2025
Survey and Improvement Strategies for Gene Prioritization with Large Language Models
Neeley M, Qi G, Wang G, Tang R, Mao D, Liu C, Pasupuleti S, Yuan B, Xia F, Liu P, Liu Z, Hu X. Survey and Improvement Strategies for Gene Prioritization with Large Language Models. Bioinformatics Advances 2025, vbaf148. DOI: 10.1093/bioadv/vbaf148.Peer-Reviewed Original ResearchNew tsetse (Glossina fuscipes fuscipes) genomes generated from wild and laboratory‐reared specimens
Bruzzese D, Weiss B, Echodu R, Mireji P, Abd‐Alla A, Aksoy S. New tsetse (Glossina fuscipes fuscipes) genomes generated from wild and laboratory‐reared specimens. Insect Science 2025 PMID: 40509668, DOI: 10.1111/1744-7917.70085.Peer-Reviewed Original ResearchHigh-quality genomesVectors of African trypanosomesSingle-copy homologsPopulation-level variationBUSCO scoreUnique orthologsAssembled genomeAnimal African trypanosomiasesGenetic diversityNatural wild populationsNanopore sequencingGenomeWild populationsLong-term captivityAfrican trypanosomesLaboratory linesGlossina fuscipes fuscipesGeographical originOrthologsLaboratory-reared specimensQV scoreVector biologyCentral African RepublicNorthwestern UgandaFliesPopulation Genetic Structure of Azara's Owl Monkey (Aotus azarae) From Northern Argentina: Insights Into Gene Flow and Dispersal Patterns in a Pair‐Living Primate
Corley M, Burchfield K, Fusco N, Fernandez‐Duque E, Caccone A. Population Genetic Structure of Azara's Owl Monkey (Aotus azarae) From Northern Argentina: Insights Into Gene Flow and Dispersal Patterns in a Pair‐Living Primate. American Journal Of Primatology 2025, 87: e70045. PMID: 40407255, DOI: 10.1002/ajp.70045.Peer-Reviewed Original ResearchConceptsPopulation genetic structureGene flowPair-living primatesAzara's owl monkeysGenetic structureGenetic differentiationGenetic diversityModerate level of genetic differentiationPattern of isolation-by-distanceGallery forestLevel of genetic differentiationPatterns of genetic diversityPatterns of gene flowEffects of habitat lossIsolation-by-distanceMitochondrial DNA sequencesAotus azaraeDispersal patternsNorthern ArgentinaSouth American Gran ChacoGran ChacoEvaluate dispersion patternsPatches of forestConservation management strategiesAssignment tests95 Assessing genetic diversity of the Pfs25 vaccine candidate: Implications for malaria transmission-blocking vaccine in Africa
Orfano A, Cisse A, Sheng Z, Guo Y, Han L, Thiam L, Mangou K, Moore A, Ba A, Li R, Pouye M, Diallo F, Sene S, Ngom E, Sadio B, Mbengue A, Membi C, Bazié T, Somé F, Olson N, Patel S, Shapiro L, Parikh S, Foy B, Cappello M, Premji Z, Dabiré R, Ouedraogo J, Bei A. 95 Assessing genetic diversity of the Pfs25 vaccine candidate: Implications for malaria transmission-blocking vaccine in Africa. Journal Of Clinical And Translational Science 2025, 9: 29-29. PMCID: PMC12050472, DOI: 10.1017/cts.2024.767.Peer-Reviewed Original ResearchSingle nucleotide polymorphismsTransmission-blocking vaccinesGenetic diversityComplex infectionSymptomatic P. falciparum infectionsMalaria transmission-blocking vaccineVaccine candidatesVariant frequenciesNovel single nucleotide polymorphismsNonsynonymous single nucleotide polymorphismsRare variantsFrequency of single nucleotide polymorphismsP. falciparum 3D7Plasmodium falciparum samplesAmplicon deep sequencingMalaria eliminationCountry-specific prevalenceEndemic African countriesPfs25 proteinGeneious softwareParasite genetic diversityProportion of mutant allelesAmplicon sequencingPfs25Mutant allelesPsychiatric genetics in the diverse landscape of Latin American populations
