Jingyi Jessica Li

Also affiliated with Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa, University of California, Los Angeles, University of Washington, Fred Hutch Cancer Center, Quantitative BioSciences, Cancer Research And Biostatistics, University of Washington Applied Physics Laboratory, Institute of Zoology

Biochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 3%percentile

1.1Author DataRank

Indexed papers

1in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 1 indexed paper attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

A genome-wide spectrum of tandem repeat expansions in 338,963 humans

Cell(2024)10.1016/j.cell.2024.03.004

Top 18%

1.1DataRank

Top 18%39 citations

Wenbin Ye, Jason Sheng Li, Jingyi Jessica Li, Éric Vilain, Tamer Sallam +2 more

Papers

Driven by 60 papers — median percentile 82. Top paper: “scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured”.

scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured

Genome biology(2021)10.1186/s13059-021-02367-2

N/A

2.7DataRank · unranked

127 citations

Dongyuan Song, Wei Vivian Li, Jingyi Jessica Li, Tianyi Sun

A genome-wide spectrum of tandem repeat expansions in 338,963 humans

Cell(2024)10.1016/j.cell.2024.03.004

Top 18%

1.1DataRank

Top 18%39 citations

Wenbin Ye, Jason Sheng Li, Jingyi Jessica Li, Éric Vilain, Tamer Sallam +2 more

Comparative analysis of regulatory information and circuits across distant species

Nature(2014)10.1038/nature13668

N/A

0.818DataRank · unranked

232 citations

Carlos L. Araya, Cathleen Brdlik, Philip Cayting, Chao Cheng, Yong Cheng +40 more

Network Modeling in Biology: Statistical Methods for Gene and Brain Networks

Statistical Science(2020)10.1214/20-sts792

N/A

0DataRank · unranked

25 citations

Lexin Li, Jingyi Jessica Li, Haiyan Huang, Y. X. Rachel Wang

Bipartite tight spectral clustering (BiTSC) algorithm for identifying conserved gene co-clusters in two species

Bioinformatics(2020)10.1093/bioinformatics/btaa741

N/A

0DataRank · unranked

6 citations

Heather J. Zhou, Jingyi Jessica Li, Yidan Eden Sun

Clipper: p-value-free FDR control on high-throughput data from two conditions

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.19.390773

N/A

0DataRank · unranked

11 citations

Yiling Elaine Chen, Dongyuan Song, MeiLu McDermott, Kyla Woyshner, Antigoni Manousopoulou +5 more

scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.17.387795

N/A

0DataRank · unranked

10 citations

Dongyuan Song, Wei Vivian Li, Jingyi Jessica Li, Tianyi Sun

Statistics or biology: the zero-inflation controversy about scRNA-seq data

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.28.424633

N/A

0DataRank · unranked

9 citations

Tianyi Sun, Dongyuan Song, Jingyi Jessica Li, Ruochen Jiang

mbImpute: an accurate and robust imputation method for microbiome data

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.07.982314

N/A

0DataRank · unranked

8 citations

Wei Vivian Li, Jingyi Jessica Li, Ruochen Jiang

PseudotimeDE: inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing data

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.17.387779

N/A

0DataRank · unranked

7 citations

Jingyi Jessica Li, Dongyuan Song

DORGE: Discovery of Oncogenes and Tumor SuppressoR Genes Using Genetic and Epigenetic Features

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.21.213702

N/A

0DataRank · unranked

6 citations

Jingyi Jessica Li, Jianzhong Su, Fanglue Peng, Yiling Elaine Chen, Xinzhou Ge +2 more

Cellular heterogeneity–adjusted clonal methylation (CHALM) provides better prediction of gene expression

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.02.23.961813

N/A

0DataRank · unranked

1 citations

Jiejun Shi, Xiaodong Cui, Ya Cui, Jingyi Jessica Li, Ajay Goel +5 more

The concurrence of DNA methylation and demethylation is associated with transcription regulation

