Gene and isoform expression signatures associated with tumor stage in kidney renal clear cell carcinoma. - Qi Liu 024; Shilin Zhao; Pei-Fang Su; Shyr Yu (BMC Syst. Biol., 2013)

Detection of internal exon deletion with exon Del. - Yan Guo; Shilin Zhao; Brian D. Lehmann; Quanhu Sheng; Timothy M. Shaver; Thomas Stricker; Jennifer A. Pietenpol; Yu Shyr (BMC Bioinform., 2014)

Heatmap3: an improved heatmap package with more powerful and convenient features. - Shilin Zhao; Yan Guo; Quanhu Sheng; Yu Shyr (BMC Bioinform., 2014)

NGSPERL: a semi-automated framework for large scale next generation sequencing data analysis. - Quanhu Sheng; Shilin Zhao; Mingsheng Guo; Yu Shyr (Int. J. Comput. Biol. Drug Des., 2015)

Facial Expression Recognition Algorithm Based on CNN and LBP Feature Fusion. - Xinli Yang; Ming Li; Shilin Zhao (ICRAI, 2017)

Robust Object Tracking Based on Collaborative Sparse Representation of Multifeature. - Shilin Zhao; Ming Li; Xinli Yang (ICRAI, 2017)

Strategies for processing and quality control of Illumina genotyping arrays. - Shilin Zhao; Jing Wang 026; David C. Samuels; Quanghu Sheng; Yu Shyr; Yan Guo (Briefings Bioinform., 2018)

RnaSeqSampleSize: real data based sample size estimation for RNA sequencing. - Shilin Zhao; Chung-I Li; Yan Guo; Quanhu Sheng; Yu Shyr (BMC Bioinform., 2018)

Traffic Classification and Application Identification Based on Machine Learning in Large-Scale Supercomputing Center. - Shilin Zhao; Kejiang Ye; Cheng-Zhong Xu 001 (HPCC/SmartCity/DSS, 2019)

Non-canonical RNA-DNA differences and other human genomic features are enriched within very short tandem repeats. - Hui Yu; Shilin Zhao; Scott Ness; Huining Kang; Quanhu Sheng; David C. Samuels; Olufunmilola Oyebamiji; Ying-Yong Zhao; Yan Guo (PLoS Comput. Biol., 2020)

Beds: Bagging Ensemble Deep Segmentation For Nucleus Segmentation With Testing Stage Stain Augmentation. - Xing Li; Haichun Yang; Jiaxin He; Aadarsh Jha; Agnes B. Fogo; Lee E. Wheless; Shilin Zhao; Yuankai Huo (ISBI, 2021)

SimTriplet: Simple Triplet Representation Learning with a Single GPU. - Quan Liu 002; Peter C. Louis; Yuzhe Lu; Aadarsh Jha; Mengyang Zhao; Ruining Deng; Tianyuan Yao; Joseph T. Roland; Haichun Yang; Shilin Zhao; Lee E. Wheless; Yuankai Huo (MICCAI (2), 2021)

MAG: A Simple Learning-Based Patient-Level Aggregation Method for Detecting Microsatellite Instability from Whole-Slide Images. - Kaifeng Pang; Zuhayr Asad; Shilin Zhao; Yuankai Huo (ISBI, 2022)

Multi-modal learning with missing data for cancer diagnosis using histopathological and genomic data. - Can Cui 006; Zuhayr Asad; William F. Dean; Isabelle T. Smith; Christopher Madden; Shunxing Bao; Bennett A. Landman; Joseph T. Roland; Lori A. Coburn; Keith T. Wilson; Jeffrey P. Zwerner; Shilin Zhao; et al. (Computer-Aided Diagnosis, 2022)

Survival Prediction of Brain Cancer with Incomplete Radiology, Pathology, Genomic, and Demographic Data. - Can Cui 006; Han Liu; Quan Liu 002; Ruining Deng; Zuhayr Asad; Yaohong Wang; Shilin Zhao; Haichun Yang; Bennett A. Landman; Yuankai Huo (MICCAI (5), 2022)

Integrate memory efficiency methods for self-supervised learning on pathological image analysis. - Quan Liu 002; Bryan A. Millis; Zuhayr Asad; Can Cui 006; William F. Dean; Isabelle T. Smith; Christopher Madden; Joseph T. Roland; Jeffrey P. Zwerner; Shilin Zhao; Lee E. Wheless; Yuankai Huo (Image Processing, 2022)

