Mark N. Lee, MD, PhD
Assistant Professor of Laboratory MedicineDownloadHi-Res Photo
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Appointments
Laboratory Medicine
Primary
Pathology
Secondary
Contact Info
Laboratory Medicine
Clinic Building 405, 333 Cedar Street
New Haven, CT 06520
United States
About
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Titles
Assistant Professor of Laboratory Medicine
Biography
Dr. Mark Lee is an Assistant Professor in the Department of Laboratory Medicine with a secondary affiliation in the Department of Pathology, and is a member of Yale's Human and Translational Immunology (HTI) Program as well as the Cancer Immunology Research Program at Yale Cancer Center. Dr. Lee received his B.S. and M.S. degrees in Molecular Biophysics & Biochemistry at Yale University, and his M.D. and Ph.D. degrees from Harvard Medical School. He performed his Ph.D. work in Immunology at Harvard Medical School and the Broad Institute of MIT and Harvard, where he studied how common genetic variants alter immune phenotypes. He completed residency in Clinical Pathology at the Brigham and Women's Hospital, followed by a fellowship in Transfusion Medicine in the Harvard Joint Program in Transfusion Medicine, and a postdoctoral fellowship at the Dana-Farber Cancer Institute. He served as an attending physician on the Blood Transfusion Service in the Department of Pathology at the Massachusetts General Hospital, prior to joining the faculty at Yale School of Medicine as a physician-scientist and Principal Investigator.
Last Updated on August 03, 2025.
Appointments
Laboratory Medicine
Assistant ProfessorPrimaryPathology
Assistant ProfessorSecondary
Other Departments & Organizations
- Cancer Immunology
- Human and Translational Immunology Program
- Immunology
- Janeway Society
- Laboratory Medicine
- Mark Lee Lab
- Molecular Medicine, Pharmacology, and Physiology
- Pathology
- Program in Translational Biomedicine (PTB)
- Yale Cancer Center
- Yale Combined Program in the Biological and Biomedical Sciences (BBS)
- Yale Medicine
Education & Training
- Fellow
- Massachusetts General Hospital (2019)
- Resident
- Brigham and Women's Hospital (2018)
- MD
- Harvard Medical School (2015)
- PhD
- Harvard Medical School, Immunology (2013)
- MS
- Yale University, Molecular Biophysics & Biochemistry (2004)
- BS
- Yale University, Molecular Biophysics & Biochemistry (2004)
Research
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Overview
Medical Research Interests
Adaptive Immunity; Antigenic Variation; Antigens; Autoimmune Diseases; Autoimmunity; Biological Variation, Individual; Clonal Selection, Antigen-Mediated; Gene Rearrangement, T-Lymphocyte; Genomics; Hematologic Diseases; Immune Checkpoint Inhibitors; Immune Evasion; Immune System Diseases; Immunologic Memory; Immunotherapy; Lymphocyte Activation; Major Histocompatibility Complex; Molecular Medicine; Neoplasms; Neoplastic Processes; Pathology; Pathology, Clinical; T-Cell Antigen Receptor Specificity; Translational Science, Biomedical; Tumor Microenvironment
ORCID
0000-0002-9576-9589- View Lab Website
Lee Lab
Research at a Glance
Yale Co-Authors
Frequent collaborators of Mark N. Lee's published research.
Publications Timeline
A big-picture view of Mark N. Lee's research output by year.
Research Interests
Research topics Mark N. Lee is interested in exploring.
