2024
Spatial transcriptomic validation of a biomimetic model of fibrosis enables re-evaluation of a therapeutic antibody targeting LOXL2
Bell J, Davies E, Brereton C, Vukmirovic M, Roberts J, Lunn K, Wickens L, Conforti F, Ridley R, Ceccato J, Sayer L, Johnston D, Vallejo A, Alzetani A, Jogai S, Marshall B, Fabre A, Richeldi L, Monk P, Skipp P, Kaminski N, Offer E, Wang Y, Davies D, Jones M. Spatial transcriptomic validation of a biomimetic model of fibrosis enables re-evaluation of a therapeutic antibody targeting LOXL2. Cell Reports Medicine 2024, 5: 101695. PMID: 39173635, PMCID: PMC11524965, DOI: 10.1016/j.xcrm.2024.101695.Peer-Reviewed Original Research
2022
Comprehensive visualization of cell–cell interactions in single-cell and spatial transcriptomics with NICHES
Raredon M, Yang J, Kothapalli N, Lewis W, Kaminski N, Niklason L, Kluger Y. Comprehensive visualization of cell–cell interactions in single-cell and spatial transcriptomics with NICHES. Bioinformatics 2022, 39: btac775. PMID: 36458905, PMCID: PMC9825783, DOI: 10.1093/bioinformatics/btac775.Peer-Reviewed Original ResearchConceptsCell-cell interactionsCell-cell signalingSingle-cell resolutionSingle-cell dataLocal cellular microenvironmentSingle-cell levelSpatial transcriptomics dataCell clustersExtracellular signalingTranscriptomic dataGene expression valuesSpatial transcriptomicsSignaling mechanismCellular microenvironmentNicheExpression valuesSupplementary dataSignalingTranscriptomicsComprehensive visualizationBioinformaticsInteraction