Publications

Selected publications and preprints.

For a full publication list, see Google Scholar.

2026

  1. Spatial Kernel Restricted Canonical Correlation Analysis: Population Targets, Identifiability, and Stability
    Zhen Miao, Yilong Qu, and Nancy R. Zhang
    arXiv (preprint), 2026
    HTML PDF
  2. Dissecting the coordinated progression of cell states in spatial transcriptomics with CoPro
    Zhen Miao, Yilong Qu, Sijia Huang, Linshan Laux, Samuel Peters, and 6 more authors
    bioRxiv (preprint), 2026
    HTML Code

2025

  1. Controlling nephron precursor differentiation to generate proximal-biased kidney organoids with emerging maturity
    Jack Schnell, Zhen Miao, MaryAnne Achieng, Connor C. Fausto, Kari Koppitch, and 11 more authors
    Nature Communications, 2025
    HTML PDF
  2. PACS_illustration.svg
    Depth-corrected multi-factor dissection of chromatin accessibility for scATAC-seq data with PACS
    Zhen Miao, Jianqiao Wang, Kernyu Park, Da Kuang, and Junhyong Kim
    Nature Communications, 2025
    HTML PDF Code

2024

  1. Modified C-type natriuretic peptide normalizes tumor vasculature, reinvigorates antitumor immunity, and improves solid tumor therapies
    Zhen Lu, Ioannis Verginadis, Motofumi Kumazoe, Gerardo M. Castillo, Yao Yao, and 27 more authors
    Science Translational Medicine, 2024
    HTML
  2. F1.large.jpg
    Uniform quantification of single-nucleus ATAC-seq data with Paired-Insertion Counting (PIC) and a model-based insertion rate estimator
    Zhen Miao, and Junhyong Kim
    Nature Methods, 2024
    HTML PDF Code

2023

  1. Direct androgen receptor control of sexually dimorphic gene expression in the mammalian kidney
    Lingyun Xiong, Jing Liu, Seung Yub Han, Kari Koppitch, Jin-Jin Guo, and 8 more authors
    Developmental Cell, 2023

2022

  1. Transient expansion and myofibroblast conversion of adipogenic lineage precursors mediate bone marrow repair after radiation
    Leilei Zhong, Lutian Yao, Nicholas Holdreith, Wei Yu, Tao Gui, and 7 more authors
    JCI insight, 2022
  2. Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease
    Hongbo Liu, Tomohito Doke, Dong Guo, Xin Sheng, Ziyuan Ma, and 7 more authors
    Nature Genetics, 2022
  3. ATF3 and CH25H regulate effector trogocytosis and anti-tumor activities of endogenous and immunotherapeutic cytotoxic T lymphocytes
    Zhen Lu, Noreen McBrearty, Jinyun Chen, Vivek S Tomar, Hongru Zhang, and 7 more authors
    Cell Metabolism, 2022

2021

  1. Single-cell transcriptomic analysis of mIHC images via antigen mapping
    Kiya W Govek, Emma C Troisi, Zhen Miao, Rachael G Aubin, Steven Woodhouse, and 1 more author
    Science Advances, 2021
  2. Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments
    Xin Sheng, Yuting Guan, Ziyuan Ma, Junnan Wu, Hongbo Liu, and 7 more authors
    Nature genetics, 2021
  3. dev_kidney_graph.jpg
    Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets
    Zhen Miao, Michael S Balzer, Ziyuan Ma, Hongbo Liu, Junnan Wu, and 9 more authors
    Nature communications, 2021
    HTML PDF
  4. A Mendelian randomization study of the role of lipoprotein subfractions in coronary artery disease
    Qingyuan Zhao, Jingshu Wang, Zhen Miao, Nancy R Zhang, Sean Hennessy, and 2 more authors
    Elife, 2021
  5. Transcriptome-wide association analysis identifies DACH1 as a kidney disease risk gene that contributes to fibrosis
    Tomohito Doke, Shizheng Huang, Chengxiang Qiu, Hongbo Liu, Yuting Guan, and 7 more authors
    The Journal of Clinical Investigation, 2021
  6. 41581_2021_463_Fig1_HTML.webp
    Multi-omics integration in the age of million single-cell data
    Zhen Miao, Benjamin D Humphreys, Andrew P McMahon, and Junhyong Kim
    Nature Reviews Nephrology, 2021
    HTML PDF
  7. A single genetic locus controls both expression of DPEP1/CHMP1A and kidney disease development via ferroptosis
    Yuting Guan, Xiujie Liang, Ziyuan Ma, Hailong Hu, Hongbo Liu, and 5 more authors
    Nature communications, 2021

2020

  1. Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment
    Leilei Zhong, Lutian Yao, Robert J Tower, Yulong Wei, Zhen Miao, and 17 more authors
    Elife, 2020
  2. APOE and TREM2 regulate amyloid-responsive microglia in Alzheimer’s disease
    Aivi T Nguyen, Kui Wang, Gang Hu, Xuran Wang, Zhen Miao, and 7 more authors
    Acta neuropathologica, 2020

2019

  1. A single point mutation in hmgA leads to melanin accumulation in Bacillus thuringiensis BMB181
    Tong-tong Tan, Xu-dong Zhang, Zhen Miao, Ying Yu, Si-ling Du, and 2 more authors
    Enzyme and microbial technology, 2019
  2. Prediction of ion channels and their types from protein sequences: comprehensive review and comparative assessment
    Jianzhao Gao, Zhen Miao, Zhaopeng Zhang, Hong Wei, and Lukasz Kurgan
    Current Drug Targets, 2019