JL
Jingyi Jessica Li
bioinformaticsGene Expression ProfilingSingle-Cell AnalysisComputational Biologyq-bio.GNSoftwaregenomicsstat.METranscriptomeq-bio.QM
On Valency
published · living versionsW_nqkkx3hk·v1 · currentpublished
TwinPoSI: Statistical Twins for Powerful Post-Selection Inference on Population-Based Regression Coefficients
with Changhu Wang, Zhifei Li
1 version
Preprints & journals
143 papers in the corpus · 2007–2026scStable: assessing scRNA-seq analysis stability under bulk-derived between-sample variation.42926404 · Jiang, Chengfeng, Li, Jingyi Jessica2026 · 16 citationsbioRxiv : the preprint server for biology. 2026
Q-SID: Detecting collusion groups from exam question scores with error quantification.42890763 · Yan, Guanao, Li, Jingyi Jessica, Biggin, Mark D2026 · 0 citationsPatterns (New York, N.Y.). 2026;7(10):101642
Beyond differential expression: Differential variability as an underappreciated axis in transcriptomics.42617588 · Jiang, Chenxin Flora, Wang, Changhu, Li, Jingyi Jessica2026 · 0 citationsCell systems. 2026;17(8):101706
IntegrateRigor: annotation-free integration optimization for cell identity recovery reveals cancer-immune interface niches.42182279 · Zhai, Zhiqian, Wang, Changhu, Jiang, Chengfeng et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
Flexible and scalable inference of spatially varying correlation in spatial transcriptomics with spCorr.42309667 · Jiang, Chenxin Flora, Yin, Yuxin, Robson, Paul et al.2026 · 0 citationsGenome research. 2026
Identifying Context-Specific Cell-Cell Interaction Genes Without Ligand-Receptor Databases from Spatial Transcriptomics10.64898/2026.05.08.723913v1 · Kim, H., Park, B., Jung, J. et al.2026 · 0 citationsbioRxiv
CIPHER: An end-to-end framework for designing optimized aggregated spatial transcriptomics experiments.41542523 · Hemminger, Zachery, De Ocampo, Haley, Xie, Fangming et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
SnakeAltPromoter Facilitates Differential Alternative Promoter Analysis.41993886 · Tan, Jiang, Wu, Yuqing, Barve, Ruteja et al.2026 · 0 citationsComputational and structural biotechnology journal. 2026;35(1):0033
Vitamin C inhibits ACSL4 to alleviate ferro-aging in primates.41819088 · Liu, Lixiao, Zheng, Zikai, You, Wanbang et al.2026 · 31 citationsCell metabolism. 2026;38(4):673-693.e17
Information Geometry Reconciles Discrete and Continuous Variation in Single-Cell and Spatial Transcriptomic Analysis10.64898/2026.02.25.707866v2 · Cai, J., Wang, Y., Qiao, Y. et al.2026 · 0 citationsbioRxiv
scDesignPop generates realistic population-scale single-cell RNA-seq for power analysis, benchmarking, and privacy protection.41808987 · Dong, Chris Y, Cen, Yihui, Song, Dongyuan et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
New paradigm for aging research: aging studies through innovative AI applications and interdisciplinary collaborations.41766693 · Gao, Zeyu, Li, Mei, Li, Jingyi et al.2026 · 2 citationsLife medicine. 2026;5(1):lnaf039
Systematic mapping of emergent transcriptional states in interacting single-cell dyads by Cell-Cell-seq.41727115 · Baghdasarian, Sevana, Wang, Qingyang, Langerman, Justin et al.2026 · 5 citationsbioRxiv : the preprint server for biology. 2026
Hypatia: Comparative Isoform Profiling Across Cell Populations from Long-Read Single-Cell Transcriptomes.41648631 · Pan, Timothy, Shiau, Cheng-Kai, Lu, Lina et al.2026 · 1 citationbioRxiv : the preprint server for biology. 2026
ClusterDE: A Statistical Software Package for Removing Double-Dipping Bias in Post-Clustering Differential Expression Analysis.41060830 · Lee, Christy, Song, Dongyuan, Chen, Siqi et al.2026 · 0 citationsJournal of computational biology : a journal of computational molecular cell biology. 2026;33(1):36-42
