Scholars@Duke
Yi Zhang

Yi Zhang

Assistant Professor of Neurosurgery
Neurosurgery, Neuro-Oncology
yi.zhang@duke.edu
203 Research Dr, MSRB1 199B, Durham, NC 27705
203 Research Dr, MSRB1 199B, Durham, NC 27705

Selected Publications

cellSTAAR: incorporating single-cell-sequencing-based functional data to boost power in rare variant association testing of noncoding regions.

Journal Article Nat Methods · December 31, 2025 Understanding how rare genetic variants influence complex traits remains a major challenge, particularly when these variants lie in noncoding regions of the genome. The effects of variants within candidate cis-regulatory elements (cCREs) often depend on th ... Full text Link to item Cite

scATAnno: Automated Cell Type Annotation for Single-cell ATAC Sequencing Data.

Journal Article Genomics Proteomics Bioinformatics · November 24, 2025 Recent advances in single-cell epigenomic techniques have created a growing demand for scATAC-seq analysis. One key analysis task is to determine cell type identity based on the epigenetic data. We introduce scATAnno, a python package designed to automatic ... Full text Link to item Cite

STHD: probabilistic cell typing of single spots in whole transcriptome spatial data with high definition.

Journal Article Genome Biol · July 18, 2025 Recent advances in spatial transcriptomics technologies have enabled gene expression profiling across the transcriptome in spots with subcellular resolution, but high sparsity and dimensionality present significant computational challenges. We present STHD ... Full text Link to item Cite

A community challenge to predict clinical outcomes after immune checkpoint blockade in non-small cell lung cancer.

Journal Article J Transl Med · February 21, 2024 BACKGROUND: Predictive biomarkers of immune checkpoint inhibitor (ICI) efficacy are currently lacking for non-small cell lung cancer (NSCLC). Here, we describe the results from the Anti-PD-1 Response Prediction DREAM Challenge, a crowdsourced initiative th ... Full text Link to item Cite

Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA.

Journal Article Nat Protoc · August 2023 RNA-sequencing (RNA-seq) has become an increasingly cost-effective technique for molecular profiling and immune characterization of tumors. In the past decade, many computational tools have been developed to characterize tumor immunity from gene expression ... Full text Link to item Cite

Leveraging epigenomes and three-dimensional genome organization for interpreting regulatory variation.

Journal Article PLoS Comput Biol · July 2023 Understanding the impact of regulatory variants on complex phenotypes is a significant challenge because the genes and pathways that are targeted by such variants and the cell type context in which regulatory variants operate are typically unknown. Cell-ty ... Full text Link to item Cite

MetaTiME integrates single-cell gene expression to characterize the meta-components of the tumor immune microenvironment.

Journal Article Nat Commun · May 6, 2023 Recent advances in single-cell RNA sequencing have shown heterogeneous cell types and gene expression states in the non-cancerous cells in tumors. The integration of multiple scRNA-seq datasets across tumors can indicate common cell types and states in the ... Full text Link to item Cite

Machine Learning Modeling of Protein-intrinsic Features Predicts Tractability of Targeted Protein Degradation.

Journal Article Genomics Proteomics Bioinformatics · October 2022 Targeted protein degradation (TPD) has rapidly emerged as a therapeutic modality to eliminate previously undruggable proteins by repurposing the cell's endogenous protein degradation machinery. However, the susceptibility of proteins for targeting by TPD a ... Full text Link to item Cite

Topical therapy for regression and melanoma prevention of congenital giant nevi.

Journal Article Cell · June 9, 2022 Giant congenital melanocytic nevi are NRAS-driven proliferations that may cover up to 80% of the body surface. Their most dangerous consequence is progression to melanoma. This risk often triggers preemptive extensive surgical excisions in childhood, produ ... Full text Link to item Cite

MYC drives aggressive prostate cancer by disrupting transcriptional pause release at androgen receptor targets.

Journal Article Nat Commun · May 13, 2022 c-MYC (MYC) is a major driver of prostate cancer tumorigenesis and progression. Although MYC is overexpressed in both early and metastatic disease and associated with poor survival, its impact on prostate transcriptional reprogramming remains elusive. We d ... Full text Link to item Cite

TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response.

Journal Article Nucleic Acids Res · January 7, 2022 Syngeneic mouse models are tumors derived from murine cancer cells engrafted on genetically identical mouse strains. They are widely used tools for studying tumor immunity and immunotherapy response in the context of a fully functional murine immune system ... Full text Link to item Cite

Checkpoint blockade-induced CD8+ T cell differentiation in head and neck cancer responders.

Journal Article J Immunother Cancer · January 2022 BACKGROUND: Immune checkpoint blockade (ICB) response in recurrent/metastatic head and neck squamous cell carcinoma (HNSCC) is limited to 15%-20% of patients and underpinnings of resistance remain undefined. METHODS: Starting with an anti-PD1 sensitive mur ... Full text Link to item Cite

In vivo CRISPR screens identify the E3 ligase Cop1 as a modulator of macrophage infiltration and cancer immunotherapy target.

