2025
Scale-free and unbiased transformer with tokenization for cell type annotation from single-cell RNA-seq data
Zhang H, Jiang Z, Zhang S, Tu L, Carlson D. Scale-free and unbiased transformer with tokenization for cell type annotation from single-cell RNA-seq data. Pattern Recognition 2025, 168: 111724. DOI: 10.1016/j.patcog.2025.111724.Peer-Reviewed Original ResearchSingle-cell RNA-seq dataHigh-throughput single-cell RNA sequencingGene pathway informationCell type annotationRNA-seq dataSingle-cell datasetsSingle-cell RNA sequencingGene expression vectorScRNA-seqPathway informationDiverse speciesRNA sequencingExpression vectorAnnotation methodGene expressionDropout eventsExpression patternsGenesSpeciesType annotationsAnnotationCellsComprehensive intra-Cell levelSequenceZooid arrangement and colony growth in Porpita porpita
Oguchi K, Maeno A, Yoshida K, Yamamoto G, Kohtsuka H, Dunn C. Zooid arrangement and colony growth in Porpita porpita. Frontiers In Zoology 2025, 22: 11. PMID: 40551163, PMCID: PMC12183843, DOI: 10.1186/s12983-025-00565-3.Peer-Reviewed Original ResearchColony developmentColony growthStructure of coloniesReproductive polypsFeeding polypsGonozooidsGastrozooidsZooidsDactylozooidsLife historyPorpitaColoniesAboral chamberStructural variationsCoenosarcMorphological observationsConclusionsOur studyGrowth zoneMature onesGrowthMicro-CT techniqueSpeciesTentaclesEcologyMorphological investigationsComplete genome sequence of a novel Acinetobacter spp. linked to an outbreak of sepsis following apheresis platelet transfusion.
Kent A, Sula E, Breaker E, McAllister G, Gable P, Chan-Riley M, Leung V, Peaper D, Jones S, Jones J, Basavaraju S, Halpin A. Complete genome sequence of a novel Acinetobacter spp. linked to an outbreak of sepsis following apheresis platelet transfusion. Microbiology Resource Announcements 2025, e0136124. PMID: 40503797, DOI: 10.1128/mra.01361-24.Peer-Reviewed Original ResearchImplications for OLE RNA as a natural integral membrane RNA.
Lyon S, Breaker R. Implications for OLE RNA as a natural integral membrane RNA. RNA 2025, rna.080489.125. PMID: 40393771, DOI: 10.1261/rna.080489.125.Peer-Reviewed Original ResearchOLE RNARNA world organismsGram-positive bacterial speciesCellular stress responseEmergence of proteinsBacterial hostsLocalized to cell membranesBilayer of membranesRibonucleoprotein complexMaster regulatorsBacterial speciesBiochemical functionsEvolutionary emergenceStress responseRNANoncoding RNAsRNA polymersCell membraneUnusual classPhospholipid bilayersRibonucleoproteinMembraneProteinSpeciesOrnateMapping pesticide-induced metabolic alterations in human gut bacteria
Chen L, Yan H, Di S, Guo C, Zhang H, Zhang S, Gold A, Wang Y, Hu M, Wu D, Johnson C, Wang X, Zhu J. Mapping pesticide-induced metabolic alterations in human gut bacteria. Nature Communications 2025, 16: 4355. PMID: 40348778, PMCID: PMC12065874, DOI: 10.1038/s41467-025-59747-6.Peer-Reviewed Original ResearchConceptsModulating gut microbiota compositionGut bacteria speciesGut microbial speciesHuman gut bacteriaGut microbiota compositionGut bacterial metabolismPesticide exposureHost healthGut bacteriaMicrobiota compositionMicrobial speciesBacterial metabolismBacteria speciesMolecular mechanismsComprehensive atlasLipid metabolismGutIn Vivo Mouse ModelPesticidesHostMetabolismSpeciesInteractive atlasMouse modelMetabolic changesSynteny Enabled Upgrade of the Galapagos Giant Tortoise Genome Improves Inferences of Runs of Homozygosity
