Jingyi Jessica Li

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 49

Top Venues

Nature communications

Proceedings of the National Academy of Sciences of the United States of America

Genome biology

bioRxiv : the preprint server for biology

University of California, Los Angeles

University of California, Berkeley (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of California, Los Angeles Jul 01 2019

United States

Associate Professor :: Department of Statistics

University of California, Los Angeles Jul 01 2013 - Jun 30 2019

United States

Assistant Profesor :: Department of Statistics

Education History

University of California, Berkeley Aug 15 2008 - May 17 2013

United States

PHD :: Interdepartmental Group of Biostatistics

Tsinghua University Aug 15 2003 - Jul 15 2007

China

BSC :: Department of Biological Sciences and Technology

Publications

Lucy Xia, Christy Lee, Jingyi Jessica Li
Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters. Nature communications 15 (1) (2024)
Lucy Xia, Christy Lee, Jingyi Jessica Li
Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters. Nature communications 15 (1) (2024)
Yuanzhong Pan, Tsu-Pei Chiu, Lili Zhou, Priscilla Chan, Tia Tyrsett Kuo, Francesca Battaglin, Shivani Soni, Priya Jayachandra, Jingyi Jessica Li, Heinz-Josef Lenz, Shannon M Mumenthaler, Remo Rohs, Evanthia Roussos Torres, Steve A Kay
Targeting circadian transcriptional programs in triple negative breast cancer through a cis-regulatory mechanism. bioRxiv : the preprint server for biology (2024)
Lucy Xia, Christy Lee, Jingyi Jessica Li
Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters. Nature communications 15 (1) (2024)
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
APIR: Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control. Genomics, proteomics & bioinformatics 22 (2) (2024)
Ashok Patowary, Pan Zhang, Connor Jops, Celine K Vuong, Xinzhou Ge, Kangcheng Hou, Minsoo Kim, Naihua N Gong, Michael Margolis, Daniel D Vo, Xusheng Wang, Yanling Liu, Bogdan Pasaniuc, Jingyi Jessica Li, Michael J Gandal, Luis de la Torre-Ubieta
Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms. Science (New York, N.Y.) 384 (6698) (2024)
Ashok Patowary, Pan Zhang, Connor Jops, Celine K Vuong, Xinzhou Ge, Kangcheng Hou, Minsoo Kim, Naihua N Gong, Michael Margolis, Daniel D Vo, Xusheng Wang, Yanling Liu, Bogdan Pasaniuc, Jingyi Jessica Li, Michael J Gandal, Luis de la Torre-Ubieta
Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms. Science (New York, N.Y.) 384 (6698) (2024)
Ashok Patowary, Pan Zhang, Connor Jops, Celine K Vuong, Xinzhou Ge, Kangcheng Hou, Minsoo Kim, Naihua N Gong, Michael Margolis, Daniel D Vo, Xusheng Wang, Yanling Liu, Bogdan Pasaniuc, Jingyi Jessica Li, Michael J Gandal, Luis de la Torre-Ubieta
Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms. Science (New York, N.Y.) 384 (6698) (2024)
Ashok Patowary, Pan Zhang, Connor Jops, Celine K Vuong, Xinzhou Ge, Kangcheng Hou, Minsoo Kim, Naihua N Gong, Michael Margolis, Daniel D Vo, Xusheng Wang, Yanling Liu, Bogdan Pasaniuc, Jingyi Jessica Li, Michael J Gandal, Luis de la Torre-Ubieta
Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms. Science (New York, N.Y.) 384 (6698) (2024)
Lucy Xia, Christy Lee, Jingyi Jessica Li
Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters. Nature communications 15 (1) (2024)
Lucy Xia, Christy Lee, Jingyi Jessica Li
Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters. Nature communications 15 (1) (2024)
Yuanzhong Pan, Tsu-Pei Chiu, Lili Zhou, Priscilla Chan, Tia Tyrsett Kuo, Francesca Battaglin, Shivani Soni, Priya Jayachandran, Jingyi Jessica Li, Heinz-Josef Lenz, Shannon M Mumenthaler, Remo Rohs, Evanthia Roussos Torres, Steve A Kay
Targeting circadian transcriptional programs in triple negative breast cancer through a cis-regulatory mechanism. bioRxiv : the preprint server for biology (2024)
Dongyuan Song, Kexin Li, Xinzhou Ge, Jingyi Jessica Li
ClusterDE: a post-clustering differential expression (DE) method robust to false-positive inflation caused by double dipping. bioRxiv : the preprint server for biology (2023)
Wei Zong, Tanbin Rahman, Li Zhu, Xiangrui Zeng, Yingjin Zhang, Jian Zou, Song Liu, Zhao Ren, Jingyi Jessica Li, Etienne Sibille, Adrian V Lee, Steffi Oesterreich, Tianzhou Ma, George C Tseng
