On May 7, 2024, students and faculty mentors were celebrated at Yale School of Medicine’s (YSM) Student Research Day, an annual tradition at YSM since 1988.
About
Research
Overview
My research focuses on the neurological complications of systemic infections, including HIV and COVID-19. After completing my clinical training in Infectious Diseases, I pursued a research fellowship in Neuro-Infectious Diseases at the Yale School of Medicine, focusing my work on neurological complications of HIV in older adults on suppressive antiretroviral therapy. In my clinical role, I care for adults with neurological complications of HIV, Lyme, Syphilis, and other infectious diseases.
Medical Research Interests
Brain; Encephalitis, Arbovirus; HIV; HIV Infections; Infectious Disease Medicine; Internal Medicine; Neurosyphilis
Public Health Interests
HIV/AIDS
Publications
Featured Publications
HIV viral transcription and immune perturbations in the CNS of people with HIV despite ART
Farhadian SF, Lindenbaum O, Zhao J, Corley MJ, Im Y, Walsh H, Vecchio A, Garcia-Milian R, Chiarella J, Chintanaphol M, Calvi R, Wang G, Ndhlovu LC, Yoon J, Trotta D, Ma S, Kluger Y, Spudich S. HIV viral transcription and immune perturbations in the CNS of people with HIV despite ART. JCI Insight 2022, 7: e160267. PMID: 35801589, PMCID: PMC9310520, DOI: 10.1172/jci.insight.160267.Peer-Reviewed Original ResearchConceptsCerebrospinal fluidHIV infectionHIV-1-infected cellsCNS viral persistenceCentral memory CD4T-cell abnormalitiesHIV-1 RNAMicroglia-like cellsT cell activationSystemic viral suppressionAbnormal CD8HIV neuropathogenesisViral suppressionMemory CD4CNS reservoirsImmune perturbationsExperience elevated ratesNeuroimmune effectsPeripheral bloodNeurological impairmentViral persistenceT cellsCell abnormalitiesUninfected controlsCell activationBorrelia miyamotoi Meningoencephalitis in an Immunocompetent Patient
Gandhi S, Narasimhan S, Workineh A, Mamula M, Yoon J, Krause PJ, Farhadian SF. Borrelia miyamotoi Meningoencephalitis in an Immunocompetent Patient. Open Forum Infectious Diseases 2022, 9: ofac295. PMID: 35873293, PMCID: PMC9301576, DOI: 10.1093/ofid/ofac295.Peer-Reviewed Original ResearchEmerging Single-cell Approaches to Understand HIV in the Central Nervous System
Corley MJ, Farhadian SF. Emerging Single-cell Approaches to Understand HIV in the Central Nervous System. Current HIV/AIDS Reports 2021, 19: 113-120. PMID: 34822063, PMCID: PMC8613726, DOI: 10.1007/s11904-021-00586-7.Peer-Reviewed Original ResearchConceptsCentral nervous systemSingle-cell sequencing methodsSingle-cell approachesStudy of genomesSingle-cell technologiesSingle-cell analysisSingle-cell levelSingle-cell studiesNervous systemMolecular identitySequencing methodsRare infected cellsViral establishmentCentral nervous system tissueInfected cellsNervous system tissueAutopsy brainsCNS reservoirsCSF cellsHIV StudyHIVTranslational studiesCNS perturbationsCNS studiesTissue compartmentsDivergent and self-reactive immune responses in the CNS of COVID-19 patients with neurological symptoms
