2024
Dynamics of clustering rates in the rhode Island HIV-1 epidemic.
Novitsky V, Steingrimsson J, Guang A, Dunn C, Howison M, Gillani F, Hague J, Fulton J, Bertrand T, Bhattarai L, MacAskill M, Bandy U, Hogan J, Kantor R. Dynamics of clustering rates in the rhode Island HIV-1 epidemic. AIDS 2024 PMID: 39527774, DOI: 10.1097/qad.0000000000004062.Peer-Reviewed Original ResearchHIV-1 epidemicAcademic-public health partnershipCountry of birthSocio-demographic characteristicsNewly-diagnosedPrevalent infectionPartial HIV-1 pol sequencesHealth partnershipsRhode IslandHIV-1 pol sequencesMental illnessNewly-diagnosed individualsTargeted interventionsHIV-1 diagnosisHIV-1 subtypesHIV transmissionClustering rateStatewide epidemicsRate trendsHIV-1Pol sequencesTransmission riskEpidemicInfectionIndividualsPhysalia gonodendra are not yet sexually mature when released
Oguchi K, Yamamoto G, Kohtsuka H, Dunn C. Physalia gonodendra are not yet sexually mature when released. Scientific Reports 2024, 14: 23011. PMID: 39362967, PMCID: PMC11450099, DOI: 10.1038/s41598-024-73611-5.Peer-Reviewed Original ResearchConceptsGerm cell maturationGene expression analysisGerm cell markersReproductive ecologySexual reproductionHaploid cellsGerm cellsReproductive biologyGonophoresExpression analysisRelated genesLife cycleGenesCell maturationGermConsistent with other studiesFlow cytometryPhysalia utriculusExpressionCnidariaCell markersCellsPhysaliaSpermHydrozoaProspective Evaluation of Routine Statewide Integration of Molecular Epidemiology and Contact Tracing to Disrupt Human Immunodeficiency Virus Transmission
Kantor R, Steingrimsson J, Fulton J, Novitsky V, Howison M, Gillani F, Bhattarai L, MacAskill M, Hague J, Guang A, Khanna A, Dunn C, Hogan J, Bertrand T, Bandy U. Prospective Evaluation of Routine Statewide Integration of Molecular Epidemiology and Contact Tracing to Disrupt Human Immunodeficiency Virus Transmission. Open Forum Infectious Diseases 2024, 11: ofae599. PMID: 39474444, PMCID: PMC11521326, DOI: 10.1093/ofid/ofae599.Peer-Reviewed Original ResearchRoutine public health activitiesPublic health activitiesHealth activitiesAcademic-public health partnershipHIV transmissionNew HIV diagnosesHIV-TRACEHealth partnershipsHIV diagnosisIdentified barriersNewly-diagnosed individualsRoutine contactStatewide studyAt-riskAt-risk contactsIdentified gapsLongitudinal integrationInitial interviewContact tracingUnique individualsImproving contact tracingMolecular epidemiologyRhode IslandCommunity characteristicsMolecular cluster analysisIntegrating HIV Cluster Analysis in Everyday Public Health Practice: Lessons Learned From a Public Health–—Academic Partnership
Fulton J, Novitsky V, Gillani F, Guang A, Steingrimsson J, Khanna A, Hague J, Dunn C, Hogan J, Howe K, MacAskill M, Bhattarai L, Bertrand T, Bandy U, Kantor R. Integrating HIV Cluster Analysis in Everyday Public Health Practice: Lessons Learned From a Public Health–—Academic Partnership. JAIDS Journal Of Acquired Immune Deficiency Syndromes 2024, 97: 48-54. PMID: 39116331, PMCID: PMC11310557, DOI: 10.1097/qai.0000000000003469.Peer-Reviewed Original ResearchHIV prevention effortsAcademic partnershipsAcademic-public health partnershipRe-interviewedPrevention effortsHIV-diagnosed personsPublic health staffPublic health practicePublic health activitiesPublic health effortsPublic health actionPublic health dataPublic health benefitsState of Rhode IslandHealth partnershipsMonthly conferenceHealth practicesTargeted interventionsDocument lessonsMultidisciplinary conferenceHIV outbreakHIVRhode IslandMolecular cluster analysisPartnershipIntegrating phylogenies into single-cell RNA sequencing analysis allows comparisons across species, genes, and cells
