Ravi Dandekar
BIOINFORMATICS PROGR 4
Neurology
School of Medicine

Publications (43)

Top publication keywords:
Herpesvirus 4, HumanReceptors, KIRHLA AntigensCentral ToleranceEpstein-Barr Virus InfectionsB-LymphocytesParaneoplastic Cerebellar DegenerationMultiple SclerosisImmunogeneticsVirus ActivationPolymorphism, GeneticAntigens, ViralAutoantibodiesEncephalitisGenotype

• Autoantibody landscapes in Long COVID with neurological symptoms show heterogeneity without a shared disease signature.
  JCI insight 2026 Chakravarty D, Dandekar R, Lashkari VD, Tilton I, McAlpine L, Chiarella J, Nelson A, Ngo T, Chen P, Wang CY, Saxena A, Castillo-Rojas B, Zorn K, Tribble DR, Burgess TH, Rubin LH, Richard SA, Agan BK, …
• Immune Profiling after treatment with an Anti-CD19 Chimeric Antigen Receptor T Cell Therapy in Treatment-Refractory Progressive Multiple Sclerosis.
  medRxiv : the preprint server for health sciences 2026 Gupta S, Seshadri MR, Dandekar R, Müller-Jensen L, McCutcheon K, Scarffe LA, Vanasupa S, Sunahara M, Hayashi F, Caspar C, Lincoln R, Okinishi N, Thomas N, Shenoy S, Zylberman S, Fouassier C, Hassan E,…
• Virus reactivation in acute and long COVID-19.
  Nature 2026 Maguire C, Chen J, Rouphael N, Morse BA, Hoch A, Pickering H, Phan HV, Glascock A, Chu V, Dandekar R, IMPACC Network, Corry D, Kheradmand F, Baden LR, Sekaly RP, McComsey GA, Haddad EK, Cairns CB, …
• Cerebrospinal fluid transcriptional immune pathways linked to survival in HIV-associated tuberculous meningitis.
  The Journal of infectious diseases 2026 Louine M, Dandekar R, Reddy SP, Karalius MC, Waldrop G, Wang S, Gakuru J, Kimuda S, Mugabi T, Musubire AK, Kagimu E, Abassi M, Kabahubya M, Williams DA, Phan HV, Dai B, Zia M, Zorn KC, Fouassier C, …
• AEGIS reveals epitope- and clone-resolved convergence of CNS B and T cell autoreactivity in ROHHAD.
  bioRxiv : the preprint server for biology 2026 Bodansky A, Ahyong V, Dayao M, Asaki J, Vanasupa S, Dandekar R, Chen S, Sabatino J, Klauer S, Knudsen G, Valenzuela CL, McCutcheon K, Zorn K, Sidhu S, Yu D, Garcia S, Quandt Z, Wang CY, Rojas BC, …

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• Autoantibody landscapes in neurological Long COVID and post-COVID cognitive impairment show heterogeneity without a shared disease signature.
  medRxiv : the preprint server for health sciences 2026 Chakravarty D, Dandekar R, Lashkari VD, Tilton I, McAlpine L, Chiarella J, Nelson A, Ngo T, Chen P, Wang G, Saxena A, Castillo-Rojas B, Zorn K, Tribble DR, Burgess TH, Rubin LH, Richard SA, Agan BK, …
• Development of a Diagnostic Autoantibody Assay to a Consensus Motif for the Risk Prediction of Epstein-Barr Virus-Related Multiple Sclerosis.
  Neurology(R) neuroimmunology & neuroinflammation 2026 McCutcheon KM, Bodansky A, Ngo TT, Caspar C, Quintana S, Asaki J, Zhou J, Caillier SJ, Sharathchandra A, Waldrop G, Dandekar R, Zorn K, Tubati A, Gupta S, Sabatino JJ, Cuneo R, Oksenberg J, Wallin MT,…
• Autoreactomes in Healthy Individuals Vary According to HLA Class II Genotype.
  bioRxiv : the preprint server for biology 2026 Suseno R, Boquett JA, Dandekar R, Ituarte T, Sharathchandra A, Alvarenga B, Vierra-Green C, Spellman S, Maiers M, DeRisi JL, Wilson MR, Hollenbach JA
• Antigen specificity of clonally enriched CD8+ T cells in multiple sclerosis.
  Nature immunology 2026 Hayashi F, Mittl K, Dandekar R, Gerdts J, Hassan E, Schubert RD, Oshiro L, Loudermilk R, Greenfield A, Augusto DG, Havton G, Anumarlu S, Surapaneni A, Ramesh A, Tran E, Koshal K, Kizer K, Dreux J, …
• Exploratory autoantibody profiling in autism spectrum disorder.
  medRxiv : the preprint server for health sciences 2025 Lun MP, Ngo TT, Tilton I, Dandekar R, Pekar M, Thurm A, Bartley CM, Wilson MR, Pleasure SJ
• Permissive central tolerance plus defective peripheral checkpoints license pathogenic memory B cells in CASPR2-antibody encephalitis.
