• Naima Ahmed Fahmi, Hsin-Sung Yeh, Jae-Woong Chang, Heba Nassereddeen, Deliang Fan, Jeongsik Yong, Wei Zhang. AS-Quant: Detection and Visualization of Alternative Splicing Events with RNA-seq Data. [BioRxiv]
  • Naima Ahmed Fahmi, Jae-Woong Chang, Heba Nassereddeen, Khandakar Tanvir Ahmed, Deliang Fan, Jeongsik Yong, Wei Zhang. APA-Scan: Detection and Visualization of 3′-UTR APA with RNA-seq and 3′-end-seq Data. [BioRxiv]
  • Sze Cheng*, Naima Ahmed Fahmi*, Meeyeon Park, Jae-Woong Chang, Jiao Sun, Kai Thao, Hsin-Sung Yeh, Wei Zhang#, Jeongsik Yong#. mTOR-driven widespread exon skipping renders multifaceted gene regulation and proteome complexity. [BioRxiv]

Peer-reviewed Publications


  • Khandakar Tanvir Ahmed, Sunho Park, Qibing Jiang, Taehyun Hwang, and Wei Zhang. Network-based Drug Sensitivity Prediction. International Conference on Intelligent Biology and Medicine (ICIBM), August 2020.
  • Wei Zhang, Raphael Petegrosso, Jae-Woong Chang, Jiao Sun, Jeongsik Yong, Jeremy Chien, and Rui Kuang. A Large-Scale Comparative Study of Isoform Expressions Measured on Four Platforms. BMC Genomics, 2020. doi:10.1186/s12864-020-6643-8
  • Shaahin Angizi, Naima Ahmed Fahmi, Wei Zhang, and Deliang Fan. PIM-Assembler: A Processing-in-Memory Platform for Genome Assembly. Design Automation Conference (DAC), July 2020.
  • Anne Showalter, Ana Martini, Daniel Nierenberg, Kristen Hosang, Naima Ahmed Fahmi, Priya Gopalan, Amr Khaled, Wei Zhang, and Annette Khaled. Investigating Chaperonin-Containing TCP-1 Subunit 2 as an Essential Component of the Chaperonin Complex for Tumorigenesis. Scientific Reports, 2020. doi:10.1038/s41598-020-57602-w
  • Shaahin Angizi, Jiao SunWei Zhang, and Deliang Fan. PIM-Aligner: A Processing-in-MRAM Platform for Biological Sequence Alignment. Design, Automation and Test in Europe (DATE), Mar 2020.


  • Jiao Sun, Jae-Woong Chang, Teng Zhang, Jeongsik Yong, Rui Kuang, and Wei Zhang#. Platform-integrated mRNA Isoform Quantification. Bioinformatics, 2019. (#Corresponding author) doi:10.1093/bioinformatics/btz932 [Download]
  • Zhibo Wang, Zhezhi He, Milan Shah, Teng Zhang, Deliang Fan, and Wei Zhang#. Network-based Multi-Task Learning Models for Biomarker Selection and Cancer Outcome Prediction. Bioinformatics, 2019. (#Corresponding author) doi:10.1093/bioinformatics/btz809 [Download]
  • Jae-Woong Chang, Hsin-Sung Yeh, Meeyeon Park, Luke Erber, Jiao Sun, Sze Cheng, Alexander M. Bui, Naima Ahmed Fahmi, Ryan Nasti, Rui Kuang, Yue Chen, Wei Zhang#, and Jeongsik Yong#. mTOR-regulated U2af1 tandem exon splicing specifies transcriptome features for translational control. Nucleic Acids Research, 2019. (#co-corresponding authors) doi:10.1093/nar/gkz761
  • Zhuliu Li, Wei Zhang, R. Stephanie Huang, and Rui Kuang. Learning a Low-rank Tensor of Pharmacogenomic Multi-relations from Biomedical Networks. IEEE International Conference on Data Mining (ICDM), Nov 2019. (9.08%=95/1046 Acceptance Ratio)
  • Raphael Petegrosso, Zhuliu Li, Molly Srour, Yousef Saad, Wei Zhang, and Rui Kuang. Scalable Remote Homology Detection and Fold Recognition in Massive Protein Networks. PROTEINS: Structure, Function, and Bioinformatics, 2019. doi:10.1002/prot.25669
  • Shaahin Angizi, Jiao SunWei Zhang, and Deliang Fan. AlignS: A Processing-In-Memory Accelerator for DNA Short Read Alignment Leveraging SOT-MRAM. Design Automation Conference (DAC), June 2019.
  • Shaahin Angizi, Jiao SunWei Zhang, and Deliang Fan. GraphS: A Graph Processing Accelerator Leveraging SOT-MRAM. Design, Automation and Test in Europe (DATE), Mar 2019.


