2024
DNA methylation in mammalian development and disease
Smith Z, Hetzel S, Meissner A. DNA methylation in mammalian development and disease. Nature Reviews Genetics 2024, 26: 7-30. PMID: 39134824, DOI: 10.1038/s41576-024-00760-8.Peer-Reviewed Original ResearchLong-read sequencing technologiesDNA methylation fieldDNA methylation landscapeGenome functionMethylation landscapeSequencing technologiesEpigenetic codeGenomic characterizationRegulatory layerDNA methylationCell physiologyMammalian developmentMammalian lifespanGenetic featuresFunctional understandingSingle-cellDNAMechanistic discoveriesSomatic transitionsPhases of discoveryDevelopmental potentialDiscoveryPhenotypeSenescencePhysiologyScalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph
Cheng H, Asri M, Lucas J, Koren S, Li H. Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph. Nature Methods 2024, 21: 967-970. PMID: 38730258, PMCID: PMC11214949, DOI: 10.1038/s41592-024-02269-8.Peer-Reviewed Original Research
2023
FLED: a full-length eccDNA detector for long-reads sequencing data
Li F, Ming W, Lu W, Wang Y, Li X, Dong X, Bai Y. FLED: a full-length eccDNA detector for long-reads sequencing data. Briefings In Bioinformatics 2023, 24: bbad388. PMID: 37930031, PMCID: PMC10632013, DOI: 10.1093/bib/bbad388.Peer-Reviewed Original ResearchConceptsLong readsNanopore long-read sequencing technologyLong-read sequencing technologiesLong-read sequencing dataShort sequence readsCancer cell line samplesNanopore long readsCis-regulatory elementsExtrachromosomal circular DNAFull-length sequenceCell linesPolymerase chain reactionCancer-related genesCell line samplesRolling Circle AmplificationCancer-related pathwaysHigh-throughput detectionSequence readsEccDNA sequencingIntact geneEccDNACancer cell linesEccDNA moleculesLinear DNARegulatory potency
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