2024
Rare Drivers at Low Prevalence with High Cancer Effects in T-Cell and B-Cell Pediatric Acute Lymphoblastic Leukemia
Mandell J, Diviti S, Xu M, Townsend J. Rare Drivers at Low Prevalence with High Cancer Effects in T-Cell and B-Cell Pediatric Acute Lymphoblastic Leukemia. International Journal Of Molecular Sciences 2024, 25: 6589. PMID: 38928295, PMCID: PMC11203805, DOI: 10.3390/ijms25126589.Peer-Reviewed Original ResearchGenomic analysisPediatric acute lymphoblastic leukemiaCancer effectsAcute lymphoblastic leukemiaT cellsTherapeutic targetSomatic substitutionsRare driversB-ALLLymphoblastic leukemiaEpistatic effectsT-cell ALL patientsMutational contributionsMutated genesCancer phenotypeMutated formDevelopment of leukemiaLow prevalenceB-cell lineageDisease mechanismsMutationsPrecision therapeuticsTherapeutic opportunitiesT-ALLALL patients
2022
Secondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassa
Wang Z, Lopez-Giraldez F, Slot J, Yarden O, Trail F, Townsend JP. Secondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassa. MSystems 2022, 7: e00232-22. PMID: 35638725, PMCID: PMC9239088, DOI: 10.1128/msystems.00232-22.Peer-Reviewed Original ResearchConceptsSM clustersComparative genomicsSecondary metabolitesAsexual growthN. crassaNeurospora crassaSecondary metabolism gene clustersSexual developmentDevelopmental stagesSecondary metabolite clustersComparative genomic analysisExtensive transcriptomic dataGene expression patternsEnvironmental conditionsFungal toxin productionLevel of RNASMC genesLife cycleRegulatory switchComputational annotationGene clusterEnvironmental signalsMetabolite clustersGenomic analysisKnockout phenotypes
2020
Comparative Genomics within and across Bilaterians Illuminates the Evolutionary History of ALK and LTK Proto-Oncogene Origination and Diversification
Dornburg A, Wang Z, Wang J, Mo ES, López-Giráldez F, Townsend JP. Comparative Genomics within and across Bilaterians Illuminates the Evolutionary History of ALK and LTK Proto-Oncogene Origination and Diversification. Genome Biology And Evolution 2020, 13: evaa228. PMID: 33196781, PMCID: PMC7851593, DOI: 10.1093/gbe/evaa228.Peer-Reviewed Original ResearchConceptsLeukocyte tyrosine kinaseEvolutionary historyPhylogenetic analysisProtein-coding genesComparative genomic analysisEarly embryonic expressionMetazoan genomesComparative genomicsPhylogenetic contextModel organismsEmbryonic expressionModel speciesHuman genesKey genesGenomic analysisImportant genesMammal systemsFunctional convergenceTyrosine kinaseMolecular homologyGenesFunctional roleVertebratesMammal modelsHomology
2018
Lvr, a Signaling System That Controls Global Gene Regulation and Virulence in Pathogenic Leptospira
Adhikarla H, Wunder EA, Mechaly AE, Mehta S, Wang Z, Santos L, Bisht V, Diggle P, Murray G, Adler B, Lopez F, Townsend JP, Groisman E, Picardeau M, Buschiazzo A, Ko AI. Lvr, a Signaling System That Controls Global Gene Regulation and Virulence in Pathogenic Leptospira. Frontiers In Cellular And Infection Microbiology 2018, 8: 45. PMID: 29600195, PMCID: PMC5863495, DOI: 10.3389/fcimb.2018.00045.Peer-Reviewed Original ResearchConceptsResponse regulatorTwo-component system proteinsDNA-binding response regulatorGlobal transcriptional regulationHybrid histidine kinaseGlobal gene regulationNovel signal pathwayComprehensive genomic analysisPhosphotransfer assaysTCS genesHistidine kinaseGene duplicationTranscriptional regulationGene regulationCorresponding genesPhylogenetic analysisGenomic analysisMolecular basisMutant strainSystem proteinsSignaling systemInfection processGenesBranched pathwayVirulence
2007
Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project
Dunlap JC, Borkovich KA, Henn MR, Turner GE, Sachs MS, Glass NL, McCluskey K, Plamann M, Galagan JE, Birren BW, Weiss RL, Townsend JP, Loros JJ, Nelson MA, Lambreghts R, Colot HV, Park G, Collopy P, Ringelberg C, Crew C, Litvinkova L, DeCaprio D, Hood HM, Curilla S, Shi M, Crawford M, Koerhsen M, Montgomery P, Larson L, Pearson M, Kasuga T, Tian C, Baştürkmen M, Altamirano L, Xu J. Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project. Advances In Genetics 2007, 57: 49-96. PMID: 17352902, PMCID: PMC3673015, DOI: 10.1016/s0065-2660(06)57002-6.Peer-Reviewed Original ResearchConceptsFunctional genomics projectsGenomics projectsFilamentous fungiFilamentous fungus NeurosporaFunctional genomic analysisNon-yeast fungiFunctional genomicsNeurospora genomeFungus NeurosporaNovel genesPositional cloningNeurospora crassaAntisense transcriptsGenomic analysisSNP mapAlternative promotersCDNA libraryExpression analysisGene replacementMutant strainSystematic disruptionExpression dataPhenotypic analysisNeurosporaConditions of growth