  • Jae-Woong Chang*, Wei Zhang*, Hsin-Sung Yeh, Meeyeon Park, Chengguo Yao, Yongsheng Shi, Rui Kuang#, and Jeongsik Yong#. An Integrative Model for Alternative Polyadenylation, IntMAP, Delineates mTOR-modulated Endoplasmic Reticulum Stress Response. Nucleic Acids Research, 2018. (*Joint first authors) doi:10.1093/nar/gky340 [Download]
  • Sk. Kayum Alam, Matteo Astone, Ping Liu, Stephanie Hall, Abbygail Coyle, Erin Dankert, Dane Hoffman, Wei Zhang, Rui Kuang, Anja Roden, Aaron Mansfield, and Luke Hoeppner. DARPP-32 and t-DARPP Promote Non-small Cell Lung Cancer Growth Through Regulation of IKKα-dependent Cell Migration. Communication Biology, 2018. doi:10.1038/s42003-018-0050-6
  • Xiaoyu Xiang, Yuanguo Wang, Hongbin Zhang, Jinhua Piao, Selvaraj Muthusamy, Lei Wang, Yibin Deng, Wei Zhang, Rui Kuang, Daniel D. Billadeau, Shengbing Huang, Jinping Lai, Raul Urrutia, and Ningling Kang. Vasodilator-stimulated phosphoprotein promotes liver metastasis of gastrointestinal cancer by activating a β1-integrin-FAK-YAP1/TAZ signaling pathway. npj Precision Oncology, 2018. doi:10.1038/s41698-017-0045-7


  • Wei Zhang, Jeremy Chien, Jeongsik Yong, and Rui Kuang. Network-based Machine Learning and Graph Theory Algorithms for Precision Oncology. npj Precision Oncology, 2017. doi:10.1038/s41698-017-0029-7
  • Hsin-Sung Yeh, Wei Zhang, Jeongsik Yong. Analyses of alternative polyadenylation: from old school biochemistry to high-throughput technologies. BMB Reports, 2017. doi:10.5483/BMBRep.2017.50.4.019

2016 and Before

  • Lining Liang, Hao Sun, Wei Zhang, Mengdan Zhang, Xiao Yang, Rui Kuang, and Hui Zheng. Meta-Analysis of EMT Datasets Reveals Different Types of EMT. PLoS One, 2016. doi:10.1371/journal.pone.0156839
  • Wei Zhang, Jae-Woong Chang, Lilong Lin, Kay Minn, Baolin Wu, Jeremy Chien, Jeongsik Yong, Hui Zheng, and Rui Kuang. Network-based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis. PLoS Comput Biol, 2015. doi:10.1371/journal.pcbi.1004465 [Download]
  • Jae-Woong Chang*, Wei Zhang*, Hsin-Sung Yeh, Ebbing de Jong, Semo Jun, Kwan-Hyun Kim, Sun Sik Bae, Kenneth Beckman, TaeHyun Hwang, Kye-Seong Kim, Do-Hyung Kim, Rui Kuang, and Jeongsik Yong. mRNA 3’UTR Shortening is a Molecular Signature of mTORC1 Activation. Nature Communications, 2015. doi:10.1038/ncomms8218 (*Joint first authors)
  • Wei Zhang, Takayo Ota, Viji Shridhar, Jeremy R Chien, Baolin Wu, and Rui Kuang. Network-based Survival Analysis Reveals Subnetwork Signatures for Predicting Outcomes of Ovarian Cancer Treatment. PLoS Comput Biol, 2013. doi:10.1371/journal.pcbi.1002975 [Download]
  • Jiaqi Yang, Wei Zhang, Baolin Wu. A note on statistical method for genotype calling of high-throughput SNP arrays. Journal of Applied Statistics, 2013. doi:10.1080/02664763.2013.785499
  • Wei Zhang, Nicholas Johnson, Baolin Wu, and Rui Kuang. Signed Network Propagation for Detecting Differential Gene Expressions and DNA Copy Number Variations. Proc. of ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB), Oct 2012. [Paper][Download]
  • TaeHyun Hwang, Wei Zhang, MaoQiang Xie, Jinfeng Liu, and Rui Kuang. Inferring Disease and Gene Set Associations with Rank Coherence in Networks. Bioinformatics, 27(19): 2692-2699, 2011. doi:10.1093/bioinformatics/btr463
  • Wei Zhang, Baryun Hwang, Baolin Wu, and Rui Kuang. Network propagation models for gene selection. Proc. of IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), Nov 2010. [Paper]
  • Mingrui Zhang, Wei Zhang, Hugues Sicotte, and Ping Yang. A New Validity Measure for a Correlation-Based Fuzzy C-means Clustering Algorithm. Conference Proc. The 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Sept 2009. [Paper]


  • Raphael Petegrosso*, Wei Zhang*, Zhuliu Li, Yousef Saad, and Rui Kuang. Low-rank Label Propagation for Semi-supervised Learning with 100 Millions Samples. (*Joint first authors) [Paper]
  • Wei Zhang, Rui Kuang, and Baolin Wu. Model Based Clustering Analysis of 16S rRNA Sequence. [Paper]