Robert Homer, MD, PhD
Professor Emeritus of Pathology and Senior Research ScientistCards
Additional Titles
Director of Medical Studies, Anatomic Pathology
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Titles
Professor Emeritus of Pathology and Senior Research Scientist
Director of Medical Studies, Anatomic Pathology
Biography
Historically, my major interests have been in diagnostic and experimental lung pathology. I was lead thoracic pathologist at Yale from 2004 to 2022 and have experience in diagnosing and classifying the full range of histopathology of clinical lung disease. I was also Director of Anatomic Pathology at VA Connecticut HealthCare system (aka the West Haven VA) from 1994 to 2022.
My PhD was on aspects of the murine MHC. My post doctoral fellowship was with Richard Flavell on development of T cell tolerance. Since then, I have helped evaluate various murine models of inflammatory lung disease, ran an NIH funded morphology core for the Yale pulmonary section, and ran a basic laboratory at West Haven VA looking at murine models of pulmonary fibrosis. I now mostly consult on various experimental models of lung disease and work with collaborators analyzing human fibrotic and neoplastic disease.
I am heavily involved in medical school curriculum development as Director of Medical Education for Pathology. I am Co-Director of the pre-clerkship YSM course Attacks and Defenses (covering immunology, infectious disease, microbiology, rheumatology and dermatology). One of my major current interests is exploring use of Large Language Models in medical education.
Appointments
Pathology
EmeritusPrimaryPathology
Senior Research ScientistSecondaryPulmonary, Critical Care & Sleep Medicine
ProfessorSecondary
Other Departments & Organizations
- All Institutions
- Cancer Signaling Networks
- Cardiovascular Pathology
- Center for Thoracic Cancers
- Creed House Affiliates
- Internal Medicine
- Interstitial Lung Disease (ILD) Program
- Occupational & Environmental Lung Diseases Program
- Pathology
- Pathology and Molecular Medicine
- Pathology Research
- Pulmonary, Critical Care & Sleep Medicine
- Surgical Pathology
- Thoracic Pathology
- Yale Cancer Center
- Yale Ventures
Education & Training
- Resident
- Yale-New Haven Hospital (1992)
- PhD
- Yale University (1987)
- MD
- Yale University (1987)
Board Certifications
Anatomic Pathology
- Certification Organization
- AB of Pathology
- Original Certification Date
- 1991
Research
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Overview
(1) Pathology of neoplastic and inflammatory lung diseases.
2) Miscellaneous interests include autopsy pathology, case reports, and quality assurance issues in pathology.
Medical Research Interests
ORCID
0000-0002-2055-5885
Research at a Glance
Yale Co-Authors
Publications Timeline
Research Interests
Naftali Kaminski, MD
Lauren Cohn, MD
David Rimm, MD, PhD
Akiko Iwasaki, PhD
Mridu Gulati, MD, MPH
Xiting Yan, PhD
Lung
Asthma
Pulmonary Fibrosis
Lung Neoplasms
Lung Diseases, Interstitial
Acute Lung Injury
Publications
2026
From complexity to clarity: GPT-4 for patient-centered prostate cancer pathology reports
Fereydooni S, Homer R, Chartash D. From complexity to clarity: GPT-4 for patient-centered prostate cancer pathology reports. Patient Education And Counseling 2026, 149: 109597. PMID: 41905268, DOI: 10.1016/j.pec.2026.109597.Peer-Reviewed Original ResearchConceptsCancer pathology reportsPathology reportsPatient comprehensionLimited health literacyReading levelHealth literacyPaired t-testProstate cancer pathologyHealth communicationCancer diagnosisClinical workflowMedical informationCancer Genome Atlas databaseMinimal burdenClinical accuracyT-testCancer pathologyAtlas databasePatientsCommon Core StandardsOriginal reportDecision-makingPathologyCore standardsReportsMild SARS-CoV-2 maternal infection in mice induces transient offspring neurodevelopmental aberrance
