About
Titles
Professor
Biography
My lab studies animal evolution, with a particular focus on better understanding our most distant animal relatives and the earliest events in the animal tree of life. Our research includes field work to collect poorly known animals, often by SCUBA diving and sometimes with remotely operated underwater vehicles. Lab bench work includes studies of anatomy and genome function. Much of my work is computational- we develop methods and tools for analyzing evolutionary relationships and using those relationships to provide an integrated perspective on genomic and anatomical evolution. I coauthored the book Practical Computing for Biologists to help more biologists become comfortable with computational methods. In addition to his studies of broad patterns of diversity across distantly related animals, my lab also focuses on siphonophores, a group of about 185 species of open-ocean animals that include the Portuguese Man of War. We address basic questions about their structure, growth, diversity, and evolution. I did my undergraduate studies at Stanford University, my graduate studies were with Günter Wagner at Yale, and postdoc studies with Mark Martindale at the University of Hawaii.
Appointments
Department of Ecology & Evolutionary Biology
ProfessorPrimaryGenetics
ProfessorSecondary
Other Departments & Organizations
Education & Training
- PhD
- Yale University, Ecology and Evolutionary Biology (2005)
- MS
- Yale University, Ecology and Evolutionary Biology
Research
Overview
Medical Research Interests
ORCID
0000-0003-0628-5150- View Lab Website
Dunn Lab
Research at a Glance
Yale Co-Authors
Publications Timeline
Research Interests
Gunter Wagner, PhD
Publications
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 ResearchConceptsHIV-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 ResearchMeSH Keywords and ConceptsConceptsGerm 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 ResearchConceptsRoutine 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 ResearchConceptsHIV 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 ResearchMeSH Keywords and ConceptsConceptsScRNA-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 ResearchConceptsTrophic 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 ResearchMeSH Keywords and ConceptsConceptsK-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 ResearchConceptsSingle-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 ResearchConceptsMolecular 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