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Journal of Computational Biology : a Journal of Computational Molecular Cell Biology|November 6, 2023
A Python Package itca for Information-Theoretic Classification Accuracy: A Criterion That Guides Data-Driven Combination of Ambiguous Outcome Labels in Multiclass ClassificationChihao Zhang, Shihua Zhang, Jingyi Jessica LiIEEE Transactions on Pattern Analysis and Machine Intelligence|October 12, 2019
Bayesian Joint Matrix Decomposition for Data Integration with Heterogeneous NoiseChihao Zhang, Shihua ZhangThe Annals of Applied Statistics|May 8, 2018
MSIQ: JOINT MODELING OF MULTIPLE RNA-SEQ SAMPLES FOR ACCURATE ISOFORM QUANTIFICATIONWei Vivian Li, Anqi Zhao, Shihua Zhang, et al.Nucleic Acids Research|October 9, 2023
STAMarker: determining spatial domain-specific variable genes with saliency maps in deep learningChihao Zhang, Kangning Dong, Kazuyuki Aihara, et al.Journal of Computational Biology : a Journal of Computational Molecular Cell Biology|October 9, 2025
mcRigor: A Statistical Software Package for Evaluating and Optimizing Metacell Partitioning in Single-Cell Data AnalysisPan Liu, Jingyi Jessica LiBMC Genomics|January 29, 2016
NMFP: a non-negative matrix factorization based preselection method to increase accuracy of identifying mRNA isoforms from RNA-seq dataYuting Ye, Jingyi Jessica LiBMC Genomics|March 18, 2017
Correspondence of D. melanogaster and C. elegans developmental stages revealed by alternative splicing characteristics of conserved exonsRuiqi Gao, Jingyi Jessica LiGenome Biology|April 30, 2021
PseudotimeDE: inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing dataDongyuan Song, Jingyi Jessica LiNature Communications|September 29, 2025
mcRigor: a statistical method to enhance the rigor of metacell partitioning in single-cell data analysisPan Liu, Jingyi Jessica LiPatterns (New York, N.Y.)|October 19, 2020
Statistical Hypothesis Testing versus Machine Learning Binary Classification: Distinctions and GuidelinesJingyi Jessica Li, Xin TongPageof 37