mcRigor: A Statistical Software Package for Evaluating and Optimizing Metacell Partitioning in Single-Cell Data Analysis.41066085 · Liu, Pan, Li, Jingyi Jessica2025 · 0 citationsJournal of computational biology : a journal of computational molecular cell biology. 2025
CellScope: high-performance cell atlas workflow with tree-structured representation.41469386 · Li, Bingjie, Lin, Runyu, Ni, Tianhao et al.2025 · 3 citationsNature communications. 2025
PseudotimeDE-fast: fast testing of differential gene expression along cell pseudotime.41117775 · Lai, Yuheng, Song, Dongyuan, Xia, Lucy et al.2025 · 0 citationsBioinformatics (Oxford, England). 2025;41(11)
spCorr: flexible and scalable inference of spatially varying correlation in spatial transcriptomics10.1101/2025.09.30.679684v1 · Jiang, C., Yin, Y., Robson, P. et al.2025 · 0 citationsbioRxiv
MelTok: 2D Tokenization for Single-Codebook Audio Compression2510.01903v3 · Jingyi Li, Zhiyuan Zhao, Zhisheng Zhang et al.2025 · 0 citationsarXiv
mcRigor: a statistical method to enhance the rigor of metacell partitioning in single-cell data analysis.41022768 · Liu, Pan, Li, Jingyi Jessica2025 · 7 citationsNature communications. 2025;16(1):8602
Systematic benchmarking of computational methods to identify spatially variable genes.40968359 · Li, Zhijian, M Patel, Zain, Song, Dongyuan et al.2025 · 18 citationsGenome biology. 2025;26(1):285
Genetic variants affecting RNA stability influence complex traits and disease risk.40913182 · Huang, Elaine, Fu, Ting, Zhang, Ling et al.2025 · 9 citationsNature genetics. 2025;57(10):2578-2588
Beware of counter-intuitive levels of false discoveries in datasets with strong intra-correlations.40826107 · Kanduri, Chakravarthi, Mamica, Maria, Olstad, Emilie Willoch et al.2025 · 12 citationsGenome biology. 2025;26(1):249
Constructing a norm for children's scientific drawing: Distribution features based on semantic similarity of large language models.40874033 · Zhang, Yi, Wei, Fan, Li, Jingyi et al.2025 · 0 citationsBiology methods & protocols. 2025;10(1):bpaf062
Nullstrap-DE: A General Framework for Calibrating FDR and Preserving Power in DE Methods, with Applications to DESeq2 and edgeR2507.20598v2 · Chenxin Jiang, Changhu Wang, Jingyi Jessica Li2025 · 0 citationsarXiv
Spatial transcriptomics iterative hierarchical clustering (stIHC): A novel method for identifying spatial gene co-expression modules.41674714 · Higgins, Catherine, Li, Jingyi Jessica, Carey, Michelle2026 · 2 citationsQuantitative biology (Beijing, China). 2025;13(4):e70011
Systematic mining and quantification reveal the dominant contribution of non-HLA variations to acute graft-versus-host disease.40033084 · Liang, Shuang, Kang, Yu-Jian, Huo, Mingrui et al.2025 · 1 citationCellular & molecular immunology. 2025;22(5):501-511
Decoding heterogeneous single-cell perturbation responses.40011559 · Song, Bicna, Liu, Dingyu, Dai, Weiwei et al.2025 · 31 citationsNature cell biology. 2025;27(3):493-504
Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq.39975282 · Zhang, Hefei, Li, Xuhang, Song, Dongyuan et al.2025 · 12 citationsbioRxiv : the preprint server for biology. 2025
Nullstrap: A Simple, High-Power, and Fast Framework for FDR Control in Variable Selection for Diverse High-Dimensional Models2501.05012v2 · Changhu Wang, Ziheng Zhang, Jingyi Jessica Li2025 · 0 citationsarXiv
Comment on "Data Fission: Splitting a Single Data Point", Data Fission for Unsupervised Learning: A Discussion on Post-Clustering Inference and the Challenges of Debiasing.40453591 · Wang, Changhu, Ge, Xinzhou, Song, Dongyuan et al.2026 · 0 citationsJournal of the American Statistical Association. 2025;120(549):174-175
A Super-Enhancer-Related Ferroptosis Signature Predicts Survival and Immune Microenvironment in Colon Cancer Based on Bioinformatics Analyses and Experimental Validation.41325548 · Wan, Luying, Li, Jingyi, Xie, Xianhe2025 · 1 citationIET systems biology. 2025;19(1):e70043
