Author

Di Zhang

Yale University

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Same name, identified by ORCID

Biology Disciplines

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Microbiology· 4 Bioengineering· 1 Bioinformatics· 1 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 5 Research Focus:cell type annotation· 4 Organism:human· 3 Organism:mouse· 3 Assay:spatial transcriptomics· 3 Research Focus:host-pathogen & immune response· 2 Assay:proteomics· 2 Assay:ATAC-seq· 1

Frequent Co-Authors

Rong FaniD· 2 shared Alex Edwards· 1 shared Arnar GeirssoniD· 1 shared Chu Qi· 1 shared David GateiD· 1 shared Deguang Song· 1 shared Dejiang WangiD· 1 shared Dongqiang WangiD· 1 shared

Activity by Year

2016-2026 · peak 5/yr

Co-Author Collaboration Network

10 top collaborators · 9 mutual co-author links

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2 shared papersBioinformatics

Rong FanORCID

Mutual co-authors in cluster

Author profile →

7 papers

Recent·Most cited

Spatially resolved host-fungal transcriptomics profiling by fungal-DBiT

Xiaohui Yu, Fu Qiang Gao, Deguang Song, Gaocai Li, Dejiang Wang, Shenjie Wang, Xiangjun Di, Shujie He, Liyun Lin, Junyi Xu, Di Zhang, Yu Jin, Jing Du, Noah W. Palm, Liu Yang

This study introduces fungal-DBiT, a spatial transcriptomic platform that maps host and fungal RNAs in tissue sections, revealing spatial heterogeneity in fungal localization and host responses during infection and under physiological conditions.

bioRxiv · Oct 19, 2026 · PreprintMicrobiology

A suture-specific oocyst wall protein COWP4 is essential for excystation and infectivity, while COWP6 links wall architecture to host interaction in Cryptosporidium parvum

Xiaodong Wu, Jigang Yin, Wei Qi, Peng Jiang, Ying Zhang, Di Zhang, Dongqiang Wang, Guan Zhu

This paper identifies COWP4 and COWP6 as distinct oocyst wall proteins in Cryptosporidium parvum, showing COWP4 is essential for suture formation and infectivity while COWP6 links wall structure to host interaction.

bioRxiv · May 6, 2026 · PreprintMicrobiology

Mosaic integration of spatial multi-omics with SpaMosaic

Xuhua Yan, Kok Siong Ang, Lynn van Olst, Alex Edwards, Thomas Watson, Ruiqing Zheng, Di Zhang, Rong Fan, Min Li, David Gate, Jinmiao Chen

SpaMosaic integrates spatial multi-omics data using contrastive learning and graph neural networks, improving spatial domain identification and missing modality imputation across diverse datasets.

Nature Genetics · Apr 24, 2026Peer-reviewedBioinformatics

Cross-Species Multi-Omics Profiling Identifies Conserved Activated Valvular Interstitial Cell Population Driving Myxomatous Mitral Valve Degeneration

Fu Gao, Ian Mason, Mingze Dong, Yue Lu, Di Zhang, Xing Lou, Irbaz Hameed, Mingyu Yang, Mei Zhong, Marcus Krane, Giovanni Ferrari, George Tellides, Yang Liu, Rong Fan, Arnar Geirsson

The paper identifies a conserved activated valvular interstitial cell population across species and disease types that drives myxomatous mitral valve degeneration.

bioRxiv · Mar 25, 2026 · PreprintMolecular Biology

Molecular basis of enfumafungin inhibition and resistance in Candida glabrata β-1,3-Glucan synthase FKS1

Ping Yang, Chu Qi, Shuchang Du, Xinlin Hu, Zhengkang Hua, Yizheng Yang, Di Zhang, Yan Ke, Mingjie Zhang, Xiaotian Liu, Tao Chen, Min Zhang, Hongjun Yu

This study determines the molecular mechanism of enfumafungin inhibition and resistance in Candida glabrata FKS1 using cryo-EM and functional analyses.

bioRxiv · Feb 8, 2026 · PreprintMicrobiology

The two-component nuclease-active KELShedu system confers broad antiphage activity via abortive infection

Hengwei Zhang, Jiajia You, Hanwen Zhou, Zan Zhang, Hongxuan Wu, Di Zhang, Xuewei Pan, Weiguo Zhang, Xian Zhang, Zhiming Rao

The paper characterizes the KELShedu system in E. coli, showing it confers antiphage activity through abortive infection by degrading DNA when NTP levels drop during phage invasion.

Science Advances · Oct 31, 2025Peer-reviewedMicrobiology

Live Cell Partial Wave Spectroscopic microscopy: Label-free Imaging of the Native, Living Cellular Nanoarchitecture

Luay M Almassalha, Greta Bauer, John Chandler, Scott Gladstein, Lusik Cherkezyan, Yolanda Stypula-Cyrus, Sam Weinberg, Di Zhang, Peder Thusgaard Ruhoff, Hemant Roy, Hariharan Subramanian, Navdeep Chandel, Igal Szleifer, Vadim Backman

This paper develops live cell Partial Wave Spectroscopic (PWS) microscopy to study chromatin nano-architecture dynamics in real-time, showing changes in chromatin structure due to DNA damage and linking it to mitochondrial membrane potential.

bioRxiv · Jul 2, 2016Bioengineering