Robert Homer, MD, PhD
Professor of Pathology and of Medicine (Pulmonary)Cards
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Director of Medical Studies, Anatomic Pathology
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Are You a Patient?
View this doctor's clinical profile on the Yale Medicine website for information about the services we offer and making an appointment.
View Doctor ProfileAdditional Titles
Director of Medical Studies, Anatomic Pathology
Contact Info
Are You a Patient?
View this doctor's clinical profile on the Yale Medicine website for information about the services we offer and making an appointment.
View Doctor ProfileAdditional Titles
Director of Medical Studies, Anatomic Pathology
Contact Info
About
Titles
Professor of Pathology and of Medicine (Pulmonary)
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
Professor Phased RetirementPrimaryPulmonary, Critical Care & Sleep Medicine
ProfessorSecondary
Other Departments & Organizations
- Autopsy
- 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 Medicine
- Yale Ventures
Education & Training
- Resident
- Yale-New Haven Hospital (1992)
- PhD
- Yale University (1987)
- MD
- Yale University (1987)
Research
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
Lauren Cohn, MD
Naftali Kaminski, MD
David Rimm, MD, PhD
Mridu Gulati, MD
Akiko Iwasaki, PhD
Farida Ahangari, MD
Lung
Asthma
Pulmonary Fibrosis
Lung Neoplasms
Lung Diseases, Interstitial
Acute Lung Injury
Publications
2025
Prediction of Lymph Node Metastasis in Non–Small Cell Lung Carcinoma Using Primary Tumor Somatic Mutation Data
Lee V, Moore N, Doyle J, Hicks D, Oh P, Bodofsky S, Hossain S, Patel A, Aneja S, Homer R, Park H. Prediction of Lymph Node Metastasis in Non–Small Cell Lung Carcinoma Using Primary Tumor Somatic Mutation Data. JCO Clinical Cancer Informatics 2025, 9: e2400303. PMID: 40446175, DOI: 10.1200/cci-24-00303.Peer-Reviewed Original ResearchAltmetricMeSH Keywords and ConceptsConceptsNon-small cell lung cancerLymph node metastasisArea under the receiver operating characteristic curveNode metastasisTreatment strategiesNon-small cell lung carcinomaPrediction of lymph node metastasisSurvival analysisSNP dataLymph node metastasis statusAssociated with lymph node metastasisCell lung carcinomaCell lung cancerLymph node metastasis predictionReceiver operating characteristic curveDiagnostic methodsPersonalized treatment strategiesSingle-nucleotide polymorphism (SNPChi-square testMedian AUCLung carcinomaClinical outcomesNon-smallRisk stratificationLogistic regression modelsAPOBEC affects tumor evolution and age at onset of lung cancer in smokers
Zhang T, Sang J, Hoang P, Zhao W, Rosenbaum J, Johnson K, Klimczak L, McElderry J, Klein A, Wirth C, Bergstrom E, Díaz-Gay M, Vangara R, Colon-Matos F, Hutchinson A, Lawrence S, Cole N, Zhu B, Przytycka T, Shi J, Caporaso N, Homer R, Pesatori A, Consonni D, Imielinski M, Chanock S, Wedge D, Gordenin D, Alexandrov L, Harris R, Landi M. APOBEC affects tumor evolution and age at onset of lung cancer in smokers. Nature Communications 2025, 16: 4711. PMID: 40394004, PMCID: PMC12092836, DOI: 10.1038/s41467-025-59923-8.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsLung cancerTumor evolutionMulti-omics profilingLung tumor samplesCell of originProgenitor-like cellsMulti-omicsMutagenic processesMutational processesOff-target activityTP53 mutationsMutational burdenSignaling pathwayKRAS mutationsMutagenesisAPOBEC mutagenesisSomatic mutationsSolid tumorsTumor samplesClonal expansionDNA damageTumor developmentCell typesMutationsStemness markersSecretory leukocyte protease inhibitor influences periarticular joint inflammation in Borrelia burgdorferi-infected mice
