David Ferguson
Senior Manager, BiorepositoryAbout
Titles
Senior Manager, Biorepository
Departments & Organizations
Education & Training
- MSc
- Quinnipiac College (1996)
- BS
- Western Conn State Coll (1984)
Research
Research at a Glance
Yale Co-Authors
Frequent collaborators of David Ferguson's published research.
Publications Timeline
A big-picture view of David Ferguson's research output by year.
Marie-Louise Landry, MD
Wade Schulz, MD, PhD
Nathan Grubaugh, PhD
Bony De Kumar, PhD
Chantal Vogels, PhD
Akiko Iwasaki, PhD
15Publications
575Citations
Publications
2024
Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections
Li K, Chaguza C, Stamp J, Chew Y, Chen N, Ferguson D, Pandya S, Kerantzas N, Schulz W, Initiative Y, Hahn A, Ogbunugafor C, Pitzer V, Crawford L, Weinberger D, Grubaugh N. Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections. PLOS Computational Biology 2024, 20: e1012469. PMID: 39288189, PMCID: PMC11432881, DOI: 10.1371/journal.pcbi.1012469.Peer-Reviewed Original ResearchMeSH Keywords and ConceptsConceptsGenome-wide association studiesSingle-nucleotide polymorphismsAssociation studiesWhole-genome sequencingAmino acid changesSingle nucleotide polymorphismsPairs of substitutionsViral copiesEpistasis testsGenome sequenceGenetic variationSpike geneAcid changesViral genomeNucleotide polymorphismsSARS-CoV-2Detect interactionsHost factorsVirus copiesCopyInfection dynamicsRT-qPCRPolymorphismOmicron BASARS-CoV-2 infection
2023
Enhanced inhibition of MHC-I expression by SARS-CoV-2 Omicron subvariants
Moriyama M, Lucas C, Monteiro V, Initiative Y, Iwasaki A, Chen N, Breban M, Hahn A, Pham K, Koch T, Chaguza C, Tikhonova I, Castaldi C, Mane S, De Kumar B, Ferguson D, Kerantzas N, Peaper D, Landry M, Schulz W, Vogels C, Grubaugh N. Enhanced inhibition of MHC-I expression by SARS-CoV-2 Omicron subvariants. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2221652120. PMID: 37036977, PMCID: PMC10120007, DOI: 10.1073/pnas.2221652120.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsMHC-I expressionBreakthrough infectionsSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variantsMajor histocompatibility complex class I expressionCell-mediated immunityInfluenza virus infectionSARS-CoV-2 VOCsMHC-I upregulationClass I expressionSARS-CoV-2T cell recognitionVirus infectionMHC II expressionSpike proteinEnhanced inhibitionInfectionCell recognitionCommon mutationsReinfectionE proteinAntibodiesViral genesSubvariantsExpressionAccelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection
Chaguza C, Hahn A, Petrone M, Zhou S, Ferguson D, Breban M, Pham K, Peña-Hernández M, Castaldi C, Hill V, Initiative Y, Billig K, Earnest R, Fauver J, Kalinch C, Kerantzas N, Koch T, De Kumar B, Landry M, Ott I, Peaper D, Tikhonova I, Vogels C, Schulz W, Swanstrom R, Roberts S, Grubaugh N. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. Cell Reports Medicine 2023, 4: 100943. PMID: 36791724, PMCID: PMC9906997, DOI: 10.1016/j.xcrm.2023.100943.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsChronic infectionEvolutionary ratesGenetic diversityIntrahost evolutionDistinct genotypesHigher viral genome copiesVirus evolutionary ratesSARS-CoV-2 evolutionUntreated chronic infectionAdvantageous mutationsNucleotide substitutionsViral genome copiesDivergent variantsInfection hypothesisVariant emergenceViral populationsInfectious virusInfectionHallmark changesGenome copiesDifferent genotypesDiversityGenotypesTemporal dynamicsEvolution
2022
Use of Whole-Genome Sequencing to Estimate the Contribution of Immune Evasion and Waning Immunity on Decreasing COVID-19 Vaccine Effectiveness
Lind M, Copin R, McCarthy S, Coppi A, Warner F, Ferguson D, Duckwall C, Borg R, Muenker M, Overton J, Hamon S, Zhou A, Cummings D, Ko A, Hamilton J, Schulz W, Hitchings M. Use of Whole-Genome Sequencing to Estimate the Contribution of Immune Evasion and Waning Immunity on Decreasing COVID-19 Vaccine Effectiveness. The Journal Of Infectious Diseases 2022, 227: 663-674. PMID: 36408616, DOI: 10.1093/infdis/jiac453.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsVaccine effectivenessImmune evasionDelta infectionVE estimatesSecond doseTest-negative case-control studySevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2Whole-genome sequencingCOVID-19 vaccine effectivenessRespiratory syndrome coronavirus 2Syndrome coronavirus 2Case-control studyCoronavirus 2Calendar periodDelta variantInfectionDoseEvasionDaysLow effectivenessImmunityVariants
2013
Comparison of Simplexa HSV 1 & 2 PCR with Culture, Immunofluorescence, and Laboratory-Developed TaqMan PCR for Detection of Herpes Simplex Virus in Swab Specimens