Synthetic control removes spurious discoveries from double dipping in single-cell and spatial transcriptomics data analyses.37546812 · Song, Dongyuan, Chen, Siqi, Lee, Christy et al.2026 · 18 citationsbioRxiv : the preprint server for biology. 2024
Systematic evaluation of methylation-based cell type deconvolution methods for plasma cell-free DNA.39702273 · Sun, Tongyue, Yuan, Jinqi, Zhu, Yacheng et al.2024 · 12 citationsGenome biology. 2024;25(1):318
Semisynthetic simulation for microbiome data analysis.39927858 · Sankaran, Kris, Kodikara, Saritha, Li, Jingyi Jessica et al.2025 · 9 citationsBriefings in bioinformatics. 2024;26(1)
Integrated molecular and functional characterization of the intrinsic apoptotic machinery identifies therapeutic vulnerabilities in glioma.39572533 · Fernandez, Elizabeth G, Mai, Wilson X, Song, Kai et al.2024 · 15 citationsNature communications. 2024;15(1):10089
Systematic dissection of epigenetic age acceleration in normal breast tissue reveals its link to estrogen signaling and cancer risk10.1101/2024.10.31.619735v1 · Sehl, M. E., Guo, W., Farrell, C. et al.2024 · 2 citationsbioRxiv
Response to "Neglecting normalization impact in semi-synthetic RNA-seq data simulation generates artificial false positives" and "Winsorization greatly reduces false positives by popular differential expression methods when analyzing human population samples".39478544 · Ge, Xinzhou, Li, Yumei, Li, Wei et al.2024 · 1 citationGenome biology. 2024;25(1):283
Targeting circadian transcriptional programs through a cis-regulatory mechanism in triple negative breast cancer.38746115 · Pan, Yuanzhong, Chiu, Tsu-Pei, Zhou, Lili et al.2024 · 1 citationbioRxiv : the preprint server for biology. 2024
Spatial Single-Cell Mapping of Transcriptional Differences Across Genetic Backgrounds in Mouse Brains.39416191 · Hemminger, Zachary, Sanchez-Tam, Gabriela, Ocampo, Haley De et al.2026 · 1 citationbioRxiv : the preprint server for biology. 2024
A genome-wide spectrum of tandem repeat expansions in 338,963 humans.39368475 · Cui, Ya, Ye, Wenbin, Li, Jason Sheng et al.2026 · 11 citationsCell. 2024;187(22):6411-6412
Categorization of 33 computational methods to detect spatially variable genes from spatially resolved transcriptomics data.38855546 · Yan, Guanao, Hua, Shuo Harper, Li, Jingyi Jessica2026 · 45 citationsArXiv. 2024
Question-Score Identity Detection (Q-SID): A Statistical Algorithm to Detect Collusion Groups with Error Quantification from Exam Question Scores2407.07420v2 · Guanao Yan, Jingyi Jessica Li, Mark D. Biggin2024 · 0 citationsarXiv
APIR: Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control.39198030 · Chen, Yiling Elaine, Ge, Xinzhou, Woyshner, Kyla et al.2024 · 3 citationsGenomics, proteomics & bioinformatics. 2024;22(2)
scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data.38783325 · Wang, Weijian, Cen, Yihui, Lu, Zezhen et al.2024 · 19 citationsGenome biology. 2024;25(1):136
A genome-wide spectrum of tandem repeat expansions in 338,963 humans.38582080 · Cui, Ya, Ye, Wenbin, Li, Jason Sheng et al.2024 · 41 citationsCell. 2024;187(9):2336-2341.e5
Systematic Evaluation of Cell Type Deconvolution Methods for Plasma Cell-free DNA10.1101/2024.03.25.586507v1 · Sun, T., Yuan, J., Zhu, Y. et al.2024 · 1 citationbioRxiv
Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters.38409103 · Xia, Lucy, Lee, Christy, Li, Jingyi Jessica2024 · 70 citationsNature communications. 2024;15(1):1753
Dissecting gene expression heterogeneity: generalized Pearson correlation squares and the K-lines clustering algorithm.39697782 · Li, Jingyi Jessica, Zhou, Heather J, Bickel, Peter J et al.2025 · 2 citationsJournal of the American Statistical Association. 2024;119(548):2450-2463
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