MOAT: efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool. - Lucas Lochovsky; Jing Zhang 062; Mark Gerstein (Bioinform., 2018)

PUB-SalNet: A Pre-Trained Unsupervised Self-Aware Backpropagation Network for Biomedical Salient Segmentation. - Feiyang Chen; Ying Jiang; Xiangrui Zeng; Jing Zhang 062; Xin Gao 001; Min Xu 009 (Algorithms, 2020)

TopicNet: a framework for measuring transcriptional regulatory network change. - Shaoke Lou; Tianxiao Li; Xiangmeng Kong; Jing Zhang 062; Jason Liu 003; Donghoon Lee 006; Mark Gerstein (Bioinform., 2020)

DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring. - Jing Zhang 062; Jason Liu 003; Donghoon Lee 006; Shaoke Lou; Zhanlin Chen; Gamze Gürsoy; Mark Gerstein (BMC Bioinform., 2020)

NIMBus: a negative binomial regression based Integrative Method for mutation Burden Analysis. - Jing Zhang 062; Jason Liu 003; Patrick D. McGillivray; Caroline Yi; Lucas Lochovsky; Donghoon Lee 006; Mark Gerstein (BMC Bioinform., 2020)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. - Esther Rheinbay; Morten Muhlig Nielsen; Federico Abascal; Jeremiah Wala; Ofer Shapira; Grace Tiao; Henrik Hornshøj; Julian M. Hess; Randi Istrup Juul; Ziao Lin; Lars Feuerbach; Radhakrishnan Sabarinathan; et al. (Nat., 2020)

Epigenome-based splicing prediction using a recurrent neural network. - Donghoon Lee 006; Jing Zhang 062; Jason Liu 003; Mark Gerstein (PLoS Comput. Biol., 2020)

Few-shot learning for classification of novel macromolecular structures in cryo-electron tomograms. - Ran Li; Liangyong Yu; Bo Zhou 009; Xiangrui Zeng; Zhenyu Wang; Xiaoyan Yang; Jing Zhang 062; Xin Gao 001; Rui Jiang 001; Min Xu 009 (PLoS Comput. Biol., 2020)

AttPNet: Attention-Based Deep Neural Network for 3D Point Set Analysis. - Yufeng Yang; Yixiao Ma; Jing Zhang 062; Xin Gao 001; Min Xu 009 (Sensors, 2020)

Unsupervised Domain Alignment Based Open Set Structural Recognition of Macromolecules Captured By Cryo-Electron Tomography. - Yuchen Zeng; Gregory Howe; Kai Yi; Xiangrui Zeng; Jing Zhang 062; Yi-Wei Chang; Min Xu 009 (ICIP, 2021)

DECODE: a Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays. - Zhanlin Chen; Jing Zhang 062; Jason Liu 003; Yi Dai; Donghoon Lee 006; Martin Renqiang Min; Min Xu 009; Mark Gerstein (Bioinform., 2021)

Active learning to classify macromolecular structures in situ for less supervision in cryo-electron tomography. - Xuefeng Du; Haohan Wang; Zhenxi Zhu; Xiangrui Zeng; Yi-Wei Chang; Jing Zhang 062; Eric P. Xing; Min Xu 009 (Bioinform., 2021)

Forest Fire Clustering: Cluster-oriented Label Propagation Clustering and Monte Carlo Verification Inspired by Forest Fire Dynamics. - Zhanlin Chen; Philip Tuckman; Jeremy Goldwasser; Jing Zhang 062; Mark Gerstein (CoRR, 2021)

Bayesian structural time series for biomedical sensor data: A flexible modeling framework for evaluating interventions. - Jason Liu 003; Daniel J. Spakowicz; Garrett I. Ash; Rebecca Hoyd; Rohan Ahluwalia; Andrew Zhang; Shaoke Lou; Donghoon Lee 006; Jing Zhang 062; Carolyn Presley; Ann Greene; Matthew Stults-Kolehmainen; et al. (PLoS Comput. Biol., 2021)

