Mustafa Khasraw, Katherine B. Peters, Dina Randazzo, John H. Sampson, Roger E. McLendon, Darell D. Bigner, David M. Ashley. 2021. "Very low mutation burden is a feature of inflamed recurrent glioblastomas responsive to cancer immunotherapy." Nature Communications , vol. 12 , no. 1 .
Joseph T Glessner, Xiurui Hou, Cheng Zhong, Jie Zhang, Munir Khan, Fabian Brand, Peter Krawitz, Patrick M A Sleiman, Hakon Hakonarson, Zhi Wei. 2021. "DeepCNV: a deep learning approach for authenticating copy number variations." Briefings in Bioinformatics , vol. 22 , no. 5 .
Tian Tian, Ruihua Cheng, Zhi Wei. 2021. "An empirical bayes change-point model for transcriptome time-course data." Annals of Applied Statistics , vol. 15 , no. 1 , pp. 509-526.
Yun Rose Li, Joseph T. Glessner, Bradley P. Coe, Jin Li, Maede Mohebnasab, Xiao Chang, John Connolly, Charlly Kao, Zhi Wei, Jonathan Bradfield, Cecilia Kim, Cuiping Hou, Munir Khan, Frank Mentch, Haijun Qiu, Marina Bakay, Christopher Cardinale, Maria Lemma, Debra Abrams, Andrew Bridglall-Jhingoor, Meckenzie Behr, Shanell Harrison, George Otieno, Alexandria Thomas, Fengxiang Wang, Rosetta Chiavacci, Lawrence Wu, Dexter Hadley, Elizabeth Goldmuntz, Josephine Elia, John Maris, Robert Grundmeier, Marcella Devoto, Brendan Keating, Michael March, Renata Pellagrino, Struan F.A. Grant, Patrick M.A. Sleiman, Mingyao Li, Evan E. Eichler, Hakon Hakonarson. 2020. "Rare copy number variants in over 100,000 European ancestry subjects reveal multiple disease associations." Nature Communications , vol. 11 , no. 1 .
Yonggang Pei, Josiah Hiu-yuen Wong, Hem Chandra Jha, Tian Tian, Zhi Wei, Erle S Robertson. 2020. "Epstein-Barr Virus Facilitates Expression of KLF14 by Regulating the Cooperative Binding of the E2F-Rb-HDAC Complex in Latent Infection." Journal of Virology , vol. 94 , no. 22 .
Liangliang Wang, Yan Gao, Gao Zhang, Dan Li, Zhenda Wang, Jie Zhang, Leandro C. Hermida, Lei He, Zhisong Wang, Jingwen Si, Shuang Geng, Rizi Ai, Fei Ning, Chaoran Cheng, Haiteng Deng, Dimiter S. Dimitrov, Yan Sun, Yanyi Huang, Dong Wang, Xiaoyu Hu, Zhi Wei, Wei Wang, Xuebin Liao. 2020. "Enhancing KDM5A and TLR activity improves the response to immune checkpoint blockade." Science translational medicine , vol. 12 , no. 560 .
Shiyan Yu, Iyshwarya Balasubramanian, Daniel Laubitz, Kevin Tong, Sheila Bandyopadhyay, Xiang Lin, Juan Flores, Rajbir Singh, Yue Liu, Carlos Macazana, Yanlin Zhao, Fabienne Béguet-Crespel, Karuna Patil, Monica T. Midura-Kiela, Daniel Wang, George S. Yap, Ronaldo P. Ferraris, Zhi Wei, Edward M. Bonder, Max M. Häggblom, Lanjing Zhang, Veronique Douard, Michael P. Verzi, Ken Cadwell, Pawel R. Kiela, Nan Gao. 2020. "Paneth Cell-Derived Lysozyme Defines the Composition of Mucolytic Microbiota and the Inflammatory Tone of the Intestine." Immunity , vol. 53 , no. 2 , pp. 398-416.e8.
Fei Tan, Tian Tian, Xiurui Hou, Xiang Yu, Lei Gu, Fernanda Mafra, Brian D. Gregory, Zhi Wei, Hakon Hakonarson. 2020. "Elucidation of DNA methylation on N <sup>6</sup>-adenine with deep learning." Nature Machine Intelligence , vol. 2 , no. 8 , pp. 466-475.
Christopher J. Cardinale, Michael E. March, Xiang Lin, Yichuan Liu, Lynn A. Spruce, Jonathan P. Bradfield, Zhi Wei, Steven H. Seeholzer, Struan F.A. Grant, Hakon Hakonarson. 2020. "Regulation of Janus Kinase 2 by an Inflammatory Bowel Disease Causal Non-coding Single Nucleotide Polymorphism." Journal of Crohn's and Colitis , vol. 14 , no. 5 , pp. 646-653.
Hongyun Yue, Zhi Wei, Qingjiang Chen, Xiaoyan Zhang. 2020. "Dynamic surface control for a class of nonlinearly parameterized systems with input time delay using neural network." Journal of the Franklin Institute , vol. 357 , no. 4 , pp. 1961-1986.
Ryan M. Carey, Karthik Rajasekaran, Tyler Seckar, Xiang Lin, Zhi Wei, Charles C.L. Tong, Viran J. Ranasinghe, Jason G. Newman, Bert W. O'Malley, Gregory S. Weinstein, Michael D. Feldman, Erle S. Robertson. 2020. "The virome of HPV-positive tonsil squamous cell carcinoma and neck metastasis." Oncotarget , vol. 11 , no. 3 , pp. 282-293.
Xiurui Hou, Kai Wang, Jie Zhang, Zhi Wei. 2020. "An Enriched Time-Series Forecasting Framework for Long-Short Portfolio Strategy." IEEE Access , vol. 8 , pp. 31992-32002.
Xiaoying Pan, Yizhe Zhao, Hao Chen, De Wei, Chen Zhao, Zhi Wei. 2020. "Fully Automated Bone Age Assessment on Large-Scale Hand X-Ray Dataset." International Journal of Biomedical Imaging , vol. 2020 .
Jin Li, Zhi Wei, Jie Zhang, Hakon Hakonarson, Scott D. Cook-Sather. 2019. "Candidate gene analyses for acute pain and morphine analgesia after pediatric day surgery: African American versus European Caucasian ancestry and dose prediction limits." Pharmacogenomics Journal , vol. 19 , no. 6 , pp. 570-581.
Andrea Aloia, Daniela Müllhaupt, Christophe D. Chabbert, Tanja Eberhart, Stefanie Flückiger-Mangual, Ana Vukolic, Ossia Eichhoff, Anja Irmisch, Leila T. Alexander, Ernesto Scibona, Dennie T. Frederick, Benchun Miao, Tian Tian, Chaoran Cheng, Lawrence N. Kwong, Zhi Wei, Ryan J. Sullivan, Genevieve M. Boland, Meenhard Herlyn, Keith T. Flaherty, Nicola Zamboni, Reinhard Dummer, Gao Zhang, Mitchell P. Levesque, Wilhelm Krek, Werner J. Kovacs. 2019. "A Fatty Acid Oxidation-dependent Metabolic Shift Regulates the Adaptation of BRAF-mutated Melanoma to MAPK Inhibitors." Clinical Cancer Research , vol. 25 , no. 22 , pp. 6852-6867.
Fentaw Abegaz, François Van Lishout, Jestinah M. Mahachie John, Kridsadakorn Chiachoompu, Archana Bhardwaj, Elena S. Gusareva, Zhi Wei, Hakon Hakonarson, Kristel Van Steen. 2019. "Epistasis Detection in Genome-Wide Screening for Complex Human Diseases in Structured Populations." Systems Medicine , vol. 2 , no. 1 , pp. 19-27.
Xiali Li, Shuai He, Zhi Wei, Licheng Wu. 2019. "Improved Online Sequential Extreme Learning Machine: A New Intelligent Evaluation Method for AZ-Style Algorithms." IEEE Access , vol. 7 , pp. 124891-124901.
Xiali Li, Zhengyu Lv, Song Wang, Zhi Wei, Licheng Wu. 2019. "A Reinforcement Learning Model Based on Temporal Difference Algorithm." IEEE Access , vol. 7 , pp. 121922--121930.
Xiali Li, Zhengyu Lv, Song Wang, Zhi Wei, Xiaochuan Zhang, Licheng Wu. 2019. "A Middle Game Search Algorithm Applicable to Low-Cost Personal Computer for Go." IEEE Access , vol. 7 , pp. 121719--121727.
