Jingyi Jessica Li*
8951 Math Sciences Bldg.
Member, Bioinformatics GPB Home Area, Genetics & Genomics GPB Home Area
My research is at the interface between statistics and biology. My primary research interest lies in developing new statistical methods for understanding biological questions, especially those related to large-scale genomic and transcriptomic data. The specific topics I have examined include
Bioinformatics / Statistical Genomics:
Statistical methods for analyzing next-generation bulk and single-cell RNA sequencing data
Using statistics to quantitate the Central Dogma, a fundamental principle in molecular biology
Comparative genomics: developing novel statistical methods to investigate conserved or divergent biological phenomena in different tissue and cell types across multiple species
Novel statistical methods for imputing missing data or extracting hidden information from various types of genomics data
Identification of gene-gene co-expression and protein-DNA and protein-RNA interactions using diverse genomic data
Measures of association
Neyman-Pearson classification that controls the prioritized type of error in binary classification
High-dimensional linear model inference and variable selection
Community detection in a bipartite network with node covariates
P-value free control of false discovery rates
Labeling ambiguity issue in multi-class classification
Jingyi Jessica Li is a Professor in the Department of Statistics (primary) and the Departments of Biostatistics, Computational Medicine, and Human Genetics (secondary) at University of California, Los Angeles (UCLA). She is also a faculty member in the Interdepartmental Ph.D. Program in Bioinformatics. Prior to joining UCLA in 2013, Jessica obtained her Ph.D. degree from the Interdepartmental Group in Biostatistics at University of California, Berkeley, where she worked with Profs. Peter J. Bickel and Haiyan Huang. Jessica received her B.S. (summa cum laude) from the Department of Biological Sciences and Technology at Tsinghua University, China in 2007. Jessica and her students focus on developing statistical and computational methods motivated by important questions in biomedical sciences and abundant information in big genomic and health related data. On the statistical methodology side, her research interests include association measures, asymmetric classification, and high-dimensional variable selection. On the biomedical application side, her research interests include bulk and single-cell RNA sequencing, comparative genomics, and information flow in the central dogma. Jessica is the recipient of the Hellman Fellowship (2015), the PhRMA Foundation Research Starter Grant in Informatics (2017), the Alfred P. Sloan Research Fellowship (2018), the Johnson & Johnson WiSTEM2D Math Scholar Award (2018), the NSF CAREER Award (2019), the UCLA DGSOM Keck W. M. Keck Foundation Junior Faculty Award (2020), and the MIT Technology Review 35 Innovators Under 35 China (2020).
A selected list of publications:
- Xi Nan Miles, Li Jingyi Jessica Benchmarking Computational Doublet-Detection Methods for Single-Cell RNA Sequencing Data Cell systems, 2021; 12(2): 176-194.e6.
- Sun Yidan Eden, Zhou Heather J, Li Jingyi Jessica Bipartite tight spectral clustering (BiTSC) algorithm for identifying conserved gene co-clusters in two species Bioinformatics (Oxford, England), 2021; 37(9): 1225-1233.
- Song Dongyuan, Li Jingyi Jessica PseudotimeDE: inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing data Genome biology, 2021; 22(1): 124.
- Jiang Ruochen, Li Wei Vivian, Li Jingyi Jessica mbImpute: an accurate and robust imputation method for microbiome data Genome biology, 2021; 22(1): 192.
- Sun Tianyi, Song Dongyuan, Li Wei Vivian, Li Jingyi Jessica scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured Genome biology, 2021; 22(1): 163.
- Song Dongyuan, Li Kexin, Hemminger Zachary, Wollman Roy, Li Jingyi Jessica scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling Bioinformatics (Oxford, England), 2021; 37(Suppl_1): i358-i366.
- Lyu Jie, Li Jingyi Jessica, Su Jianzhong, Peng Fanglue, Chen Yiling Elaine, Ge Xinzhou, Li Wei DORGE: Discovery of Oncogenes and tumoR suppressor genes using Genetic and Epigenetic features Science advances, 2020; 6(46): 176-194.e6.
- Li Jingyi Jessica, Tong Xin Statistical Hypothesis Testing versus Machine Learning Binary Classification: Distinctions and Guidelines Patterns (New York, N.Y.), 2020; 1(7): 100115.
- Li Wei Vivian, Li Jingyi Jessica A statistical simulator scDesign for rational scRNA-seq experimental design Bioinformatics (Oxford, England), 2019; 35(14): i41-i50.