Bruxel E, Rovaris D, Belangero S, Chavarría-Soley G, Cuellar-Barboza A, Martínez-Magaña J, Nagamatsu S, Nievergelt C, Núñez-Ríos D, Ota V, Peterson R, Sloofman L, Adams A, Albino E, Alvarado A, Andrade-Brito D, Arguello-Pascualli P, Bandeira C, Bau C, Bulik C, Buxbaum J, Cappi C, Corral-Frias N, Corrales A, Corsi-Zuelli F, Crowley J, Cupertino R, da Silva B, De Almeida S, De la Hoz J, Forero D, Fries G, Gelernter J, González-Giraldo Y, Grevet E, Grice D, Hernández-Garayua A, Hettema J, Ibáñez A, Ionita-Laza I, Lattig M, Lima Y, Lin Y, López-León S, Loureiro C, Martínez-Cerdeño V, Martínez-Levy G, Melin K, Moreno-De-Luca D, Muniz Carvalho C, Olivares A, Oliveira V, Ormond R, Palmer A, Panzenhagen A, Passos-Bueno M, Peng Q, Pérez-Palma E, Prieto M, Roussos P, Sanchez-Roige S, Santamaría-García H, Shansis F, Sharp R, Storch E, Tavares M, Tietz G, Torres-Hernández B, Tovo-Rodrigues L, Trelles P, Trujillo-ChiVacuan E, Velásquez M, Vera-Urbina F, Voloudakis G, Wegman-Ostrosky T, Zhen-Duan J, Zhou H, Santoro M, Nicolini H, Atkinson E, Giusti-Rodríguez P, Montalvo-Ortiz J. Psychiatric genetics in the diverse landscape of Latin American populations. Nature Genetics 2025, 57: 1074-1088. PMID: 40175716, PMCID: PMC12133068, DOI: 10.1038/s41588-025-02127-z.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesPsychiatric genomicsPsychiatric genome-wide association studiesLarge-scale genome-wide association studiesGenetic risk lociNon-European populationsGenetic diversityRisk lociGenetic admixtureBurden of psychiatric disordersAssociation studiesPsychiatric disordersEuropean ancestryPsychiatric geneticsGenomeHealthcare disparitiesConsortium effortLatin American populationsPromote equityEnvironmental factorsDiversityAmerican populationDiverse landscapeLociAncestryPlant graph-based pangenomics: techniques, applications, and challenges
Du Z, He J, Jiao W. Plant graph-based pangenomics: techniques, applications, and challenges. ABIOTECH 2025, 1-16. DOI: 10.1007/s42994-025-00206-7.Peer-Reviewed Original ResearchNovo-assembled genomeMolecular breeding of cropsDNA sequencing technologiesInvestigate population diversityAgronomically important genesBreeding of cropsPangenome graphsGenetic mapSmall variantsGenomic regionsGenetic diversityGraph pangenomeSequencing technologiesGenomic analysisPangenomic studiesGenomic studiesGenetic variationImportant genesMolecular breedingStructural variantsPangenomeGenomeCrop breedingPlantsVariants
2024
Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon
Cabrera-Sosa L, Safarpour M, Kattenberg J, Ramirez R, Vinetz J, Rosanas-Urgell A, Gamboa D, Delgado-Ratto C. Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon. Frontiers In Genetics 2024, 15: 1488109. PMID: 39748949, PMCID: PMC11693692, DOI: 10.3389/fgene.2024.1488109.Peer-Reviewed Original ResearchInvestigate population geneticsPopulation geneticsSNP barcodesPairwise F<sub>ST<Pairwise genetic differentiationPolyclonal infectionsMalaria parasitesPopulation genetic estimatesPer-sample costProportion of polyclonal infectionsPlasmodium falciparum</i> parasitesPlasmodium vivax</i>Genetic differentiationGenetic resolutionGenetic diversityPeruvian AmazonGenetic estimatesMicrosatelliteSNPsAmpliSeqBarcodingDiversity trendsMolecular surveillanceResource availabilityMS panelPhenotypic Heterogeneity in Pathogens
