2019
Genomic sites hypersensitive to ultraviolet radiation
Premi S, Han L, Mehta S, Knight J, Zhao D, Palmatier MA, Kornacker K, Brash DE. Genomic sites hypersensitive to ultraviolet radiation. Proceedings Of The National Academy Of Sciences Of The United States Of America 2019, 116: 24196-24205. PMID: 31723047, PMCID: PMC6883822, DOI: 10.1073/pnas.1907860116.Peer-Reviewed Original ResearchMeSH Keywords5' Untranslated RegionsCells, CulturedDNA DamageFibroblastsGene Expression RegulationGenome, HumanHigh-Throughput Nucleotide SequencingHumansMelanocytesMelanomaMutationPromoter Regions, GeneticProtein BiosynthesisPyrimidine DimersPyrimidine NucleotidesSkin NeoplasmsTOR Serine-Threonine KinasesUltraviolet RaysConceptsCyclobutane pyrimidine dimersETS family transcription factorsIndividual gene promotersFamily transcription factorsRNA-binding proteinPrimary human melanocytesSingle-base resolutionEpigenetic marksGenomic averageTranslation regulationGenomic sitesMotif locationsTranscription factorsCell physiologyGene promoterCancer driversGenomeHuman melanocytesCell typesTumor evolutionCell pathwaysRare mutationsUV targetPyrimidine dimersApurinic sites
2014
Enhancing the detection of barcoded reads in high throughput DNA sequencing data by controlling the false discovery rate
Buschmann T, Zhang R, Brash DE, Bystrykh LV. Enhancing the detection of barcoded reads in high throughput DNA sequencing data by controlling the false discovery rate. BMC Bioinformatics 2014, 15: 264. PMID: 25099007, PMCID: PMC4133078, DOI: 10.1186/1471-2105-15-264.Peer-Reviewed Original ResearchAnimalsDNADNA ContaminationDNA PrimersFalse Positive ReactionsGenomeHigh-Throughput Nucleotide SequencingMiceReference StandardsSequence Analysis, DNASodium-Potassium-Exchanging ATPaseCommon Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes
Laurence M, Hatzis C, Brash DE. Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes. PLOS ONE 2014, 9: e97876. PMID: 24837716, PMCID: PMC4023998, DOI: 10.1371/journal.pone.0097876.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceBradyrhizobiumDNA ContaminationDNA, BacterialHigh-Throughput Nucleotide SequencingMicrobiotaMolecular Sequence DataSequence AlignmentSequence Analysis, DNAConceptsLow-abundance microbesNCBI genome databaseHigh-throughput sequencingShotgun DNA librariesUnbiased high-throughput sequencingNovel microbesGenome databaseDNA libraryNext-generation sequencingComplete genomeGenome ProjectKnown sequencesSequencing runMicrobesSequencing applicationsGenomeCommon contaminantsSequencingLaboratory contaminantsClinical specimensGenusNCBISpeciesDiversityReads