Sagarika Banerjee, James C. Alwine, Zhi Wei, Tian Tian, Natalie Shih, Colin Sperling, Thomas Guzzo, Michael D. Feldman, Erle S. Robertson. 2019. "Microbiome signatures in prostate cancer." Carcinogenesis , vol. 40 , no. 6 , pp. 749-764.
Jie Zhang, Zhi Wei, Zhenyu Yan, Mengchu Zhou, Abhishek Pani. 2019. "Online Change-Point Detection in Sparse Time Series with Application to Online Advertising." IEEE Transactions on Systems, Man, and Cybernetics: Systems , vol. 49 , no. 6 , pp. 1141-1151.
Fei Tan, Chaoran Cheng, Zhi Wei. 2019. "Modeling and elucidation of housing price." Data Mining and Knowledge Discovery , vol. 33 , no. 3 , pp. 636-662.
Fei Tan, Xiurui Hou, Jie Zhang, Zhi Wei, Zhenyu Yan. 2019. "A Deep Learning Approach to Competing Risks Representation in Peer-to-Peer Lending." IEEE Transactions on Neural Networks and Learning Systems , vol. 30 , no. 5 , pp. 1565-1574.
Tian Tian, Ji Wan, Qi Song, Zhi Wei. 2019. "Clustering single-cell RNA-seq data with a model-based deep learning approach." Nature Machine Intelligence , vol. 1 , no. 4 , pp. 191.
Jie Zhang, Zhigen Zhao, Kai Zhang, Zhi Wei. 2019. "A feature sampling strategy for analysis of high dimensional genomic data." IEEE/ACM Transactions on Computational Biology and Bioinformatics , vol. 16 , no. 2 , pp. 434-441.
Rani Ojha, Nektaria M. Leli, Angelique Onorati, Shengfu Piao, Ioannis I. Verginadis, Feven Tameire, Vito W. Rebecca, Cynthia I. Chude, Sengottuvelan Murugan, Colin Fennelly, Estela Noguera-Ortega, Shujing Liu, Xiaowei Xu, Clemens Krepler, Min Xiao, Wei Xu, Zhi Wei, Dennie T. Frederick, Genevieve Boland, Tara C. Mitchell, Giorgos C. Karakousis, Lynn M. Schuchter, Keith T. Flaherty, Gao Zhang, Meenhard Herlyn, Constantinos Koumenis, Ravi K. Amaravadi. 2019. "Er translocation of the mapk pathway drives therapy resistance in BRAF-mutant melanoma." Cancer Discovery , vol. 9 , no. 3 , pp. 396-415.
Avinash Das Sahu, Joo S Lee, Zhiyong Wang, Gao Zhang, Ramiro Iglesias-Bartolome, Tian Tian, Zhi Wei, Benchun Miao, Nishanth Ulhas Nair, Olga Ponomarova, Adam A. Friedman, Arnaud Amzallag, Tabea Moll, Gyulnara Kasumova, Patricia Greninger, Regina K. Egan, Leah J. Damon, Dennie T. Frederick, Livnat Jerby-Arnon, Allon Wagner, Kuoyuan Cheng, Seung Gu Park, Welles Robinson, Kevin Gardner, Genevieve Boland, Sridhar Hannenhalli, Meenhard Herlyn, Cyril Benes, Keith Flaherty, Ji Luo, J. Silvio Gutkind, Eytan Ruppin. 2019. "Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy." Molecular Systems Biology , vol. 15 , no. 3 .
Chengqian Yin, Bo Zhu, Ting Zhang, Tongzheng Liu, Shuyang Chen, Yu Liu, Xin Li, Xiao Miao, Shanshan Li, Xia Mi, Jie Zhang, Li Li, Guo Wei, Zhi xiang Xu, Xiumei Gao, Canhua Huang, Zhi Wei, Colin R. Goding, Peng Wang, Xianming Deng, Rutao Cui. 2019. "Pharmacological Targeting of STK19 Inhibits Oncogenic NRAS-Driven Melanomagenesis." Cell , vol. 176 , no. 5 , pp. 1113-1127.e16.
Xin Gao, Zhi Wei, Hakon Hakonarson. 2019. "TRNA-DL: A Deep Learning Approach to Improve tRNAscan-SE Prediction Results." Human Heredity , vol. 83 , no. 3 , pp. 163-172.
Jie Zhang, Zhi Wei, Christopher J. Cardinale, Elena S. Gusareva, Kristel Van Steen, Patrick Sleiman, Hakon Hakonarson. 2019. "Multiple epistasis interactions within MHC are associated with ulcerative colitis." Frontiers in Genetics , vol. 10 .
Xiaoping Xiong, Wenliang Wu, Ning Li, Lu Yang, Jie Zhang, Zhi Wei. 2019. "Risk-based multi-objective optimization of distributed generation based on GPSO-BFA algorithm." IEEE Access , vol. 7 , pp. 30563-30572.
Yan Sun, Xueming Yao, Michael E. March, Xinyi Meng, Junyi Li, Zhi Wei, Patrick M.A. Sleiman, Hakon Hakonarson, Qianghua Xia, Jin Li. 2019. "Target genes of autism risk loci in brain frontal cortex." Frontiers in Genetics , vol. 10 , no. JUL .
Q. Kang, L. Shi, Mengchu Zhou, Xianqin Wang, Q. Wu, Zhi Wei. 2018. "A Distance-Based Weighted Undersampling Scheme for Support Vector Machines and its Application to Imbalanced Classification." IEEE Transactions on Neural Networks and Learning Systems , vol. 29 , no. 9 , pp. 4152-4165.
The International League Against Epilepsy Consortium on Complex Epilepsies, Zhi Wei. 2018. "Genome-wide mega-analysis identifies 16 loci and highlights diverse biological mechanisms in the common epilepsies." Nature Communications , vol. 9 , pp. 5269.
Yukihide Momozawa, Julia Dmitrieva, Emilie Theatre, Valerie Deffontaine, Souad Rahmouni, Benoit Charloteaux, Francois Crins, Elisa Docampo, Mahmoud Elansary, Ann-Stephan Gori, Christelle Lecut, Rob Mariman, Myriam Mni, Cecile Oury, Ilya Altukhov, Dmitry Alexeev, Yuri Aulchenko, Leila Amininejad, Gerd Bouma, Frank Hoentjen, Mark Lowenberg, Bas Oldenburg, Marieke J Pierik, vander Meulen-de Jong, Andrea E, van der Woude, C Janneke, Marijn C Visschedijk, Consortium IBD Genetics, Zhi Wei, Mark Lathrop, Jean-Pierre Hugot, Rinse K Weersma, Martine De Vos, Denis Franchimont, Severine Vermeire, Michiaki Kubo, Edouard Louis, Michel Georges. 2018. "IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes." NATURE COMMUNICATIONS , vol. 9 , pp. 2427.
Shujing Liu, Gao Zhang, Jianping Guo, Xiang Chen, Jingce Lei, Kan Ze, Liyun Dong, Xiangpeng Dai, Yang Gao, Daisheng Song, Brett Ecker, Ruifeng Yang, Caitlin Feltcher, Kai Peng, Cheng Feng, Hui Chen, Rebecca X. Lee, Heddy Kerestes, Jingwen Niu, Suresh Kumar, Weiting Xu, Jie Zhang, Zhi Wei, James S. Martin, Xiaoming Liu, Gordon Mills, Yiling Lu, Wei Guo, Lunquan Sun, Lin Zhang, Ashani Weeraratna, Meenhard Herlyn, Wenyi Wei, Frank S. Lee, Xiaowei Xu. 2018. "Loss of Phd2 cooperates with BRAF <sup>V600E</sup> to drive melanomagenesis." Nature Communications , vol. 9 , no. 1 .
Jane F. Ferguson, Chenyi Xue, Yuanfeng Gao, Tian Tian, Jianting Shi, Xuan Zhang, Ying Wang, Yuhuang D. Li, Zhi Wei, Mingyao Li, Hanrui Zhang, Muredach P. Reilly. 2018. "Tissue-Specific Differential Expression of Novel Genes and Long Intergenic Noncoding RNAs in Humans With Extreme Response to Evoked Endotoxemia." Circulation. Genomic and precision medicine , vol. 11 , no. 11 , pp. e001907.
Turki Turki, Zhi Wei. 2018. "Boosting support vector machines for cancer discrimination tasks." Computers in Biology and Medicine , vol. 101 , pp. 236-249.