Journal Article Cell · October 14, 2021 Despite remarkable clinical efficacy of immune checkpoint blockade (ICB) in cancer treatment, ICB benefits for triple-negative breast cancer (TNBC) remain limited. Through pooled in vivo CRISPR knockout (KO) screens in syngeneic TNBC mouse models, we found ... Full text Link to item Cite

Abstract 65: Therapeutically increasing MHC-I expression potentiates immune checkpoint blockade

Journal Article Cancer Research · July 1, 2021 AbstractImmune checkpoint blockade (ICB) therapy revolutionized cancer treatment, but many patients with impaired MHC-I expression remain refractory. Here, we combined FACS-based genome-wide CRISPR screens w ... Full text Cite

Molecular and cellular features of CTLA-4 blockade for relapsed myeloid malignancies after transplantation.

Journal Article Blood · June 10, 2021 Relapsed myeloid disease after allogeneic stem cell transplantation (HSCT) remains largely incurable. We previously demonstrated the potent activity of immune checkpoint blockade in this clinical setting with ipilimumab or nivolumab. To define the molecula ... Full text Link to item Cite

Therapeutically Increasing MHC-I Expression Potentiates Immune Checkpoint Blockade.

Journal Article Cancer Discov · June 2021 Immune checkpoint blockade (ICB) therapy revolutionized cancer treatment, but many patients with impaired MHC-I expression remain refractory. Here, we combined FACS-based genome-wide CRISPR screens with a data-mining approach to identify drugs that can upr ... Full text Link to item Cite

Neural network architecture search with AMBER

Journal Article Nature Machine Intelligence · May 1, 2021 Full text Cite

Functional analysis of low-grade glioma genetic variants predicts key target genes and transcription factors.

Journal Article Neuro Oncol · April 12, 2021 BACKGROUND: Large-scale genome-wide association studies (GWAS) have implicated thousands of germline genetic variants in modulating individuals' risk to various diseases, including cancer. At least 25 risk loci have been identified for low-grade gliomas (L ... Full text Link to item Cite

Local and Systemic Effects of Immune Checkpoint Blockade on Relapsed Myeloid Malignancies Following Allogeneic Hematopoietic Stem Cell Transplantation

Journal Article Blood · November 5, 2020 Relapse after allogeneic hematopoietic stem cell transplantation (HSCT) remains an unmet medical need. The ETCTN 9204 study evaluated in 71 study subjects if immune checkpoint blockade with anti-CTLA-4 (Ipilimumab (Ipi), n = 43) or anti-PD-1 (Nivol ... Full text Cite

Clonal tracing reveals diverse patterns of response to immune checkpoint blockade.

Journal Article Genome Biol · October 15, 2020 BACKGROUND: Immune checkpoint blockade (ICB) therapy has improved patient survival in a variety of cancers, but only a minority of cancer patients respond. Multiple studies have sought to identify general biomarkers of ICB response, but elucidating the mol ... Full text Link to item Cite

ABC-GWAS: Functional Annotation of Estrogen Receptor-Positive Breast Cancer Genetic Variants.

Journal Article Front Genet · 2020 Over the past decade, hundreds of genome-wide association studies (GWAS) have implicated genetic variants in various diseases, including cancer. However, only a few of these variants have been functionally characterized to date, mainly because the majority ... Full text Link to item Cite

SequencEnG: an interactive knowledge base of sequencing techniques.

Journal Article Bioinformatics · April 15, 2019 SUMMARY: Next-generation sequencing (NGS) techniques are revolutionizing biomedical research by providing powerful methods for generating genomic and epigenomic profiles. The rapid progress is posing an acute challenge to students and researchers to stay a ... Full text Link to item Cite

Abstract 1220: Integrative genomic analysis discovers the causative regulatory mechanisms of a breast cancer-associated genetic variant

Journal Article Cancer Research · July 1, 2018 AbstractGenome-wide association studies (GWAS) have identified genetic variants that may significantly modulate breast cancer susceptibility. However, the precise molecular mechanisms behind these associatio ... Full text Cite

Integrative Genomic Analysis Predicts Causative Cis-Regulatory Mechanisms of the Breast Cancer-Associated Genetic Variant rs4415084.

Journal Article Cancer Res · April 1, 2018 Previous genome-wide association studies (GWAS) have identified several common genetic variants that may significantly modulate cancer susceptibility. However, the precise molecular mechanisms behind these associations remain largely unknown; it is often n ... Full text Link to item Cite

ClusterEnG: an interactive educational web resource for clustering and visualizing high-dimensional data.

Journal Article PeerJ Comput Sci · 2018 SUMMARY: Clustering is one of the most common techniques used in data analysis to discover hidden structures by grouping together data points that are similar in some measure into clusters. Although there are many programs available for performing clusteri ... Full text Link to item Cite