Current Appointments & Affiliations
Assistant Professor of Biostatistics & Bioinformatics
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2020 - Present
Biostatistics & Bioinformatics, Division of Integrative Genomics,
Biostatistics & Bioinformatics
Recent Publications
Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis.
Journal Article Nat Methods · August 2024 Here we demonstrate that the large language model GPT-4 can accurately annotate cell types using marker gene information in single-cell RNA sequencing analysis. When evaluated across hundreds of tissue and cell types, GPT-4 generates cell type annotations ... Full text Link to item CiteGeneSegNet: a deep learning framework for cell segmentation by integrating gene expression and imaging.
Journal Article Genome Biol · October 19, 2023 When analyzing data from in situ RNA detection technologies, cell segmentation is an essential step in identifying cell boundaries, assigning RNA reads to cells, and studying the gene expression and morphological features of cells. We developed a deep-lear ... Full text Link to item CiteControlling taxa abundance improves metatranscriptomics differential analysis.
Journal Article BMC Microbiol · March 7, 2023 BACKGROUND: A common task in analyzing metatranscriptomics data is to identify microbial metabolic pathways with differential RNA abundances across multiple sample groups. With information from paired metagenomics data, some differential methods control fo ... Full text Link to item CiteRecent Grants
computational methods for spatial transcriptomics
ResearchPrincipal Investigator · Awarded by National Institutes of Health · 2024 - 2029Perinatal Per- and Polyfluoroalkyl Substances (PFAS) exposure and Immunotoxicity
ResearchInvestigator · Awarded by National Institute of Environmental Health Sciences · 2023 - 2028NSF Engineering Research Center for Precision Microbiome Engineering (PreMiEr)
ResearchInvestigator · Awarded by National Science Foundation · 2022 - 2027View All Grants