Sherry J, Rego E. Phenotypic Heterogeneity in Pathogens. Annual Review Of Genetics 2024, 58: 183-209. PMID: 39083846, DOI: 10.1146/annurev-genet-111523-102459.Peer-Reviewed Original ResearchPhenotypic heterogeneityGenetically identical populationSalmonella typhimurium</i>Genetic diversityPathogen diversityPathogen populationsBacterial pathogensPathogen subpopulationsGenetic heterogeneityInvading pathogensHost organismFluctuating environmentsInfectious disease progressionPathogensIdentical populationsTreatment escapeInfection outcomesHeterogeneous subpopulationsDisease progressionInfecting organismDiversityCausative linkGeneticsSubpopulationsPhenotypeVaccine-induced human monoclonal antibodies to PfRH5 show broadly neutralizing activity against P. falciparum clinical isolates
Thiam L, McHugh K, Ba A, Li R, Guo Y, Pouye M, Cisse A, Pipini D, Diallo F, Sene S, Patel S, Thiam A, Sadio B, Mbengue A, Vigan-Womas I, Sheng Z, Shapiro L, Draper S, Bei A. Vaccine-induced human monoclonal antibodies to PfRH5 show broadly neutralizing activity against P. falciparum clinical isolates. Npj Vaccines 2024, 9: 198. PMID: 39448626, PMCID: PMC11502735, DOI: 10.1038/s41541-024-00986-x.Peer-Reviewed Original ResearchP. falciparum clinical isolatesClinical isolatesNext-generation sequencingEarly clinical studiesDose-dependent inhibitionGrowth inhibition activitySingle B cellsOccurrence of novel mutationsNext-generation sequencing analysisBlood-stageNo significant differencePfRH5MAb combinationsNovel mutationsClinical studiesNeutralizing activityAntibody susceptibilityIgG responsesPre-clinicalGenotype/phenotype relationshipsMonoclonal antibodiesVaccine alleleGenetic diversitySignificant differenceMAbAnalysis of Powassan Virus Genome Sequences from Human Cases Reveals Substantial Genetic Diversity with Implications for Molecular Assay Development
Klontz E, Chowdhury N, Holbrook N, Solomon I, Telford S, Aliota M, Vogels C, Grubaugh N, Helgager J, Hughes H, Velez J, Piantadosi A, Chiu C, Lemieux J, Branda J. Analysis of Powassan Virus Genome Sequences from Human Cases Reveals Substantial Genetic Diversity with Implications for Molecular Assay Development. Viruses 2024, 16: 1653. PMID: 39599768, PMCID: PMC11599074, DOI: 10.3390/v16111653.Peer-Reviewed Original ResearchGenome sequenceDiversity of genomic sequencesHuman infectionsPCR assay designVirus genome sequencesAssay designIn silico analysisBiology of infectionViral genomic dataGenetic diversityGenomic dataSensitivity of PCRGenomeCladePCR assayHuman diseasesVirulent strainsPCR designPowassan virusSequenceImmunocompromised patientsPCRTick-borne virusesAssay developmentClinical diagnosticsPrevalence and Genetic Diversity of Deer Tick Virus (Powassan Virus, Lineage II) in Ixodes scapularis Ticks in Five Habitats at a Nature Reserve in Southern Maine, United States
Robich R, Piantadosi A, Elias S, Cosenza D, Schneider E, Baxter L, LaFon E, Lubelczyk C, Meagher M, Vogels C, Smith R. Prevalence and Genetic Diversity of Deer Tick Virus (Powassan Virus, Lineage II) in Ixodes scapularis Ticks in Five Habitats at a Nature Reserve in Southern Maine, United States. American Journal Of Tropical Medicine And Hygiene 2024, 111: 1311-1319. PMID: 39406212, PMCID: PMC11619509, DOI: 10.4269/ajtmh.23-0643.Peer-Reviewed Original ResearchDeer tick virusHabitat typesGenetic diversityIxodes scapularis ticksInvasive vegetationAdult ticksLong-distance dispersalTick virusShort-range dispersalVirus prevalenceTick-borne encephalitis virusPhylogenetic analysisLineage IIHabitatPowassan virus lineage IIEnzootic fociNature ReserveNative vegetationTicksDeerNational Estuarine Research ReserveCompared to 0UnderstoryEncephalitis virusForestGenomic surveillance of malaria parasites in an indigenous community in the Peruvian Amazon
