Publications

Peer-reviewed Publications

2024

  • Jiao Sun, Jin-Young Kim, Semo Jun, Meeyeon Park, Ebbing de Jong, Jae-Woong Chang, Sze Cheng, Deliang Fan, Yue Chen, Timothy Griffin, Ho Jin You, Jung-Hee Lee, Wei Zhang#, and Jeongsik Yong#. Dichotomous Intronic Polyadenylation Profiles Reveal Multifaceted Gene Functions in the Pan-cancer Transcriptome. Experimental & Molecular Medicine, 2024 (IF = 11.7).
  • Sudipto Baul, Khandakar Tanvir Ahmed, Qibing Jiang, Guangyu Wang, Qian Li, Jeongsik Yong, and Wei Zhang#. Integrating Spatial Transcriptomics and Bulk RNA-seq: Predicting Gene Expression with Enhanced Resolution through Graph Attention Networks. Briefings in Bioinformatics, 2024. doi:10.1093/bib/bbae316 [Download]
  • Ehtesamul Azim, Dongjie Wang, Kunpeng Liu, Wei Zhang, and Yanjie Fu. Feature Interaction-Aware Automated Data Representation Transformation. SIAM International Conference on Data Mining (SDM), April 2024. 10.1137/1.9781611978032.100
  • Alexandra Nowak, Nadia Saadat, Jiao Sun, Anna Forsman, Xiaoyu Liang, Cara Joyce, Christopher Engeland, Jennifer Woo, Dawn Misra, Carmen Giurgescu, Wei Zhang, and Cindy Anderson. Preterm Birth in African American Women: A Multi-Omic Pilot Study in Early Pregnancy. Biological Research for Nursing , 2024 (accept).
  • Fan Zhang, Amitesh Sridharan, Wangxin He, Injune Yeo, Maximilian Liehr, Wei Zhang, Nathaniel Cady, Yu Cao, Jae-Sun Seo, and Deliang Fan. A 65-nm RRAM Compute-in-Memory Macro for Genome Processing. IEEE Journal of Solid-State Circuits, 2024. 10.1109/JSSC.2024.3396429
  • Lauren J. Sundby, William M. Southern, Jiao Sun, Xiaobai Patrinostro, Wei Zhang, Jeongsik Yong, and James M. Ervasti. Deletion of exons 2 and 3 from Actb and cell immortalization leads to widespread, beta-actin independent alterations in gene expression associated with cell cycle control. European Journal of Cell Biology, 2024. 10.1016/j.ejcb.2024.151397
  • Shaahin Angizi, Naima Ahmed Fahmin, Deniz Najafi, Wei Zhang, and Deliang Fan. PANDA: Processing in Magnetic Random-Access Memory-Accelerated de Bruijn Graph-Based DNA Assembly. Journal of Low Power Electronics and Applications, 2024. 10.3390/jlpea14010009

2023

  • Khandakar Tanvir Ahmed, Sudipto Baul, Yanjie Fu, and Wei Zhang#. Attention-Based Multi-modal Missing Value Imputation for Time Series Data with High Missing Rate. SIAM International Conference on Data Mining (SDM), April 2023. 10.1137/1.9781611977653.ch53
  • Fareesa Aftab, Alice Rodriguez-Fuguet, Luis Silva, Ikei Kobayashi, Jiao Sun, Katerina Politi, Elena Levantini, Wei Zhang, Susumu Kobayashi, and Wencai Zhang. An Intrinsic Purine Metabolite AICAR Blocks Lung Tumor Growth by Targeting Oncoprotein Mucin 1. British Journal of Cancer, 2023. 10.1038/s41416-023-02196-z
  • Fan Zhang, Shaahin Angizi, Jiao Sun, Wei Zhang, and Deliang Fan. Aligner-D: Leveraging in-DRAM Computing to Accelerate DNA Short Read Alignment. IEEE Journal on Emerging and Selected Topics in Circuits and Systems, 2023. 10.1109/JETCAS.2023.3241545

