2024
Giants among Cnidaria: Large Nuclear Genomes and Rearranged Mitochondrial Genomes in Siphonophores
Ahuja N, Cao X, Schultz D, Picciani N, Lord A, Shao S, Jia K, Burdick D, Haddock S, Li Y, Dunn C. Giants among Cnidaria: Large Nuclear Genomes and Rearranged Mitochondrial Genomes in Siphonophores. Genome Biology And Evolution 2024, 16: evae048. PMID: 38502059, PMCID: PMC10980510, DOI: 10.1093/gbe/evae048.Peer-Reviewed Original ResearchConceptsK-mer spectraMitochondrial genomeGenomic diversityK-mersNuclear genomeEstimate nuclear genome sizesMitochondrial gene orderNuclear genome sizeGenome assembly projectsRearranged mitochondrial genomesK-mer countingGenome skimmingGene orderGenome sizeRead coverageSequencing depthPhylogenetic samplingIllumina sequencingCnidarian speciesGenomeAssembly projectsSiphonophoresZooplankton communityAbundant predatorsSpecies
2017
A sequence-based method to predict the impact of regulatory variants using random forest
Liu Q, Gan M, Jiang R. A sequence-based method to predict the impact of regulatory variants using random forest. BMC Systems Biology 2017, 11: 7. PMID: 28361702, PMCID: PMC5374684, DOI: 10.1186/s12918-017-0389-1.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphismsGenome-wide association studiesK-mer featuresK-mersGenome sequenceChromatin regionsDNA sequencesGenetic variantsImpact of regulatory variantsRandom genomic sequencesSequence conservation featuresIdentification of genetic risk factorsDisease-Associated VariantsSequence-based methodsK-mer countingImpact of single nucleotide polymorphismsBreast cancer cell linesRegulatory variantsGenetic risk factorsNoncoding regionsComplex traitsAssociation studiesRegulatory elementsCancer cell linesPermutation experiments
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