Cabrera-Sosa L, Nolasco O, Kattenberg J, Fernandez-Miñope C, Valdivia H, Barazorda K, Arévalo de los Rios S, Rodriguez-Ferrucci H, Vinetz J, Rosanas-Urgell A, Van geertruyden J, Gamboa D, Delgado-Ratto C. Genomic surveillance of malaria parasites in an indigenous community in the Peruvian Amazon. Scientific Reports 2024, 14: 16291. PMID: 39009685, PMCID: PMC11250820, DOI: 10.1038/s41598-024-66925-x.Peer-Reviewed Original ResearchConceptsPassive case detectionPf parasitesPersistent malaria transmissionPfhrp2/3 gene deletionsDeep sequencing assaySulfadoxine-pyrimethamineMalaria casesMalaria eliminationPlasmodium vivaxMalaria parasitesMalaria transmissionP. falciparumResistance mutationsImported infectionsMalariaPopulation genetic indicesSequencing assayCase detectionGene deletionPV populationResistance markersGenetic diversityPeruvian AmazonGenomic surveillanceGenetic indicesGenetic diversity of North African populations in the 17q21 genomic region
Messaoudi M, Pakstis A, Ezzaher T, Boussetta S, Ben Ammar Elgaaied A, Kidd K, Cherni L. Genetic diversity of North African populations in the 17q21 genomic region. Mammalian Genome 2024, 35: 445-460. PMID: 38965090, DOI: 10.1007/s00335-024-10051-6.Peer-Reviewed Original ResearchNorth African populationsSingle-nucleotide polymorphismsGenetic structureGenetic diversityDemographic history of human populationsHaplotype analysisAutosomal single-nucleotide polymorphismsHistory of human populationsAfrican populationsSouthwest Asian populationsComplex demographic historyHeterogeneous genetic structureNorth AfricaAutosomal markersDemographic historyGenetic flowGenomic regionsGenome ProjectGenetic compositionGenetic heterogeneityGlobal contextHistory of North AfricaMigration processNorth AfricansCultural factorsVibrio cholerae O1 experiences mild bottlenecks through the gastrointestinal tract in some but not all cholera patients
Lypaczewski P, Chac D, Dunmire C, Tandoc K, Chowdhury F, Khan A, Bhuiyan T, Harris J, LaRocque R, Calderwood S, Ryan E, Qadri F, Shapiro B, Weil A. Vibrio cholerae O1 experiences mild bottlenecks through the gastrointestinal tract in some but not all cholera patients. Microbiology Spectrum 2024, 12: e00785-24. PMID: 38916318, PMCID: PMC11302224, DOI: 10.1128/spectrum.00785-24.Peer-Reviewed Original ResearchGenetic diversityVibrio cholerae</i> O1Short-read dataLong-read sequencingDiarrheal disease choleraReduced genetic variationBacterial population sizeSingle-nucleotide variationsPangenome analysisGene presence/absencePilus operonPopulation bottlenecksDisease choleraMild bottleneckGene presenceGut colonizationGenetic variationAdaptive mutationsGenomeCholera patientsPopulation sizeGut resultsSites of active infectionGutStool samplesDengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus
Vogels C, Hill V, Breban M, Chaguza C, Paul L, Sodeinde A, Taylor-Salmon E, Ott I, Petrone M, Dijk D, Jonges M, Welkers M, Locksmith T, Dong Y, Tarigopula N, Tekin O, Schmedes S, Bunch S, Cano N, Jaber R, Panzera C, Stryker I, Vergara J, Zimler R, Kopp E, Heberlein L, Herzog K, Fauver J, Morrison A, Michael S, Grubaugh N. DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus. BMC Genomics 2024, 25: 433. PMID: 38693476, PMCID: PMC11062901, DOI: 10.1186/s12864-024-10350-x.Peer-Reviewed Original ResearchConceptsAmplicon sequencing protocolsPrimer schemeSequencing protocolGenomic surveillanceDengue virus serotypesAmplicon sequencing workflowClinical specimensHigh genome coverageWhole-genome sequencingDengue virusVirus serotypesGenome coverageVirus stocksGenetic diversitySequencing instrumentsSequencing workflowGenotype VIDiverse serotypesSequence of samplesGenotype IVPrimersSurveillance of dengue virusSerotypesVirus copiesSerotype-specificThe multidimensional roles of intermediate filaments - bridging genetic diversity with form, functions, and targets
