publications

publications in reversed chronological order.

2025

  1. Genome Biol.
    Cross-species imputation and comparison of single-cell transcriptomic profiles
    Ran Zhang, Mu Yang, Jacob Schreiber, and 6 more authors
    Genome Biology, 2025

2024

  1. NeurIPS
    Into the Single Cell Multiverse: an End-to-End Dataset for Procedural Knowledge Extraction in Biomedical Texts
    Ruth Dannenfelser, Jeffrey Zhong, Ran Zhang, and 1 more author
    Advances in Neural Information Processing Systems, 2024
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  2. bioRxiv
    An integrated view of the structure and function of the human 4D nucleome
    Job Dekker, Betul Akgol Oksuz, Yang Zhang, and 8 more authors
    bioRxiv, 2024
  3. bioRxiv
    Astrocyte-derived extracellular matrix proteins regulate synapse remodeling in stress-induced depression
    Ran Zhang, Patricia Rodriguez-Rodriguez, Lucian Medrihan, and 8 more authors
    bioRxiv, 2024
  4. bioRxiv
    Multi-condition and multi-modal temporal profile inference during mouse embryonic development
    Ran Zhang, Chengxiang Qiu, Gala Filippova, and 6 more authors
    bioRxiv, 2024
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2023

  1. bioRxiv
    Pseudotime analysis for time-series single-cell sequencing and imaging data
    Gang Li, Hyeon-Jin Kim, Sriram Pendyala, and 6 more authors
    bioRxiv, 2023
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  2. Bioinform.
    LSMMD-MA: scaling multimodal data integration for single-cell genomics data analysis
    Laetitia Meng-Papaxanthos, Ran Zhang, Gang Li, and 3 more authors
    Bioinformatics, 2023
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  3. Lab. Investig.
    A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomes
    Daniel Mar, Ilona M Babenko, Ran Zhang, and 4 more authors
    Laboratory Investigation, 2023
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2022

  1. RECOMB
    Semi-supervised single-cell cross-modality translation using polarbear
    Ran Zhang, Laetitia Meng-Papaxanthos, Jean-Philippe Vert, and 1 more author
    In Research in Computational Molecular Biology: 26th Annual International Conference, RECOMB 2022, San Diego, CA, USA, May 22–25, 2022, Proceedings, 2022
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  2. J. Comput. Biol.
    Multimodal Single-Cell Translation and Alignment with Semi-Supervised Learning
    Ran Zhang, Laetitia Meng-Papaxanthos, Jean-philippe Vert, and 1 more author
    Journal of Computational Biology, 2022
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  3. bioRxiv
    Identifying genes and pathways linking astrocyte regional specificity to Alzheimer’s disease susceptibility
    Ran Zhang, Margarete Knudsen, Pedro Del Cioppo Vasques, and 6 more authors
    bioRxiv, 2022
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2021

  1. Cell Syst.
    Tissue-specific enhancer functional networks for associating distal regulatory regions to disease
    Xi Chen, Jian Zhou, Ran Zhang, and 4 more authors
    Cell systems, 2021
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  2. Mol. Psychiatry
    Presenilin 1 phosphorylation regulates amyloid-βdegradation by microglia
    Jose Henrique Ledo, Thomas Liebmann, Ran Zhang, and 7 more authors
    Molecular Psychiatry, 2021
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2020

  1. PLoS One
    Lack of a site-specific phosphorylation of Presenilin 1 disrupts microglial gene networks and progenitors during development
    Jose Henrique Ledo, Ran Zhang, Luka Mesin, and 5 more authors
    PloS one, 2020
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2016

  1. Nat. Neurosci
    Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder
    Arjun Krishnan*, Ran Zhang*, Victoria Yao, and 7 more authors
    Nature neuroscience, 2016
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2015

  1. Nat. Genet
    Understanding multicellular function and disease with human tissue-specific networks
    Casey S Greene, Arjun Krishnan, Aaron K Wong, and 8 more authors
    Nature genetics, 2015
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  2. Nat. Methods
    Targeted exploration and analysis of large cross-platform human transcriptomic compendia
    Qian Zhu, Aaron K Wong, Arjun Krishnan, and 8 more authors
    Nature methods, 2015
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2014

  1. Sci. China Life Sci.
    Atg5 regulates late endosome and lysosome biogenesis
    JunYa Peng, Ran Zhang, YiTong Cui, and 8 more authors
    Science China Life Sciences, 2014
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