Church S, Mah J, Dunn C. Integrating phylogenies into single-cell RNA sequencing analysis allows comparisons across species, genes, and cells. PLOS Biology 2024, 22: e3002633. PMID: 38787797, PMCID: PMC11125556, DOI: 10.1371/journal.pbio.3002633.Peer-Reviewed Original ResearchConceptsScRNA-seqPhylogenetic comparative approachCellular gene expressionScRNA-seq analysisSingle-cell RNA sequencingRNA sequencing analysisGene treesSpecies treeCell phylogenyPhylogenetic approachPhylogenetic treeEvolutionary historyPairwise alignmentSingle-cell RNA sequencing analysisSequence analysisCellular lifeRNA sequencingGene expressionGenesCell evolutionCell lineagesPhylogenySpeciesCell functionCellsVertical trophic structure and niche partitioning of gelatinous predators in a pelagic food web: Insights from stable isotopes of siphonophores
Hetherington E, Close H, Haddock S, Damian‐Serrano A, Dunn C, Wallsgrove N, Doherty S, Choy C. Vertical trophic structure and niche partitioning of gelatinous predators in a pelagic food web: Insights from stable isotopes of siphonophores. Limnology And Oceanography 2024, 69: 902-919. DOI: 10.1002/lno.12536.Peer-Reviewed Original ResearchTrophic positionPelagic food webFood websGelatinous zooplanktonTrophic ecologyCSIA-AASuspended particlesCalifornia Current EcosystemStable isotope valuesCollection depthIsotope valuesTrophic diversityBasal resourcesNiche overlapTrophic levelsTrophic structureFeeding ecologyAnalysis of individual amino acidsCurrent EcosystemGelatinous predatorsVertical habitatNiche partitioningSmall crustaceansPelagic ecosystemRemotely operated vehicleGiants among Cnidaria: Large Nuclear Genomes and Rearranged Mitochondrial Genomes in Siphonophores
Ahuja N, Cao X, Schultz D, Picciani N, Lord A, Shao S, Jia K, Burdick D, Haddock S, Li Y, Dunn C. Giants among Cnidaria: Large Nuclear Genomes and Rearranged Mitochondrial Genomes in Siphonophores. Genome Biology And Evolution 2024, 16: evae048. PMID: 38502059, PMCID: PMC10980510, DOI: 10.1093/gbe/evae048.Peer-Reviewed Original ResearchConceptsK-mer spectraMitochondrial genomeGenomic diversityK-mersNuclear genomeEstimate nuclear genome sizesMitochondrial gene orderNuclear genome sizeGenome assembly projectsRearranged mitochondrial genomesK-mer countingGenome skimmingGene orderGenome sizeRead coverageSequencing depthPhylogenetic samplingIllumina sequencingCnidarian speciesGenomeAssembly projectsSiphonophoresZooplankton communityAbundant predatorsSpeciesCell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data
Mah J, Dunn C. Cell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data. Nature Ecology & Evolution 2024, 8: 325-338. PMID: 38182680, DOI: 10.1038/s41559-023-02281-9.Peer-Reviewed Original ResearchSingle-cell datasetsCell typesSingle-cell RNA sequencing dataFundamental evolutionary questionsCell type evolutionSister cell typesGene expression dynamicsRNA sequencing dataSingle-cell dataEvolutionary relationshipsEvolutionary questionsEvolutionary historyEvolutionary biologyExpression dynamicsPhylogenetic methodsPhylogenetic charactersMarker genesPhylogenySequencing dataEye cellsCladeType evolutionSpeciesCellsNon-myelinating Schwann cells
2023
2899. Integrating HIV Partner Services and Molecular Epidemiology Data to Enhance HIV Transmission Disruption in Rhode Island: Findings from a Public Health-Academic Partnership