Ultra-Low-Loss Graphene Coated Optical Fiber Polarizer with PMMA Enhancement. - Jianwei Li; Xinwei Deng; Shilin Zhao; Ziyu Wang; Xinyue Wang (OECC/PSC, 2022)

Comprehensive evaluation of noise reduction methods for single-cell RNA sequencing data. - Shih-Kai Chu; Shilin Zhao; Yu Shyr; Qi Liu 024 (Briefings Bioinform., 2022)

Survival Prediction of Brain Cancer with Incomplete Radiology, Pathology, Genomics, and Demographic Data. - Can Cui 006; Han Liu; Quan Liu 002; Ruining Deng; Zuhayr Asad; Yaohong Wang; Shilin Zhao; Haichun Yang; Bennett A. Landman; Yuankai Huo (CoRR, 2022)

Deep Multi-modal Fusion of Image and Non-image Data in Disease Diagnosis and Prognosis: A Review. - Can Cui 006; Haichun Yang; Yaohong Wang; Shilin Zhao; Zuhayr Asad; Lori A. Coburn; Keith T. Wilson; Bennett A. Landman; Yuankai Huo (CoRR, 2022)

Omni-Seg+: A Scale-aware Dynamic Network for Pathological Image Segmentation. - Ruining Deng; Quan Liu 002; Can Cui 006; Tianyuan Yao; Jun Long; Zuhayr Asad; R. Michael Womick; Zheyu Zhu; Agnes B. Fogo; Shilin Zhao; Haichun Yang; Yuankai Huo (CoRR, 2022)

Multimodality in meta-learning: A comprehensive survey. - Yao Ma; Shilin Zhao; Weixiao Wang; Yaoman Li; Irwin King (Knowl. Based Syst., 2022)

Partial Discharge Localization on Power Cables Based on a Novel Signal Relay System. - Kai Zhou; Yao Fu; Guangya Zhu; Shilin Zhao; Lu Lu 005; Xianjin Wang; Yuan Li 020; Pengfei Meng; Shiyu Ma (IEEE Trans. Instrum. Meas., 2022)

Segment Anything Model (SAM) for Digital Pathology: Assess Zero-shot Segmentation on Whole Slide Imaging. - Ruining Deng; Can Cui 006; Quan Liu 002; Tianyuan Yao; Lucas W. Remedios; Shunxing Bao; Bennett A. Landman; Lee E. Wheless; Lori A. Coburn; Keith T. Wilson; Yaohong Wang; Shilin Zhao; et al. (CoRR, 2023)

Spatial Pathomics Toolkit for Quantitative Analysis of Podocyte Nuclei with Histology and Spatial Transcriptomics Data in Renal Pathology. - Jiayuan Chen 003; Yu Wang; Ruining Deng; Quan Liu 002; Can Cui 006; Tianyuan Yao; Yilin Liu; Jianyong Zhong; Agnes B. Fogo; Haichun Yang; Shilin Zhao; Yuankai Huo (CoRR, 2023)

Evaluation Kidney Layer Segmentation on Whole Slide Imaging using Convolutional Neural Networks and Transformers. - Muhao Liu; Chenyang Qi; Shunxing Bao; Quan Liu 002; Ruining Deng; Yu Wang; Shilin Zhao; Haichun Yang; Yuankai Huo (CoRR, 2023)

Omni-Seg: A Scale-Aware Dynamic Network for Renal Pathological Image Segmentation. - Ruining Deng; Quan Liu 002; Can Cui 006; Tianyuan Yao; Jun Long; Zuhayr Asad; R. Michael Womick; Zheyu Zhu; Agnes B. Fogo; Shilin Zhao; Haichun Yang; Yuankai Huo (IEEE Trans. Biomed. Eng., 2023)

PrPSeg: Universal Proposition Learning for Panoramic Renal Pathology Segmentation. - Ruining Deng; Quan Liu 002; Can Cui 006; Tianyuan Yao; Jialin Yue; Juming Xiong; Lining Yu; Yifei Wu; Mengmeng Yin; Yu Wang; Shilin Zhao; Yucheng Tang; et al. (CVPR, 2024)

HATs: Hierarchical Adaptive Taxonomy Segmentation for Panoramic Pathology Image Analysis. - Ruining Deng; Quan Liu 002; Can Cui 006; Tianyuan Yao; Juming Xiong; Shunxing Bao; Hao Li; Mengmeng Yin; Yu Wang; Shilin Zhao; Yucheng Tang; Haichun Yang; et al. (MICCAI (4), 2024)