Nature Communications(2021)10.1038/s41467-021-25521-7

N/A

0DataRank · unranked

100 citations

Jianfeng Xu, Yiling Elaine Chen, Jason Sheng Li, Ya Cui, Lanlan Shen +3 more

PseudotimeDE: inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing data

Genome biology(2021)10.1186/s13059-021-02341-y

N/A

0DataRank · unranked

94 citations

Jingyi Jessica Li, Dongyuan Song

mbImpute: an accurate and robust imputation method for microbiome data

Genome biology(2021)10.1186/s13059-021-02400-4

N/A

0DataRank · unranked

75 citations

Wei Vivian Li, Jingyi Jessica Li, Ruochen Jiang

Clipper: p-value-free FDR control on high-throughput data from two conditions

Genome biology(2021)10.1186/s13059-021-02506-9

N/A

0DataRank · unranked

55 citations

Yiling Elaine Chen, Dongyuan Song, MeiLu McDermott, Kyla Woyshner, Antigoni Manousopoulou +5 more

scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling

Bioinformatics(2021)10.1093/bioinformatics/btab273

N/A

0DataRank · unranked

31 citations

Kexin Li, Zachary Hemminger, Roy Wollman, Jingyi Jessica Li, Dongyuan Song

Cellular Heterogeneity–Adjusted cLonal Methylation (CHALM) improves prediction of gene expression

Nature Communications(2021)10.1038/s41467-020-20492-7

N/A

0DataRank · unranked

29 citations

Jiejun Shi, Xiaodong Cui, Ya Cui, Jingyi Jessica Li, Ajay Goel +5 more

Identifying the combinatorial control of signal-dependent transcription factors

PLoS Computational Biology(2021)10.1371/journal.pcbi.1009095

N/A

0DataRank · unranked

26 citations

Diane Lefaudeux, Anup Mazumder, Jingyi Jessica Li, Alexander Hoffmann, Ning Wang

Protocol for executing and benchmarking eight computational doublet-detection methods in single-cell RNA sequencing data analysis

STAR Protocols(2021)10.1016/j.xpro.2021.100699

N/A

0DataRank · unranked

4 citations

Jingyi Jessica Li, Nan Miles Xi

A large-sample crisis? Exaggerated false positives by popular differential expression methods

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.08.25.457733

N/A

0DataRank · unranked

5 citations

Xinzhou Ge, Fanglue Peng, Wei Li, Jingyi Jessica Li, Yumei Li

scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.09.430550

N/A

0DataRank · unranked

2 citations

Kexin Li, Zachary Hemminger, Roy Wollman, Jingyi Jessica Li, Dongyuan Song

APIR: Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.08.459494

N/A

0DataRank · unranked

1 citations

Xinzhou Ge, Kyla Woyshner, MeiLu McDermott, Antigoni Manousopoulou, Scott B. Ficarro +5 more

The Competition between DNA Methylation and Demethylation is Associated with Transcription Regulation and Tumorigenesis

Research Square(2021)10.21203/rs.3.rs-123209/v1

N/A

0DataRank · unranked

0 citations

Jiejun Shi, Jianfeng Xu, Yi‐Ling Chen, Jingyi Jessica Li, Lanlan Shen +1 more

Single-cell generalized trend model (scGTM): a flexible and interpretable model of gene expression trend along cell pseudotime

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.25.470059

N/A

0DataRank · unranked

0 citations

Dongyuan Song, Weng Kee Wong, Jingyi Jessica Li, Elvis Han Cui

Statistics or biology: the zero-inflation controversy about scRNA-seq data

Genome biology(2022)10.1186/s13059-022-02601-5

N/A

0DataRank · unranked

649 citations

Tianyi Sun, Dongyuan Song, Jingyi Jessica Li, Ruochen Jiang

Exaggerated false positives by popular differential expression methods when analyzing human population samples

Genome biology(2022)10.1186/s13059-022-02648-4

N/A

0DataRank · unranked

320 citations

Xinzhou Ge, Fanglue Peng, Wei Li, Jingyi Jessica Li, Yumei Li

The interplay between translational efficiency, poly(A) tails, microRNAs, and neuronal activation

RNA(2022)10.1261/rna.079046.121

N/A

0DataRank · unranked

16 citations

Jingyi Jessica Li, David P. Bartel, Timothy J. Eisen

Single-cell generalized trend model (scGTM): a flexible and interpretable model of gene expression trend along cell pseudotime

