2020
SCELLECTOR: ranking amplification bias in single cells using shallow sequencing
Sarangi V, Jourdon A, Bae T, Panda A, Vaccarino F, Abyzov A. SCELLECTOR: ranking amplification bias in single cells using shallow sequencing. BMC Bioinformatics 2020, 21: 521. PMID: 33183232, PMCID: PMC7663899, DOI: 10.1186/s12859-020-03858-y.Peer-Reviewed Original ResearchConceptsMultiple displacement amplificationShallow sequencingSingle-cell platformsSingle-cell sequencingCoverage sequencing dataSingle cellsHuman neuronal cellsMosaic mutationsAmount of DNAAmplification qualityCell sequencingCoverage sequencingHigh-coverage dataSequencing dataHaplotype informationPhi29 polymeraseDNA damageIndividual cellsNeuronal cellsSequencingAmplification biasAllelic imbalancePresence of sitesMutationsFragment lengthComplex mosaic structural variations in human fetal brains
Sekar S, Tomasini L, Proukakis C, Bae T, Manlove L, Jang Y, Scuderi S, Zhou B, Kalyva M, Amiri A, Mariani J, Sedlazeck F, Urban AE, Vaccarino F, Abyzov A. Complex mosaic structural variations in human fetal brains. Genome Research 2020, 30: gr.262667.120. PMID: 33122304, PMCID: PMC7706730, DOI: 10.1101/gr.262667.120.Peer-Reviewed Original ResearchMeSH KeywordsBrainClonal EvolutionDNA, CircularFemaleGenomic Structural VariationGenotyping TechniquesGestational AgeHumansMosaicismNeurogenesisPregnancySequence Analysis, DNAConceptsSingle nucleotide variantsCopy number variantsStructural variantsMegabase-scale copy number variantsHuman fetal brainFunctional consequencesMobile element insertionsSimilar functional consequencesFetal brainMosaic single-nucleotide variantsAdult brain neuronsStructural variationsPotential functional consequencesKilobase scaleDNA eventsGenomic fragmentDifferent chromosomesElement insertionsClonal approachHuman brain cellsFetal human brainNucleotide variantsReplication errorsHuman brainNumber variants
1999
Identification, Chromosomal Assignment, and Expression Analysis of the Human Homeodomain-Containing Gene Orthopedia (OTP)
Lin X, State M, Vaccarino F, Greally J, Hass M, Leckman J. Identification, Chromosomal Assignment, and Expression Analysis of the Human Homeodomain-Containing Gene Orthopedia (OTP). Genomics 1999, 60: 96-104. PMID: 10458915, DOI: 10.1006/geno.1999.5882.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBase SequenceBrainChromosome BandingChromosome MappingChromosomes, Human, Pair 5DNA, ComplementaryDrosophila ProteinsExonsGene ExpressionGene Expression Regulation, DevelopmentalGenesHomeodomain ProteinsHumansImmunohistochemistryIn Situ Hybridization, FluorescenceIntronsMolecular Sequence DataNerve Tissue ProteinsRatsRats, Sprague-DawleySequence AlignmentSequence Analysis, DNASequence Homology, Amino AcidConceptsHuman cDNAHuman homologueRadiation hybrid panel mappingDeduced amino acid sequenceHelix transcription factorOpen reading frameAmino acid sequenceHuman HomeodomainChromosomal assignmentHomeodomain genesCell fateGenomic libraryTranscription factorsHuman chromosomesReading frameGene productsAcid sequenceHD geneExpression analysisC-terminusYAC clonesNovel polyclonal antibodyOrthopediaCell migration patternsHuman fetal brain tissue