Integrating longitudinal clinical and microbiome data to predict growth faltering in preterm infants. - Jose Lugo-Martinez; Siwei Xu; Justine Levesque; Daniel Gallagher; Leslie A. Parker; Josef Neu; Christopher J. Stewart; Janet E. Berrington; Nicholas D. Embleton; Gregory Young; Katherine E. Gregory; Misty Good; et al. (J. Biomed. Informatics, 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)

Expediting knowledge acquisition by a web framework for Knowledge Graph Exploration and Visualization (KGEV): case studies on COVID-19 and Human Phenotype Ontology. - Jacqueline Peng; David Xu 007; Ryan Lee; Siwei Xu; Yunyun Zhou; Kai Wang 049 (BMC Medical Informatics Decis. Mak., 2022)

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)