Biclustering of Linear Patterns In Gene Expression Data. - Qinghui Gao; Christine Ho; Yingmin Jia; Jingyi Jessica Li; Haiyan Huang (J. Comput. Biol., 2012)

Comparative analysis of regulatory information and circuits across distant species Open. - Alan P. Boyle; Carlos L. Araya; Cathleen Brdlik; Philip Cayting; Chao Cheng; Yong Cheng; Kathryn Gardner; LaDeana W. Hillier; Judith Janette; Lixia Jiang; Dionna Kasper; Trupti Kawli; et al. (Nat., 2014)

Epigenome overlap measure (EPOM) for comparing tissue/cell types based on chromatin states. - Wei Vivian Li; Zahra S. Razaee; Jingyi Jessica Li (BMC Genom., 2016)

NMFP: a non-negative matrix factorization based preselection method to increase accuracy of identifying mRNA isoforms from RNA-seq data. - Yuting Ye; Jingyi Jessica Li (BMC Genom., 2016)

Hybrid Statistical and Mechanistic Mathematical Model Guides Mobile Health Intervention for Chronic Pain. - Sara M. Clifton; Chaeryon Kang; Jingyi Jessica Li; Qi Long; Nirmish Shah; Daniel M. Abrams (J. Comput. Biol., 2017)

Modeling and analysis of RNA-seq data: a review from a statistical perspective. - Wei Vivian Li; Jingyi Jessica Li (Quant. Biol., 2018)

A statistical simulator scDesign for rational scRNA-seq experimental design. - Wei Vivian Li; Jingyi Jessica Li (Bioinform., 2019)

Word and Sentence Embedding Tools to Measure Semantic Similarity of Gene Ontology Terms by Their Definitions. - Dat Duong; Wasi Uddin Ahmad; Eleazar Eskin; Kai-Wei Chang; Jingyi Jessica Li (J. Comput. Biol., 2019)

Matched Bipartite Block Model with Covariates. - Zahra S. Razaee; Arash A. Amini; Jingyi Jessica Li (J. Mach. Learn. Res., 2019)

Bridging Cost-sensitive and Neyman-Pearson Paradigms for Asymmetric Binary Classification. - Wei Vivian Li; Xin Tong; Jingyi Jessica Li (CoRR, 2020)

Statistical Hypothesis Testing versus Machine Learning Binary Classification: Distinctions and Guidelines. - Jingyi Jessica Li; Xin Tong (Patterns, 2020)

RAD: a web application to identify region associated differentially expressed genes. - Yixin Guo; Ziwei Xue; Ruihong Yuan; Jingyi Jessica Li; William A. Pastor; Wanlu Liu (Bioinform., 2021)

scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling. - Dongyuan Song; Kexin Li; Zachary Hemminger; Roy Wollman; Jingyi Jessica Li (Bioinform., 2021)

Bipartite tight spectral clustering (BiTSC) algorithm for identifying conserved gene co-clusters in two species. - Yidan Eden Sun; Heather J. Zhou; Jingyi Jessica Li (Bioinform., 2021)

A flexible model-free prediction-based framework for feature ranking. - Jingyi Jessica Li; Yiling Elaine Chen; Xin Tong (J. Mach. Learn. Res., 2021)

Identifying the combinatorial control of signal-dependent transcription factors. - Ning Wang; Diane Lefaudeux; Anup Mazumder; Jingyi Jessica Li; Alexander Hoffmann (PLoS Comput. Biol., 2021)

Single-cell generalized trend model (scGTM): a flexible and interpretable model of gene expression trend along cell pseudotime. - Elvis Han Cui; Dongyuan Song; Weng Kee Wong; Jingyi Jessica Li (Bioinform., 2022)

scSampler: fast diversity-preserving subsampling of large-scale single-cell transcriptomic data. - Dongyuan Song; Nan Miles Xi; Jingyi Jessica Li; Lin Wang 044 (Bioinform., 2022)

Hierarchical Neyman-Pearson Classification for Prioritizing Severe Disease Categories in COVID-19 Patient Data. - Lijia Wang; Y. X. Rachel Wang; Jingyi Jessica Li; Xin Tong (CoRR, 2022)

Simulating Single-Cell Gene Expression Count Data with Preserved Gene Correlations by scDesign2. - Tianyi Sun; Dongyuan Song; Wei Vivian Li; Jingyi Jessica Li (J. Comput. Biol., 2022)

Information-theoretic Classification Accuracy: A Criterion that Guides Data-driven Combination of Ambiguous Outcome Labels in Multi-class Classification. - Chihao Zhang 002; Yiling Elaine Chen; Shihua Zhang; Jingyi Jessica Li (J. Mach. Learn. Res., 2022)

A Python Package itca for Information-Theoretic Classification Accuracy: A Criterion That Guides Data-Driven Combination of Ambiguous Outcome Labels in Multiclass Classification. - Chihao Zhang 002; Shihua Zhang; Jingyi Jessica Li (J. Comput. Biol., 2023)

Semisynthetic simulation for microbiome data analysis. - Kris Sankaran; Saritha Kodikara; Jingyi Jessica Li; Kim-Anh Lê Cao (Briefings Bioinform., 2024)

APIR: Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control. - Yiling Elaine Chen; Xinzhou Ge; Kyla Woyshner; Meilu McDermott; Antigoni Manousopoulou; Scott B. Ficarro; Jarrod A. Marto; Kexin Li; Leo David Wang; Jingyi Jessica Li (Genom. Proteom. Bioinform., 2024)

mcRigor: A Statistical Method to Enhance the Rigor of Metacell Partitioning in Single-Cell RNA-seq and ATAC-seq Data Analysis. - Pan Liu; Jingyi Jessica Li (RECOMB, 2025)

Synthetic Control Removes Spurious Discoveries from Double Dipping in Single-Cell and Spatial Transcriptomics Data Analyses. - Dongyuan Song; Siqi Chen; Christy Lee; Kexin Li; Xinzhou Ge; Jingyi Jessica Li (RECOMB, 2025)