Transcriptomic congruence analysis for evaluating model organisms. Proceedings of the National Academy of Sciences of the United States of America 120 (6) (2023)
Wei Zong, Tanbin Rahman, Li Zhu, Xiangrui Zeng, Yingjin Zhang, Jian Zou, Song Liu, Zhao Ren, Jingyi Jessica Li, Etienne Sibille, Adrian V Lee, Steffi Oesterreich, Tianzhou Ma, George C Tseng
Transcriptomic congruence analysis for evaluating model organisms. Proceedings of the National Academy of Sciences of the United States of America 120 (6) (2023)
Jingyi Jessica Li, Dongyuan Song, Kexin Li, Xinzhou Ge
ClusterDE: a post-clustering differential expression (DE) method robust to false-positive inflation caused by double dipping. Research square (2023)
Wei Zong, Tanbin Rahman, Li Zhu, Xiangrui Zeng, Yingjin Zhang, Jian Zou, Song Liu, Zhao Ren, Jingyi Jessica Li, Etienne Sibille, Adrian V Lee, Steffi Oesterreich, Tianzhou Ma, George C Tseng
Transcriptomic congruence analysis for evaluating model organisms. Proceedings of the National Academy of Sciences of the United States of America 120 (6) (2023)
Guanao Yan, Dongyuan Song, Jingyi Jessica Li
scReadSim: a single-cell RNA-seq and ATAC-seq read simulator. Nature communications 14 (1) (2023)
Wei Zong, Tanbin Rahman, Li Zhu, Xiangrui Zeng, Yingjin Zhang, Jian Zou, Song Liu, Zhao Ren, Jingyi Jessica Li, Etienne Sibille, Adrian V Lee, Steffi Oesterreich, Tianzhou Ma, George C Tseng
Transcriptomic congruence analysis for evaluating model organisms. Proceedings of the National Academy of Sciences of the United States of America 120 (6) (2023)
Lucy Xia, Christy Lee, Jingyi Jessica Li
scDEED: a statistical method for detecting dubious 2D single-cell embeddings. bioRxiv : the preprint server for biology (2023)
Wei Zong, Tanbin Rahman, Li Zhu, Xiangrui Zeng, Yingjin Zhang, Jian Zou, Song Liu, Zhao Ren, Jingyi Jessica Li, Etienne Sibille, Adrian V Lee, Steffi Oesterreich, Tianzhou Ma, George C Tseng
Transcriptomic congruence analysis for evaluating model organisms. Proceedings of the National Academy of Sciences of the United States of America 120 (6) (2023)
Jingyi Jessica Li
How the Monty Hall problem is similar to the false discovery rate in high-throughput data analysis. Nature biotechnology (2023)
Chihao Zhang, Tinghu Zhang, Jingyi Jessica Li
A Python Package itca for Information-Theoretic Classification Accuracy: A Criterion That Guides Data-Driven Combination of Ambiguous Outcome Labels in Multiclass Classification. Journal of computational biology : a journal of computational molecular cell biology (2023)
Dongyuan Song, Qingyang Wang, Guanao Yan, Tianyang Liu, Tianyi Sun, Jingyi Jessica Li
scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics. Nature biotechnology (2023)
Lucy Xia, Christy Lee, Jingyi Jessica Li
scDEED: a statistical method for detecting dubious 2D single-cell embeddings. bioRxiv : the preprint server for biology (2023)
Wei Zong, Tanbin Rahman, Li Zhu, Xiangrui Zeng, Yingjin Zhang, Jian Zou, Song Liu, Zhao Ren, Jingyi Jessica Li, Etienne Sibille, Adrian V Lee, Steffi Oesterreich, Tianzhou Ma, George C Tseng
Transcriptomic congruence analysis for evaluating model organisms. Proceedings of the National Academy of Sciences of the United States of America 120 (6) (2023)
Wei Zong, Tanbin Rahman, Li Zhu, Xiangrui Zeng, Yingjin Zhang, Jian Zou, Song Liu, Zhao Ren, Jingyi Jessica Li, Etienne Sibille, Adrian V Lee, Steffi Oesterreich, Tianzhou Ma, George C Tseng
Transcriptomic congruence analysis for evaluating model organisms. Proceedings of the National Academy of Sciences of the United States of America 120 (6) (2023)
Wei Zong, Tanbin Rahman, Li Zhu, Xiangrui Zeng, Yingjin Zhang, Jian Zou, Song Liu, Zhao Ren, Jingyi Jessica Li, Etienne Sibille, Adrian V Lee, Steffi Oesterreich, Tianzhou Ma, George C Tseng
Transcriptomic congruence analysis for evaluating model organisms. Proceedings of the National Academy of Sciences of the United States of America 120 (6) (2023)
Yiming Wu, Meiling Jin, Mike Minh Fernandez, Kevyn Lopez Hart, Aijun Liao, Xinzhou Ge, Stacey M Fernandes, Tinisha McDonald, Zhenhua Chen, Daniel Röth, Lucy Y Ghoda, Guido Marcucci, Markus Kalkum, Raju K Pillai, Alexey V Danilov, Jingyi Jessica Li, Jianjun Chen, Jennifer R Brown, Steven T Rosen, Tanya Siddiqi, Lili Wang