Jensen E, Marchisio C, Ochoa A, Gray R, Parra V, Miller J, Çilingir F, Caccone A. Synteny Enabled Upgrade of the Galapagos Giant Tortoise Genome Improves Inferences of Runs of Homozygosity. Ecology And Evolution 2025, 15: e71358. PMID: 40290375, PMCID: PMC12032190, DOI: 10.1002/ece3.71358.Peer-Reviewed Original ResearchContiguous genomeGiant tortoisesGenome assemblyGalapagos giant tortoisesChromosome-level genome assemblySynteny-based methodsGenome resequencing dataEstimates of inbreedingWhole-genome sequencingHigh-quality DNAAldabra giant tortoiseReference genomeResequencing dataComplete genomeImproved genomeSpecies groupsExtinct speciesGenomeTortoisesHomozygositySpeciesSequenceAssemblyImprove inferenceGalapagosConstraint Optimisation Approaches for Designing Group-Living Captive Breeding Programmes
Forshaw M, Gray R, VonHoldt B, Ochoa A, Miller J, Brzeski K, Caccone A, Jensen E. Constraint Optimisation Approaches for Designing Group-Living Captive Breeding Programmes. Proceedings Of The AAAI Conference On Artificial Intelligence 2025, 39: 27989-27997. DOI: 10.1609/aaai.v39i27.35016.Peer-Reviewed Original ResearchCaptive breeding programsBreeding program designsBreeding programsCaptive populationsEffective population sizeCaptive breeding programmesGalapagos giant tortoisesMultiple malesPrevent inbreedingCaptive breeding centresSpecies ecologyBreeding pairsReintroduction effortsGenetic healthBreeding programmesGiant tortoisesBreed groupsBreeding centresEndangered speciesBiodiversity crisisPopulation sizeBreedingRelatednessSpeciesComputational toolsMolecular detection and characterization of Rickettsia felis, R. asembonensis, and Yersinia pestis from peri-domestic fleas in Uganda
Eneku W, Erima B, Maranda A, Gillian N, Atim G, Tugume T, Aquino Q, Kibuuka H, Mworozi E, Douglas C, William J, von Fricken Emery M, Tweyongyere R, Wabwire-Mangen F, Karuhize D. Molecular detection and characterization of Rickettsia felis, R. asembonensis, and Yersinia pestis from peri-domestic fleas in Uganda. Infection Ecology & Epidemiology 2025, 15: 2473159. PMID: 40041476, PMCID: PMC11878166, DOI: 10.1080/20008686.2025.2473159.Peer-Reviewed Original ResearchZoonotic agentsFlea speciesFlea-borne pathogensR. asembonensisR. senegalensisDomestic animalsRickettsia felisPeridomestic environmentsPublic health riskRainy seasonFleasDry seasonHost speciesMolecular detectionPredominant speciesYear-roundSppSeasonCollection timeHuman dwellingsSpeciesYersinia pestisRodent speciesGoatsSub-Saharan AfricaViral genomic features predict Orthopoxvirus reservoir hosts
Tseng K, Koehler H, Becker D, Gibb R, Carlson C, Pilar Fernandez M, Seifert S. Viral genomic features predict Orthopoxvirus reservoir hosts. Communications Biology 2025, 8: 309. PMID: 40000824, PMCID: PMC11862092, DOI: 10.1038/s42003-025-07746-0.Peer-Reviewed Original ResearchConceptsHost speciesViral genomic featuresHost ecological traitsPotential host speciesGenomic featuresHistorical rangeEcological traitsParts of Southeast AsiaWildlife surveillanceHuman populationCausative agent of smallpoxHost predictionAgent of smallpoxSpeciesSoutheast AsiaCausative agentGeographic regionsOrthopoxvirusesNon-disruptive matrix turnover is a conserved feature of biofilm aggregate growth in paradigm pathogenic species