Tung W, Yuen M, Cai H, Cho H, Lu P, Kliman H, Homer R, Herrerias A, Salla N, Rivera A, Liu Y, Pattabiraman K, Iwasaki A. Mild SARS-CoV-2 maternal infection in mice induces transient offspring neurodevelopmental aberrance. Proceedings Of The National Academy Of Sciences Of The United States Of America 2026, 123: e2518294123. PMID: 41849379, PMCID: PMC13012083, DOI: 10.1073/pnas.2518294123.Peer-Reviewed Original ResearchAltmetricMeSH Keywords and ConceptsConceptsSARS-CoV-2 infectionPlacental inflammationEffects of maternal SARS-CoV-2 infectionMaternal SARS-CoV-2 infectionMouse modelMaternal viral infectionPostnatal day 5Systemic immune responsesMild COVID-19Object recognition testMaternal infectionMicroglial abundanceInfected mothersNeurodevelopmental abnormalitiesNeurodevelopmental aberrationsImmune responseDay 5Soluble factorsRisk factorsViral infectionCerebral cortexRespiratory tractSynaptic densityInfectionSARS-CoV-2Genomic Characterization of Lung Cancer in Never-Smokers Using Deep Learning
Saha M, Tran T, Bhawsar P, Zhang T, Zhao W, Hoang P, Mutreja K, Lawrence S, Rothman N, Lan Q, Homer R, Baine M, Sholl L, Joubert P, Leduc C, Travis W, Chanock S, Shi J, Yang S, Almeida J, Landi M. Genomic Characterization of Lung Cancer in Never-Smokers Using Deep Learning. Modern Pathology 2026, 39: 100973. PMID: 41638573, PMCID: PMC12975288, DOI: 10.1016/j.modpat.2026.100973.Peer-Reviewed Original ResearchConceptsWhole-slide imagesDeep learningCustomized deep convolutional neural networkDeep convolutional neural networkHistological whole-slide imagesConvolutional neural networkHotspot mutationsLung cancerMultilabel classificationBottleneck layerClassification headResidual blockCharacterization of lung cancerKRAS hotspot mutationsResNet50 architectureComputational complexityTumor mutational burdenInception-v3Neural networkReceiver operating characteristic curveHistologically distinctive subsetAPOBEC mutational signaturesOperating characteristics curveALK fusionsCDKN2A deletionAberrant cellular communities underlying disease heterogeneity in chronic obstructive pulmonary disease
Zhang Y, Wei H, Nouws J, Jiang W, Brewster R, Nguyen J, Liang S, Pass S, Wang W, Collin F, Oill A, Kim S, Siller S, Liu J, Zhao A, Hansbro P, Dela Cruz C, Britto C, Gomez J, Cloonan S, Herzog E, Lam T, Banovich N, Raredon M, Zhang X, Mangiola S, Homer R, Kaminski N, McDonough J, Polverino F, Yan X, Sauler M. Aberrant cellular communities underlying disease heterogeneity in chronic obstructive pulmonary disease. Nature Genetics 2026, 58: 376-391. PMID: 41578022, PMCID: PMC12900648, DOI: 10.1038/s41588-025-02480-z.Peer-Reviewed Original ResearchAltmetricMeSH Keywords and ConceptsConceptsChronic obstructive pulmonary diseaseObstructive pulmonary diseasePlasma biomarkersPulmonary diseaseComposite symptom scoreStudy participantsCell statesEarly COPDCellular landscapeNonimmune cellsCell communication analysisSymptom scoresImmune populationsSingle-nucleus RNA sequencingDisease progressionTherapeutic strategiesLung functionLung tissueChronic obstructive pulmonary disease heterogeneityMolecular driversDisease heterogeneityRegenerative stateCell compositionPathological cellsCell-autonomousCommentary on: Update of the international multidisciplinary classification of the interstitial pneumonias: an ERS/ATS statement
Homer R. Commentary on: Update of the international multidisciplinary classification of the interstitial pneumonias: an ERS/ATS statement. European Respiratory Journal 2026, 67: 2501947. PMID: 41506684, DOI: 10.1183/13993003.01947-2025.Peer-Reviewed Original Research
2025
Microbiome analysis of 940 lung cancers in never-smokers reveals lack of clinically relevant associations