David A. Hafler, MD, FANA
18Publications
3,617Citations
Autoimmune Diseases
Autoimmunity
Adaptive Immunity
Publications
2021
Antigen identification for HLA class I– and HLA class II–restricted T cell receptors using cytokine-capturing antigen-presenting cells
Lee M, Meyerson M. Antigen identification for HLA class I– and HLA class II–restricted T cell receptors using cytokine-capturing antigen-presenting cells. Science Immunology 2021, 6 PMID: 33483338, PMCID: PMC8320540, DOI: 10.1126/sciimmunol.abf4001.Peer-Reviewed Original ResearchCitationsAltmetricMeSH KeywordsAntigen PresentationAntigen-Presenting CellsCD4-Positive T-LymphocytesCD8-Positive T-LymphocytesCell EngineeringCytokinesEpitope MappingEpitopes, T-LymphocyteHEK293 CellsHeLa CellsHigh-Throughput Screening AssaysHistocompatibility Antigens Class IHistocompatibility Antigens Class IIHumansJurkat CellsPeptide LibraryReceptors, Antigen, T-Cell
2018
Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection
Ye C, Chen J, Villani A, Gate R, Subramaniam M, Bhangale T, Lee M, Raj T, Raychowdhury R, Li W, Rogel N, Simmons S, Imboywa S, Chipendo P, McCabe C, Lee M, Frohlich I, Stranger B, De Jager P, Regev A, Behrens T, Hacohen N. Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection. Genome Research 2018, 28: 1812-1825. PMID: 30446528, PMCID: PMC6280757, DOI: 10.1101/gr.240390.118.Peer-Reviewed Original ResearchCitationsAltmetricMeSH KeywordsAdolescentAdultAlternative SplicingAminopeptidasesChromosome MappingComputational BiologyDendritic CellsFemaleGene Expression ProfilingGene Expression RegulationGene OntologyGenetic Predisposition to DiseaseGenetic TestingGenetic VariationHost-Pathogen InteractionsHumansInfluenza A virusInfluenza, HumanInterferon Type IMaleMiddle AgedModels, BiologicalMolecular Sequence AnnotationMonocytesQuantitative Trait LociTranscriptomeYoung Adult
2017
Systematic STAT3 sequencing in patients with unexplained cytopenias identifies unsuspected large granular lymphocytic leukemia
Morgan E, Lee M, DeAngelo D, Steensma D, Stone R, Kuo F, Aster J, Gibson C, Lindsley R. Systematic STAT3 sequencing in patients with unexplained cytopenias identifies unsuspected large granular lymphocytic leukemia. Blood Advances 2017, 1: 1786-1789. PMID: 29296824, PMCID: PMC5728102, DOI: 10.1182/bloodadvances.2017011197.Peer-Reviewed Original ResearchCitationsAltmetric
2016
Persistently High Cardiac Troponin T with a Negative Cardiac Workup
Lee M, Skali H, Jarolim P. Persistently High Cardiac Troponin T with a Negative Cardiac Workup. Clinical Chemistry 2016, 62: 896-897. PMID: 27235467, DOI: 10.1373/clinchem.2015.248377.Peer-Reviewed Original ResearchAltmetricHigh-Dose Biotin Treatment for Secondary Progressive Multiple Sclerosis May Interfere with Thyroid Assays
Minkovsky A, Lee M, Dowlatshahi M, Angell T, Mahrokhian L, Petrides A, Melanson S, Marqusee E, Woodmansee W. High-Dose Biotin Treatment for Secondary Progressive Multiple Sclerosis May Interfere with Thyroid Assays. AACE Clinical Case Reports 2016, 2: e370-e373. PMID: 27917400, PMCID: PMC5134919, DOI: 10.4158/ep161261.cr.Peer-Reviewed Original ResearchCitationsAltmetricConceptsHigh dose biotinLaboratory valuesLaboratory assessment of thyroid functionLaboratory evidenceThyroid-stimulating hormone <Elevated thyroid hormone levelsAssessment of thyroid functionLaboratory assessmentFree thyroxine >Thyroid hormone levelsProgressive multiple sclerosisMultiple sclerosis patientsLaboratory interferenceHigh-dosePatient demographicsThyroid functionCase reportHormone levelsThyroid assaysBiotin treatmentPlasma samplesMultiple sclerosisPatientsThyrotoxicosisThyroidParsing the Interferon Transcriptional Network and Its Disease Associations
Mostafavi S, Yoshida H, Moodley D, LeBoité H, Rothamel K, Raj T, Ye C, Chevrier N, Zhang S, Feng T, Lee M, Casanova J, Clark J, Hegen M, Telliez J, Hacohen N, De Jager P, Regev A, Mathis D, Benoist C, Consortium T. Parsing the Interferon Transcriptional Network and Its Disease Associations. Cell 2016, 164: 564-578. PMID: 26824662, PMCID: PMC4743492, DOI: 10.1016/j.cell.2015.12.032.Peer-Reviewed Original ResearchCitationsAltmetric
2014
O3‐04‐05: EXPRESSION QTL ANALYSIS FROM PRIMARY IMMUNE CELLS IDENTIFIES NOVEL REGULATORY EFFECTS UNDERLYING ALZHEIMER'S DISEASE SUSCEPTIBILITY