Adapting Mouse Pathological Model to Human Glomerular Lesion Segmentation. - Lining Yu; Mengmeng Yin; Ruining Deng; Quan Liu 002; Tianyuan Yao; Can Cui 006; Yu Wang; Yaohong Wang; Shilin Zhao; Haichun Yang; Yuankai Huo (CoRR, 2024)

Cross-Species Data Integration for Enhanced Layer Segmentation in Kidney Pathology. - Junchao Zhu; Mengmeng Yin; Ruining Deng; Yitian Long; Yu Wang; Yaohong Wang; Shilin Zhao; Haichun Yang; Yuankai Huo (CoRR, 2024)

How Good Are We? Evaluating Cell AI Foundation Models in Kidney Pathology with Human-in-the-Loop Enrichment. - Junlin Guo; Siqi Lu; Can Cui 006; Ruining Deng; Tianyuan Yao; Zhewen Tao; Yizhe Lin; Marilyn Lionts; Quan Liu 002; Juming Xiong; Yu Wang; Shilin Zhao; et al. (CoRR, 2024)

Glo-In-One-v2: Holistic Identification of Glomerular Cells, Tissues, and Lesions in Human and Mouse Histopathology. - Lining Yu; Mengmeng Yin; Ruining Deng; Quan Liu 002; Tianyuan Yao; Can Cui 006; Junlin Guo; Yu Wang; Yaohong Wang; Shilin Zhao; Haichun Yang; Yuankai Huo (CoRR, 2024)

ASIGN: An Anatomy-aware Spatial Imputation Graphic Network for 3D Spatial Transcriptomics. - Junchao Zhu; Ruining Deng; Tianyuan Yao; Juming Xiong; Chongyu Qu; Junlin Guo; Siqi Lu; Mengmeng Yin; Yu Wang; Shilin Zhao; Haichun Yang; Yuankai Huo (CVPR, 2025)

stImage: a versatile framework for optimizing spatial transcriptomic analysis through customizable deep histology and location informed integration. - Yu Wang; Haichun Yang; Ruining Deng; Yuankai Huo; Qi Liu 024; Yu Shyr; Shilin Zhao (Briefings Bioinform., 2025)

Fault localization using sliding adaptive data segmentation and improved k-nearest neighbour with application to railway track circuits. - Shilin Zhao; Guangwu Chen; Peng Li; Jianqiang Shi; Vyacheslav Potekhin (Comput. Electr. Eng., 2025)

PySpatial: A High-Speed Whole Slide Image Pathomics Toolkit. - Yuechen Yang; Yu Wang; Tianyuan Yao; Ruining Deng; Mengmeng Yin; Shilin Zhao; Haichun Yang; Yuankai Huo (CoRR, 2025)

KPIs 2024 Challenge: Advancing Glomerular Segmentation from Patch- to Slide-Level. - Ruining Deng; Tianyuan Yao; Yucheng Tang; Junlin Guo; Siqi Lu; Juming Xiong; Lining Yu; Quan Huu Cap; Pengzhou Cai; Libin Lan; Ze Zhao; Adrian Galdran; et al. (CoRR, 2025)

MagNet: Multi-Level Attention Graph Network for Predicting High-Resolution Spatial Transcriptomics. - Junchao Zhu; Ruining Deng; Tianyuan Yao; Juming Xiong; Chongyu Qu; Junlin Guo; Siqi Lu; Yucheng Tang; Daguang Xu; Mengmeng Yin; Yu Wang; Shilin Zhao; et al. (CoRR, 2025)

The improved mountain gazelle optimizer for spatiotemporal support vector regression: a novel method for railway subgrade settlement prediction integrating multi-source information. - Guangwu Chen; Shilin Zhao; Peng Li; Shilin Wang; Xin Zhou; Vyacheslav Potekhin (Appl. Intell., 2025)

IRS: Incremental Relationship-guided Segmentation for Digital Pathology. - Ruining Deng; Junchao Zhu; Juming Xiong; Can Cui 006; Tianyuan Yao; Junlin Guo; Siqi Lu; Marilyn Lionts; Mengmeng Yin; Yu Wang; Shilin Zhao; Yucheng Tang; et al. (CoRR, 2025)

Img2ST-Net: Efficient High-Resolution Spatial Omics Prediction from Whole Slide Histology Images via Fully Convolutional Image-to-Image Learning. - Junchao Zhu; Ruining Deng; Junlin Guo; Tianyuan Yao; Juming Xiong; Chongyu Qu; Mengmeng Yin; Yu Wang; Shilin Zhao; Haichun Yang; Daguang Xu; Yucheng Tang; et al. (CoRR, 2025)