Bioinformatics(2022)10.1093/bioinformatics/btac423

N/A

0DataRank · unranked

7 citations

Dongyuan Song, Weng Kee Wong, Jingyi Jessica Li, Elvis Han Cui

A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.09.20.508796

N/A

0DataRank · unranked

6 citations

Qingyang Wang, Guanao Yan, Tianyang Liu, Jingyi Jessica Li, Dongyuan Song

PCA outperforms popular hidden variable inference methods for molecular QTL mapping

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.09.483661

N/A

0DataRank · unranked

4 citations

Lei Li, Yumei Li, Wei Li, Jingyi Jessica Li, Heather J. Zhou

scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics

Nature Biotechnology(2023)10.1038/s41587-023-01772-1

N/A

0DataRank · unranked

151 citations

Qingyang Wang, Guanao Yan, Tianyang Liu, Tianyi Sun, Jingyi Jessica Li +1 more

METTL3-Mediated m6A Modification Controls Splicing Factor Abundance and Contributes to Aggressive CLL

Blood Cancer Discovery(2023)10.1158/2643-3230.bcd-22-0156

N/A

0DataRank · unranked

28 citations

Meiling Jin, Mike M. Fernandez, Kevyn L. Hart, Aijun Liao, Xinzhou Ge +16 more

Functional characterization of age-dependent p16 epimutation reveals biological drivers and therapeutic targets for colorectal cancer

Journal of Experimental & Clinical Cancer Research(2023)10.1186/s13046-023-02689-y

N/A

0DataRank · unranked

22 citations

Xiaomin Chen, Christy Lee, Jiejun Shi, Emily B. Lawrence, Lanjing Zhang +11 more

scReadSim: a single-cell RNA-seq and ATAC-seq read simulator

Nature Communications(2023)10.1038/s41467-023-43162-w

N/A

0DataRank · unranked

15 citations

Dongyuan Song, Jingyi Jessica Li, Guanao Yan

Transcriptomic congruence analysis for evaluating model organisms

Proceedings of the National Academy of Sciences(2023)10.1073/pnas.2202584120

N/A

0DataRank · unranked

8 citations

Tanbin Rahman, Li Zhu, Xiangrui Zeng, Yingjin Zhang, Jian Zou +9 more

Exploring the optimization of autoencoder design for imputing single-cell RNA sequencing data

Computational and Structural Biotechnology Journal(2023)10.1016/j.csbj.2023.07.041

N/A

0DataRank · unranked

6 citations

Jingyi Jessica Li, Nan Miles Xi

How the Monty Hall problem is similar to the false discovery rate in high-throughput data analysis

Nature Biotechnology(2023)10.1038/s41587-023-01794-9

N/A

0DataRank · unranked

1 citations

Jingyi Jessica Li

Synthetic control removes spurious discoveries from double dipping in single-cell and spatial transcriptomics data analyses

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.21.550107

N/A

0DataRank · unranked

17 citations

Siqi Chen, Christy Lee, Kexin Li, Xinzhou Ge, Jingyi Jessica Li +1 more

ClusterDE: a post-clustering differential expression (DE) method robust to false-positive inflation caused by double dipping

Research Square(2023)10.21203/rs.3.rs-3211191/v1

N/A

0DataRank · unranked

6 citations

Dongyuan Song, Kexin Li, Xinzhou Ge, Jingyi Jessica Li

scDEED: a statistical method for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.21.537839

N/A

0DataRank · unranked

5 citations

Christy Lee, Jingyi Jessica Li, Lucy Xia

Decoding Heterogenous Single-cell Perturbation Responses

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.30.564796

N/A

0DataRank · unranked

5 citations

Dingyu Liu, Weiwei Dai, Natalie F. McMyn, Qingyang Wang, Dapeng Yang +19 more

ClipperQTL: ultrafast and powerful eGene identification method

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.28.555191

N/A

0DataRank · unranked

3 citations

Xinzhou Ge, Jingyi Jessica Li, Heather J. Zhou

Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters

Nature Communications(2024)10.1038/s41467-024-45891-y

N/A

0DataRank · unranked

64 citations

Christy Lee, Jingyi Jessica Li, Lucy Xia

Integrated molecular and functional characterization of the intrinsic apoptotic machinery identifies therapeutic vulnerabilities in glioma

