Author

Zilu Zhou

University of PennsylvaniaORCID 0000-0002-5554-8490Unclaimed ORCID profile · follow to get notified of new preprints

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Zilu Zhou1 paper

Biology Disciplines

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Bioinformatics· 5 Immunology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 5 Assay:scRNA-seq· 4 Research Focus:cell type annotation· 2 Approach:deep learning· 2 Research Focus:differential expression· 2 Organism:human· 2 Organism:mouse· 2 Research Focus:phylogenetics / evolution· 2

Frequent Co-Authors

Nancy Ruonan ZhangiD· 5 shared Chengzhong YeiD· 2 shared Jingshu WangiD· 2 shared Andy J. MinniD· 1 shared Bihui Xu· 1 shared Divyansh AgarwaliD· 1 shared Eugene Urrutia· 1 shared Gang HuiD· 1 shared

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2018-2025 · peak 2/yr

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10 top collaborators · 16 mutual co-author links

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5 shared papersBioinformatics

Nancy Ruonan ZhangORCID

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6 papers

Recent·Most cited

Hemin Inhibits the Activation of STING in Macrophages by Inducing HO-1, Promoting Endometriosis Development

Qinglin Mo, Ruoshui Chang, LY Zhang, Lei Huang, W Huang, Xiaoyu Liang, XL Xue, Qibo Zhang, Xiaorui Hou, Lin Yc, Zilu Zhou, Yongwen Chen, Wei Zhu, LW Hao, Shuai Wu

This study shows hemin induces HO-1 in macrophages, inhibiting STING pathway activation and promoting endometriosis development.

bioRxiv · Oct 25, 2025 · PreprintImmunology

Surface protein imputation from single cell transcriptomes by deep neural networks

Zilu Zhou, Chengzhong Ye, Jingshu Wang, Nancy Ruonan Zhang

The paper introduces a deep learning framework to impute surface protein abundances from scRNA-seq data using transfer learning.

Nature Communications · Jan 31, 2020Peer-reviewedBioinformatics

Genetic Heterogeneity Profiling by Single Cell RNA Sequencing

Zilu Zhou, Bihui Xu, Andy J. Minn, Nancy Ruonan Zhang

DENDRO profiles genetic heterogeneity in scRNA-seq data by detecting subclones, assigning cells to subclones, and reconstructing phylogenetic trees.

bioRxiv · Oct 17, 2019 · PreprintBioinformatics

Data Denoising with transfer learning in single-cell transcriptomics

Jingshu Wang, Divyansh Agarwal, Mo Chao Huang, Gang Hu, Zilu Zhou, Chengzhong Ye, Nancy Ruonan Zhang

This paper improves scRNA-seq data quality using transfer learning by combining a deep autoencoder with a Bayesian model to extract gene-gene relationships across diverse datasets.

Nature Methods · Aug 30, 2019Peer-reviewedBioinformatics

Integrative DNA copy number detection and genotyping from sequencing and array-based platforms

Zilu Zhou, Weixin Wang, Li‐San Wang, Nancy Ruonan Zhang

The paper introduces iCNV, a statistical framework for detecting and genotyping DNA copy number variations from sequencing and array data, improving sensitivity and accuracy.

Bioinformatics · Feb 22, 2018Peer-reviewedBioinformatics

Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny

Eugene Urrutia, Hao Chen, Zilu Zhou, Nancy Ruonan Zhang, Yuchao Jiang

The paper introduces a computational pipeline called MARATHON for copy number profiling and tumor phylogeny inference, addressing challenges in cancer genomics.

Bioinformatics · Feb 2, 2018Peer-reviewedBioinformatics