Khanna A, Novitsky V, Guang A, Howison M, Gillani F, Steingrimsson J, Dunn C, Fulton J, Bertrand T, Howe K, Bhattarai L, Ronquillo G, MacAskill M, Bandy U, Kantor R. 2899. Integrating HIV Partner Services and Molecular Epidemiology Data to Enhance HIV Transmission Disruption in Rhode Island: Findings from a Public Health-Academic Partnership. Open Forum Infectious Diseases 2023, 10: ofad500.170. PMCID: PMC10678557, DOI: 10.1093/ofid/ofad500.170.Peer-Reviewed Original ResearchMolecular epidemiology dataEpidemiology dataMolecular epidemiologyHIV partner servicesSignificant public health concernLocal HIV epidemicPublic health concernPublic healthOnly moderate concordanceRhode Island DepartmentHIV transmissionHealth contactsHIV epidemicBackground HIVModerate concordanceContact tracingHealth concernPartner servicesConclusion IntegrationEpidemiologyConcordanceHealthUniversity investigatorsUnique personPersonsNormalizing need not be the norm: count-based math for analyzing single-cell data
Church S, Mah J, Wagner G, Dunn C. Normalizing need not be the norm: count-based math for analyzing single-cell data. Theory In Biosciences 2023, 143: 45-62. PMID: 37947999, DOI: 10.1007/s12064-023-00408-x.Peer-Reviewed Original Research
2022
Incorporating Within-Host Diversity in Phylogenetic Analyses for Detecting Clusters of New HIV Diagnoses
Guang A, Howison M, Ledingham L, D’Antuono M, Chan P, Lawrence C, Dunn C, Kantor R. Incorporating Within-Host Diversity in Phylogenetic Analyses for Detecting Clusters of New HIV Diagnoses. Frontiers In Microbiology 2022, 12: 803190. PMID: 35250908, PMCID: PMC8891961, DOI: 10.3389/fmicb.2021.803190.Peer-Reviewed Original ResearchCluster inferenceNext-generation sequencingPhylogenetic inferencePhylogenetic analysisConsensus sequenceSingle consensus sequenceCluster detectionInferenceConsensus sequence approachHost viral diversitySequence diversitySequence variationGene regionNetwork featuresSummary methodsSequence approachViral diversityConventional approachesDiversityIntegrating siphonophores into marine food‐web ecology
Hetherington E, Damian‐Serrano A, Haddock S, Dunn C, Choy C. Integrating siphonophores into marine food‐web ecology. Limnology And Oceanography Letters 2022, 7: 81-95. DOI: 10.1002/lol2.10235.Peer-Reviewed Original ResearchFood web ecologyFood web structureFood web topologyDeep pelagic habitatPredator-prey interactionsDiversity of taxaTrophic complexityTrophic ecologyTrophic nicheWeb structureNiche differentiationTrophic differencesAbundant predatorsPelagic ecosystemFeeding ecologyOceanic ecosystemsDepth habitatGelatinous zooplanktonDeep pelagicSiphonophore speciesEcologyDiet differencesWater columnColonial hydrozoansEcosystems
2021
The Evolutionary History of Siphonophore Tentilla: Novelties, Convergence, and Integration
Damian-Serrano A, Haddock S, Dunn C. The Evolutionary History of Siphonophore Tentilla: Novelties, Convergence, and Integration. Integrative Organismal Biology 2021, 3: obab019. PMID: 34355122, PMCID: PMC8331849, DOI: 10.1093/iob/obab019.Peer-Reviewed Original ResearchEvolutionary historyMorphological diversityComplex evolutionary historyBroad morphological diversityEvolutionary gainPhenotypic integrationEvolutionary timeHydrozoan cnidariansMorphological convergenceFunctional diversityMorphological charactersStructured diversityCharacter correlationsFeeding habitsPrey captureUnique biological structureSiphonophore speciesNematocyst typesTentillaDiversityKinematic diversitySpeciesBiological structuresNematocyst dischargeCnidarians
2018
Description of Tottonophyes enigmatica gen. nov., sp. nov. (Hydrozoa, Siphonophora, Calycophorae), with a reappraisal of the function and homology of nectophoral canals
PUGH P, DUNN C, HADDOCK S. Description of Tottonophyes enigmatica gen. nov., sp. nov. (Hydrozoa, Siphonophora, Calycophorae), with a reappraisal of the function and homology of nectophoral canals. Zootaxa 2018, 4415: 452-472. PMID: 30313611, DOI: 10.11646/zootaxa.4415.3.3.Peer-Reviewed Original Research
2017
Insights into the Biodiversity, Behavior, and Bioluminescence of Deep-Sea Organisms Using Molecular and Maritime Technology