Fiona Simpkins, Kibeom Jang, Hyunho Yoon, Karina E. Hew, Minsoon Kim, Diana J. Azzam, Jun Sun, Dekuang Zhao, Tan A. Ince, Wenbin Liu, Wei Guo, Zhi Wei, Gao Zhang, Gordon B. Mills, Joyce M. Slingerland. 2018. "Dual Src and MEK inhibition decreases ovarian cancer growth and targets tumor initiating stem-like cells." Clinical Cancer Research , vol. 24 , no. 19 , pp. 4874-4886.
Gao Zhang, Lawrence W. Wu, Ilgen Mender, Michal Barzily-Rokni, Marc R. Hammond, Omotayo Ope, Chaoran Cheng, Themistoklis Vasilopoulos, Sergio Randell, Norah Sadek, Aurelie Beroard, Min Xiao, Tian Tian, Jiufeng Tan, Umar Saeed, Eric Sugarman, Clemens Krepler, Patricia Brafford, Katrin Sproesser, Sengottuvelan Murugan, Rajasekharan Somasundaram, Bradley Garman, Bradley Wubbenhorst, Jonathan Woo, Xiangfan Yin, Qin Liu, Dennie T. Frederick, Benchun Miao, Wei Xu, Giorgos C. Karakousis, Xiaowei Xu, Lynn M. Schuchter, Tara C. Mitchell, Lawrence N. Kwong, Ravi K. Amaravadi, Yiling Lu, Genevieve M. Boland, Zhi Wei, Katherine Nathanson, Utz Herbig, Gordon B. Mills, Keith T. Flaherty, Meenhard Herlyn, Jerry W. Shay. 2018. "Induction of telomere dysfunction prolongs disease control of therapy-resistant melanoma." Clinical Cancer Research , vol. 24 , no. 19 , pp. 4771-4784.
Q. Kang, L. Shi, Mengchu Zhou, X. Wang, Q. Wu, Zhi Wei. 2018. "A Distance-Based Weighted Undersampling Scheme for Support Vector Machines and its Application to Imbalanced Classification." IEEE Transactions on Neural Networks and Learning Systems , vol. 29 , no. 9 , pp. 4152-4165.
Tian Tian, Ji Wan, Yan Han, Haoran Liu, Feng Gao, Youdong Pan, Qi Song, Zhi Wei. 2018. "A comprehensive survey of immune cytolytic activity-associated gene co-expression networks across 17 tumor and normal tissue types." Cancers , vol. 10 , no. 9 .
Tian Tian, Zhi Wei, Xiao Chang, Yichuan Liu, Raquel E. Gur, Patrick M. A. Sleiman, Hakon Hakonarson. 2018. "The Long Noncoding RNA Landscape in Amygdala Tissues from Schizophrenia Patients." EBioMedicine , vol. 34 , pp. 171-181.
Noam Auslander, Gao Zhang, Joo Sang Lee, Dennie T. Frederick, Benchun Miao, Tabea Moll, Tian Tian, Zhi Wei, Sanna Madan, Ryan J. Sullivan, Genevieve Boland, Keith Flaherty, Meenhard Herlyn, Eytan Ruppin. 2018. "Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma." Nature Medicine , no. 24 , pp. 1545–1549.
Israel Cañadas, Rohit Thummalapalli, Jong Wook Kim, Shunsuke Kitajima, Russell William Jenkins, Camilla Laulund Christensen, Marco Campisi, Yanan Kuang, Yanxi Zhang, Evisa Gjini, Gao Zhang, Tian Tian, Debattama Rai Sen, Diana Miao, Yu Imamura, Tran Thai, Brandon Piel, Hideki Terai, Amir Reza Aref, Timothy Hagan, Shohei Koyama, Masayuki Watanabe, Hideo Baba, Anika Elise Adeni, Christine Anne Lydon, Pablo Tamayo, Zhi Wei, Meenhard Herlyn, Thanh Uyen Barbie, Ravindra Uppaluri, Lynnette Marie Sholl, Ewa Sicinska, Jacob Sands, Scott Rodig, Kwok Kin Wong, Cloud Peter Paweletz, Hideo Watanabe, David Allen Barbie. 2018. "Tumor innate immunity primed by specific interferon-stimulated endogenous retroviruses." Nature Medicine , vol. 24 , no. 8 , pp. 1143-1150.
Turki Turki, Zhi Wei, Jason T. Wang. 2018. "A transfer learning approach via procrustes analysis and mean shift for cancer drug sensitivity prediction." J Bioinform Comput Biol , vol. 16 , no. 3 , pp. 1840014.
R. Dajani, S. J. Shbailat, A. Arafat, S. A. Sober, H. A. Albitar, R. Tayyem, Zhi Wei, H. Hakonarson. 2018. "Association of genetic variants with macronutrient intake in Circassian and Chechan populations in relation to diabetes." Meta Gene , vol. 16 , pp. 199-207.
L. Yang, Y. Li, Zhi Wei, X. Chang. 2018. "Coexpression network analysis identifies transcriptional modules associated with genomic alterations in neuroblastoma." Biochim Biophys Acta , vol. 1864 , no. 6 Pt B , pp. 2341-2348.
L. Yang, Y. Li, T. Turki, H. Tan, Zhi Wei, X. Chang. 2018. "Weighted Gene Co-Expression Network Analysis Reveals Dysregulation of Mitochondrial Oxidative Phosphorylation in Eating Disorders." Genes , vol. 9 , no. 7 , pp. 325.
Verneri Anttila, Brendan Bulik-Sullivan, Hilary K. Finucane, Raymond K. Walters, Jose Bras, Laramie Duncan, Valentina Escott-Price, Guido J. Falcone, Padhraig Gormley, Rainer Malik, Nikolaos A. Patsopoulos, Stephan Ripke, Zhi Wei, Dongmei Yu, Phil H. Lee, Patrick Turley, Benjamin Grenier-Boley, Vincent Chouraki, Yoichiro Kamatani, Claudine Berr, Luc Letenneur, Didier Hannequin, Philippe Amouyel, Anne Boland, Jean-François Deleuze, Emmanuelle Duron, Badri N. Vardarajan, Christiane Reitz, Alison M. Goate, Matthew J. Huentelman, M. Ilyas Kamboh, Eric B. Larson, Ekaterina Rogaeva, Peter St George-Hyslop, Hakon Hakonarson, Walter A. Kukull, Lindsay A. Farrer, Lisa L. Barnes, Thomas G. Beach, F. Yesim Demirci, Elizabeth Head, Christine M. Hulette, Gregory A. Jicha, John S. K. Kauwe, Jeffrey A. Kaye, James B. Leverenz, Allan I. Levey, Andrew P. Lieberman, Vernon S. Pankratz, Wayne W. Poon, Joseph F. Quinn, Andrew J. Saykin, Lon S. Schneider, Amanda G. Smith, Joshua A. Sonnen, Robert A. Stern, Vivianna M. Van Deerlin, Linda J. Van Eldik, Denise Harold, Giancarlo Russo, David C. Rubinsztein, Anthony Bayer, Magda Tsolaki, Petra Proitsi, Nick C. Fox, Harald Hampel, Michael J. Owen, Simon Mead, Peter Passmore, Kevin Morgan, Markus M. Nöthen, Jonathan M. Schott, Martin Rossor, Michelle K. Lupton, Per Hoffmann, Johannes Kornhuber, Brian Lawlor, Andrew McQuillin, Ammar Al-Chalabi, Joshua C. Bis, Agustin Ruiz, Mercè Boada, Sudha Seshadri, Alexa Beiser, Kenneth Rice, van der Lee, Sven J., Philip L. De Jager, Daniel H. Geschwind, Matthias Riemenschneider, Steffi Riedel-Heller, Jerome I. Rotter, Gerhard Ransmayr, Bradley T. Hyman, Carlos Cruchaga, Montserrat Alegret, Bendik Winsvold, Priit Palta, Kai-How Farh, Ester Cuenca-Leon, Nicholas Furlotte, others. 2018. "Analysis of shared heritability in common disorders of the brain." Science , vol. 360 , no. 6395 , pp. eaap8757.
S. Banerjee, T. Tian, Zhi Wei, N. Shih, M. D. Feldman, K. N. Peck, A. M. DeMichele, J. C. Alwine, E. S. Robertson. 2018. "Distinct Microbial Signatures Associated With Different Breast Cancer Types." Front Microbiol , no. 9 , pp. 951.
Jie Zhang, Zhi Wei, Jun Chen. 2018. "A distance-based approach for testing the mediation effect of the human microbiome." Bioinformatics , vol. 34 , no. 11 , pp. 1875-1883.