Yu Q, Tang X, Hart T, Homer R, Belperron A, Bockenstedt L, Ring A, Nakamura A, Fikrig E. Secretory leukocyte protease inhibitor influences periarticular joint inflammation in Borrelia burgdorferi-infected mice. ELife 2025, 14: rp104913. PMID: 40392222, PMCID: PMC12092001, DOI: 10.7554/elife.104913.Peer-Reviewed Original ResearchAltmetricMeSH Keywords and ConceptsConceptsSecretory leukocyte protease inhibitorJoint inflammationC57BL/6 miceHigher infection loadTick-borne infectionsWild-type control miceClinical manifestations of infectionDevelopment of Lyme arthritisElevated serum levelsExcessive pro-inflammatory responsesManifestations of infectionProtease inhibitorsPro-inflammatory responseAnkle joint tissueInfection loadPromote tissue repairAnti-inflammatory effectsSerum levelsPeriarticular swellingClinical manifestationsControl miceTibiotarsal jointMMP-8Lyme diseaseIL-6Secretory leukocyte protease inhibitor influences periarticular joint inflammation in Borrelia burgdorferi-infected mice
Yu Q, Tang X, Hart T, Homer R, Belperron A, Bockenstedt L, Ring A, Nakamura A, Fikrig E. Secretory leukocyte protease inhibitor influences periarticular joint inflammation in Borrelia burgdorferi-infected mice. ELife 2025, 14 DOI: 10.7554/elife.104913.4.Peer-Reviewed Original ResearchConceptsSecretory leukocyte protease inhibitorSLPI-deficient miceJoint inflammationC57BL/6 miceDeficient miceB. burgdorferiHigher infection loadTick-borne infectionsWild-type control miceDeficient C57BL/6 miceClinical manifestations of infectionDevelopment of Lyme arthritisElevated serum levelsExcessive pro-inflammatory responsesManifestations of infectionProtease inhibitorsPro-inflammatory responseAnkle joint tissueInfection loadPromote tissue repairAnti-inflammatory effectsSerum levelsPeriarticular swellingClinical manifestationsControl mice
2024
SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data
Liu Y, Li N, Qi J, Xu G, Zhao J, Wang N, Huang X, Jiang W, Wei H, Justet A, Adams T, Homer R, Amei A, Rosas I, Kaminski N, Wang Z, Yan X. SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data. Genome Biology 2024, 25: 271. PMID: 39402626, PMCID: PMC11475911, DOI: 10.1186/s13059-024-03416-2.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsCharacterizing interstitial lung disease in patients with psoriasis: a cross-sectional analysis in the National Institutes of Health’s All of Us Research Program
Shaw V, Damsky W, Homer R, Cohen J. Characterizing interstitial lung disease in patients with psoriasis: a cross-sectional analysis in the National Institutes of Health’s All of Us Research Program. Clinical And Experimental Dermatology 2024, 49: 1083-1084. PMID: 38618708, DOI: 10.1093/ced/llae132.Peer-Reviewed Original ResearchConceptsElectronic health recordsUs Research ProgramCross-sectional analysisNational Institutes of HealthHealth recordsInstitutes of HealthConfounding variablesRate of interstitial lung diseaseMultivariate modelNational InstituteLung diseaseAssociationInterstitial lung diseaseConfoundingHealthORParticipantsASCL1 Drives Tolerance to Osimertinib in EGFR Mutant Lung Cancer in Permissive Cellular Contexts.
Hu B, Wiesehöfer M, de Miguel F, Liu Z, Chan L, Choi J, Melnick M, Arnal Estape A, Walther Z, Zhao D, Lopez-Giraldez F, Wurtz A, Cai G, Fan R, Gettinger S, Xiao A, Yan Q, Homer R, Nguyen D, Politi K. ASCL1 Drives Tolerance to Osimertinib in EGFR Mutant Lung Cancer in Permissive Cellular Contexts. Cancer Research 2024, 84: 1303-1319. PMID: 38359163, DOI: 10.1158/0008-5472.can-23-0438.Peer-Reviewed Original ResearchCitationsAltmetricConceptsTyrosine kinase inhibitorsPatient-derived xenograftsEGFR mutant lung cancerMutant lung cancerPre-treatment tumorsResidual diseaseDrug toleranceLung cancerResidual tumor cells in vivoEGFR mutant lung adenocarcinomaTyrosine kinase inhibitor osimertinibEGFR tyrosine kinase inhibitorsTyrosine kinase inhibitor treatmentTumor cells in vivoMutant lung adenocarcinomaMaximal tumor regressionTranscription factor Ascl1Drug-tolerant cellsTime of maximal responseEvidence of cellsCells in vivoOsimertinib treatmentTumor regressionSingle cell transcriptional profilingTumor cellsEGFR-Driven Lung Adenocarcinomas Co-opt Alveolar Macrophage Metabolism and Function to Support EGFR Signaling and Growth.