Nature Communications(2024)10.1038/s41467-024-54138-9

N/A

0DataRank · unranked

12 citations

X. Wilson, Kai Song, Nicholas Bayley, Jiyoon Kim, Henan Zhu +15 more

Semisynthetic simulation for microbiome data analysis

Briefings in Bioinformatics(2024)10.1093/bib/bbaf051

N/A

0DataRank · unranked

7 citations

Saritha Kodikara, Jingyi Jessica Li, Kim-Anh Lȇ Cao, Kris Sankaran

APIR: Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control

Genomics Proteomics & Bioinformatics(2024)10.1093/gpbjnl/qzae042

N/A

0DataRank · unranked

3 citations

Xinzhou Ge, Kyla Woyshner, MeiLu McDermott, Antigoni Manousopoulou, Scott B. Ficarro +5 more

Dissecting Gene Expression Heterogeneity: Generalized Pearson Correlation Squares and the K -Lines Clustering Algorithm

Journal of the American Statistical Association(2024)10.1080/01621459.2024.2342639

N/A

0DataRank · unranked

2 citations

Heather J. Zhou, Peter J. Bickel, Xin Tong, Jingyi Jessica Li

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"

Genome biology(2024)10.1186/s13059-024-03232-8

N/A

0DataRank · unranked

1 citations

Yumei Li, Wei Li, Jingyi Jessica Li, Xinzhou Ge

Targeting circadian transcriptional programs through a cis-regulatory mechanism in triple negative breast cancer

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.26.590360

N/A

0DataRank · unranked

1 citations

Tsu-Pei Chiu, Lili Zhou, Priscilla Chan, Tia Tyrsett Kuo, Francesca Battaglin +9 more

Categorization of 34 computational methods to detect spatially variable genes from spatially resolved transcriptomics data

Nature Communications(2025)10.1038/s41467-025-56080-w

N/A

0DataRank · unranked

37 citations

Shuo Harper Hua, Jingyi Jessica Li, Guanao Yan

Systematic benchmarking of computational methods to identify spatially variable genes

Genome biology(2025)10.1186/s13059-025-03731-2

N/A

0DataRank · unranked

13 citations

Z. Patel, Dongyuan Song, Sai Nirmayi Yasa, Robrecht Cannoodt, Guanao Yan +3 more

Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq

Nature Communications(2025)10.1038/s41467-025-60154-0

N/A

0DataRank · unranked

7 citations

Xuhang Li, Dongyuan Song, Onur Yukselen, Shivani Nanda, Alper Küçükural +4 more

mcRigor: a statistical method to enhance the rigor of metacell partitioning in single-cell data analysis

Nature Communications(2025)10.1038/s41467-025-63626-5

N/A

0DataRank · unranked

5 citations

Jingyi Jessica Li, Pan Liu

Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.02.02.636107

N/A

0DataRank · unranked

4 citations

Xuhang Li, Dongyuan Song, Onur Yukselen, Shivani Nanda, Alper Küçükural +4 more

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

Journal of the American Statistical Association(2025)10.1080/01621459.2024.2412191

N/A

0DataRank · unranked

0 citations

Xinzhou Ge, Dongyuan Song, Jingyi Jessica Li, Changhu Wang

ClipperQTL: ultrafast and powerful eGene identification method

Genome biology(2025)10.1186/s13059-025-03662-y

N/A

0DataRank · unranked

0 citations

Xinzhou Ge, Jingyi Jessica Li, Heather J. Zhou

PseudotimeDE-fast: fast testing of differential gene expression along cell pseudotime

Bioinformatics(2025)10.1093/bioinformatics/btaf573

N/A

0DataRank · unranked

0 citations

Dongyuan Song, Lucy Xia, Jingyi Jessica Li, Yuheng Lai

Benchmarking Computational Doublet-Detection Methods for Single-Cell RNA Sequencing Data

Cell Systems(2020)10.1016/j.cels.2020.11.008

N/A

0DataRank · unranked

223 citations

Jingyi Jessica Li, Nan Miles Xi

DORGE: Discovery of Oncogenes and tumoR suppressor genes using Genetic and Epigenetic features

Science Advances(2020)10.1126/sciadv.aba6784

N/A

0DataRank · unranked

68 citations

Jingyi Jessica Li, Jianzhong Su, Fanglue Peng, Yiling Elaine Chen, Xinzhou Ge +2 more

Jingyi Jessica Li

Indexed papers

Top data-sharing exemplar

Papers