Ileabett M Echevarría‐Vargas, Patricia I Reyes‐Uribe, Adam N Guterres, Xiangfan Yin, Andrew V Kossenkov, Qin Liu, Gao Zhang, Clemens Krepler, Chaoran Cheng, Zhi Wei, Rajasekharan Somasundaram, Giorgos Karakousis, Wei Xu, Jennifer JD Morrissette, Yiling Lu, Gordon B Mills, Ryan J Sullivan, Miao Benchun, Dennie T Frederick, Genevieve Boland, Keith T Flaherty, Ashani T Weeraratna, Meenhard Herlyn, Ravi Amaravadi, Lynn M Schuchter, Christin E Burd, Andrew E Aplin, Xiaowei Xu, Jessie Villanueva. 2018. "Co‐targeting <scp>BET</scp> and <scp>MEK</scp> as salvage therapy for <scp>MAPK</scp> and checkpoint inhibitor‐resistant melanoma." EMBO Molecular Medicine , vol. 10 , no. 5 .
L. Yang, N. Hang, Zhi Wei. 2018. "Dual M-Convex Variable Subsets Family and Extremum Analysis for the OPF Problem." IEEE Access , vol. 6 , pp. 27018-27027.
I. M. Echevarria-Vargas, P. I. Reyes-Uribe, A. N. Guterres, X. Yin, A. V. Kossenkov, Q. Liu, G. Zhang, C. Krepler, C. Cheng, Zhi Wei, R. Somasundaram, G. Karakousis, W. Xu, J. J. Morrissette, Y. Lu, G. B. Mills, R. J. Sullivan, M. Benchun, D. T. Frederick, G. Boland, K. T. Flaherty, A. T. Weeraratna, M. Herlyn, R. Amaravadi, L. M. Schuchter, C. E. Burd, A. E. Aplin, X. Xu, J. Villanueva. 2018. "Co-targeting BET and MEK as salvage therapy for MAPK and checkpoint inhibitor-resistant melanoma." EMBO Mol Med , vol. 10 , no. 5 , pp. e8446.
X. Gao, J. Zhang, Zhi Wei, H. Hakonarson. 2018. "DeepPolyA: A Convolutional Neural Network Approach for Polyadenylation Site Prediction." IEEE Access , vol. 6 , pp. 24340-24349.
G. Zhang, L. W. Wu, I. Mender, M. Barzily-Rokni, M. R. Hammond, O. Ope, C. Cheng, T. Vasilopoulos, S. Randell, N. Sadek, A. Beroard, M. Xiao, T. Tian, J. Tan, U. Saeed, E. Sugarman, C. Krepler, P. Brafford, K. Sproesser, S. Murugan, R. Somasundaram, B. Garman, B. Wubbenhorst, J. Woo, X. Yin, Q. Liu, D. T. Frederick, B. Miao, W. Xu, G. C. Karakousis, X. Xu, L. M. Schuchter, T. C. Mitchell, L. N. Kwong, R. K. Amaravadi, Y. Lu, G. M. Boland, Zhi Wei, K. Nathanson, U. Herbig, G. B. Mills, K. T. Flaherty, M. Herlyn, J. W. Shay. 2018. "Induction of Telomere Dysfunction Prolongs Disease Control of Therapy-Resistant Melanoma." Clin Cancer Res .
R. W. Jenkins, A. R. Aref, P. H. Lizotte, E. Ivanova, S. Stinson, C. W. Zhou, M. Bowden, J. Deng, H. Liu, D. Miao, M. X. He, W. Walker, G. Zhang, T. Tian, C. Cheng, Zhi Wei, S. Palakurthi, M. Bittinger, H. Vitzthum, J. W. Kim, A. Merlino, M. Quinn, C. Venkataramani, J. A. Kaplan, A. Portell, P. C. Gokhale, B. Phillips, A. Smart, A. Rotem, R. E. Jones, L. Keogh, M. Anguiano, L. Stapleton, Z. Jia, M. Barzily-Rokni, I. Canadas, T. C. Thai, M. R. Hammond, R. Vlahos, E. S. Wang, H. Zhang, S. Li, G. J. Hanna, W. Huang, M. P. Hoang, A. Piris, J. P. Eliane, A. O. Stemmer-Rachamimov, L. Cameron, M. J. Su, P. Shah, B. Izar, M. Thakuria, N. R. LeBoeuf, G. Rabinowits, V. Gunda, S. Parangi, J. M. Cleary, B. C. Miller, S. Kitajima, R. Thummalapalli, B. Miao, T. U. Barbie, V. Sivathanu, J. Wong, W. G. Richards, R. Bueno, C. H. Yoon, J. Miret, M. Herlyn, L. A. Garraway, E. M. Van Allen, G. J. Freeman, P. T. Kirschmeier, J. H. Lorch, P. A. Ott, F. S. Hodi, K. T. Flaherty, R. D. Kamm, G. M. Boland, K. K. Wong, D. Dornan, C. P. Paweletz, D. A. Barbie. 2018. "Ex Vivo Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids." Cancer Discov , vol. 8 , no. 2 , pp. 196-215.
J Chen, E King, R Deek, Zhi Wei, Y Yu, D Grill, K Ballman, O Stegle. 2018. "An omnibus test for differential distribution analysis of microbiome sequencing data.." Bioinformatics (Oxford, England) , vol. 34 , no. 4 , pp. 643-651.
M. V. Heppt, J. X. Wang, D. M. Hristova, Zhi Wei, L. Li, B. Evans, M. Beqiri, S. Zaman, J. Zhang, M. Irmler, C. Berking, R. Besch, J. Beckers, F. J. Rauscher, 3rd, R. A. Sturm, D. E. Fisher, M. Herlyn, M. Fukunaga-Kalabis. 2018. "MSX1-Induced Neural Crest-Like Reprogramming Promotes Melanoma Progression." J Invest Dermatol , vol. 138 , no. 1 , pp. 141-149.
B. Zhu, S. Chen, H. Wang, C. Yin, C. Han, C. Peng, Z. Liu, L. Wan, X. Zhang, J. Zhang, C. G. Lian, P. Ma, Z. X. Xu, S. Prince, T. Wang, X. Gao, Y. Shi, D. Liu, M. Liu, W. Wei, Zhi Wei, J. Pan, Y. Wang, Z. Xuan, J. Hess, N. K. Hayward, C. R. Goding, X. Chen, J. Zhou, R. Cui. 2018. "The protective role of DOT1L in UV-induced melanomagenesis." Nat Commun , vol. 9 , no. 1 , pp. 259.
J. Zhang, Zhi Wei, Zhipeng Yan, Mengchu Zhou, A. Pani. 2017. "Online Change-Point Detection in Sparse Time Series With Application to Online Advertising." IEEE Transactions on Systems, Man, and Cybernetics: Systems .
F. Liu, Q. Niu, X. Fan, C. Liu, J. Zhang, Zhi Wei, W. Hou, T. D. Kanneganti, M. L. Robb, J. H. Kim, N. L. Michael, J. Sun, L. Soong, H. Hu. 2017. "Priming and Activation of Inflammasome by Canarypox Virus Vector ALVAC via the cGAS/IFI16-STING-Type I IFN Pathway and AIM2 Sensor." J Immunol , vol. 199 , no. 9 , pp. 3293-3305.
Vito W. Rebecca, Michael C. Nicastri, Noel McLaughlin, Colin Fennelly, Quentin McAfee, Amruta Ronghe, Michel Nofal, Chun-Yan Lim, Eric Witze, Cynthia I. Chude, Gao Zhang, Gretchen M. Alicea, Shengfu Piao, Sengottuvelan Murugan, Rani Ojha, Samuel M. Levi, Zhi Wei, Julie S. Barber-Rotenberg, Maureen E. Murphy, Gordon B. Mills, Yiling Lu, Joshua Rabinowitz, Ronen Marmorstein, Qin Liu, Shujing Liu, Xiaowei Xu, Meenhard Herlyn, Roberto Zoncu, Donita C. Brady, David W. Speicher, Jeffrey D. Winkler, Ravi K. Amaravadi. 2017. "A Unified Approach to Targeting the Lysosome’s Degradative and Growth Signaling Roles." Cancer Discovery , vol. 7 , no. 11 , pp. 1260-1283.
Turki Turki, Zhi Wei. 2017. "A link prediction approach to cancer drug sensitivity prediction." BMC Systems Biology , vol. 11 , no. Suppl 5 , pp. 94.