Reichhardt C, Matwichuk M, Lewerke L, Jacobs H, Yan J, Parsek M. Non-disruptive matrix turnover is a conserved feature of biofilm aggregate growth in paradigm pathogenic species. MBio 2025, 16: e03935-24. PMID: 39982068, PMCID: PMC11898600, DOI: 10.1128/mbio.03935-24.Peer-Reviewed Original ResearchConceptsSynthesize EPSBiofilm aggregatesBiofilm matrixBiofilm matrix exopolysaccharidesBiofilm-forming speciesBiofilm matrix compositionStudy of biofilmsMatrix exopolysaccharidesVibrio cholerae</i>.Cellular biomassPathogenic speciesModel organismsBacterial speciesExtracellular DNAExopolysaccharideBiofilm stabilityMulticellular aggregatesCell-free matricesBiofilmCell-free formSpeciesMatrix turnoverAggregate peripheryBacteriaMatrix componentsMacaqueNet: Advancing comparative behavioural research through large‐scale collaboration
De Moor D, Skelton M, MacaqueNet, Amici F, Arlet M, Balasubramaniam K, Ballesta S, Berghänel A, Berman C, Bernstein S, Bhattacharjee D, Bliss‐Moreau E, Brotcorne F, Butovskaya M, Campbell L, Carosi M, Chatterjee M, Cooper M, Cowl V, De la O C, De Marco A, Dettmer A, Dhawale A, Erinjery J, Evans C, Fischer J, García‐Nisa I, Giraud G, Hammer R, Hansen M, Holzner A, Kaburu S, Konečná M, Kumara H, Larrivaz M, Leca J, Legrand M, Lehmann J, Li J, Lezé A, MacIntosh A, Majolo B, Maréchal L, Marty P, Massen J, Maulany R, McCowan B, McFarland R, Merieau P, Meunier H, Micheletta J, Mishra P, Sah S, Molesti S, Morrow K, Müller‐Klein N, Ngakan P, Palagi E, Petit O, Pflüger L, di Sorrentino E, Raghaven R, Raimbault G, Ram S, Reichard U, Riley E, Rincon A, Ruppert N, Sadoughi B, Santhosh K, Schino G, Sheeran L, Silk J, Singh M, Sinha A, Sosa S, Stribos M, Sueur C, Tiddi B, Tkaczynski P, Trebouet F, Widdig A, Whitehouse J, Wooddell L, Xia D, von Fersen L, Young C, Schülke O, Ostner J, Neumann C, Duboscq J, Brent L. MacaqueNet: Advancing comparative behavioural research through large‐scale collaboration. Journal Of Animal Ecology 2025, 94: 519-534. PMID: 39934999, PMCID: PMC11962231, DOI: 10.1111/1365-2656.14223.Peer-Reviewed Original ResearchA widespread and ancient bacterial machinery assembles cytochrome OmcS nanowires essential for extracellular electron transfer
Shen C, Salazar-Morales A, Jung W, Erwin J, Gu Y, Coelho A, Gupta K, Yalcin S, Samatey F, Malvankar N. A widespread and ancient bacterial machinery assembles cytochrome OmcS nanowires essential for extracellular electron transfer. Cell Chemical Biology 2025, 32: 239-254.e7. PMID: 39818215, PMCID: PMC11845295, DOI: 10.1016/j.chembiol.2024.12.013.Peer-Reviewed Original ResearchConceptsExtracellular electron transferPhylogenetically diverse speciesATP-dependent mannerMicrobial extracellular electron transferBacterial machineryDiverse prokaryotesDiverse speciesBiotechnological applicationsGeobacter sulfurreducensCell growthSurface-displayedMorphology maintenanceBiophysical methodsMulti-heme cytochromesCytochromeElectron transferOsCHSProkaryotesPhylogeneticallySulfurreducensGeobacterOverexpressionSpeciesMachineryPathogens and planetary change