  Science advances 2025 Sun B, Fernandes D, Soltys J, Kienzler AK, Paneva S, Harrison R, Ramanathan S, Harrison AL, Makuch M, Fichtner ML, Donat RF, Akdeniz D, Bayuangga H, Im MG, Williams R, Vasconcelos A, Thomsen S, Fower …
• Permissive central tolerance plus defective peripheral checkpoints licence pathogenic memory B cells in CASPR2-antibody encephalitis.
  bioRxiv : the preprint server for biology 2025 Sun B, Fernandes D, Kienzler AK, Paneva S, Harrison R, Ramanathan S, Harrison AL, Makuch M, Fichtner ML, Donat RF, Akdeniz D, Bayuangga H, Im MG, Williams R, Vasconcelos A, Thomsen S, Fower A, Sun R, …
• Chronic Viral Reactivation and Associated Host Immune Response and Clinical Outcomes in Acute COVID-19 and Post-Acute Sequelae of COVID-19.
  bioRxiv : the preprint server for biology 2024 Maguire C, Chen J, Rouphael N, Pickering H, Phan HV, Glascock A, Chu V, Dandekar R, Corry D, Kheradmand F, Baden LR, Selaky R, McComsey GA, Haddad EK, Cairns CB, Pulendran B, Fernandez-Sesma A, Simon …
• Antigen-Specific T Cell Receptor Discovery for Treating Progressive Multifocal Leukoencephalopathy.
  bioRxiv : the preprint server for biology 2024 Gupta S, Martinov T, Thelen A, Sunahara M, Mureli S, Vazquez A, Gerdts J, Dandekar R, Cortese I, Fouassier C, Schanzer E, Urnov FD, Marson A, Shy BR, Greenberg PD, Wilson MR
• Antigen specificity of clonally-enriched CD8+ T cells in multiple sclerosis.
  bioRxiv : the preprint server for biology 2024 Mittl K, Hayashi F, Dandekar R, Schubert RD, Gerdts J, Oshiro L, Loudermilk R, Greenfield A, Augusto DG, Ramesh A, Tran E, Koshal K, Kizer K, Dreux J, Cagalingan A, Schustek F, Flood L, Moore T, …
• An autoantibody signature predictive for multiple sclerosis.
  Nature medicine 2024 Zamecnik CR, Sowa GM, Abdelhak A, Dandekar R, Bair RD, Wade KJ, Bartley CM, Kizer K, Augusto DG, Tubati A, Gomez R, Fouassier C, Gerungan C, Caspar CM, Alexander J, Wapniarski AE, Loudermilk RP, …
• Features of acute COVID-19 associated with post-acute sequelae of SARS-CoV-2 phenotypes: results from the IMPACC study.
  Nature communications 2024 Ozonoff A, Jayavelu ND, Liu S, Melamed E, Milliren CE, Qi J, Geng LN, McComsey GA, Cairns CB, Baden LR, Schaenman J, Shaw AC, Samaha H, Seyfert-Margolis V, Krammer F, Rosen LB, Steen H, Syphurs C, …
• Detection of High-Risk Paraneoplastic Antibodies against TRIM9 and TRIM67 Proteins.
  Annals of neurology 2023 Bartley CM, Ngo TT, Do LD, Zekeridou A, Dandekar R, Muñiz-Castrillo S, Alvarenga BD, Zorn KC, Tubati A, Pinto AL, Browne WD, Hullett PW, Terrelonge M, Schubert RD, Piquet AL, Yang B, Montalvo M, Kung …
• T cell deletional tolerance restricts AQP4 but not MOG CNS autoimmunity.
  Proceedings of the National Academy of Sciences of the United States of America 2023 Sagan SA, Moinfar Z, Moseley CE, Dandekar R, Spencer CM, Verkman AS, Ottersen OP, Sobel RA, Sidney J, Sette A, Anderson MS, Steinman L, Wilson MR, Sabatino JJ, Zamvil SS
• Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients.
  Cell reports. Medicine 2023 Diray-Arce J, Fourati S, Doni Jayavelu N, Patel R, Maguire C, Chang AC, Dandekar R, Qi J, Lee BH, van Zalm P, Schroeder A, Chen E, Konstorum A, Brito A, Gygi JP, Kho A, Chen J, Pawar S, Gonzalez-…
• A Predictive Autoantibody Signature in Multiple Sclerosis.
  medRxiv : the preprint server for health sciences 2023 Zamecnik CR, Sowa GM, Abdelhak A, Dandekar R, Bair RD, Wade KJ, Bartley CM, Tubati A, Gomez R, Fouassier C, Gerungan C, Alexander J, Wapniarski AE, Loudermilk RP, Eggers EL, Zorn KC, Ananth K, …
• CAR-T Cell-Mediated B-Cell Depletion in Central Nervous System Autoimmunity.
