J. Li

发表

System wide analyses have underestimated protein abundances and the importance of transcription in mammals

P. Bickel, M. Biggin, J. Li, 2012, PeerJ.

DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila

James B. Brown, P. Bickel, J. Stamatoyannopoulos, 2012, Proceedings of the National Academy of Sciences.

Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data

Steven E Brenner, Haiyan Huang, Peter J Bickel, 2014, Genome research.

Comparative Analysis of the Transcriptome across Distant Species

Peter J. Bickel, Raymond K. Auerbach, Peter J. Park, 2014, Nature.

Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation

James B. Brown, P. Bickel, Haiyan Huang, 2011, Proceedings of the National Academy of Sciences.

Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis

J. Li, S. Jacobsen, Li Feng, 2018, Proceedings of the National Academy of Sciences.

Spliceosome Profiling Visualizes Operations of a Dynamic RNP at Nucleotide Resolution

J. Yates, H. Madhani, J. Li, 2018, Cell.

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

Haiyan Huang, Lexin Li, J. Li, 2021, Statistical science : a review journal of the Institute of Mathematical Statistics.

AIDE: annotation-assisted isoform discovery with high precision

J. Li, Xin Tong, Hubing Shi, 2019, Genome research.

Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell states

Zhi John Lu, Yang Yang, Yu-Cheng T. Yang, 2016, Nucleic acids research.

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

J. Li, Jianzhong Su, Jie Lyu, 2020, Science Advances.

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

J. Li, Jianzhong Su, Jie Lyu, 2020, Science Advances.

TROM: A Testing-Based Method for Finding Transcriptomic Similarity of Biological Samples

J. Li, W. Li, Y. Chen, 2016, Statistics in biosciences.

Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes

M. Biggin, J. Li, G. Chew, 2019, bioRxiv.

Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes

M. Biggin, J. Li, G. Chew, 2019, Genome Biology.

Quantitating translational control: mRNA abundance-dependent and independent contributions and the mRNA sequences that specify them

M. Biggin, J. Li, G. Chew, 2017, bioRxiv.

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

J. Li, Ruochen Jiang, Tianyi Sun, 2020, Genome Biology.

EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequences

Soo Bin Kwon, J. Li, Haowen Zhang, 2019, bioRxiv.

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

J. Li, N. Xi, 2020, Cell systems.

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

J. Li, J. Issa, Xi Chen, 2020, bioRxiv.

scReadSim: a single-cell multi-omics read simulator

J. Li, Guanao Yan, 2022 .

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

J. Li, Lanlan Shen, Jiejun Shi, 2021 .

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

D. Bartel, J. Li, Timothy J. Eisen, 2022, RNA.

PCA outperforms popular hidden variable inference methods for molecular QTL mapping

J. Li, Lei Li, Wei Li, 2022, bioRxiv.

Spliceosome profiling visualizes the operations of a dynamic RNP in vivo at nucleotide resolution

J. Yates, H. Madhani, J. Li, 2017, bioRxiv.

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

J. Li, Dongyuan Song, Tianyang Liu, 2022, bioRxiv.

Resource Spliceosome Profiling Visualizes Operations of a Dynamic RNP at Nucleotide Resolution Graphical

J. Yates, H. Madhani, J. Li, 2018 .

TRANSCRIPTOME ANALYSIS USING NEXT-GENERATION SEQUENCING

Xuegong Zhang, Haiyan Huang, J. Li, 2015 .

CAMO: A molecular congruence analysis framework for evaluating model organisms

J. Li, Xiangrui Zeng, Tianzhou Ma, 2021, bioRxiv.

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

Jingyi Jessica Li, Dongyuan Song, J. Li, 2020, Genome Biology.

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

J. Li, Ruochen Jiang, Tianyi Sun, 2022, bioRxiv.

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

J. Li, W. Li, Tianyi Sun, 2021, Genome Biology.

APIR: a universal FDR-control framework for boosting peptide identification power by aggregating multiple proteomics database search algorithms

Leo D. Wang, S. Ficarro, J. Li, 2021 .