MBARI, Haddock S, Christianson L, Francis W, Martini S, Powers M, Dunn C, Pugh P, Mills C, Osborn K, Seibel B, Choy A, Schnitzler C, Matsumoto G, Messié M, Schultz D, Winnikoff J, Gasca R, Browne W, Johnsen S, Schlining K, von Thun S, Erwin B, Ryan J, Thuesen E. Insights into the Biodiversity, Behavior, and Bioluminescence of Deep-Sea Organisms Using Molecular and Maritime Technology. Oceanography 2017, 30: 38-47. DOI: 10.5670/oceanog.2017.422.Peer-Reviewed Original Research
2016
Comparative genomics and the diversity of life
Dunn C, Munro C. Comparative genomics and the diversity of life. Zoologica Scripta 2016, 45: 5-13. DOI: 10.1111/zsc.12211.Peer-Reviewed Original ResearchGenomic analysisComparative genome analysisComparative genomic analysisNumber of speciesDiversity of lifeGenome functionGene duplicationComparative genomicsOrganism's phenotypeLaboratory model systemPhylogenetic analysisGene homologyGenome sequenceGenome analysisMore speciesBiodiversity researchGenomicsNomenclatural systemSpeciesModel systemCentral roleSystematicsOrthologsPhylogeneticsPowerful window
2015
Correction to Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda
Zapata F, Wilson N, Howison M, Andrade S, Jörger K, Schrödl M, Goetz F, Giribet G, Dunn C. Correction to Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda. Proceedings Of The Royal Society B 2015, 282: 20142941. PMCID: PMC4344162, DOI: 10.1098/rspb.2014.2941.Peer-Reviewed Original Research
2014
Animal Phylogeny and Its Evolutionary Implications
Dunn C, Giribet G, Edgecombe G, Hejnol A. Animal Phylogeny and Its Evolutionary Implications. Annual Review Of Ecology Evolution And Systematics 2014, 45: 1-25. DOI: 10.1146/annurev-ecolsys-120213-091627.Peer-Reviewed Original ResearchAnimal phylogenyAnimal treeEvolution of developmentEvolutionary radiationEvolutionary implicationsMore homoplasyFossil recordPhylogenySpiraliaDeep branchLate NeoproterozoicEarly CambrianRemarkable patternAnimal relationshipsAlternative hypothesisTreesXenacoelomorphaBilateriaEcdysozoaMonophylyProtostomiaGenomeHomoplasyRecent progressNervous system
2013
The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes
Bracken-Grissom H, Collins A, Collins T, Crandall K, Distel D, Dunn C, Giribet G, Haddock S, Knowlton N, Martindale M, Medina M, Messing C, O'Brien S, Paulay G, Putnam N, Ravasi T, Rouse G, Ryan J, Schulze A, Wörheide G, Adamska M, Bailly X, Breinholt J, Browne W, Diaz M, Evans N, Flot J, Fogarty N, Johnston M, Kamel B, Kawahara A, Laberge T, Lavrov D, Michonneau F, Moroz L, Oakley T, Osborne K, Pomponi S, Rhodes A, Santos S, Satoh N, Thacker R, Van de Peer Y, Voolstra C, Welch D, Winston J, Zhou X. The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes. Journal Of Heredity 2013, 105: 1-18. PMID: 24336862, PMCID: PMC4072906, DOI: 10.1093/jhered/est084.Peer-Reviewed Original ResearchConceptsGenome/transcriptome sequencingInvertebrate genomesMetazoan speciesPhyletic diversityMarine taxaPhylogenetic placementTaxonomic spectrumTranscriptome sequencingStudy taxaWhole genomeGenomeConservation researchInvertebratesSpeciesTaxaSequencingComparative approachPlacozoaCnidariaTranscriptomeCtenophoraPoriferaHuman healthArthropodaGenomicsSTEFAN SIEBERT, PHIL R. PUGH, STEVEN H. D. HADDOCK & CASEY W. DUNN (2013) Re-evaluation of characters in Apolemiidae (Siphonophora), with description of two new species from Monterey Bay, California. Zootaxa 3702 (3), 201–232
SIEBERT S, PUGH P, HADDOCK S, DUNN C. STEFAN SIEBERT, PHIL R. PUGH, STEVEN H. D. HADDOCK & CASEY W. DUNN (2013) Re-evaluation of characters in Apolemiidae (Siphonophora), with description of two new species from Monterey Bay, California. Zootaxa 3702 (3), 201–232. Zootaxa 2013, 3710: 100-100. DOI: 10.11646/zootaxa.3710.1.9.Peer-Reviewed Original Research