Scholars@Duke
Zhicheng Ji

Zhicheng Ji

Assistant Professor of Biostatistics & Bioinformatics
Biostatistics & Bioinformatics, Division of Integrative Genomics

Selected 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 Cite

GeneSegNet: 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 Cite

Controlling 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 Cite

Palo: spatially aware color palette optimization for single-cell and spatial data.

Journal Article Bioinformatics · July 11, 2022 SUMMARY: In the exploratory data analysis of single-cell or spatial genomic data, single-cells or spatial spots are often visualized using a two-dimensional plot where cell clusters or spot clusters are marked with different colors. With tens of clusters, ... Full text Link to item Cite

Global gene expression and chromatin accessibility of the peripheral nervous system in animal models of persistent pain.

Journal Article J Neuroinflammation · August 26, 2021 BACKGROUND: Efforts to understand genetic variability involved in an individual's susceptibility to chronic pain support a role for upstream regulation by epigenetic mechanisms. METHODS: To examine the transcriptomic and epigenetic basis of chronic pain th ... Full text Link to item Cite

Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers.

Journal Article Nature · August 2021 PD-1 blockade unleashes CD8 T cells1, including those specific for mutation-associated neoantigens (MANA), but factors in the tumour microenvironment can inhibit these T cell responses. Single-cell transcriptomics have revealed global T cell dysfunction pr ... Full text Link to item Cite

Discussion of "Exponential-family Embedding with Application to Cell Developmental Trajectories for Single-cell RNA-seq Data".

Journal Article J Am Stat Assoc · 2021 Exponential-family singular value decomposition (eSVD) is a new approach for embedding multivariate data into a lower-dimensional space. It provides an elegant dimension reduction framework with flexibility to handle one-parameter exponential family distri ... Full text Link to item Cite

Single cell transcriptomics of mouse kidney transplants reveals a myeloid cell pathway for transplant rejection.

Journal Article JCI Insight · October 15, 2020 Myeloid cells are increasingly recognized as major players in transplant rejection. Here, we used a murine kidney transplantation model and single cell transcriptomics to dissect the contribution of myeloid cell subsets and their potential signaling pathwa ... Full text Open Access Link to item Cite

Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data.

Journal Article Lancet Oncol · January 2017 BACKGROUND: Improvements to prognostic models in metastatic castration-resistant prostate cancer have the potential to augment clinical trial design and guide treatment strategies. In partnership with Project Data Sphere, a not-for-profit initiative allowi ... Full text Link to item Cite