H. Lu, S. Liu, G. Zhang, Wu Bin, Y. Zhu, D. T. Frederick, Y. Hu, W. Zhong, S. Randell, N. Sadek, W. Zhang, G. Chen, C. Cheng, J. Zeng, L. W. Wu, J. Zhang, X. Liu, W. Xu, C. Krepler, K. Sproesser, M. Xiao, B. Miao, J. Liu, C. D. Song, J. Y. Liu, G. C. Karakousis, L. M. Schuchter, Y. Lu, G. Mills, Y. Cong, J. Chernoff, J. Guo, G. M. Boland, R. J. Sullivan, Zhi Wei, J. Field, R. K. Amaravadi, K. T. Flaherty, M. Herlyn, X. Xu, W. Guo. 2017. "PAK signalling drives acquired drug resistance to MAPK inhibitors in BRAF-mutant melanomas." Nature , vol. 550 , no. 7674 , pp. 133-136.
R. Somasundaram, G. Zhang, M. Fukunaga-Kalabis, M. Perego, C. Krepler, X. Xu, C. Wagner, D. Hristova, J. Zhang, T. Tian, Zhi Wei, Q. Liu, K. Garg, J. Griss, R. Hards, M. Maurer, C. Hafner, M. Mayerhofer, G. Karanikas, A. Jalili, V. Bauer-Pohl, F. Weihsengruber, K. Rappersberger, J. Koller, R. Lang, C. Hudgens, G. Chen, M. Tetzlaff, L. Wu, D. T. Frederick, R. A. Scolyer, G. V. Long, M. Damle, C. Ellingsworth, L. Grinman, H. Choi, B. J. Gavin, M. Dunagin, A. Raj, N. Scholler, L. Gross, M. Beqiri, K. Bennett, I. Watson, H. Schaider, M. A. Davies, J. Wargo, B. J. Czerniecki, L. Schuchter, D. Herlyn, K. Flaherty, M. Herlyn, S. N. Wagner. 2017. "Tumor-associated B-cells induce tumor heterogeneity and therapy resistance." Nat Commun , vol. 8 , no. 1 , pp. 607.
X. Chang, Y. Zhao, C. Hou, J. Glessner, L. McDaniel, M. A. Diamond, K. Thomas, J. Li, Zhi Wei, Y. Liu, Y. Guo, F. D. Mentch, H. Qiu, C. Kim, P. Evans, Z. Vaksman, S. J. Diskin, E. F. Attiyeh, P. Sleiman, J. M. Maris, H. Hakonarson. 2017. "Common variants in MMP20 at 11q22.2 predispose to 11q deletion and neuroblastoma risk." Nat Commun , vol. 8 , no. 1 , pp. 569.
Rana Dajani, Jin Li, Zhi Wei, Michael E March, Qianghua Xia, Yousef Khader, Nancy Hakooz, Raja Fatahallah, Mohammed El-Khateeb, Ala Arafat, others. 2017. "Genome-wide association study identifies novel type II diabetes risk loci in Jordan subpopulations." PeerJ , vol. 5 , pp. e3618.
JI Leu, Thibaut Barnoud, Gao Zhang, Tian Tian, Zhi Wei, Meenhard Herlyn, Maureen E Murphy, Donna L George. 2017. "Inhibition of stress-inducible HSP70 impairs mitochondrial proteostasis and function.." Oncotarget , vol. 8 , no. 28 , pp. 45656–45669.
Sagarika Banerjee, Tian Tian, Zhi Wei, Kristen N Peck, Natalie Shih, Ara A Chalian, O'Malley, Bert W, Gregory S Weinstein, Michael D Feldman, James Alwine, others. 2017. "Microbial Signatures Associated with Oropharyngeal and Oral Squamous Cell Carcinomas." Scientific Reports , vol. 7 , no. 1 , pp. 4036.
Sagarika Banerjee, Tian Tian, Zhi Wei, Natalie Shih, Michael D Feldman, James C Alwine, George Coukos, Erle S Robertson. 2017. "The ovarian cancer oncobiome." Oncotarget , vol. 8 , no. 22 , pp. 36225.
Dongmei Zhang, Gao Zhang, Xiaowen Hu, Lawrence Wu, Yi Feng, Sidan He, Youyou Zhang, Zhongyi Hu, Lu Yang, Tian Tian, Weiting Xu, Zhi Wei, Yiling Lu, Keith T. Flaherty, Xiaomin Zhong, Gordon B. Mills, Phyllis A. Gimotty, Xiaowei Xu, Meenhard Herlyn, Lin Zhang. 2017. "Oncogenic RAS regulates long non-coding RNA Orilnc1 in human cancer." Cancer Research , vol. 77 , no. 14 , pp. 3745-3757.
Turki Turki, Zhi Wei, Jason T. L. Wang. 2017. "Transfer Learning Approaches to Improve Drug Sensitivity Prediction in Multiple Myeloma Patients." IEEE Access , vol. 5 , pp. 7381-7393.
E. O. Melo, D. M. Cordeiro, R. Pellegrino, Zhi Wei, Z. J. Daye, R. C. Nishimura, M. A. N. Dode. 2017. "Identification of molecular markers for oocyte competence in bovine cumulus cells." Animal Genetics , vol. 48 , no. 1 , pp. 19-29.
J Li , Zhi Wei, Y R Li , S M Maggadottir, X Chang, A Desai, H Hakonarson. 2016. "Understanding the genetic and epigenetic basis of common variable immunodeficiency disorder through omics approaches.." Biochimica et biophysica acta , vol. 1860 , no. 11 Pt B , pp. 2656-63.
Mizuho Fukunaga-Kalabis, Markus V Heppt, Joshua X Wang, Denitsa M Hristova, Zhi Wei, Martin Irmler, Carola Berking, Robert Besch, Johannes Beckers, Frank J Rauscher, others. 2016. "MSX1 promotes melanoma progression via neural crest-like reprogramming." Journal of Dermatological Science , vol. 84 , no. 1 , pp. e87.
G van Ingen, J Li , A Goedegebure, R Pandey, Y R Li , M E March, V W Jaddoe, M Bakay, F D Mentch, K Thomas, Zhi Wei, X Chang, H S Hain, A G Uitterlinden, H A Moll, C M van Duijn, F Rivadeneira, H Raat, R J de Baatenburg Jong, P M Sleiman, M P van der Schroeff, H Hakonarson. 2016. "Genome-wide association study for acute otitis media in children identifies FNDC1 as disease contributing gene.." Nature communications , vol. 7 , pp. 12792.
B Shannan, A Watters, Q Chen, S Mollin, M Dörr, E Meggers, X Xu, P A Gimotty, M Perego, L Li , J Benci, C Krepler, P Brafford, J Zhang, Zhi Wei, G Zhang, Q Liu, X Yin, K L Nathanson, M Herlyn, A Vultur. 2016. "PIM kinases as therapeutic targets against advanced melanoma.." Oncotarget .
J Li , Zhi Wei, X Chang, C J Cardinale, C E Kim, R N Baldassano, H Hakonarson. 2016. "Pathway-based Genome-wide Association Studies Reveal the Association Between Growth Factor Activity and Inflammatory Bowel Disease.." Inflammatory bowel diseases , vol. 22 , no. 7 , pp. 1540-51.
J Zhang, Zhi Wei. 2016. "An empirical Bayes change-point model for identifying 3' and 5' alternative splicing by next-generation RNA sequencing.." Bioinformatics (Oxford, England) , vol. 32 , no. 12 , pp. 1823-31.
D Hristova, X Hua, J Wang, L Li, M Beqiri, A Watters, A Vultur, Zhi Wei, M Herlyn, M Fukunaga-Kalabis. 2016. "Numb is induced by GSK3 inhibition and inhibits melanoma migration, invasion and metastasis." Journal of Investigative Dermatology , vol. 136 , no. 5 , pp. S117.
G Zhang, D T Frederick, L Wu, Zhi Wei, C Krepler, S Srinivasan, Y C Chae, X Xu, H Choi, E Dimwamwa, O Ope, B Shannan, D Basu, D Zhang, M Guha, M Xiao, S Randell, K Sproesser, Weiting Xu, J Liu, G C Karakousis, L M Schuchter, T C Gangadhar, R K Amaravadi, Mengnan Gu, C Xu, A Ghosh, W Xu, Tian Tian, Jie Zhang, S Zha, Q Liu, P Brafford, A Weeraratna, M A Davies, J A Wargo, N G Avadhani, Y Lu, G B Mills, D C Altieri, K T Flaherty, M Herlyn. 2016. "Targeting mitochondrial biogenesis to overcome drug resistance to MAPK inhibitors.." The Journal of clinical investigation , vol. 126 , no. 5 , pp. 1834-56.
