2024
Integrating phylogenies into single-cell RNA sequencing analysis allows comparisons across species, genes, and cells
Church S, Mah J, Dunn C. Integrating phylogenies into single-cell RNA sequencing analysis allows comparisons across species, genes, and cells. PLOS Biology 2024, 22: e3002633. PMID: 38787797, PMCID: PMC11125556, DOI: 10.1371/journal.pbio.3002633.Peer-Reviewed Original ResearchConceptsScRNA-seqPhylogenetic comparative approachCellular gene expressionScRNA-seq analysisSingle-cell RNA sequencingRNA sequencing analysisGene treesSpecies treeCell phylogenyPhylogenetic approachPhylogenetic treeEvolutionary historyPairwise alignmentSingle-cell RNA sequencing analysisSequence analysisCellular lifeRNA sequencingGene expressionGenesCell evolutionCell lineagesPhylogenySpeciesCell functionCellsCell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data
Mah J, Dunn C. Cell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data. Nature Ecology & Evolution 2024, 8: 325-338. PMID: 38182680, DOI: 10.1038/s41559-023-02281-9.Peer-Reviewed Original ResearchSingle-cell datasetsCell typesSingle-cell RNA sequencing dataFundamental evolutionary questionsCell type evolutionSister cell typesGene expression dynamicsRNA sequencing dataSingle-cell dataEvolutionary relationshipsEvolutionary questionsEvolutionary historyEvolutionary biologyExpression dynamicsPhylogenetic methodsPhylogenetic charactersMarker genesPhylogenySequencing dataEye cellsCladeType evolutionSpeciesCellsNon-myelinating Schwann cells
2023
Normalizing need not be the norm: count-based math for analyzing single-cell data
Church S, Mah J, Wagner G, Dunn C. Normalizing need not be the norm: count-based math for analyzing single-cell data. Theory In Biosciences 2023, 143: 45-62. PMID: 37947999, DOI: 10.1007/s12064-023-00408-x.Peer-Reviewed Original Research