2014
Common 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 ResearchConceptsLow-abundance microbesNCBI genome databaseHigh-throughput sequencingShotgun DNA librariesUnbiased high-throughput sequencingNovel microbesGenome databaseDNA libraryNext-generation sequencingComplete genomeGenome ProjectKnown sequencesSequencing runMicrobesSequencing applicationsGenomeCommon contaminantsSequencingLaboratory contaminantsClinical specimensGenusNCBISpeciesDiversityReads
2009
Influence of cytosine methylation on ultraviolet-induced cyclobutane pyrimidine dimer formation in genomic DNA
Rochette PJ, Lacoste S, Therrien JP, Bastien N, Brash DE, Drouin R. Influence of cytosine methylation on ultraviolet-induced cyclobutane pyrimidine dimer formation in genomic DNA. Mutation Research/Fundamental And Molecular Mechanisms Of Mutagenesis 2009, 665: 7-13. PMID: 19427505, DOI: 10.1016/j.mrfmmm.2009.02.008.Peer-Reviewed Original ResearchConceptsLigation-mediated PCRX chromosomeFMR1 geneGenomic DNAInactive X chromosomeDimer formationCyclobutane pyrimidine dimer formationTumor suppressor genePyrimidine dimer formationConstitutive methylationCytosine methylationMethylated cytosineUnmethylated cytosinesSuppressor geneP53 tumor suppressor geneGenesMethylationCPD formationChromosomesCytosineDNAMutationsSunlight-induced mutationsDipyrimidine sitesPGK1
1995
Intragenic Domains of Strand-specific Repair inEscherichia coli
Kunala S, Brash D. Intragenic Domains of Strand-specific Repair inEscherichia coli. Journal Of Molecular Biology 1995, 246: 264-272. PMID: 7869378, DOI: 10.1006/jmbi.1994.0082.Peer-Reviewed Original ResearchConceptsTranscription-repair coupling factorTranscription start siteStart siteEscherichia coli genesUV-induced cyclobutane pyrimidine dimersStrand-specific repairMfd mutationExcision repair mechanismChromatin domainsIntragenic domainsGenomic organizationMfd geneColi geneCyclobutane pyrimidine dimersLacZ transcriptionDNA repairInEscherichia coliDownstream domainIndividual nucleotidesRepair mechanismsGenesTranscriptionRepair systemDNA strandsInduced levels
1993
Local recurrence versus new primary: Clinical analysis of 82 breast relapses and potential applications for genetic fingerprinting
Haffty B, Carter D, Flynn S, Fischer D, Brash D, Simons J, Ziegler A, Fischer J. Local recurrence versus new primary: Clinical analysis of 82 breast relapses and potential applications for genetic fingerprinting. International Journal Of Radiation Oncology • Biology • Physics 1993, 27: 575-583. PMID: 8226151, DOI: 10.1016/0360-3016(93)90382-6.Peer-Reviewed Original ResearchConceptsNew primary tumorsBreast relapsePrimary tumorTrue recurrenceNew primaryConservative surgeryLocal recurrencePathological criteriaRadiation therapyOriginal tumorSurvival rateClinical pathological analysisSecond primary tumorsShorter median timeTrue local recurrenceSignificant prognostic implicationsDNA flow cytometryLocal relapseMedian timePrognostic implicationsResidual diseaseTumor bedPathological analysisRelapseTherapeutic implications
1992
Excision repair at individual bases of the Escherichia coli lacI gene: relation to mutation hot spots and transcription coupling activity.
Kunala S, Brash DE. Excision repair at individual bases of the Escherichia coli lacI gene: relation to mutation hot spots and transcription coupling activity. Proceedings Of The National Academy Of Sciences Of The United States Of America 1992, 89: 11031-11035. PMID: 1438309, PMCID: PMC50477, DOI: 10.1073/pnas.89.22.11031.Peer-Reviewed Original ResearchConceptsTranscribed strandMutation hot spotsChromosomal DNAExcision repairIndividual nucleotidesEscherichia coli chromosomeExcision repair systemColi chromosomeMfd geneDistribution of mutationsGene fragmentsDNA fragmentsEnzymatic incisionCell extractsLacI geneUV-induced mutationsSite of labelingEscherichia coliRepair systemSpecific gene fragmentsUV photoproductsGenesBase variationsMutationsNucleotidesStatus of the p53 tumor suppressor gene in human squamous carcinoma cell lines.