Deep Active Learning for Cryo-Electron Tomography Classification. - Tianyang Wang; Bo Li; Jing Zhang 062; Xiangrui Zeng; Mostofa Rafid Uddin; Wei Wu; Min Xu 009 (ICIP, 2022)

Unsupervised Multi-Task Learning for 3D Subtomogram Image Alignment, Clustering and Segmentation. - Haoyi Zhu; Chuting Wang; Yuanxin Wang 001; Zhaoxin Fan; Mostofa Rafid Uddin; Xin Gao 001; Jing Zhang 062; Xiangrui Zeng; Min Xu 009 (ICIP, 2022)

Deep-Precognitive Diagnosis: Preventing Future Pandemics by Novel Disease Detection With Biologically-Inspired Conv-Fuzzy Network. - Aviral Chharia; Rahul Upadhyay; Vinay Kumar; Chao Cheng; Jing Zhang 062; Tianyang Wang; Min Xu 009 (IEEE Access, 2022)

Translator: A Transfer Learning Approach to Facilitate Single-Cell ATAC-Seq Data Analysis from Reference Dataset. - Siwei Xu; Mario Skarica; Ahyeon Hwang; Yi Dai; Cheyu Lee; Matthew J. Girgenti; Jing Zhang 062 (J. Comput. Biol., 2022)

Structure Detection in Three-Dimensional Cellular Cryoelectron Tomograms by Reconstructing Two-Dimensional Annotated Tilt Series. - Xiangrui Zeng; Ziqian Lin; Mostofa Rafid Uddin; Bo Zhou 009; Chao Cheng; Jing Zhang 062; Zachary Freyberg; Min Xu 009 (J. Comput. Biol., 2022)

Venus: An efficient virus infection detection and fusion site discovery method using single-cell and bulk RNA-seq data. - Cheyu Lee; Yuhang Chen; Ziheng Duan; Min Xu 009; Matthew J. Girgenti; Ke Xu 010; Mark Gerstein; Jing Zhang 062 (PLoS Comput. Biol., 2022)

iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease. - Ziheng Duan; Yi Dai; Ahyeon Hwang; Cheyu Lee; Kaichi Xie; Chutong Xiao; Min Xu 009; Matthew J. Girgenti; Jing Zhang 062 (PLoS Comput. Biol., 2023)

Understanding Transcriptional Regulatory Redundancy by Learnable Global Subset Perturbations. - Junhao Liu 001; Siwei Xu; Dylan Riffle; Ziheng Duan; Martin Renqiang Min; Jing Zhang 062 (ACML, 2024)

iHAST: Integrating Hybrid Attention for Super-Resolution in Spatial Transcriptomics. - Xi Li; Jing Zhang 062; Ziheng Duan; Yi Dai; Siwei Xu (BMVC, 2024)

iMIRACLE: An Iterative Multi-View Graph Neural Network to Model Intercellular Gene Regulation From Spatial Transcriptomic Data. - Ziheng Duan; Siwei Xu; Cheyu Lee; Dylan Riffle; Jing Zhang 062 (CIKM, 2024)

scACT: Accurate Cross-modality Translation via Cycle-consistent Training from Unpaired Single-cell Data. - Siwei Xu; Junhao Liu 001; Jing Zhang 062 (CIKM, 2024)

scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding. - Ziheng Duan; Siwei Xu; Shushrruth Sai Srinivasan; Ahyeon Hwang; Cheyu Lee; Feng Yue; Mark Gerstein; Yu Luan; Matthew J. Girgenti; Jing Zhang 062 (Briefings Bioinform., 2024)

Single-Cell Omics Arena: A Benchmark Study for Large Language Models on Cell Type Annotation Using Single-Cell Data. - Junhao Liu 001; Siwei Xu; Lei Zhang 201; Jing Zhang 062 (CoRR, 2024)