T H Finkel, J Li , Zhi Wei, W Wang, H Zhang, E M Behrens, E L Reuschel, S Limou, C Wise, M Punaro, M L Becker, J E Munro, B Flatø, Ø Førre, S D Thompson, C D Langefeld, D N Glass, J T Glessner, C E Kim, E Frackelton, D K Shivers, K A Thomas, R M Chiavacci, C Hou, K Xu, J Snyder, H Qiu, F Mentch, K Wang, C A Winkler, B A Lie, J A Ellis, H Hakonarson. 2016. "Variants in CXCR4 associate with juvenile idiopathic arthritis susceptibility.." BMC medical genetics , vol. 17 , pp. 24.
K Hew, C Miller, D El-Ashry, J Sun, A Besser, T A Ince, M Gu, Zhi Wei, G Zhang, P Brafford, W Guo, Y Lu, G Mills, J Slingerland, F Simpkins. 2016. "MAPK activation predicts poor outcome and the MEK inhibitor, selumetininb, reverses antiestrogen resistance in high grade serous ovarian cancer." Clinical Cancer Research , vol. 22 , no. 4 , pp. 935-947.
J Li , Zhi Wei, H Hakonarson. 2016. "Application of computational methods in genetic study of inflammatory bowel disease.." World journal of gastroenterology , vol. 22 , no. 3 , pp. 949-60.
Y Guo, Zhi Wei, B J Keating, H Hakonarson. 2016. "Machine learning derived risk prediction of anorexia nervosa.." BMC medical genomics , vol. 9 , pp. 4.
Xiang Ji, Soon Ae Chun, Zhi Wei, James Geller. 2015. "Twitter sentiment classification for measuring public health concerns." Social Network Analysis and Mining , vol. 5 , no. 1 , pp. 1–25.
X Chang, J Glessner, A Tin, J Li , Y Guo, Zhi Wei, Y Liu, F D Mentch, C Hou, Y Zhao, T Wang, H Qiu, C Kim, P M Sleiman, H Hakonarson. 2015. "Genome-wide association study reveals two loci for serum magnesium concentrations in European-American children.." Scientific reports , vol. 5 , pp. 18792.
Elena S Gusareva, Zhi Wei, James A Traherne, Jean-Pierre Hugot, Isabelle Cleynen, Judy H Cho, Hakon Hakonarson, Kristel Van Steen. 2015. "Epistasis associated to inflammatory bowel disease (IBD) in humans." GENETIC EPIDEMIOLOGY , vol. 39 , no. 7 , pp. 554–555.
S Banerjee, Zhi Wei, F Tan, K N Peck, N Shih, M Feldman, T R Rebbeck, J C Alwine, E S Robertson. 2015. "Distinct microbiological signatures associated with triple negative breast cancer." Scientific Reports , vol. 5 , no. 15162 .
Y R Li , J Li , S D Zhao, J P Bradfield, F D Mentch, S M Maggadottir, C Hou, D J Abrams, D Chang, F Gao, Y Guo, Zhi Wei, J J Connolly, C J Cardinale, M Bakay, J T Glessner, D Li , C Kao, K A Thomas, H Qiu, R M Chiavacci, C E Kim, F Wang, J Snyder, M D Richie, B Flatø, Ø Førre, L A Denson, S D Thompson, M L Becker, S L Guthery, A Latiano, E Perez, E Resnick, R K Russell, D C Wilson, M S Silverberg, V Annese, B A Lie, M Punaro, M C Dubinsky, D S Monos, C Strisciuglio, A Staiano, E Miele, S Kugathasan, J A Ellis, J E Munro, K E Sullivan, C A Wise, H Chapel, C Cunningham-Rundles, S F Grant, J S Orange, P M Sleiman, E M Behrens, A M Griffiths, J Satsangi, T H Finkel, A Keinan, E T Prak, C Polychronakos, R N Baldassano, H Li , B J Keating, H Hakonarson. 2015. "Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases.." Nature medicine , vol. 21 , no. 9 , pp. 1018-27.
R Dajani, Li, Zhi Wei, J Glessner, X Chang, C Cardinale, R Pellegrino, T Wang, N Hakooz, Y Khader, A Sheshani, D Zandaki, H Hakonarson. 2015. "CNV Analysis Associates AKNAD1 with Type-2 Diabetes in Jordan Subpopulations." Scientific Reports , vol. 5 , pp. 13391.
J Li, I Fung, J Glessner, P Pandey, Zhi Wei, m Bakay, F Mentch, R Pellegrino, T Wang, C E Kim, c Hou, F Wang, Rosetta M Chiavacci, K A Thomas, J M Spergel, H Hakonarson, P MA Sleiman. 2015. "Copy Number Variations in CTNNA3 and RBFOX1 Associate with Pediatric Food Allergy." The Journal of Immunology , vol. 195 , no. 4 , pp. 1599-1607.
S Liu, M Tetzlaff, R Yang, L Xie, G Zhang, C Krepler, M Xiao, M Beqiri, W Xu, G Karakousis, L Schuchter, R Amaravadi, Weiting Xu, Zhi Wei, Y Yao, L Zhang, Y Wang, L Zhang, X Xu. 2015. "miR‐200c/Bmi1 Axis and Epithelial‐Mesenchymal Transition Contribute to Acquired Resistance to BRAF Inhibitor Treatment." Pigment Cell & Melanoma Research , vol. 28 , no. 4 , pp. 431–441.
S Wen, Zhi Wei. 2015. "Hierarchical recognition of sparse patterns in large-scale simultaneous inference." Biometrika , vol. 102 , no. 2 , pp. 267-280.
M Fukunaga-Kalabis, D Hristova, J Wang, L Li, M Heppt, Zhi Wei, A Gyurdieva, M R Webster, A T Weeraratna, M Herlyn. 2015. "UV-Induced Wnt7a in the Human Skin Microenvironment Specifies the Fate of Neural Crest–Like Cells via Suppression of Notch." Journal of Investigative Dermatology , vol. 135 , pp. 1521–1532.
Christopher Ochs, James Geller, Yehoshua Perl, Yan Chen, Julia Xu, Hua Min, James T Case, Zhi Wei. 2015. "Scalable quality assurance for large SNOMED CT hierarchies using subject-based subtaxonomies." J American Medical Informatics Association , vol. 22 , no. 3 , pp. 507-518.
X Chang, J Li, Y Guo, Zhi Wei, F Mentch, C Hou, Y Zhao, H Qiu, C Kim, P Sleiman, H Hakonarson. 2015. "Genome-Wide Association Study of Serum Minerals Levels in Children of Different Ethnic Background." PLOS ONE , vol. 10 , no. 4 , pp. e0123499.
S. Melkorka Maggadottir, Jin Li, Joseph T. Glessner, Yun Rose Li, Zhi Wei, Xiao Chang, Frank D. Mentch, Kelly A. Thomas, Cecilia E. Kim, Yan Zhao, Cuiping Hou, Fengxiang Wang, Silje F. Jørgensen, Elena E. Perez, Kathleen E. Sullivan, Jordan S. Orange, Tom H. Karlsen, Helen Chapel, Charlotte Cunningham-Rundles, Hakon Hakonarson. 2015. "Rare variants at 16p11. 2 are associated with common variable immunodeficiency." Journal of Allergy and Clinical Immunology , vol. 135 , no. 6 , pp. 1569–1577.
Haitao Hu, M Eller, S Zafar, Y Zhou, Mengnan Gu, Zhi Wei, J R, M A Marovich, H N Kibuuka, R T Bailer, R A Koup, M L Robb, N L Michael, J H Kim, S Ratto-Kim. 2014. "Preferential infection of human Ad5-specific CD4 T cells by HIV in Ad5 naturally exposed and recombinant Ad5-HIV vaccinated individuals." Proceedings of the National Academy of Sciences , vol. 111 , no. 37 , pp. 13439-13444.
Ruifeng Yang, Ying Zheng, Ling Li, Shujing Liu, Michelle Burrows, Zhi Wei, Arben Nace, Meenhard Herlyn, Rutao Cui, Wei Guo, George Cotsarelis, Xiaowei Xu. 2014. "Direct conversion of mouse and human fibroblasts to functional melanocytes by defined factors." Nature Communications , vol. 5 , no. 1 .
International League Against Epilepsy Consortium on Complex Epilepsies , Zhi Wei. 2014. "Genetic determinants of common epilepsies: a meta-analysis of genome-wide association studies." Lancet , vol. 13 , no. 9 , pp. 893 - 903.