2022

  • Khandakar Tanvir Ahmed, Sze Cheng, Qian Li, Jeongsik Yong, and Wei Zhang#. Incomplete Time-Series Gene Expression in Integrative Study for Islet Autoimmunity Prediction. Briefings in Bioinformatics, 2022. doi:10.1093/bib/bbac537 [Download]
  • Naima Ahmed Fahmi, Khandakar Tanvir Ahmed, Jae-Woong Chang, Heba Nassereddeen, Deliang Fan, Jeongsik Yong, and Wei Zhang#. APA-Scan: Detection and Visualization of 3′-UTR APA with RNA-seq and 3′-end-seq Data. BMC Bioinformatics, 2022. (#Corresponding author) doi:10.1186/s12859-022-04939-w [Download]
  • Sudipto Baul, Khandakar Tanvir Ahmed, Joseph Filipek, and Wei Zhang#. omicsGAT: Graph Attention Network for Cancer Subtype Analyses. International Journal of Molecular Sciences, 2022. (#Corresponding author) doi:10.3390/ijms231810220 [Download]

  • Qibing Jiang, Praneeth Sudalagunta, Maria C. Silva, Rafael R. Canevarolo, Xiaohong Zhao, Khandakar Tanvir Ahmed, Raghunandan Reddy Alugubelli, Gabriel DeAvila, Alexandre Tungesvik, Lia Perez, Robert Gatenby, Robert Gillies, Rachid Baz, Mark B. Meads, Kenneth H. Shain, Ariosto S. Silva, and Wei Zhang#. CancerCellTracker: A Brightfield Time-lapse Microscopy Framework for Cancer Drug Sensitivity Estimation. Bioinformatics, 2022. (#Corresponding author) doi:10.1093/bioinformatics/btac417 [Download]
  • Sze Cheng*, Naima Ahmed Fahmi*, Meeyeon Park, Jiao Sun, Kaitlyn Thao, Hsin-Sung Yeh, Wei Zhang#, and Jeongsik Yong#. mTOR contributes to the proteome diversity through transcriptome-wide alternative splicing. International Journal of Molecular Sciences, 2022.
  • TingTing Wu, Semo Jun, Eun-Ji Choi, Jiao Sun, Eun-Bi Yang, Hyun-Seo Lee, Sang-Yong Kim, Naima Ahmed Fahmi, Qibing Jiang, Wei Zhang, Jeongsik Yong, Jung-Hee Lee, Ho Jin You. 53BP1-ACLY-SLBP-coordinated activation of replication-dependent histone biogenesis maintains genomic integrity. Nucleic Acids Research, 2022. doi:10.1093/nar/gkab1300

2021

  • Jiao Sun*, Naima Ahmed Fahmi*, Heba Nassereddeen, Sze Cheng, Irene Martinez, Deliang Fan, Jeongsik Yong, and Wei Zhang#. Computational Methods to Study Human Transcript Variants in COVID-19 Infected Lung Cancer Cells. International Journal of Molecular Sciences, 2021. (#Corresponding author) doi:10.3390/ijms22189684

  • Khandakar Tanvir Ahmed*, Jiao Sun*, William Chen, Irene Martinez, Sze Cheng, Wencai Zhang, Jeongsik Yong, and Wei Zhang#. In Silico Model for miRNA-mediated Regulatory Network in Cancer. Briefings in Bioinformatics, 2021. (#Corresponding author) doi.org/10.1093/bib/bbab264 [Download]

  • Khandakar Tanvir Ahmed, Jiao Sun, Sze Cheng, Jeongsik Yong, and Wei Zhang#. Multi-omics Data Integration by Generative Adversarial Network. Bioinformatics, 2021. (#Corresponding author) doi:10.1093/bioinformatics/btab608 [Download]

  • Naima Ahmed Fahmi, Heba Nassereddeen, Jae-Woong Chang, Meeyeon Park, Hsin-Sung Yeh, Jiao Sun, Deliang Fan, Jeongsik Yong#, and Wei Zhang#. AS-Quant: Detection and Visualization of Alternative Splicing Events with RNA-seq Data. International Journal of Molecular Sciences, 2021. (#Corresponding author) doi.org/10.3390/ijms22094468 [Download]

