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Nature Computational Science|February 25, 2026
Partially shared multi-modal embedding learns holistic representation of cell stateXinyi Zhang, G V Shivashankar, Caroline UhlerNature Communications|December 3, 2022
Graph-based autoencoder integrates spatial transcriptomics with chromatin images and identifies joint biomarkers for Alzheimer's diseaseXinyi Zhang, Xiao Wang, G V Shivashankar, et al.Cell Systems|May 13, 2025
Image2Reg: Linking chromatin images to gene regulation using genetic and chemical perturbation screensDaniel Paysan, Adityanarayanan Radhakrishnan, Xinyi Zhang, et al.Bioarchitecture|July 20, 2016
Geometric control and modeling of genome reprogrammingCaroline Uhler, G V ShivashankarTrends in Cancer|April 3, 2018
Nuclear Mechanopathology and Cancer DiagnosisCaroline Uhler, G V ShivashankarTrends in Cell Biology|July 22, 2017
Chromosome Intermingling: Mechanical Hotspots for Genome RegulationCaroline Uhler, G V ShivashankarNature Reviews. Molecular Cell Biology|October 19, 2017
Regulation of genome organization and gene expression by nuclear mechanotransductionCaroline Uhler, G V ShivashankarNature Communications|July 19, 2024
Unsupervised representation learning of chromatin images identifies changes in cell state and tissue organization in DCISXinyi Zhang, Saradha Venkatachalapathy, Daniel Paysan, et al.Biorxiv : the Preprint Server for Biology|December 18, 2023
Adhesome Receptor Clustering is Accompanied by the Colocalization of the Associated Genes in the Cell NucleusLouis V Cammarata, Caroline Uhler, G V ShivashankarMolecular Biology of the Cell|June 16, 2017
Orientation and repositioning of chromosomes correlate with cell geometry-dependent gene expressionYejun Wang, Mallika Nagarajan, Caroline Uhler, et al.Pageof 131