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Genome Research|November 8, 2019
AIDE: annotation-assisted isoform discovery with high precisionWei Vivian Li, Shan Li, Xin Tong, et al.Plos Computational Biology|June 4, 2026
CIPHER: An end-to-end framework for designing optimized aggregated spatial transcriptomics experimentsZachary Hemminger, Haley De Ocampo, Fangming Xie, et al.Nucleic Acids Research|May 3, 2019
EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequencesXinzhou Ge, Haowen Zhang, Lingjue Xie, et al.Nature Communications|December 30, 2025
CellScope: high-performance cell atlas workflow with tree-structured representationBingjie Li, Runyu Lin, Tianhao Ni, et al.Genome Biology|August 18, 2025
Beware of counter-intuitive levels of false discoveries in datasets with strong intra-correlationsChakravarthi Kanduri, Maria Mamica, Emilie Willoch Olstad, et al.Kidney International|March 22, 2017
Single-cell RNA-sequence analysis of mouse glomerular mesangial cells uncovers mesangial cell essential genesYuqiu Lu, Yuting Ye, Qianqian Yang, et al.Bioinformatics (Oxford, England)|March 8, 2021
Bipartite graph-based approach for clustering of cell lines by gene expression-drug response associationsCalvin Chi, Yuting Ye, Bin Chen, et al.The Journal of Chemical Physics|December 3, 2015
Conformation of a flexible polymer in explicit solvent: Accurate solvation potentials for Lennard-Jones chainsMark P Taylor, Yuting Ye, Shishir R AdhikariPsychoneuroendocrinology|February 23, 2023
Sex-specific effects of human chemosignal on perception of angry but not fearful facesYuting Ye, Yu Nan, Ran Wei, et al.Small Methods|November 28, 2025
Large-Area Nanowire Arrays Achieving Surface Lattice Resonance for Highly Sensitive SERS ApplicationsYuting Ye, Yongda Yan, Chen Li, et al.Pageof 21