Wei Wang, Zhi Wei, Hongzhe Li. 2014. "A change-point model for identifying 3'UTR switching by next-generation RNA sequencing." Bioinformatics , vol. 30 , no. 15 , pp. 2162-2170.
Wei Wang, Zhi Wei. 2014. "Collapsing singletons may boost signal for associating rare variants in sequencing study." BMC Proceedings , vol. 8 , pp. S50.
L Shi, Z Zhang, A M Yu, Wei Wang, Zhi Wei, E Akhter, K Maurer, P Costa Reis, L Song, M Petri, K E Sullivan. 2014. "The SLE Transcriptome Exhibits Evidence of Chronic Endotoxin Exposure and Has Widespread Dysregulation of Non-Coding and Coding RNAs." PLOS ONE , vol. 9 , no. 5 , pp. e93846.
C Cardinale, Zhi Wei, J Li, Junfei Zhu, M Gu, R Baldassano, S Grant, H Hakonarson. 2014. "Transcriptome Profiling of Human Ulcerative Colitis Mucosa Reveals Altered Expression of Pathways Enriched in Genetic Susceptibility Loci." PLOS ONE , vol. 9 , no. 5 , pp. e96153.
Ruifeng Yang, Ying Zheng, Michelle Burrows, Shujing Liu, Zhi Wei, Arben Nace, Wei Guo, Suresh Kumar, George Cotsarelis, Xiaowei Xu. 2014. "Generation of folliculogenic human epithelial stem cells from induced pluripotent stem cells." Nature Communications , vol. 5 .
Zhigen Zhao, Wei Wang, Zhi Wei. 2013. "An empirical Bayes testing procedure for detecting variants in analysis of next generation sequencing data." Annals of Applied Statistics , vol. 7 , no. 4 , pp. 2229-2248.
C Cardinale, Zhi Wei, J Li, Junfei Zhu, R Baldassano, S Grant, H Hakonarson. 2013. "Expression of Transcripts in Ulcerative Colitis Biopsies and Genome-wide Association Study Loci Overlap Substantially in Pathway-based Analysis." Inflammatory Bowel Diseases , vol. 19 , pp. S14.
S Fish, Zhi Wei, J Bradfield, K Gupta, G Spengler, A Martin, C Judge, C Escajadillo, L Ghanem, H Hakonarson, R Baldassano, J Kelsen. 2013. "SLC11A1 Polymorphism Increases the Risk of Early Surgery in Pediatric Patients With Inflammatory Bowel Disease." Inflammatory Bowel Diseases , vol. 19 , pp. S111-S112.
Zhang Zhang, Anna Maria Pinto, L Wan, Wei Wang, M G Berg, Isabela Oliva, Larry N Singh, Christopher Dengler, Zhi Wei, G Dreyfuss. 2013. "Dysregulation of synaptogenesis genes antecedes motor neuron pathology in spinal muscular atrophy." Proceedings of the National Academy of Sciences , vol. 110 , no. 48 , pp. 19348-19353.
B G Bitler, F S Fink, Zhi Wei, J R Peterson, R Zhang. 2013. "A High-Content Screening Assay for Small-Molecule Modulators of Oncogene-Induced Senescence." Journal of biomolecular screening , vol. 18 , no. 9 , pp. 1054-61.
B A Bruce, J Li, J M McDonough, Zhi Wei, C Kim, R Chiavacci, F Mentch, J B Caboot, J Spergel, J L Allen, P MA Sleiman, H Hakonarson. 2013. "Gene Network Analysis in a Pediatric Cohort Identifies Novel Lung Function Genes." PLOS ONE , vol. 8 , no. 9 , pp. e72899.
C J Cardinale, Zhi Wei, S Panossian, F Wang, C E Kim, F D Mentch, R M Chiavacci, K E Kachelries, R Pandey, S FA Grant, R N Baldassano, H Hakonarson. 2013. "Targeted resequencing identifies defective variants of decoy receptor 3 in pediatric-onset inflammatory bowel disease." Genes and immunity , vol. 14 , pp. 447–452.
I Younis, K Dittmar, Wei Wang, S W Foley, M G Berg, K Y Hu, Zhi Wei, L Wan, G Dreyfuss. 2013. "Minor introns are embedded molecular switches regulated by highly unstable U6atac snRNA." eLife , vol. 2 , pp. e00780.
Zhi Wei, Wei Wang, J P Bradfield, J Li, C Cardinale, E Frackelton, C Kim, F D Mentch, K Van Steen, P M Visscher, R N Baldassano, H Hakonarson. 2013. "Large Sample Size, Wide Variant Spectrum, and Advanced Machine-Learning Technique Boost Risk Prediction for Inflammatory Bowel Disease." The American Journal of Human Genetics , vol. 92 , no. 6 , pp. 1008–1012.
K M Aird, G Zhang, H Li, Z Tu, B G Bilter, A Garipov, H Wu, Zhi Wei, S N Wagner, M Herlyn, R Zhang. 2013. "Suppression of Nucleotide Metabolism Underlies the Establishment and Maintenance of Oncogene-Induced Senescence." Cell reports , vol. 3 , no. 4 , pp. 1252–1265.
J Li, J T Glessner, H Zhang, Cuiping Hou, Zhi Wei, J P Bradfield, F D Mentch, Y Guo, C Kim, Q Xia, R M Chiavacci, K A Thomas, H Qiu, S FA Grant, S L Furth, H Hakonarson, P MA Sleiman. 2013. "GWAS of blood cell traits identifies novel associated loci and epistatic interactions in Caucasian and African-American children." Human molecular genetics , vol. 22 , no. 7 , pp. 1457-1464.
J O'Rawe, T Jiang, G Sun, Y Wu, Wei Wang, P Bodily, L Tian, H Hakonarson, W E Johnson, Zhi Wei, K Wang, G Lyon. 2013. "Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing." Genome Medicine , vol. 5 , no. 3 , pp. Article 28.
H Hu, M Nau, P Ehrenberg, A Chenine, C Macedo, Y Zhou, Z Daye, Zhi Wei, M Vahey, N Michael, J Kim, M Marovich, S Ratto-Kim. 2013. "Distinct gene-expression profiles associated with the susceptibility of pathogen-specific CD4 T cells to HIV-1 infection." Blood , vol. 121 , no. 7 , pp. 1136-1144.
Wei Wang, Weicheng Hu, Fang Hou, Pingzhao Hu, Zhi Wei. 2012. "SNVerGUI: a desktop tool for variant analysis of next-generation sequencing data." Journal of Medical Genetics , vol. 49 , no. 12 , pp. 753-755.
J Jostins, S K Ripke, R H Duerr, D P McGovern, Ken Y Hui, J C Lee, P Schumm, Y Sharma, C A Anderson, J Essers, M Mitrovic, K Ning, I Cleynen, E Theatre, S L Spain, S Raychaudhuri, P Goyette, Zhi Wei, C Abraham, J Achkar, T Ahmad, L Amininejad, A N Ananthakrishnan, V Andersen, J M Andrews, L Baidoo, T Balschun, P A Bampton, A Bitton, G Boucher, S Brand, C Büning, A Cohain, S Cichon, M D’Amato, D De Jong, K L Devaney, M Dubinsky, C Edwards, D Ellinghaus, l R Ferguson, D Franchimont, K Fransen, R Gearry, M Georges, C Gieger, J Glas, T Haritunians, A Hart, C Hawkey, M Hedl, X Hu, T H Karlsen, L Kupcinskas, S Kugathasan, A Latiano, D Laukens, I C Lawrance, C W Lees, E Louis, G Mahy, J Mansfield, A R Morgan, C Mowat, W Newman, O Palmieri, C Ponsioen, U Potocnik, N J Prescott, M Regueiro, J I Rotter, R K Russell, J D Sanderson, M Sans, J Satsangi, S Schreiber, L A Simms, J Sventoraityte, S T Targan, K D Taylor, M M Tremelling, H W Verspaget, M De Vos, C Wijmenga, D C Wilson, J Winkelmann, R J Xavier, S Zeissig, B Zhang, C K Zhang, H Zhao, M S Silverberg, V Annese, H Hakonarson, S R Brant, G Radford-Smith, C G Mathew, J D Rioux, E E Schadt, M J Daly, A Franke, M Parkes, S Vermeire, J C Barrett, J H Cho. 2012. "Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease." Nature , vol. 491 , no. 7422 , pp. 119-124.
