Jingyi Jessica Li

31 papers B 2Journal 29

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Harmonizing qualitative and quantitative analyses in scRNA-seq via information geometry. Briefings Bioinform. Jinpu Cai, Yuxuan Wang, Yunhao Qiao, Cheng Wang, Ziqi Rong, Luting Zhou, Haoyang Liu, Jingyi Jessica Li, Hongyi Xin
2025	J	`jnl`	PseudotimeDE-fast: fast testing of differential gene expression along cell pseudotime. Bioinform. Yuheng Lai, Dongyuan Song, Lucy Xia, Jingyi Jessica Li
2025	J	`jnl`	Semisynthetic simulation for microbiome data analysis. Briefings Bioinform. Kris Sankaran, Saritha Kodikara, Jingyi Jessica Li, Kim-Anh Lê Cao
2025	J	`jnl`	Spatial transcriptomics iterative hierarchical clustering (stIHC): A novel method for identifying spatial gene co-expression modules. Quant. Biol. Catherine Higgins, Jingyi Jessica Li, Michelle Carey
2025	B	`conf`	Synthetic Control Removes Spurious Discoveries from Double Dipping in Single-Cell and Spatial Transcriptomics Data Analyses. RECOMB Dongyuan Song, Siqi Chen, Christy Lee, Kexin Li, Xinzhou Ge, Jingyi Jessica Li
2025	B	`conf`	mcRigor: A Statistical Method to Enhance the Rigor of Metacell Partitioning in Single-Cell RNA-seq and ATAC-seq Data Analysis. RECOMB Pan Liu, Jingyi Jessica Li
2024	J	`jnl`	APIR: Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control. Genom. Proteom. Bioinform. 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
2023	J	`jnl`	A Python Package J. Comput. Biol. Chihao Zhang, Shihua Zhang, Jingyi Jessica Li
2022	J	`jnl`	Hierarchical Neyman-Pearson Classification for Prioritizing Severe Disease Categories in COVID-19 Patient Data. CoRR Lijia Wang, Y. X. Rachel Wang, Jingyi Jessica Li, Xin Tong
2022	J	`jnl`	Information-theoretic Classification Accuracy: A Criterion that Guides Data-driven Combination of Ambiguous Outcome Labels in Multi-class Classification. J. Mach. Learn. Res. Chihao Zhang, Yiling Elaine Chen, Shihua Zhang, Jingyi Jessica Li
2022	J	`jnl`	Simulating Single-Cell Gene Expression Count Data with Preserved Gene Correlations by scDesign2. J. Comput. Biol. Tianyi Sun, Dongyuan Song, Wei Vivian Li, Jingyi Jessica Li
2022	J	`jnl`	Single-cell generalized trend model (scGTM): a flexible and interpretable model of gene expression trend along cell pseudotime. Bioinform. Elvis Han Cui, Dongyuan Song, Weng Kee Wong, Jingyi Jessica Li
2022	J	`jnl`	scSampler: fast diversity-preserving subsampling of large-scale single-cell transcriptomic data. Bioinform. Dongyuan Song, Nan Miles Xi, Jingyi Jessica Li, Lin Wang
2021	J	`jnl`	A flexible model-free prediction-based framework for feature ranking. J. Mach. Learn. Res. Jingyi Jessica Li, Yiling Elaine Chen, Xin Tong
2021	J	`jnl`	Bipartite tight spectral clustering (BiTSC) algorithm for identifying conserved gene co-clusters in two species. Bioinform. Yidan Eden Sun, Heather J. Zhou, Jingyi Jessica Li
2021	J	`jnl`	Identifying the combinatorial control of signal-dependent transcription factors. PLoS Comput. Biol. Ning Wang, Diane Lefaudeux, Anup Mazumder, Jingyi Jessica Li, Alexander Hoffmann
2021	J	`jnl`	Information-theoretic Classification Accuracy: A Criterion that Guides Data-driven Combination of Ambiguous Outcome Labels in Multi-class Classification. CoRR Chihao Zhang, Yiling Elaine Chen, Shihua Zhang, Jingyi Jessica Li
2021	J	`jnl`	RAD: a web application to identify region associated differentially expressed genes. Bioinform. Yixin Guo, Ziwei Xue, Ruihong Yuan, Jingyi Jessica Li, William A. Pastor, Wanlu Liu
2021	J	`jnl`	scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling. Bioinform. Dongyuan Song, Kexin Li, Zachary Hemminger, Roy Wollman, Jingyi Jessica Li
2020	J	`jnl`	Bridging Cost-sensitive and Neyman-Pearson Paradigms for Asymmetric Binary Classification. CoRR Wei Vivian Li, Xin Tong, Jingyi Jessica Li
2020	J	`jnl`	Statistical Hypothesis Testing versus Machine Learning Binary Classification: Distinctions and Guidelines. Patterns Jingyi Jessica Li, Xin Tong
2019	J	`jnl`	A statistical simulator scDesign for rational scRNA-seq experimental design. Bioinform. Wei Vivian Li, Jingyi Jessica Li
2019	J	`jnl`	Matched Bipartite Block Model with Covariates. J. Mach. Learn. Res. Zahra S. Razaee, Arash A. Amini, Jingyi Jessica Li
2019	J	`jnl`	Word and Sentence Embedding Tools to Measure Semantic Similarity of Gene Ontology Terms by Their Definitions. J. Comput. Biol. Dat Duong, Wasi Uddin Ahmad, Eleazar Eskin, Kai-Wei Chang, Jingyi Jessica Li
2018	J	`jnl`	Modeling and analysis of RNA-seq data: a review from a statistical perspective. Quant. Biol. Wei Vivian Li, Jingyi Jessica Li
2017	J	`jnl`	Hybrid Statistical and Mechanistic Mathematical Model Guides Mobile Health Intervention for Chronic Pain. J. Comput. Biol. Sara M. Clifton, Chaeryon Kang, Jingyi Jessica Li, Qi Long, Nirmish Shah, Daniel M. Abrams
2017	J	`jnl`	Matched bipartite block model with covariates. CoRR Zahra S. Razaee, Arash A. Amini, Jingyi Jessica Li
2016	J	`jnl`	Epigenome overlap measure (EPOM) for comparing tissue/cell types based on chromatin states. BMC Genom. Wei Vivian Li, Zahra S. Razaee, Jingyi Jessica Li
2016	J	`jnl`	NMFP: a non-negative matrix factorization based preselection method to increase accuracy of identifying mRNA isoforms from RNA-seq data. BMC Genom. Yuting Ye, Jingyi Jessica Li
2014	J	`jnl`	Comparative analysis of regulatory information and circuits across distant species Open. Nat. 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, Pouya Kheradpour, Anshul Kundaje, Jingyi Jessica Li, Lijia Ma, Wei Niu, E. Jay Rehm, Joel S. Rozowsky, Matthew Slattery, Rebecca Spokony, Robert Terrell, Dionne Vafeados, Daifeng Wang, Peter Weisdepp, Yi-Chieh Wu, Dan Xie, Koon-Kiu Yan, Elise A. Feingold, Peter J. Good, Michael J. Pazin, Haiyan Huang, Peter J. Bickel, Steven E. Brenner, Valerie Reinke, Robert H. Waterston, Mark Gerstein, Kevin P. White, Manolis Kellis, Michael Snyder
2012	J	`jnl`	Biclustering of Linear Patterns In Gene Expression Data. J. Comput. Biol. Qinghui Gao, Christine Ho, Yingmin Jia, Jingyi Jessica Li, Haiyan Huang