METTL3-Mediated m6A Modification Controls Splicing Factor Abundance and Contributes to Aggressive CLL. Blood cancer discovery (2023)
Heather J Zhou, Xinzhou Ge, Jingyi Jessica Li
ClipperQTL: ultrafast and powerful eGene identification method. bioRxiv : the preprint server for biology (2023)
Elvis Han Cui, Dongyuan Song, Weng Kee Wong, Jingyi Jessica Li
Single-cell generalized trend model (scGTM): a flexible and interpretable model of gene expression trend along cell pseudotime. Bioinformatics (Oxford, England) 38 (16) (2022)
Yumei Li, Xinzhou Ge, Fanglue Peng, Wei Li, Jingyi Jessica Li
Exaggerated false positives by popular differential expression methods when analyzing human population samples. Genome biology 23 (1) (2022)
Ruochen Jiang, Tianyi Sun, Dongyuan Song, Jingyi Jessica Li
Statistics or biology: the zero-inflation controversy about scRNA-seq data. Genome biology 23 (1) (2022)
Heather J Zhou, Lei Li, Yumei Li, Weibo Xie, Jingyi Jessica Li
PCA outperforms popular hidden variable inference methods for molecular QTL mapping. Genome biology 23 (1) (2022)
Dongyuan Song, Nan Miles Xi, Jingyi Jessica Li, Lin Wang
scSampler: fast diversity-preserving subsampling of large-scale single-cell transcriptomic data. Bioinformatics (Oxford, England) 38 (11) (2022)
Tianyi Sun, Dongyuan Song, Wei Vivian Li, Jingyi Jessica Li
Simulating Single-Cell Gene Expression Count Data with Preserved Gene Correlations by scDesign2. Journal of computational biology : a journal of computational molecular cell biology 29 (1) (2022)
Timothy J Eisen, Jingyi Jessica Li, David P Bartel
The interplay between translational efficiency, poly(A) tails, microRNAs, and neuronal activation. RNA (New York, N.Y.) 28 (6) (2022)
Jianfeng Xu, Jiejun Shi, Xiaodong Cui, Ya Cui, Jingyi Jessica Li, Ajay Goel, Xi Chen, Jean-Pierre J Issa, Jianzhong Su, Weibo Xie
Cellular Heterogeneity-Adjusted cLonal Methylation (CHALM) improves prediction of gene expression. Nature communications 12 (1) (2021)
Tianyi Sun, Dongyuan Song, Wei Vivian Li, Jingyi Jessica Li
scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured. Genome biology 22 (1) (2021)
Xinzhou Ge, Yiling Elaine Chen, Dongyuan Song, MeiLu McDermott, Kyla Woyshner, Antigoni Manousopoulou, Ning Wang, Wei Li, Leo D Wang, Jingyi Jessica Li
Clipper: p-value-free FDR control on high-throughput data from two conditions. Genome biology 22 (1) (2021)
Ruochen Jiang, Wei Vivian Li, Jingyi Jessica Li
mbImpute: an accurate and robust imputation method for microbiome data. Genome biology 22 (1) (2021)
Jiejun Shi, Jianfeng Xu, Yiling Elaine Chen, Jason Sheng Li, Ya Cui, Lanlan Shen, Jingyi Jessica Li, Weibo Xie
The concurrence of DNA methylation and demethylation is associated with transcription regulation. Nature communications 12 (1) (2021)
Ning Wang, Diane Lefaudeux, Anup Mazumder, Jingyi Jessica Li, Alexander Hoffmann
Identifying the combinatorial control of signal-dependent transcription factors. PLoS computational biology 17 (6) (2021)
Jie Lyu, Jingyi Jessica Li, Jianzhong Su, Fanglue Peng, Yiling Elaine Chen, Xinzhou Ge, Weibo Xie
DORGE: Discovery of Oncogenes and tumoR suppressor genes using Genetic and Epigenetic features. Science advances 6 (46) (2020)
Wei Vivian Li, Shan Li, Xin Tong, Ling Deng, Hubing Shi, Jingyi Jessica Li
AIDE: annotation-assisted isoform discovery with high precision. Genome research 29 (12) (2019)
Yu Zhang, C Jake Harris, Qikun Liu, Wanlu Liu, Israel Ausin, Yanping Long, Lidan Xiao, Li Feng, Xu Chen, Yubin Xie, Xinyuan Chen, Lingyu Zhan, Suhua Feng, Jingyi Jessica Li, Haifeng Wang, Jixian Zhai, Steven E Jacobsen
Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 115 (5) (2018)
Wei Vivian Li, Jingyi Jessica Li
An accurate and robust imputation method scImpute for single-cell RNA-seq data. Nature communications 9 (1) (2018)
Xin Tong, Yang Feng, Jingyi Jessica Li
Neyman-Pearson classification algorithms and NP receiver operating characteristics. Science advances 4 (2) (2018)
Ruiqi Gao, Jingyi Jessica Li
Correspondence of D. melanogaster and C. elegans developmental stages revealed by alternative splicing characteristics of conserved exons. BMC genomics 18 (1) (2017)

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Publication Activity (10 Years)

Top Topics

Top Venues

Jingyi Jessica Li