McElderry J, Zhang T, Zhao W, Hoang P, Anyaso-Samuel S, Sang J, Khandekar A, Hartman C, Colón-Matos F, Miraftab M, Saha M, Lee O, Sharma S, Jones K, Zhu B, Díaz-Gay M, Mas L, Arrieta O, Edell E, Santamaría J, Schabath M, Yendamuri S, Manczuk M, Lissowska J, Świątkowska B, Mukeria A, Shangina O, Zaridze D, Holcatova I, Janout V, Mates D, Ognjanovic S, Savic M, Kontic M, Bossé Y, Gould Rothberg B, Christiani D, Gaborieau V, Brennan P, Liu G, Hofman P, Wong M, Leung K, Chen C, Hsiung C, Rothman N, Leduc C, Baine M, Travis W, Sholl L, Joubert P, Homer R, Yang S, Lan Q, Nowak M, Wedge D, Alexandrov L, Chanock S, Vogtmann E, Abnet C, Shi J, Landi M. Microbiome analysis of 940 lung cancers in never-smokers reveals lack of clinically relevant associations. Nature Communications 2025, 17: 192. PMID: 41387456, PMCID: PMC12780107, DOI: 10.1038/s41467-025-66780-y.Peer-Reviewed Original ResearchAltmetricConceptsWhole-genome sequencingRNA-seqMicrobiome associationsRRNA gene sequencesMicrobial readsGene sequencesMicrobiome studiesSpecies levelTissue microbiomeGenetic ancestryMultiple data typesCommensal bacteriaMicrobiome analysisBacterial DNACancer microbiomeMicrobiomeLow biomassGenomic alterationsPaired normal lung tissuesHuman cancersSequenceLung cancerNormal lung tissuesLung tissueGenusUncovering the role of LINE-1 in the evolution of lung adenocarcinoma
Zhang T, Zhao W, Wirth C, Díaz-Gay M, Yin J, Cecati M, Marchegiani F, Hoang P, Leduc C, Baine M, Travis W, Sholl L, Joubert P, Sang J, McElderry J, Antony M, Klein A, Khandekar A, Hartman C, Rosenbaum J, Colón-Matos F, Miraftab M, Saha M, Lee O, Jones K, Caporaso N, Wong M, Leung K, Hsiung C, Chen C, Edell E, Santamaría J, Schabath M, Yendamuri S, Manczuk M, Lissowska J, Świątkowska B, Mukeria A, Shangina O, Zaridze D, Holcatova I, Mates D, Milosavljevic S, Savic M, Bossé Y, Rothberg B, Christiani D, Gaborieau V, Brennan P, Liu G, Hofman P, Homer R, Yang S, Pesatori A, Consonni D, Yang L, Zhu B, Shi J, Brown K, Rothman N, Chanock S, Alexandrov L, Choi J, Cardelli M, Lan Q, Nowak M, Wedge D, Landi M. Uncovering the role of LINE-1 in the evolution of lung adenocarcinoma. Nature 2025, 650: 230-241. PMID: 41372401, PMCID: PMC12823094, DOI: 10.1038/s41586-025-09825-y.Peer-Reviewed Original ResearchCitationsAltmetricConceptsLung adenocarcinomaEvolution of lung adenocarcinomaPoor overall survivalCopy-number alterationsTobacco smoke exposureEGFR mutationsNeoantigen burdenOverall survivalHypoxia scoreNever-smokersAggressive phenotypeSubclonal diversificationTreatment planningDeep whole-genome sequencingPromoter demethylationMetastasis propensityTumorSmoke exposureWhole-genome sequencingClonal architectureFemale individualsMutational signaturesShort latencyAdenocarcinomaIndividuals of European ancestryA Prognostic Signature for Lung Adenocarcinoma in Patients Who Have Never Smoked.
Zhao W, Zhang T, Hua X, Hoang P, Miraftab M, Saha M, McElderry J, Sang J, Lee O, Hartman C, Khandekar A, Sharma S, Colón-Matos F, Anyaso-Samuel S, Wang D, Jones K, Hutchinson A, Hicks B, Rosenbaum J, Zhong X, Yang Y, Pesatori A, Consonni D, Christiani D, Leung K, Wong M, Manczuk M, Lissowska J, Świątkowska B, Mukeria A, Shangina O, Zaridze D, Holcatova I, Mates D, Milosavljevic S, Ognjanovic S, Savic M, Kontic M, Gaborieau V, Brennan P, Arrieta O, Bossé Y, Edell E, Schabath M, Hofman P, Mas L, Yendamuri S, Chen C, Chang I, Hsiung C, Liu G, Martinez Santamaría J, Gould Rothberg B, Mutreja K, Lawrence S, Rothman N, Alexandrov L, Leduc C, Baine M, Joubert P, Sholl L, Travis W, Homer R, Lan Q, Chanock S, Yang L, Yang S, Shi J, Landi M. A Prognostic Signature for Lung Adenocarcinoma in Patients Who Have Never Smoked. Cancer Discovery 2025, 16: 460-477. PMID: 41165571, PMCID: PMC12822368, DOI: 10.1158/2159-8290.cd-25-0581.Peer-Reviewed Original ResearchCitationsAltmetricConceptsDriver gene alterationsLung adenocarcinomaStage I tumorsEpithelial-to-mesenchymal transition markersI tumorsTP53 mutationsTumor stageProlonged survivalAggressive subtypeGene alterationsProliferation markersImmune evasionLow proliferationHistological characteristicsPrognostic signatureHistological dataRNA-seq dataTransition markersTumor cell dynamicsClinical settingSubtypesCell compositionAdenocarcinomaTumorPrognosisIntranasal hemagglutinin protein boosters induce protective mucosal immunity against influenza A viruses in mice