Carlson C, Brookson C, Becker D, Cummings C, Gibb R, Halliday F, Heckley A, Huang Z, Lavelle T, Robertson H, Vicente-Santos A, Weets C, Poisot T. Pathogens and planetary change. Nature Reviews Biodiversity 2025, 1: 32-49. DOI: 10.1038/s44358-024-00005-w.Peer-Reviewed Original ResearchBiodiversity lossAnthropogenic environmental changesLand-use changeBiodiversity conservationWildlife healthLand-useEcological costsDie-offGlobal changeBiodiversityEnvironmental changesEcological interventionsLive animal marketsInfectious disease riskPathogen surveillanceHuman-animal contactPathogensVector-borne diseasesSpeciesEvolutionary principlesWildlifeHigh-risk virusesEcosystemGlobal gapConservationA Rare Case of Cyberlindnera jadinii Fungemia in a Kidney Transplant Recipient: A Case Report
Patil J, Sogawa H, Mulligan D. A Rare Case of Cyberlindnera jadinii Fungemia in a Kidney Transplant Recipient: A Case Report. Case Reports In Transplantation 2025, 2025 DOI: 10.1155/crit/3478928.Peer-Reviewed Original ResearchKidney transplant recipientsTransplant recipientsRare caseSolid organ transplant recipientsAspergillus speciesOrgan transplant recipientsAntifungal prophylaxisFungal infectionsCausative agentGraft rejectionPerioperative mortalityCase reportKidney transplantationCardiovascular eventsFungemiaEarly diagnosisQuality of lifeSpeciesKidneyImmunosuppressive pathologyMortalityRecipientsInfectionCandidaAspergillus
2024
Investigating Environmental Determinants of Hookworm Transmission using GPS Tracking and Metagenomics Technologies
Sumboh J, Agyenkwa-Mawuli K, Schwinger E, Donkor I, Akorli J, Dwomoh D, Ashong Y, Osabutey D, Ababio F, Nusbaum O, Humphries D, Cappello M, Koram K, Kwofie S, Wilson M. Investigating Environmental Determinants of Hookworm Transmission using GPS Tracking and Metagenomics Technologies. American Journal Of Tropical Medicine And Hygiene 2024, 112: 561-570. PMID: 39813691, PMCID: PMC11884298, DOI: 10.4269/ajtmh.24-0384.Peer-Reviewed Original ResearchConceptsEffective cation exchange capacityCation exchange capacitySandy-loam soilDominant helminth speciesSoil samplesClay contentSoil parametersExchange capacityHelminth larvaeAnalysis of DNA sequencesGPS trackingSoilParastrongyloides trichosuriAssociated with exposureLarvaeChemical propertiesPotential sourcesMovement dataSpeciesPredominant speciesHelminth speciesLarval countsMetagenomic technologiesDNA sequencesMetagenomic analysisThe Current and Future State of Vaccines for Lyme Disease
Plotkin S, Shapiro E. The Current and Future State of Vaccines for Lyme Disease. Clinical Infectious Diseases 2024, ciae639. PMID: 39711074, DOI: 10.1093/cid/ciae639.Peer-Reviewed Original ResearchDiverse phage communities are maintained stably on a clonal bacterial host
Pyenson N, Leeks A, Nweke O, Goldford J, Schluter J, Turner P, Foster K, Sanchez A. Diverse phage communities are maintained stably on a clonal bacterial host. Science 2024, 386: 1294-1300. PMID: 39666794, PMCID: PMC7617280, DOI: 10.1126/science.adk1183.Peer-Reviewed Original ResearchConceptsPhage communitiesBacterial hostsPhage speciesEcology of bacteriophagesDiverse biological entitiesPhage diversityGrowth phenotypeCommunity ecologyEcological mechanismsPhageBacterial cellsPhenotypic heterogeneityHost populationsBacteriophageBiological entitiesDiversityHostSpeciesPhylogeneticallyNichePhenotypeStrainCellsCommunityTargetTau‐1: Design of a phase 2 trial to evaluate the efficacy, safety, and tolerability of BMS‐986446, an anti‐MTBR tau monoclonal antibody, in patients with early Alzheimer’s disease
