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Bioinformatics (Oxford, England)|May 6, 2025
scACCorDiON: a clustering approach for explainable patient level cell-cell communication graph analysisJames S Nagai, Tiago Maié, Michael T Schaub, et al.
Bioinformatics Advances|January 26, 2023
scMEGA: single-cell multi-omic enhancer-based gene regulatory network inferenceZhijian Li, James S Nagai, Christoph Kuppe, et al.
Bioinformatics (Oxford, England)|January 15, 2022
CrossTalkeR: analysis and visualization of ligand-receptorne tworksJames S Nagai, Nils B Leimkühler, Michael T Schaub, et al.
Plos One|October 25, 2021
A stomata classification and detection system in microscope images of maize cultivarsAlexandre H Aono, James S Nagai, Gabriella da S M Dickel, et al.
Plos One|January 2, 2024
Correction: A stomata classification and detection system in microscope images of maize cultivarsAlexandre H Aono, James S Nagai, Gabriella da S M Dickel, et al.
Nature Methods|October 23, 2025
PHLOWER leverages single-cell multimodal data to infer complex, multi-branching cell differentiation trajectoriesMingbo Cheng, Jitske Jansen, Katharina C Reimer, et al.
Nature Communications|June 10, 2022
Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq dataDaniel Dimitrov, Dénes Türei, Martin Garrido-Rodriguez, et al.
Experimental Hematology|March 28, 2022
Single-cell analysis of cultured bone marrow stromal cells reveals high similarity to fibroblasts in situUrsula S A Stalmann, Bella Banjanin, Inge A M Snoeren, et al.
Molecular Systems Biology|January 4, 2024
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)Mehdi Joodaki, Mina Shaigan, Victor Parra, et al.
Proceedings of the National Academy of Sciences of the United States of America|January 10, 2025
<i>Salmonella</i> infection accelerates postnatal maturation of the intestinal epitheliumStefan Schlößer, Anna-Lena Ullrich, Nastaran Fazel Modares, et al.
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