Moriyama M, Rodrigues G, Wang J, Jayewickreme R, Hudak A, Dong H, Homer R, Ma S, Iwasaki A. Intranasal hemagglutinin protein boosters induce protective mucosal immunity against influenza A viruses in mice. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2422171122. PMID: 40991437, PMCID: PMC12501169, DOI: 10.1073/pnas.2422171122.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsInfluenza A virusProtein boosterA virusMucosal immunityHeterologous influenza virusesParenteral influenza vaccinationRespiratory tractLocal mucosal immune responsesImmune memory responseInduce mucosal immunityMucosal immune responsesSystemic antibody responsesMucosal humoral responsesUpper respiratory tractInfluenza vaccineInfluenza virusViral burdenRecombinant hemagglutininVaccine-matchedOld miceMemory responsesHumoral responseImmune responseAntibody responseViral replicationThe mutagenic forces shaping the genomes of lung cancer in never smokers
Díaz-Gay M, Zhang T, Hoang P, Leduc C, Baine M, Travis W, Sholl L, Joubert P, Khandekar A, Zhao W, Steele C, Otlu B, Nandi S, Vangara R, Bergstrom E, Kazachkova M, Pich O, Swanton C, Hsiung C, Chang I, Wong M, Leung K, Sang J, McElderry J, Hartman C, Colón-Matos F, Miraftab M, Saha M, Lee O, Jones K, Gallego-García P, Yang Y, Zhong X, Edell E, Santamaría J, Schabath M, Yendamuri S, Manczuk M, Lissowska J, Świątkowska B, Mukeria A, Shangina O, Zaridze D, Holcatova I, Mates D, Milosavljevic S, Kontic M, Bossé Y, Rothberg B, Christiani D, Gaborieau V, Brennan P, Liu G, Hofman P, Yang L, Nowak M, Shi J, Rothman N, Wedge D, Homer R, Yang S, Pesatori A, Consonni D, Lan Q, Zhu B, Chanock S, Choi J, Alexandrov L, Landi M. The mutagenic forces shaping the genomes of lung cancer in never smokers. Nature 2025, 644: 133-144. PMID: 40604281, PMCID: PMC12667038, DOI: 10.1038/s41586-025-09219-0.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsExposure to secondhand smokeExposure to second-hand tobacco smokeSecond-hand tobacco smokeHighest prevalenceLung cancerSecondhand smokeTP53 mutationsNever smokersLevels of air pollutionAir pollution levelsTobacco smokeAir pollutionTreatment-naive individualsPrevalence of eGFRSmokersDose-response effectEGFR mutationsSmokingCancer genomesEast AsiaKRAS mutationsDriver mutationsSomatic mutationsAdenocarcinomaCancer
Clinical Trials
Current Trials
Determining Mechanisms of Sensitivity and Resistance to Anti-Cancer Therapy for Advanced Lung Cancer
IRB ID1603017333RoleSub InvestigatorPrimary Completion Date06/20/2026Recruiting Participants
Academic Achievements & Community Involvement
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Activities
activity American Journal of Pathology
08/04/2023 - PresentJournal ServiceEditorial Board Memberactivity APC Advocacy committee
08/25/2023 - 08/08/2025Advisory BoardsBoard MemberDetailsAssociation of Pathology ChairsAcademically-focused advocacy objectives in education, practice and research.activity From Bots to Docs, Harnessing AI in the medical education journey
07/10/2023 - 07/12/2023LectureAssociation of Pathology Chairs, Undergraduate Medical Education SectionDetailsChicago, IL, United States
Honors
honor Keynote address
06/24/2009International AwardPulmonary Pathology SocietyDetailsUnited States
News & Links
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Media
- Eosinophilic response in fibrotic lung disease.
News
- June 21, 2024Source: College of American Pathologists Today
How-well-does-chatgpt-do-on-pathology-questions?
- April 01, 2024
Yale Faculty Present Groundbreaking Clinical Research at the 2024 American College of Cardiology Scientific Sessions
- August 03, 2023
Lung Adenocarcinomas: New Findings About Resistance to Targeted Therapies
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