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Bioinformatics (Oxford, England)|January 31, 2025
scatterbar: an R package for visualizing proportional data across spatially resolved coordinatesDee Velazquez, Jean FanBiorxiv : the Preprint Server for Biology|January 7, 2026
Spatial Transcriptomics As Rasterized Image Tensors (STARIT) characterizes cell states with subcellular molecular heterogeneityDee Velazquez, Caleb Hallinan, Roujin An, et al.Genome Biology|June 20, 2026
Spatiotemporal transcriptomic analysis during cold ischemic injury to the murine kidney reveals compartment-specific changesSrujan Singh, Shishir Kumar Patel, Ryo Matsuura, et al.Biorxiv : the Preprint Server for Biology|June 12, 2025
Spatiotemporal transcriptomic analysis during cold ischemic injury to the murine kidney reveals compartment-specific changesSrujan Singh, Shishir Kumar Patel, Ryo Matsuura, et al.Plos Computational Biology|July 2, 2026
Another 10 years of PLOS Computational Biology: A data-driven reflection on trends in genomics researchJean FanBioinformatics (Oxford, England)|September 9, 2021
VeloViz: RNA velocity-informed embeddings for visualizing cellular trajectoriesLyla Atta, Arpan Sahoo, Jean FanExperimental & Molecular Medicine|September 15, 2020
Single-cell transcriptomics in cancer: computational challenges and opportunitiesJean Fan, Kamil Slowikowski, Fan ZhangBiorxiv : the Preprint Server for Biology|September 18, 2025
Impact of Data Quality on Deep Learning Prediction of Spatial Transcriptomics from Histology ImagesCaleb Hallinan, Calixto-Hope G Lucas, Jean FanBiorxiv : the Preprint Server for Biology|April 16, 2025
Evidence of off-target probe binding in the 10x Genomics Xenium v1 Human Breast Gene Expression Panel compromises accuracy of spatial transcriptomic profilingCaleb Hallinan, Hyun Joo Ji, Steven L Salzberg, et al.Pageof 7