  • Xiaohong Zhao, Michelle Y. Wang, Huijuan Jiang, Tint Lwin, Paul M. Park, Jing Gao, Mark B. Meads, Yuan Ren, Tao Li, Jiao Sun, Naima Ahmed Fahmi, Satish Kumar Singh, Lalit Sehgal, Xuefeng Wang, Ariosto S. Silva, Eduardo M. Sotomayor, Kenneth H. Shain, John L. Cleveland, Michael Wang, Wei Zhang, Jun Qi, Bijal D. Shah, and Jianguo Tao. Transcriptional Programming Drives Ibrutinib-resistance Evolution in Mantle Cell Lymphoma. Cell Reports, 2021. doi:10.1016/j.celrep.2021.108870

  • Md Hasan, Kavya Ganapathy, Jiao Sun, Ayman Khatib, Thomas Andl, Julia Soulakova, Domenico Coppola, Wei Zhang, and Ratna Chakrabarti. LncRNA PAINT is Associated with Aggressive Prostate Cancer and Dysregulation of Cancer Hallmark Genes. International Journal of Cancer, 2021. doi.org/10.1002/ijc.33569

  • Michelle Wang, Tao Li, Yuan Ren, Bijal Shah, Tint Lwin, Jing Gao, Kenneth Shain, Wei Zhang, Xiaohong Zhao, and Jianguo Tao. MCL-1 dependency as a novel vulnerability for aggressive B-cell lymphomas. Blood Cancer Journal, 2021. doi:10.1038/s41408-020-00402-2

  • Fan Zhang, Shaahin Angizi, Naima Ahmed Fahmi, Wei Zhang, and Deliang Fan. PIM-Quantifier: A Processing-in-Memory Platform for Genome Quantification. Design Automation Conference (DAC), Dec 2021. doi: 10.1109/DAC18074.2021.9586144

  • Kunpeng Liu, Haibo Huang, Wei Zhang, Yanjie Fu, and Hua Kien. Multi-Armed Bandit Guided Feature Subspace Exploration. SIAM International Conference on Data Mining (SDM), April 2021

2020

  • 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. BMC Medical Genomics, 2020. (#Corresponding author) doi:10.1186/s12920-020-00829-3 [Download]

  • 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 [Download]

  • Jiao Sun, Jae-Woong Chang, Teng Zhang, Jeongsik Yong, Rui Kuang, and Wei Zhang#. Platform-integrated mRNA Isoform Quantification. Bioinformatics, 2020. (#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, 2020. (#Corresponding author) doi:10.1093/bioinformatics/btz809 [Download]

  • Shaahin Angizi, Wei Zhang, and Deliang Fan. Exploring DNA Alignment-in-Memory Leveraging Emerging SOT-MRAM. Great Lakes Symposium on VLSI, Sept 2020. doi:10.1145/3386263.3407590

  • 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. doi:10.1109/DAC18072.2020.9218653

  • 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 Sun, Wei Zhang, and Deliang Fan. PIM-Aligner: A Processing-in-MRAM Platform for Biological Sequence Alignment. Design, Automation and Test in Europe (DATE), Mar 2020. doi:10.23919/DATE48585.2020.9116303

2019

  • 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. doi:10.1109/ICDM.2019.00051 (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 Sun, Wei Zhang, and Deliang Fan. AlignS: A Processing-In-Memory Accelerator for DNA Short Read Alignment Leveraging SOT-MRAM. Design Automation Conference (DAC), June 2019. doi:10.1145/3316781.3317764

  • Shaahin Angizi, Jiao Sun, Wei Zhang, and Deliang Fan. GraphS: A Graph Processing Accelerator Leveraging SOT-MRAM. Design, Automation and Test in Europe (DATE), Mar 2019. doi:10.23919/DATE.2019.8715270

2018

  • 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

2017

  • 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]

OTHER MANUSCRIPTS

  • Wei Zhang, Zhongming Zhao, Kai Wang, Li Shen, and Xinghua Shi. The International Conference on Intelligent Biology and Medicine (ICIBM) 2020: Scalable techniques and algorithms for computational genomics. BMC Genomics, 2020. [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]