Song E, Bartley CM, Chow RD, Ngo TT, Jiang R, Zamecnik CR, Dandekar R, Loudermilk RP, Dai Y, Liu F, Sunshine S, Liu J, Wu W, Hawes IA, Alvarenga BD, Huynh T, McAlpine L, Rahman NT, Geng B, Chiarella J, Goldman-Israelow B, Vogels CBF, Grubaugh ND, Casanovas-Massana A, Phinney BS, Salemi M, Alexander JR, Gallego JA, Lencz T, Walsh H, Wapniarski AE, Mohanty S, Lucas C, Klein J, Mao T, Oh J, Ring A, Spudich S, Ko AI, Kleinstein SH, Pak J, DeRisi JL, Iwasaki A, Pleasure SJ, Wilson MR, Farhadian SF. Divergent and self-reactive immune responses in the CNS of COVID-19 patients with neurological symptoms. Cell Reports Medicine 2021, 2: 100288. PMID: 33969321, PMCID: PMC8091032, DOI: 10.1016/j.xcrm.2021.100288.Peer-Reviewed Original ResearchNeurological symptomsImmune responseCerebrospinal fluidAnti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodiesCOVID-19Self-reactive immune responsesSARS-CoV-2 antibodiesCompartmentalized immune responseCSF immunoglobulin GRole of autoimmunityCOVID-19 patientsB cell responsesCoronavirus disease 2019Immune surveyNeurologic sequelaePulmonary infectionBrain infectionSerum antibodiesDisease 2019Monoclonal antibody targetsAnimal modelsTarget epitopesCell activationCell responsesSingle-cell RNA sequencingNeurologic Complications of Babesiosis, United States, 2011–2021 - Volume 29, Number 6—June 2023 - Emerging Infectious Diseases journal - CDC
Locke S, O’Bryan J, Zubair A, Rethana M, Moffarah A, Krause P, Farhadian S. Neurologic Complications of Babesiosis, United States, 2011–2021 - Volume 29, Number 6—June 2023 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2023, 29: 1127-1135. PMID: 37209667, PMCID: PMC10202888, DOI: 10.3201/eid2906.221890.Peer-Reviewed Original ResearchConceptsNeurologic complicationsNeurologic symptomsRisk factorsYale-New Haven HospitalInfectious Diseases journal - CDCHigh-grade parasitemiaNeurologic risk factorsRange of symptomsAdult patientsRenal failureDiabetes mellitusFrequent symptomsHospital admissionImpaired consciousnessMedical recordsEndemic areasParasitic infectionsPatientsSymptomsIntraerythrocytic protozoaComplicationsBabesiosisNew HavenDeliriumMellitusSingle-cell RNA sequencing reveals microglia-like cells in cerebrospinal fluid during virologically suppressed HIV
Farhadian SF, Mehta SS, Zografou C, Robertson K, Price RW, Pappalardo J, Chiarella J, Hafler DA, Spudich SS. Single-cell RNA sequencing reveals microglia-like cells in cerebrospinal fluid during virologically suppressed HIV. JCI Insight 2018, 3: e121718. PMID: 30232286, PMCID: PMC6237230, DOI: 10.1172/jci.insight.121718.Peer-Reviewed Original ResearchConceptsCerebrospinal fluidHIV infectionImmune activationAntiretroviral therapyNeuronal injuryCentral nervous system immune activationLong-term suppressive antiretroviral therapySingle-cell RNA sequencingCNS immune activationDisease-associated microgliaSuppressive antiretroviral therapyImmune cell subsetsMicroglia-like cellsGene expression signaturesNeuronal damageNeuroinflammatory diseasesRNA sequencingCell subsetsCNS cellsNeurological conditionsRare subsetNeurocognitive impairmentMyeloid cellsCellular subsetsInfectionHIV and Age Do Not Synergistically Affect Age-Related T-Cell Markers
Farhadian S, Jalbert E, Deng Y, Goetz MB, Park LS, Justice A, Dubrow R, Emu B. HIV and Age Do Not Synergistically Affect Age-Related T-Cell Markers. JAIDS Journal Of Acquired Immune Deficiency Syndromes 2018, 77: 337-344. PMID: 29140874, PMCID: PMC5807137, DOI: 10.1097/qai.0000000000001595.Peer-Reviewed Original ResearchConceptsCD8 T cellsT-cell markersCD4 T cellsHIV infectionT cellsAntiretroviral therapyEffector memory CD4 T cellsImmune systemVeterans Aging Cohort StudyMemory CD4 T cellsNaive CD4 T cellsAging Cohort StudyT cell subsetsT-cell phenotypeCopies/mLCross-sectional studyRace/ethnicityChronic HIVUninfected subjectsUninfected menCohort studyHIV diseaseHigher proportionHIV serostatusHIV status
2025
HIV, smoking, and the brain: a convergence of neurotoxicities