Reiss M, Brash DE, Muñoz-Antonia T, Simon JA, Ziegler A, Vellucci VF, Zhou ZL. Status of the p53 tumor suppressor gene in human squamous carcinoma cell lines. Oncology Research Featuring Preclinical And Clinical Cancer Therapeutics 1992, 4: 349-57. PMID: 1486218.Peer-Reviewed Original Research
1991
A role for sunlight in skin cancer: UV-induced p53 mutations in squamous cell carcinoma.
Brash DE, Rudolph JA, Simon JA, Lin A, McKenna GJ, Baden HP, Halperin AJ, Pontén J. A role for sunlight in skin cancer: UV-induced p53 mutations in squamous cell carcinoma. Proceedings Of The National Academy Of Sciences Of The United States Of America 1991, 88: 10124-10128. PMID: 1946433, PMCID: PMC52880, DOI: 10.1073/pnas.88.22.10124.Peer-Reviewed Original ResearchConceptsSquamous cell carcinomaCell carcinomaP53 mutationsMajor epidemiologic risk factorsUV-induced p53 mutationsInvasive squamous cell carcinomaEpidemiologic risk factorsUV-specific mutationsP53 tumor suppressor geneInternal malignancySwedish patientsRisk factorsSkin cancerTumor progressionTT double-base changesTumor suppressor geneCarcinomaHuman cancersCancerDipyrimidine sitesSuppressor geneT substitutionSkinMutationsPatients
1989
Ultraviolet photoproducts at the ochre suppressor mutation site in the gln U gene of Escherichia coli: Relevance to “mutation frequency decline”
Garvey N, Witkin E, Brash D. Ultraviolet photoproducts at the ochre suppressor mutation site in the gln U gene of Escherichia coli: Relevance to “mutation frequency decline”. Molecular Genetics And Genomics 1989, 219: 359-364. PMID: 2695824, DOI: 10.1007/bf00259607.Peer-Reviewed Original Research
1987
Photoproduct frequency is not the major determinant of UV base substitution hot spots or cold spots in human cells.
Brash DE, Seetharam S, Kraemer KH, Seidman MM, Bredberg A. Photoproduct frequency is not the major determinant of UV base substitution hot spots or cold spots in human cells. Proceedings Of The National Academy Of Sciences Of The United States Of America 1987, 84: 3782-3786. PMID: 3473483, PMCID: PMC304960, DOI: 10.1073/pnas.84.11.3782.Peer-Reviewed Original Research
1986
Substrate range of the 40,000-dalton DNA-photoreactivating enzyme from Escherichia coli.
Sutherland B, Oliveira O, Ciarrocchi G, Brash D, Haseltine W, Lewis R, Hanawalt P. Substrate range of the 40,000-dalton DNA-photoreactivating enzyme from Escherichia coli. Biochemistry 1986, 25: 681-7. PMID: 3513832, DOI: 10.1021/bi00351a026.Peer-Reviewed Original Research
1982
UV-induced mutation hotspots occur at DNA damage hotspots
Brash D, Haseltine W. UV-induced mutation hotspots occur at DNA damage hotspots. Nature 1982, 298: 189-192. PMID: 7045692, DOI: 10.1038/298189a0.Peer-Reviewed Original ResearchNew Approaches to DNA Damage and Repair: The Ultraviolet Light Example
Haseltine W, Gordon L, Lindan C, Lippke J, Brash D, Lo K, Royer-Pokora B. New Approaches to DNA Damage and Repair: The Ultraviolet Light Example. 1982, 20: 315-332. PMID: 7115270, DOI: 10.1007/978-1-4613-3476-7_21.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus Statements
1981
Distribution of UV light-induced damage in a defined sequence of human DNA: detection of alkaline-sensitive lesions at pyrimidine nucleoside-cytidine sequences.
Lippke JA, Gordon LK, Brash DE, Haseltine WA. Distribution of UV light-induced damage in a defined sequence of human DNA: detection of alkaline-sensitive lesions at pyrimidine nucleoside-cytidine sequences. Proceedings Of The National Academy Of Sciences Of The United States Of America 1981, 78: 3388-3392. PMID: 6943547, PMCID: PMC319573, DOI: 10.1073/pnas.78.6.3388.Peer-Reviewed Original Research