Lusk C, Eriksson J. The multidimensional roles of intermediate filaments - bridging genetic diversity with form, functions, and targets. Current Opinion In Cell Biology 2024, 88: 102354. PMID: 38604107, DOI: 10.1016/j.ceb.2024.102354.Peer-Reviewed Original ResearchGenetic diversityDiversityInvasion genomics of lionfish in the Mediterranean Sea
Bernardi G, Azzurro E, Bariche M, Jimenez C, Kalogirou S, Kleitou P. Invasion genomics of lionfish in the Mediterranean Sea. Ecology And Evolution 2024, 14: e11087. PMID: 38450316, PMCID: PMC10915480, DOI: 10.1002/ece3.11087.Peer-Reviewed Original ResearchLionfish invasionEvidence of population structureMediterranean SeaEffects of lionfishRate of biological invasionsRed SeaInvasion genomicsInvasion successGenetic diversityGenomic approachesPopulation structureInvasive rangeGenomic markersBiological invasionsEvolutionary patternsFuture invasionsLionfishFish speciesPopulation dynamicsCaribbean SeaSuez CanalCentral MediterraneanMediterraneanInvasionSea
2023
Establishment genomics of the Indo-Pacific damselfish Neopomacentrus cyanomos, in the Greater Caribbean
Bernardi G, Cohn F, Dominguez-Dominguez O, Kingon K, Tornabene L, Robertson D. Establishment genomics of the Indo-Pacific damselfish Neopomacentrus cyanomos, in the Greater Caribbean. Biological Invasions 2023, 26: 1017-1031. DOI: 10.1007/s10530-023-03226-w.Peer-Reviewed Original ResearchNon-native speciesNon-native populationsGreater CaribbeanReef fishesNative rangeNatural selectionTrinidad populationIndo-Pacific reef fishMitochondrial DNA lineagesProtein coding genesSeparate genetic clustersDNA lineagesGenetic differentiationCoding genesAtlantic individualsRocky reefsGenetic clustersGenetic diversityEstablishment successRAD sequencesPopulation structureIsolated populationCoral reefsAdaptable speciesNearby reefsTransposable elements cause the loss of self‐incompatibility in citrus
Hu J, Liu C, Du Z, Guo F, Song D, Wang N, Wei Z, Jiang J, Cao Z, Shi C, Zhang S, Zhu C, Chen P, Larkin R, Lin Z, Xu Q, Ye J, Deng X, Bosch M, Franklin‐Tong V, Chai L. Transposable elements cause the loss of self‐incompatibility in citrus. Plant Biotechnology Journal 2023, 22: 1113-1131. PMID: 38038155, PMCID: PMC11022811, DOI: 10.1111/pbi.14250.Peer-Reviewed Original ResearchConceptsMiniature inverted-repeat transposable elementsMiniature inverted-repeat transposable element insertionSelf-incompatibilityTransposable elementsS-locusS-RNaseS-RNase-based SI systemPromoter regionLoss of self-incompatibilityPromote genetic diversityS-RNase allelesPrezygotic mechanismsGenetic diversityInbreeding depressionSelf-compatibleNucleotide mutationsFlowering plantsLoss of SiTransgenic experimentsBreeding strategiesCitrus genusAllelesSI phenotypePromoterCitrusComparative Genomics of Bacillus subtilis Phages Related to phiNIT1 from Desert Soils of the Southwest United States
Vill A, Delesalle V, Magness L, Chaudhry B, Lichty K, Strine M, Guffey A, DeCurzio J, Krukonis G. Comparative Genomics of Bacillus subtilis Phages Related to phiNIT1 from Desert Soils of the Southwest United States. PHAGE 2023, 4: 173-180. PMID: 40134794, PMCID: PMC11932518, DOI: 10.1089/phage.2023.0027.Peer-Reviewed Original ResearchGenomic structureBacillus phagesBacillus subtilis phageGram-positive bacteriumPathogenic Bacillus speciesDiverse genomesIntergenic regionSequence similarityGenetic diversityRepeat sequencesProtein familyRepresentative phagesPhageB. subtilisBacillus subtilisHost rangeBacillus speciesGenomeVirion structureCapsid structureDesert soilsTail lengthSequenceMyovirusesLysis assay
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