Raj T, Replogle J, Ryan K, Chibnik L, Ye J, Mostafavi S, Lee M, Rothamel K, McCabe C, Von Korff A, Bradshaw E, Evans D, Bennett D, Benoist C, Stranger B, De Jager P. O3‐04‐05: EXPRESSION QTL ANALYSIS FROM PRIMARY IMMUNE CELLS IDENTIFIES NOVEL REGULATORY EFFECTS UNDERLYING ALZHEIMER'S DISEASE SUSCEPTIBILITY. Alzheimer's & Dementia 2014, 10: p216-p216. DOI: 10.1016/j.jalz.2014.04.290.Peer-Reviewed Original ResearchPolarization of the Effects of Autoimmune and Neurodegenerative Risk Alleles in Leukocytes
Raj T, Rothamel K, Mostafavi S, Ye C, Lee MN, Replogle JM, Feng T, Lee M, Asinovski N, Frohlich I, Imboywa S, Von Korff A, Okada Y, Patsopoulos NA, Davis S, McCabe C, Paik HI, Srivastava GP, Raychaudhuri S, Hafler DA, Koller D, Regev A, Hacohen N, Mathis D, Benoist C, Stranger BE, De Jager PL. Polarization of the Effects of Autoimmune and Neurodegenerative Risk Alleles in Leukocytes. Science 2014, 344: 519-523. PMID: 24786080, PMCID: PMC4910825, DOI: 10.1126/science.1249547.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsMeSH KeywordsAdaptive ImmunityAllelesAlzheimer DiseaseAutoimmune DiseasesAutoimmunityCD4-Positive T-LymphocytesEthnicityGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansImmunity, InnateMonocytesMultiple SclerosisNeurodegenerative DiseasesParkinson DiseasePolymorphism, Single NucleotideQuantitative Trait LociRheumatic FeverTranscriptomeConceptsSpecific immune cell typesHuman immune functionImmune cell typesMulti-ethnic cohortCell-autonomous effectsAutoimmune diseasesT cellsImmune functionParkinson's diseaseHealthy individualsInnate immunityRisk allelesDiseaseExpression quantitative trait loci (eQTL) studiesQuantitative trait loci studiesSusceptibility allelesPutative functional assignmentsCausal regulatory variantsDisease-associated lociDisease susceptibility variantsCell typesSusceptibility variantsTrans-eQTLsFunctional assignmentRegulatory variantsCommon Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells
Lee MN, Ye C, Villani AC, Raj T, Li W, Eisenhaure TM, Imboywa SH, Chipendo PI, Ran FA, Slowikowski K, Ward LD, Raddassi K, McCabe C, Lee MH, Frohlich IY, Hafler DA, Kellis M, Raychaudhuri S, Zhang F, Stranger BE, Benoist CO, De Jager PL, Regev A, Hacohen N. Common Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells. Science 2014, 343: 1246980. PMID: 24604203, PMCID: PMC4124741, DOI: 10.1126/science.1246980.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsMeSH KeywordsAdultAutoimmune DiseasesCommunicable DiseasesDendritic CellsEscherichia coliFemaleGene-Environment InteractionGenetic LociGenome-Wide Association StudyHEK293 CellsHost-Pathogen InteractionsHumansInfluenza A virusInterferon Regulatory Factor-7Interferon-betaLipopolysaccharidesMaleMiddle AgedPolymorphism, Single NucleotideQuantitative Trait LociSTAT Transcription FactorsTranscriptomeYoung AdultConceptsGenetic variationPathogen-responsive genesHuman genetic variationGenetic variantsIRF transcription factorsCommon genetic variantsType I IFN inductionFunctional annotationExpression responsesTranscription factorsI IFN inductionCausal variantsPathogen sensingEnvironmental stimuliComplex diseasesCommon variantsCommon allelesIFN inductionComputational approachVariantsCellsInductionGenesInterindividual variationSTAT
2012
Identification of regulators of the innate immune response to cytosolic DNA and retroviral infection by an integrative approach
Lee M, Roy M, Ong S, Mertins P, Villani A, Li W, Dotiwala F, Sen J, Doench J, Orzalli M, Kramnik I, Knipe D, Lieberman J, Carr S, Hacohen N. Identification of regulators of the innate immune response to cytosolic DNA and retroviral infection by an integrative approach. Nature Immunology 2012, 14: 179-185. PMID: 23263557, PMCID: PMC3838897, DOI: 10.1038/ni.2509.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsMeSH KeywordsAnimalsATP-Binding Cassette TransportersCell Cycle ProteinsChaperoninsCytosolDendritic CellsDNA, ViralFibroblastsGene Expression RegulationGene SilencingHIV-1HMGB2 ProteinHSP90 Heat-Shock ProteinsHumansImmunity, InnateMiceMice, TransgenicNuclear ProteinsPhosphoproteinsProtein Serine-Threonine KinasesProteomicsRNA, Small InterferingSignal TransductionSmall Molecule LibrariesVesiculovirus
Academic Achievements & Community Involvement
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Honors
honor AABB Foundation Scientific Research Grant Award
07/01/2022National AwardAABB (Association for the Advancement of Blood & Biotherapies)DetailsUnited States
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Laboratory Medicine
Clinic Building 405, 333 Cedar Street
New Haven, CT 06520
United States
Locations
CB405
Lab
Clinic Building
789 Howard Avenue
New Haven, CT 06519