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

R. Wollman, J. Li, Dongyuan Song, 2021, bioRxiv.

A statistical simulator scDesign for rational scRNA-seq experimental design

Jingyi Jessica Li, Wei Vivian Li, J. Li, 2018, bioRxiv.

scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data

J. Li, Wanlu Liu, Chaochen Wang, 2022, bioRxiv.

System Wide Analyses have Underestimated Protein Abundances and Transcriptional Importance in Animals

P. Bickel, M. Biggin, J. Li, 2012 .

Comparative analysis of regulatory information and circuits across distant species

Peter J. Bickel, Mark Gerstein, Philip Cayting, 2014, Nature.

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

J. Li, W. Li, Tianyi Sun, 2021, Genome Biology.

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

Wei Vivian Li, Jingyi Jessica Li, Tianyi Sun, 2020, bioRxiv.

An accurate and robust imputation method scImpute for single-cell RNA-seq data

Wei Vivian Li, Jingyi Jessica Li, J. Li, 2018, Nature Communications.

mbImpute: an accurate and robust imputation method for microbiome data

Wei Vivian Li, Jingyi Jessica Li, Ruochen Jiang, 2020, Genome Biology.

Biclustering of Linear Patterns In Gene Expression Data

Yingmin Jia, Haiyan Huang, Christine Ho, 2012, J. Comput. Biol..

Simulating Single-Cell Gene Expression Count Data with Preserved Gene Correlations by scDesign2

J. Li, W. Li, Tianyi Sun, 2022, J. Comput. Biol..

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

J. Li, Wei Li, Fanglue Peng, 2022, Genome Biology.

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

J. Li, Ruochen Jiang, Tianyi Sun, 2022, Genome Biology.

Quantitating translational control: mRNA abundance-dependent and independent contributions and the mRNA sequences that specify them

M. Biggin, J. Li, G. Chew, 2017, bioRxiv.

Statistics requantitates the central dogma

Mark D. Biggin, Jingyi Jessica Li, M. Biggin, 2015, Science.

Modeling and analysis of RNA-seq data: a review from a statistical perspective

Wei Vivian Li, Jingyi Jessica Li, J. Li, 2018, Quantitative Biology.

Comprehensive mapping of mammalian transcriptomes identifies conserved genes associated with different cell differentiation states

Yu-Cheng T. Yang, J. Li, Xiaohua Shen, 2015, bioRxiv.

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

Jingyi Jessica Li, Dongyuan Song, Wei Li, 2020, Genome Biology.

Correspondence of D. melanogaster and C. elegans developmental stages revealed by alternative splicing characteristics of conserved exons

J. Li, Ruiqi Gao, 2017, BMC Genomics.

Epigenome overlap measure (EPOM) for comparing tissue/cell types based on chromatin states

Wei Vivian Li, Zahra S. Razaee, Jingyi Jessica Li, 2016, BMC Genomics.

RAD: a web application to identify region associated differentially expressed genes

William A. Pastor, J. Li, Wanlu Liu, 2020, bioRxiv.

Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis

K. Au, Xiu-Jie Wang, J. Li, 2017, F1000Research.

Integrin-Src-YAP1 signaling mediates the melanoma acquired resistance to MAPK and PI3K/mTOR dual targeted therapy

M. Zhang, J. Li, Jiang Lan, 2020, Molecular Biomedicine.

Title Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell states Permalink

Yu-Cheng T. Yang, Z. Lu, J. Li, 2016 .

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

J. Li, N. Xi, 2021, STAR protocols.

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

J. Li, J. Issa, Xi Chen, 2021, Nature Communications.

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

J. Li, Guanao Yan, 2023, bioRxiv.

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

W. Wong, J. Li, Dongyuan Song, 2021, bioRxiv.

Bipartite Tight Spectral Clustering (BiTSC) Algorithm for Identifying Conserved Gene Co-clusters in Two Species

Jingyi Jessica Li, Yidan Sun, Heather Zhou, 2019, bioRxiv.

Wilcoxon rank-sum test still outperforms dearseq after accounting for the normalization impact in semi-synthetic RNA-seq data simulation

J. Li, Wei Li, Fanglue Peng, 2022, bioRxiv.

Identifying the combinatorial control of signal-dependent transcription factors

Diane Lefaudeux, Ning Wang, Jingyi Jessica Li, 2021, PLoS Comput. Biol..

Annotating Gene Ontology terms for protein sequences with the Transformer model

Eleazar Eskin, Kai-Wei Chang, Jingyi Jessica Li, 2020, bioRxiv.