Kuhlmann-Hogan A, Cordes T, Xu Z, Kuna R, Traina K, Robles-Oteíza C, Ayeni D, Kwong E, Levy S, Globig A, Nobari M, Cheng G, Leibel S, Homer R, Shaw R, Metallo C, Politi K, Kaech S. EGFR-Driven Lung Adenocarcinomas Co-opt Alveolar Macrophage Metabolism and Function to Support EGFR Signaling and Growth. Cancer Discovery 2024, of1-of22. PMID: 38270272, DOI: 10.1158/2159-8290.cd-23-0434.Peer-Reviewed Original ResearchCitationsAltmetricConceptsLung adenocarcinomaGM-CSFEGFR-mutant lung adenocarcinomaT cell-based immunotherapyTransformed epitheliumOncogenic signalingGM-CSF secretionProinflammatory immune responseSuppress tumor progressionLocal immunosuppressionStatin therapyTherapeutic combinationsNovel therapiesTumor cellsTumor progressionTumor growthLung cancerLung adenocarcinoma cellsEGFR phosphorylationImmune responseImmunological supportCancer cellsInflammatory functionsAlveolar macrophagesIncreased cholesterol synthesisEGFR-driven lung adenocarcinomas coopt alveolar macrophage metabolism and function to support EGFR signaling and growth.
Kuhlmann-Hogan A, Cordes T, Xu Z, Kuna R, Traina K, Robles-Oteiza C, Ayeni D, Kwong E, Levy S, Globig A, Nobari M, Cheng G, Leibel S, Homer R, Shaw R, Metallo C, Politi K, Kaech S. EGFR-driven lung adenocarcinomas coopt alveolar macrophage metabolism and function to support EGFR signaling and growth. Cancer Discovery 2024, 14: 524-545. PMID: 38241033, PMCID: PMC11258210, DOI: 10.1158/2159-8290.cd-23-0434.Peer-Reviewed Original ResearchCitationsAltmetricConceptsLung adenocarcinomaGM-CSFEGFR-mutant lung adenocarcinomaGM-CSF secretionProinflammatory immune responseSuppress tumor progressionLocal immunosuppressionStatin therapyTherapeutic combinationsNovel therapiesTumor cellsTumor progressionTumor growthLung adenocarcinoma cellsEGFR phosphorylationImmune responseTransformed epitheliumCancer cellsInflammatory functionsEGFR signalingMacrophage metabolismAlveolar macrophagesIncreased cholesterol synthesisMetabolic supportOncogenic signaling
2023
Alveolar Vascular Remodeling in Nonspecific Interstitial Pneumonia: Replacement of Normal Lung Capillaries with COL15A1-Positive Endothelial Cells.
Schupp J, Manning E, Chioccioli M, Kamp J, Christian L, Ryu C, Herzog E, Kühnel M, Prasse A, Kaminski N, Jonigk D, Homer R, Neubert L, Ius F, stringJustet A, Hariri L, Seeliger B, Welte T, Knipe R, Gottlieb J. Alveolar Vascular Remodeling in Nonspecific Interstitial Pneumonia: Replacement of Normal Lung Capillaries with COL15A1-Positive Endothelial Cells. American Journal Of Respiratory And Critical Care Medicine 2023, 208: 819-822. PMID: 37552025, PMCID: PMC10563189, DOI: 10.1164/rccm.202303-0544le.Peer-Reviewed Original ResearchCitationsAltmetric
Clinical Trials
Current Trials
Determining Mechanisms of Sensitivity and Resistance to Anti-Cancer Therapy for Advanced Lung Cancer
HIC ID1603017333RoleSub InvestigatorPrimary Completion Date06/20/2026Recruiting Participants
Academic Achievements & Community Involvement
Activities
activity American Journal of Pathology
08/04/2023 - PresentJournal ServiceEditorial Board Memberactivity APC Advocacy committee
08/25/2023 - PresentAdvisory 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
Clinical Care
Overview
Robert Homer, MD, PhD, a pathologist, specializes in detecting diseases including cancers in and around the lungs. He is particularly interested in lung diseases leading to fibrosis, including those from exposures to foreign materials. He became interested in pathology as a graduate student—he wanted to know more about the structure and mechanisms of disease.
Dr. Homer is a professor of pathology at Yale School of Medicine.
Clinical Specialties
Fact Sheets
Interstitial Lung Disease (ILD)
Learn More on Yale Medicine
Board Certifications
Anatomic Pathology
- Certification Organization
- AB of Pathology
- Original Certification Date
- 1991
Yale Medicine News
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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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Are You a Patient? View this doctor's clinical profile on the Yale Medicine website for information about the services we offer and making an appointment.