Gitman MR, Ferguson D, Landry ML. Comparison of Simplexa HSV 1 & 2 PCR with Culture, Immunofluorescence, and Laboratory-Developed TaqMan PCR for Detection of Herpes Simplex Virus in Swab Specimens. Journal Of Clinical Microbiology 2013, 51: 3765-3769. PMID: 24006008, PMCID: PMC3889765, DOI: 10.1128/jcm.01413-13.Peer-Reviewed Original ResearchCitationsAltmetricMeSH KeywordsAdolescentAdultAgedAged, 80 and overChildChild, PreschoolClinical Laboratory TechniquesCosts and Cost AnalysisFemaleFluorescent Antibody TechniqueHerpes SimplexHumansInfantInfant, NewbornMaleMiddle AgedPolymerase Chain ReactionSensitivity and SpecificitySimplexvirusTime FactorsVirus CultivationYoung Adult
2009
Polymerase chain reaction and the diagnosis of viral gastrointestinal disease due to cytomegalovirus, herpes simplex virus and adenovirus
Landry ML, Ferguson D. Polymerase chain reaction and the diagnosis of viral gastrointestinal disease due to cytomegalovirus, herpes simplex virus and adenovirus. Journal Of Clinical Virology 2009, 45: 83-84. PMID: 19324590, DOI: 10.1016/j.jcv.2009.02.007.Peer-Reviewed Original ResearchCitationsMeSH Keywords and Concepts
2008
An Outbreak of Concurrent Echovirus 30 and Coxsackievirus A1 Infections Associated with Sea Swimming among a Group of Travelers to Mexico
Begier EM, Oberste MS, Landry ML, Brennan T, Mlynarski D, Mshar PA, Frenette K, Rabatsky-Ehr T, Purviance K, Nepaul A, Nix WA, Pallansch MA, Ferguson D, Cartter ML, Hadler JL. An Outbreak of Concurrent Echovirus 30 and Coxsackievirus A1 Infections Associated with Sea Swimming among a Group of Travelers to Mexico. Clinical Infectious Diseases 2008, 47: 616-623. PMID: 18637756, DOI: 10.1086/590562.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsEchovirus 30Enteroviral infectionNucleic acid amplification testingIllness onset datesUninfected control subjectsPoint-source exposureMultiple enterovirusesAseptic meningitisFrequent symptomsIllness onsetViral cultureAmplification testingControl subjectsCerebrospinal fluidHuman stoolInfectionNauseaConnecticut DepartmentStoolCoxsackievirus (CV) A1Public healthIllnessEnterovirusesMolecular amplificationGroups of travelers
2006
Coronavirus HKU1 Infection in the United States - Volume 12, Number 5—May 2006 - Emerging Infectious Diseases journal - CDC
Esper F, Weibel C, Ferguson D, Landry ML, Kahn JS. Coronavirus HKU1 Infection in the United States - Volume 12, Number 5—May 2006 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2006, 12: 775-779. PMID: 16704837, PMCID: PMC3374449, DOI: 10.3201/eid1205.051316.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsHCoV-HKU1Respiratory specimensLower respiratory tract infectionsLower respiratory tract diseaseHCoV-HKU1 infectionRespiratory tract infectionsRespiratory syncytial virusRespiratory tract diseaseReverse transcription-polymerase chain reactionNew human coronavirusYears of ageTranscription-polymerase chain reactionTract infectionsSyncytial virusPositive childrenParainfluenza virusTract diseaseRespiratory tractHuman coronavirusesPositive specimensInfluenza virusInfectionChain reactionChildrenVirus
2004
Automated detection of immunofluorescently labeled cytomegalovirus‐infected cells in isolated peripheral blood leukocytes using decision tree analysis
Ladanyi A, Sher AC, Herlitz A, Bergsrud DE, Kraeft S, Kepros J, McDaid G, Ferguson D, Landry ML, Chen LB. Automated detection of immunofluorescently labeled cytomegalovirus‐infected cells in isolated peripheral blood leukocytes using decision tree analysis. Cytometry Part A 2004, 58A: 147-156. PMID: 15057968, DOI: 10.1002/cyto.a.20016.Peer-Reviewed Original ResearchCitationsMeSH Keywords and ConceptsConceptsPeripheral blood leukocytesBlood leukocytesPatient samplesDecision tree analysisImage cytometryCytomegalovirus-infected cellsCMV infectionCytomegalovirus infectionAntiviral therapyViral antigensCellular featuresCytospin preparationsLeukocytesInfectionCytometryManual microscopic analysisImage cytometerRare cellsCellsSimilar resultsPatientsCMVTherapyAntigenDiagnosis
2001
Evaluation of Biosite Triage Clostridium difficile Panel for Rapid Detection of Clostridium difficile in Stool Samples
Landry M, Topal J, Ferguson D, Giudetti D, Tang Y. Evaluation of Biosite Triage Clostridium difficile Panel for Rapid Detection of Clostridium difficile in Stool Samples. Journal Of Clinical Microbiology 2001, 39: 1855-1858. PMID: 11326003, PMCID: PMC88038, DOI: 10.1128/jcm.39.5.1855-1858.2001.Peer-Reviewed Original ResearchCitationsMeSH Keywords and ConceptsConceptsNegative predictive valuePositive predictive valueCommon antigenStool samplesPredictive valueC. difficile toxin AHigh negative predictive valueAntigen-positive patientsDifficile-negative patientsAntigen positive resultDifficile toxin ADifficile carriersContact precautionsAntibiotic treatmentToxin ACytotoxin titersTriage PanelUnnecessary useClostridium difficilePatients