Orlinick B, Farhadian S. HIV, smoking, and the brain: a convergence of neurotoxicities. AIDS Research And Therapy 2025, 22: 13. PMID: 39915881, PMCID: PMC11804093, DOI: 10.1186/s12981-025-00714-y.Peer-Reviewed Original ResearchConceptsHuman immunodeficiency virusCholinergic anti-inflammatory pathwayAnti-inflammatory pathwayNeurocognitive impairmentTobacco smokeEffect of human immunodeficiency virusEffects of tobacco smokingNeurotoxic effectsBrain volume changesClinically significant impactIncreased oxidative stressImmunodeficiency virusAlpha7 nicotinic acetylcholine receptorPWHBrain regionsMicroglial activationCognitive functionBrain healthIncreased neuroinflammationNeuronal apoptosisTherapeutic targetAcetylcholine receptorsGeneral populationNeurotoxicitySmoking
2024
PP7.7 – 00092 Single-Nucleus Multiomic Sequencing Uncovers Differential Chromatin Accessibility and Gene Regulation in Cerebrospinal Fluid Cells of PWH
Lu C, Orlinick B, Das B, Filippidis P, Mehta S, Spudich S, Pang A, Kluger Y, Corley M, Farhadian S. PP7.7 – 00092 Single-Nucleus Multiomic Sequencing Uncovers Differential Chromatin Accessibility and Gene Regulation in Cerebrospinal Fluid Cells of PWH. Journal Of Virus Eradication 2024, 10: 87-88. DOI: 10.1016/j.jve.2024.100530.Peer-Reviewed Original ResearchPP7.9 – 00031 Memory B Cells in the CSF of People with HIV Exhibit Changes in Interferon Signaling and Antigen Presentation Capacity
Filippidis P, Corley M, Spudich S, Wang M, Kleinstein S, Farhadian S. PP7.9 – 00031 Memory B Cells in the CSF of People with HIV Exhibit Changes in Interferon Signaling and Antigen Presentation Capacity. Journal Of Virus Eradication 2024, 10: 89-90. DOI: 10.1016/j.jve.2024.100532.Peer-Reviewed Original Research
Academic Achievements & Community Involvement
Clinical Care
Overview
Shelli Farhadian, MD, PhD, is an infectious diseases specialist who cares for people with a range of infections, including HIV, Lyme disease, and syphilis. She has additional expertise in the management of neurological infections.
As an assistant professor of medicine (infectious diseases) at Yale School of Medicine and an assistant professor of epidemiology of microbial diseases at Yale School of Public Health, Dr. Farhadian studies how infections like HIV and COVID-19 affect the central nervous system. She collaborates with colleagues in neurology, geriatrics, and public health to bring a cross-disciplinary approach to her work.
Dr. Farhadian completed her medical training at Weill Cornell Medical College and a doctorate degree at the Rockefeller University in New York City. She completed her internship and residency in internal medicine at Yale New Haven Hospital, followed by a fellowship in infectious diseases at Yale School of Medicine.
“I was drawn to infectious diseases because it combines detective work with deep human connection. Every patient brings a unique story, and solving medical puzzles in this field often requires both scientific curiosity and compassion,” she says. “I see each patient as a partner in their own care, and I’m committed to bringing both empathy and the best available science to every encounter.”
Clinical Specialties
Infectious Diseases; HIV & AIDs Medicine
Fact Sheets
Sepsis
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News
- March 11, 2025
Yale Department of Internal Medicine Faculty Promotions and Appointments (March 2025)
- January 06, 2025
Request for Nominations: 2025 Iva Dostanic Award
- October 10, 2024
Yale Researchers Shed Light on Epigenetic Differences in Patients with Syphilis and Neurosyphilis
- May 14, 2024
Students and Faculty Mentors Celebrated at Student Research Day
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