- Li Wei Vivian, Li Shan, Tong Xin, Deng Ling, Shi Hubing, Li Jingyi Jessica AIDE: annotation-assisted isoform discovery with high precision Genome research, 2019; 29(12): 2056-2072.
- Ge Xinzhou, Zhang Haowen, Xie Lingjue, Li Wei Vivian, Kwon Soo Bin, Li Jingyi Jessica EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequences Nucleic acids research, 2019; 47(13): e77.
- Li Jingyi Jessica, Chew Guo-Liang, Biggin Mark Douglas Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Genome biology, 2019; 20(1): 162.
- Duong Dat, Ahmad Wasi Uddin, Eskin Eleazar, Chang Kai-Wei, Li Jingyi Jessica Word and Sentence Embedding Tools to Measure Semantic Similarity of Gene Ontology Terms by Their Definitions Journal of computational biology : a journal of computational molecular cell biology, 2019; 26(1): 38-52.
- Li Wei Vivian, Li Jingyi Jessica An accurate and robust imputation method scImpute for single-cell RNA-seq data Nature communications, 2018; 9(1): 997.
- Li Wei Vivian, Zhao Anqi, Zhang Shihua, Li Jingyi Jessica MSIQ: JOINT MODELING OF MULTIPLE RNA-SEQ SAMPLES FOR ACCURATE ISOFORM QUANTIFICATION The annals of applied statistics, 2018; 12(1): 510-539.
- Li Wei Vivian, Li Jingyi Jessica Modeling and analysis of RNA-seq data: a review from a statistical perspective Quantitative biology (Beijing, China), 2018; 6(3): 195-209.
- Tong Xin, Feng Yang, Li Jingyi Jessica Neyman-Pearson classification algorithms and NP receiver operating characteristics Science advances, 2018; 4(2): eaao1659.
- Burke Jordan E, Longhurst Adam D, Merkurjev Daria, Sales-Lee Jade, Rao Beiduo, Moresco James J, Yates John R, Li Jingyi Jessica, Madhani Hiten D Spliceosome Profiling Visualizes Operations of a Dynamic RNP at Nucleotide Resolution Cell, 2018; 173(4): 1014-1030.e17.
- Gao Ruiqi, Li Jingyi Jessica Correspondence of D. melanogaster and C. elegans developmental stages revealed by alternative splicing characteristics of conserved exons BMC genomics, 2017; 18(1): 234.
- Clifton Sara M, Kang Chaeryon, Li Jingyi Jessica, Long Qi, Shah Nirmish, Abrams Daniel M Hybrid Statistical and Mechanistic Mathematical Model Guides Mobile Health Intervention for Chronic Pain Journal of computational biology : a journal of computational molecular cell biology, 2017; 24(7): 675-688.
- Yang Yang, Yang Yu-Cheng T, Yuan Jiapei, Lu Zhi John, Li Jingyi Jessica Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell states Nucleic acids research, 2017; 45(4): 1657-1672.
- Li Jingyi Jessica, Chew Guo-Liang, Biggin Mark D Quantitating translational control: mRNA abundance-dependent and independent contributions and the mRNA sequences that specify them Nucleic acids research, 2017; 45(20): 11821-11836.
- Li Wei Vivian, Chen Yiling, Li Jingyi Jessica TROM: A Testing-Based Method for Finding Transcriptomic Similarity of Biological Samples Statistics in biosciences, 2017; 9(1): 105-136.
- Li Wei Vivian, Razaee Zahra S, Li Jingyi Jessica Epigenome overlap measure (EPOM) for comparing tissue/cell types based on chromatin states BMC genomics, 2016; 17 Suppl 1(4): 10.
- Ye Yuting, Li Jingyi Jessica NMFP: a non-negative matrix factorization based preselection method to increase accuracy of identifying mRNA isoforms from RNA-seq data BMC genomics, 2016; 17 Suppl 1(4): 11.
- Li Jingyi Jessica, Biggin Mark D Gene expression. Statistics requantitates the central dogma Science (New York, N.Y.), 2015; 347(6226): 1066-7.
- Boyle Alan P, Araya Carlos L, Brdlik Cathleen, Cayting Philip, Cheng Chao, Cheng Yong, Gardner Kathryn, Hillier LaDeana W, Janette Judith, Jiang Lixia, Kasper Dionna, Kawli Trupti, Kheradpour Pouya, Kundaje Anshul, Li Jingyi Jessica, Ma Lijia, Niu Wei, Rehm E Jay, Rozowsky Joel, Slattery Matthew, Spokony Rebecca, Terrell Robert, Vafeados Dionne, Wang Daifeng, Weisdepp Peter, Wu Yi-Chieh, Xie Dan, Yan Koon-Kiu, Feingold Elise A, Good Peter J, Pazin Michael J, Huang Haiyan, Bickel Peter J, Brenner Steven E, Reinke Valerie, Waterston Robert H, Gerstein Mark, White Kevin P, Kellis Manolis, Snyder Michael Comparative analysis of regulatory information and circuits across distant species Nature, 2014; 512(7515): 453-6.