Renata Pellegrino, Daniele Y. Sunaga, Camila Guindalini, Raquel C. S. Martins, Diego Robles Mazzotti, Zhi Wei, Z. John Daye, Monica Levy Andersen, Sergio Tufik. 2012. "Whole-blood genome-wide gene expression profile in males after prolonged wakefulness and sleep recovery." Physiological Genomics , vol. 44 , no. 21 , pp. 1003-1012.
H Hu, M Nau, P Ehrenberg, A Chenine, Z Daye, Zhi Wei, N Michael, M Vahey, J Kim, M Marovich, S Ratto-Kim. 2012. "Distinct gene expression profiles associated with the susceptibility of pathogen-specific CD4+ T cells to HIV-1 infection." Retrovirology , vol. 9 , no. s2 , pp. O46.
Yingbin Ge, Rikka Azuma, Bethsebah Gekonge, Alfonso Lopez-Coral, Min Xiao, Gao Zhang, Xiaowei Xu, Luis J. Montaner, Zhi Wei, Meenhard Herlyn, Tao Wang, Russel E. Kaufman. 2012. "Induction of metallothionein expression during monocyte to melanoma-associated macrophage differentiation." Frontiers in Biology , vol. 7 , no. 4 , pp. 359–367.
Zhi Wei, Tao Wang, Yingbin Ge, Min Xiao, Alfonso Lopez-Coral, Rikka Azuma, Rajasekharan Somasundaram, Gao Zhang, Xiaowei Xu, Frank J. Rauscher III, Meenhard Herlyn, Russel E. Kaufman. 2012. "Melanoma‐Derived Conditioned Media Efficiently Induce the Differentiation of Monocytes to Macrophages that Display a Highly Invasive Gene Signature." Pigment Cell & Melanoma Research , vol. 25 , no. 4 , pp. 493–505.
Z. John Daye, Hongzhe Li, Zhi Wei. 2012. "A powerful test for multiple rare variants association studies that incorporates sequencing qualities ." Nucleic Acids Research , vol. 40 , no. 8 .
Zhi Wei, Wei Wang, Pingzhao Hu, Gholson J. Lyon, Hakon Hakonarson. 2011. "SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data." Nucleic Acids Research , vol. 39 , no. 19 .
Weixin Wang, Zhi Wei, Tak-Wah Lam, Junwen Wang. 2011. "Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions." Scientific Reports , vol. 1 .
Gholson J Lyon, Tao Jiang, Richard Van Wijk, Wei Wang , Paul Mark Bodily, Jinchuan Xing, Lifeng Tian, Redi J Robison, Mark Clement, Lin Yang, Peng Zhang, Ying Liu, Barry Moore, Joseph T Glessner, Josephine Elia, Fred Reimherr, Wouter W. van Solinge, Mark Yankell, Hakon Hakonarson, Jun Wang, William Evan Johnson, Zhi Wei, Kai Wang. 2011. "Exome Sequencing and Unrelated Findings in the Context of Complex Disease Research: Ethical and Clinical Implications." Discovery Medicine , vol. 12 , no. 62 .
Wenguang Sun, Zhi Wei. 2011. "Multiple Testing for Pattern Identification, with Applications to Microarray Time Course Experiments." Journal of the American Statistical Association , vol. 106 , no. 493 , pp. 73–88.
Usman W. Roshan, Satishc Chikkagoudar, Zhi Wei, Kai Wang, Hakon Hakonarson. 2011. "Ranking causal variants and associated regions in genome-wide association studies by the support vector machine and random forest ." Nucleic Acids Research .
Wei Wang, Zhi Wei, Wenguang Sun. 2010. "Simultaneous set-wise testing under dependence, with applications to genome-wide association studies." Statistics and Its Interface , vol. 3 , no. 4 , pp. 501-512.
Satish Chikkagoudar, Zhi Wei, Usman W. Roshan. 2010. "PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences." Nucleic Acids Research , vol. 38 , no. Suppl 2 , pp. W59-W63.
Hongzhe Li, Zhi Wei, John Maris. 2010. "A Hidden Markov Random Field Model for Genome-wide Association Studies." Biostatistics , vol. 11 , no. 1 , pp. 139-150.
Caiyan Li, Zhi Wei, Hongzhe Li. 2010. "Network-based Empirical Bayes Methods for Linear Models with Applications to Genomic Data." Journal of Biopharmaceutical Statistics , vol. 20 , no. 2 , pp. 209-222 .
Zhi Wei, Wenguang Sun, Kai Wang, Hakon Hakonarson. 2009. "Multiple Testing in Genome-Wide Association Studies via Hidden Markov Models." Bioinformatics , vol. 25 , no. 21 , pp. 2802-2808.
Zhi Wei, Kai Wang, Hui-Qi Qu, Haitao Zhang, Jonathan Bradfield, Cecilia Kim, Edward Frackleton, Cuiping Hou, Joseph T. Glessner, Rosetta Chiavacci, Charles Stanley, Dimitri Monos, Struan F. A. Grant, Constantin Polychronakos, Hakon Hakonarson. 2009. "From Disease Association to Risk Assessment: An Optimistic View from Genome-Wide Association Studies on Type 1 Diabetes." PLoS Genetics , vol. 10 , no. 5 , pp. e1000678.
Zhi Wei, Mingyao Li, Timothy Rebbeck, Hongzhe Li. 2008. "U-Statistics-based Tests for Multiple Genes in Genetic Association Studies." Annals of Human Genetics/Blackwell Publishing Ltd/University College London , vol. 72 , no. 6 , pp. 821-833.
Zhi Wei, Hongzhe Li. 2008. "A Hidden Spatial-Temporal Markov Random Field Model For Network-Based Analysis Of Time Course Gene Expression Data." Annals of Applied Statistics , vol. 2 , no. 1 , pp. 408-429.
Zhi Wei, Mingyao Li. 2007. "Genome-wide Association Analysis of Rheumatoid Arthritis in a Canadian Population." BMC Proceedings , vol. 1 , no. S1 , pp. S19.
Zhi Wei, Hongzhe Li. 2007. "A Markov Random Field Model for Network-based Analysis of Genomic Data." Bioinformatics , vol. 23 , no. 12 , pp. 1537-1544.
Zhi Wei, Hongzhe Li. 2007. "Nonparametric Pathway-Based Regression Models for Analysis of Genomic Data." Biostatistics , vol. 8 , no. 2 , pp. 265-284.
Zhi Wei, Shane T Jensen. 2006. "A Markov Random Field Model for Network-based Analysis of Genomic Data." Bioinformatics , vol. 22 , no. 13 , pp. 1577-1584.
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"Erratum: Epstein-barr virus facilitates expression of KLF14 by regulating the cooperative binding of the E2F-Rb-HDAC complex in latent infection (Journal of Virology (2020) 94:22 (e01209-e01220) DOI: 10.1128/JVI.01209-20)"
Journal of Virology, February, 2021.
"Author Correction: Loss of Phd2 cooperates with BRAFV600E to drive melanomagenesis (Nature Communications, (2018), 9, 1, (5426), 10.1038/s41467-018-07126-9)"
Nature Communications, December, 2019.
Journal of Virology, February, 2021.
"Author Correction: Loss of Phd2 cooperates with BRAFV600E to drive melanomagenesis (Nature Communications, (2018), 9, 1, (5426), 10.1038/s41467-018-07126-9)"
Nature Communications, December, 2019.
Chapter
Zhi Wei, J Minturn, E Rappaport, G Brodeur, H Li.
"Network-Based Analysis of Multivariate Gene Expression Data."
pp. 121-139. Statistical Methods for Microarray Data Analysis/Springer, 2013.
Zhi Wei, S Baldassano, H Hakonarson. "Genetics of Inflammatory Bowel Diseases." In Petar Mamula, Jonathan E. Markowitz, Robert N. Baldassano, eds., pp. 3-12. Pediatric Inflammatory Bowel Disease/Springer, 2012.
Zhi Wei. "Hidden Markov Models for Controlling False Discovery Rate in Genome-Wide Association Analysis." In Junbai Wang, Aik Choon Tan,Tianhai Tian, eds., Next Generation Microarray Bioinformatics/Humana Press, 2011.
Zhi Wei, S Baldassano, H Hakonarson. "Genetics of Inflammatory Bowel Diseases." In Petar Mamula, Jonathan E. Markowitz, Robert N. Baldassano, eds., pp. 3-12. Pediatric Inflammatory Bowel Disease/Springer, 2012.
Zhi Wei. "Hidden Markov Models for Controlling False Discovery Rate in Genome-Wide Association Analysis." In Junbai Wang, Aik Choon Tan,Tianhai Tian, eds., Next Generation Microarray Bioinformatics/Humana Press, 2011.