van Dyck C, Kahl A, Abelian G, Donovan M, Ahuja M, Watson D, Ossenkoppele R, Iwatsubo T, Hansson O. TargetTau‐1: Design of a phase 2 trial to evaluate the efficacy, safety, and tolerability of BMS‐986446, an anti‐MTBR tau monoclonal antibody, in patients with early Alzheimer’s disease. Alzheimer's & Dementia 2024, 20: e094677. PMCID: PMC11712654, DOI: 10.1002/alz.094677.Peer-Reviewed Original ResearchMicrotubule binding regionTau monoclonal antibodiesTau speciesTau proteinMicrotubule-associated protein tauNeurotoxic tau speciesTau-induced neurotoxicityIntracellular neurofibrillary tanglesCell surface receptorsAD clinical progressionProtein tauNeurofibrillary tanglesBinding regionMonoclonal antibodiesTau transmissionSynaptic lossExtracellular accumulationSurface receptorsTau concentrationsCerebrospinal fluid correlateAlzheimer's diseaseTauIn vitro activity studiesSelf-associationSpeciesNasal, dermal, oral and indoor dust microbe and their interrelationship in children with allergic rhinitis
Tang H, Du S, Niu Z, Zhang D, Tang Z, Chen H, Chen Z, Zhang M, Xu Y, Sun Y, Fu X, Norback D, Shao J, Zhao Z. Nasal, dermal, oral and indoor dust microbe and their interrelationship in children with allergic rhinitis. BMC Microbiology 2024, 24: 505. PMID: 39614169, PMCID: PMC11606197, DOI: 10.1186/s12866-024-03668-9.Peer-Reviewed Original ResearchConceptsSpecies levelBacterial speciesAR childrenNasal cavityMethodsIn this case–control studyBody sitesControl groupBacterial diversityCase-control studyB-diversityOral swab samplesS. epidermidisStaphylococcus epidermidisStaphylococcus aureusBacterial characterizationMicrobesAllergic rhinitisSpeciesHealthy subjectsBackgroundAllergic rhinitisSwab samplesHealthy onesConclusionsOur studyMicroorganismsRhinitisGENCODE 2025: reference gene annotation for human and mouse
Mudge J, Carbonell-Sala S, Diekhans M, Martinez J, Hunt T, Jungreis I, Loveland J, Arnan C, Barnes I, Bennett R, Berry A, Bignell A, Cerdán-Vélez D, Cochran K, Cortés L, Davidson C, Donaldson S, Dursun C, Fatima R, Hardy M, Hebbar P, Hollis Z, James B, Jiang Y, Johnson R, Kaur G, Kay M, Mangan R, Maquedano M, Gómez L, Mathlouthi N, Merritt R, Ni P, Palumbo E, Perteghella T, Pozo F, Raj S, Sisu C, Steed E, Sumathipala D, Suner M, Uszczynska-Ratajczak B, Wass E, Yang Y, Zhang D, Finn R, Gerstein M, Guigó R, Hubbard T, Kellis M, Kundaje A, Paten B, Tress M, Birney E, Martin F, Frankish A. GENCODE 2025: reference gene annotation for human and mouse. Nucleic Acids Research 2024, 53: d966-d975. PMID: 39565199, PMCID: PMC11701607, DOI: 10.1093/nar/gkae1078.Peer-Reviewed Original ResearchGene annotationLong-read transcriptome sequencingMulti-genome alignmentsRibo-Seq experimentsUCSC Genome BrowserState-of-the-art proteomicsGenome browserRibo-seqSpecies genomesMouse genomeTranscriptome sequencingGENCODEGenomeAnnotation workflowAnnotationSequencePangenomeMiceGenesetsState-of-the-artUCSCProteomicsTranscriptionGenesSpecies
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