- Gerstein Mark B*, Rozowsky Joel*, Yan Koon-Kiu*, Wang Daifeng*, Cheng Chao*, Brown James B*, Davis Carrie A*, Hillier LaDeana*, Sisu Cristina*, Li Jingyi Jessica*, Pei Baikang*, Harmanci Arif O*, Duff Michael O*, Djebali Sarah* (joint first authors), Alexander Roger P, Alver Burak H, Auerbach Raymond, Bell Kimberly, Bickel Peter J, Boeck Max E, Boley Nathan P, Booth Benjamin W, Cherbas Lucy, Cherbas Peter, Di Chao, Dobin Alex, Drenkow Jorg, Ewing Brent, Fang Gang, Fastuca Megan, Feingold Elise A, Frankish Adam, Gao Guanjun, Good Peter J, GuigÃ³ Roderic, Hammonds Ann, Harrow Jen, Hoskins Roger A, Howald CÃ©dric, Hu Long, Huang Haiyan, Hubbard Tim J P, Huynh Chau, Jha Sonali, Kasper Dionna, Kato Masaomi, Kaufman Thomas C, Kitchen Robert R, Ladewig Erik, Lagarde Julien, Lai Eric, Leng Jing, Lu Zhi, MacCoss Michael, May Gemma, McWhirter Rebecca, Merrihew Gennifer, Miller David M, Mortazavi Ali, Murad Rabi, Oliver Brian, Olson Sara, Park Peter J, Pazin Michael J, Perrimon Norbert, Pervouchine Dmitri, Reinke Valerie, Reymond Alexandre, Robinson Garrett, Samsonova Anastasia, Saunders Gary I, Schlesinger Felix, Sethi Anurag, Slack Frank J, Spencer William C, Stoiber Marcus H, Strasbourger Pnina, Tanzer Andrea, Thompson Owen A, Wan Kenneth H, Wang Guilin, Wang Huaien, Watkins Kathie L, Wen Jiayu, Wen Kejia, Xue Chenghai, Yang Li, Yip Kevin, Zaleski Chris, Zhang Yan, Zheng Henry, Brenner Steven E, Graveley Brenton R, Celniker Susan E, Gingeras Thomas R, Waterston Robert Comparative analysis of the transcriptome across distant species Nature, 2014; 512(7515): 445-8.
- Li Jingyi Jessica, Huang Haiyan, Bickel Peter J, Brenner Steven E Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data Genome research, 2014; 24(7): 1086-101.
- Li Jingyi Jessica, Bickel Peter J, Biggin Mark D System wide analyses have underestimated protein abundances and the importance of transcription in mammals PeerJ, 2014; 2(1): e270.
- The ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome Nature, 2012; 489(7414): 57-74.
- Gao Qinghui, Ho Christine, Jia Yingmin, Li Jingyi Jessica, Huang Haiyan Biclustering of linear patterns in gene expression data Journal of computational biology : a journal of computational molecular cell biology, 2012; 19(6): 619-31.
- Fisher William W, Li Jingyi Jessica, Hammonds Ann S, Brown James B, Pfeiffer Barret D, Weiszmann Richard, MacArthur Stewart, Thomas Sean, Stamatoyannopoulos John A, Eisen Michael B, Bickel Peter J, Biggin Mark D, Celniker Susan E DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila Proceedings of the National Academy of Sciences of the United States of America, 2012; 109(52): 21330-5.
- Li Jingyi Jessica, Jiang Ci-Ren, Brown James B, Huang Haiyan, Bickel Peter J Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation Proceedings of the National Academy of Sciences of the United States of America, 2011; 108(50): 19867-72.
- MacArthur Stewart*, Li Xiao-Yong*, Li Jingyi* (joint first authors), Brown James B, Chu Hou Cheng, Zeng Lucy, Grondona Brandi P, Hechmer Aaron, Simirenko Lisa, KerÃ¤nen Soile V E, Knowles David W, Stapleton Mark, Bickel Peter, Biggin Mark D, Eisen Michael B Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions Genome biology, 2009; 10(7): R80.