Our single-cell and spatial omics simulator scDesign3 is now online: nature.com/articles/s4158…
scDesign3 has two functionalities: (1) synthetic data simulation and (2) real data interpretation and modification 1/
Jingyi Jessica Li (李婧翌)
529 posts
Jingyi Jessica Li (李婧翌)
@jsb_ucla
Professor & Program Head, Biostatistics @FredHutch | Affiliate Professor @UWBiostat | Formerly @UCLA | Junction of Statistics & Biology; Rigor & Reproducibility
Joined March 2018
- Our review about zeroes in scRNA-seq data: clarify statistical and biological concepts; introduce 5 mechanisms of adding non-biological zeros for fair method benchmarking; compare 3 input data types: observed, imputed, and binarized counts: tinyurl.com/2p8rtfvd @GenomeBiology
- I feel so fortunate to start my career at UCLA in 2013 after my PhD at Berkeley. I owe many thanks my dept chair Hongquan and colleagues for supporting my promotion to full professor. I should thank my PhD advisors Peter Bickel and Haiyan Huang for their consistent support. 1/
- I’m honored to join Fred Hutch as Professor and Program Head of Biostatistics, and as the Donald and Janet K. Guthrie Endowed Chair in Statistics. Excited to be part of a deeply collaborative and scientifically vibrant community with a rich legacy of impact.
- Our single-cell RNA-seq and ATAC-seq read simulator scReadSim is now online at @NatureComms nature.com/articles/s4146… scReadSim mimics real data at read-sequence and read-count levels, and it provides ground truths: UMI counts for RNA-seq and open chromatin regions for ATAC. 1/
- Lesson learned from DE gene analysis on immunotherapy data: with large sample sizes, permutation analysis offers sanity check for FDR control & Wilcoxon rank-sum test works genomebiology.biomedcentral.com/articles/10.11… thanks to collaboration w/ @superweili lab for concretizing stats concepts for real
- Congratulations to Dr. Dongyuan Song for completing his PhD and joining UConn Health Dept. of Genetics and Genome Sciences as Assistant Professor! Dongyuan has been a cornerstone of our lab for the past 5 years. Wish him continued success in his independent career!@SongDongyuan
- We propose Clipper as a general statistical framework for controlling FDR in high-throughout genomics data analysis. Clipper does not require high-resolution p-values, thus saving null distribution derivation and many rounds of permutations:
- The order of actions matters in probability calculation: from the Monty Hall problem to the false discovery rate in high-throughput data analysis. Here is my correspondence piece @NatureBiotech :nature.com/articles/s4158… 1/
- I'm glad to share our method #scDEED to detect dubious 2D embeddings and optimize hyperparameters of #tSNE and #UMAP. Paper at@NatureComms nature.com/articles/s4146…… Thanks to my collaborator, Dr. Lucy Xia at HKUST, and my Ph.D. student, Christy Lee! 1/
- In molecular QTL mapping, hidden variables are inferred from the individual-by-molecular_feature matrix. Our paper benchmarked hidden variable inference methods including PCA, PEER, SVA, and HCP on 362 synthetic and 110 real data sets. PCA is the top. genomebiology.biomedcentral.com/articles/10.11… 1/
- I was surprised and then deeply honored to be recognized by the @iscb award committee. I couldn’t have had all the opportunities without the illuminating mentorship of my advisors, the support of my colleagues, and the talents and tremendous work of my students. Truly grateful…Jingyi Jessica Li is the 2023 recipient of the Overton Prize compmed.ucla.edu/news/jingyi-je… @jsb_ucla @uclastat @iscb
- It was my great honor to give the Overton keynote lecture about using synthetic null to enhance the rigor of data analysis #ISMBECCB2023 Talk slides: jsb.ucla.edu/sites/default/… Preprint of our new method ClusterDE: doi.org/10.1101/2023.0…
- The last piece of my Ph.D. work (10+ years back) is finally online in the Journal of the American Statistical Association. We generalized Pearson correlation squares and developed the K-lines clustering algorithm to find line clusters in a 2D scatterplot: tandfonline.com/doi/full/10.10…