A quantitative proteomic analysis of cellular responses to high glucose media in Chinese hamster ovary cells

J. Li, Sangwon Cha, B. Karger, 2015, Biotechnology progress.

Cell-type-specificity of isoform diversity in the developing human neocortex informs mechanisms of neurodevelopmental disorders

J. Li, B. Pasaniuc, Kangcheng Hou, 2023, bioRxiv.

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

J. Li, L. Ghoda, S. Fernandes, 2023, Blood cancer discovery.

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

Leo D. Wang, J. Li, A. Manousopoulou, 2021, Genome Biology.

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

J. Li, Dongyuan Song, Tianyang Liu, 2023, bioRxiv.

Hybrid Statistical and Mechanistic Mathematical Model Guides Mobile Health Intervention for Chronic Pain

Qi Long, Chaeryon Kang, Jingyi Jessica Li, 2017, J. Comput. Biol..

DreamAI: algorithm for the imputation of proteomics data

Thomas Yu, Shrabanti Chowdhury, Jun Zhu, 2020, bioRxiv.

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

J. Li, Dongyuan Song, Guanao Yan, 2023, bioRxiv.

scSampler: fast diversity-preserving subsampling of large-scale single-cell transcriptomic data

J. Li, Dongyuan Song, N. Xi, 2022, bioRxiv.

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, J. Li, 2016, BMC Genomics.

scImpute: accurate and robust imputation for single cell RNA-seq data

Wei Vivian Li, Jingyi Jessica Li, J. Li, 2017, bioRxiv.

Issues arising from benchmarking single-cell RNA sequencing imputation methods.

Wei Vivian Li, Jingyi Jessica Li, J. Li, 2019, 1908.07084.

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

J. Li, Xinzhou Ge, Dongyuan Song, 2023, bioRxiv.

A novel Word2vec based tool to estimate semantic similarity of genes by using Gene Ontology terms

Eleazar Eskin, Jingyi Jessica Li, Dat Duong, 2017 .

AIDE: annotation-assisted isoform discovery and abundance estimation with high precision

Wei Vivian Li, Jingyi Jessica Li, Xin Tong, 2018, bioRxiv.

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

J. Li, W. Li, Tianyi Sun, 2021, Genome Biology.

A new bioinformatics tool to recover missing gene expression in single-cell RNA sequencing data

J. Li, 2020, Journal of molecular cell biology.

Zeros in scRNA-seq data: good or bad? How to embrace or tackle zeros in scRNA-seq data analysis?

J. Li, Ruochen Jiang, Tianyi Sun, 2020 .

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

J. Li, Dongyuan Song, 2021, Genome Biology.

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

J. Li, W. Li, Fanglue Peng, 2021, bioRxiv.

Word and sentence embedding tools to measure semantic similarity of Gene Ontology terms by their definitions

Eleazar Eskin, Kai-Wei Chang, Jingyi Jessica Li, 2017, bioRxiv.

Transcriptomic congruence analysis for evaluating model organisms

Adrian V. Lee, G. Tseng, J. Li, 2023, Proceedings of the National Academy of Sciences of the United States of America.

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

J. Li, Tianyi Sun, Dongyuan Song, 2023, Nature biotechnology.

Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation

James B. Brown, P. Bickel, Haiyan Huang, 2011, Proceedings of the National Academy of Sciences.

Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms

J. Li, B. Pasaniuc, Kangcheng Hou, 2023, bioRxiv.

TROM: A Testing-Based Method for Finding Transcriptomic Similarity of Biological Samples

J. Li, W. Li, Y. Chen, 2017, Statistics in Biosciences.

scImpute: accurate and robust imputation for single cell RNA-seq data

J. Li, W. Li, 2017, bioRxiv.

Modeling and analysis of RNA-seq data: a review from a statistical perspective

J. Li, W. Li, 2018, Quantitative Biology.

Dissecting gene expression heterogeneity: generalized Pearson correlation squares and the K-lines clustering algorithm

J. Li, Heather J. Zhou, Peter J. Bickel, 2024, Journal of the American Statistical Association.

A statistical simulator scDesign for rational scRNA-seq experimental design

J. Li, W. Li, 2018, bioRxiv.

Spatial Single-Cell Mapping of Transcriptional Differences Across Genetic Backgrounds in Mouse Brains

J. Li, Dongyuan Song, Zachary Hemminger, 2024, bioRxiv.