  Neurology(R) neuroimmunology & neuroinflammation 2023 Gupta S, Simic M, Sagan SA, Shepherd C, Duecker J, Sobel RA, Dandekar R, Wu GF, Wu W, Pak JE, Hauser SL, Lim W, Wilson MR, Zamvil SS
• Anti-SARS-CoV-2 and Autoantibody Profiling of a COVID-19 Patient With Subacute Psychosis Who Remitted After Treatment With Intravenous Immunoglobulin.
  Biological psychiatry 2022 McAlpine LS, Lifland B, Check JR, Angarita GA, Ngo TT, Chen P, Dandekar R, Alvarenga BD, Browne WD, Pleasure SJ, Wilson MR, Spudich SS, Farhadian SF, Bartley CM
• Multiple sclerosis therapies differentially affect SARS-CoV-2 vaccine-induced antibody and T cell immunity and function.
  JCI insight 2022 Sabatino JJ, Mittl K, Rowles WM, McPolin K, Rajan JV, Laurie MT, Zamecnik CR, Dandekar R, Alvarenga BD, Loudermilk RP, Gerungan C, Spencer CM, Sagan SA, Augusto DG, Alexander JR, DeRisi JL, Hollenbach…
• Remarkably Low KIR and HLA Diversity in Amerindians Reveals Signatures of Strong Purifying Selection Shaping the Centromeric KIR Region.
  Molecular biology and evolution 2022 Vargas LB, Beltrame MH, Ho B, Marin WM, Dandekar R, Montero-Martín G, Fernández-Viña MA, Hurtado AM, Hill KR, Tsuneto LT, Hutz MH, Salzano FM, Petzl-Erler ML, Hollenbach JA, Augusto DG
• Anti-SARS-CoV-2 and Autoantibody Profiles in the Cerebrospinal Fluid of 3 Teenaged Patients With COVID-19 and Subacute Neuropsychiatric Symptoms.
  JAMA neurology 2021 Bartley CM, Johns C, Ngo TT, Dandekar R, Loudermilk RL, Alvarenga BD, Hawes IA, Zamecnik CR, Zorn KC, Alexander JR, Wapniarski AE, DeRisi JL, Francisco C, Nash KB, Wietstock SO, Pleasure SJ, Wilson MR
• Impact of multiple sclerosis disease-modifying therapies on SARS-CoV-2 vaccine-induced antibody and T cell immunity.
  medRxiv : the preprint server for health sciences 2021 Sabatino JJ, Mittl K, Rowles W, Mcpolin K, Rajan JV, Zamecnik CR, Dandekar R, Alvarenga BD, Loudermilk RP, Gerungan C, Spencer CM, Sagan SA, Augusto DG, Alexander J, Hollenbach JA, Wilson MR, Zamvil …
• High-throughput Interpretation of Killer-cell Immunoglobulin-like Receptor Short-read Sequencing Data with PING.
  PLoS computational biology 2021 Marin WM, Dandekar R, Augusto DG, Yusufali T, Heyn B, Hofmann J, Lange V, Sauter J, Norman PJ, Hollenbach JA
• High-Resolution Characterization of KIR Genes in a Large North American Cohort Reveals Novel Details of Structural and Sequence Diversity.
  Frontiers in immunology 2021 Amorim LM, Augusto DG, Nemat-Gorgani N, Montero-Martin G, Marin WM, Shams H, Dandekar R, Caillier S, Parham P, Fernández-Viña MA, Oksenberg JR, Norman PJ, Hollenbach JA
• Divergent and self-reactive immune responses in the CNS of COVID-19 patients with neurological symptoms.
  Cell reports. Medicine 2021 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…
• Exploratory neuroimmune profiling identifies CNS-specific alterations in COVID-19 patients with neurological involvement.
  bioRxiv : the preprint server for biology 2020 Song E, Bartley CM, Chow RD, Ngo TT, Jiang R, Zamecnik CR, Dandekar R, Loudermilk RP, Dai Y, Liu F, Hawes IA, Alvarenga BD, Huynh T, McAlpine L, Rahman NT, Geng B, Chiarella J, Goldman-Israelow B, …
• Gut microbiota-specific IgA+ B cells traffic to the CNS in active multiple sclerosis.
  Science immunology 2020 Pröbstel AK, Zhou X, Baumann R, Wischnewski S, Kutza M, Rojas OL, Sellrie K, Bischof A, Kim K, Ramesh A, Dandekar R, Greenfield AL, Schubert RD, Bisanz JE, Vistnes S, Khaleghi K, Landefeld J, Kirkish …
• A splice acceptor variant in HLA-DRA affects the conformation and cellular localization of the class II DR alpha-chain.
  Immunology 2020 Didonna A, Damotte V, Shams H, Matsunaga A, Caillier SJ, Dandekar R, Misra MK, Mofrad MRK, Oksenberg JR, Hollenbach JA
• A pathogenic and clonally expanded B cell transcriptome in active multiple sclerosis.
  Proceedings of the National Academy of Sciences of the United States of America 2020 Ramesh A, Schubert RD, Greenfield AL, Dandekar R, Loudermilk R, Sabatino JJ, Koelzer MT, Tran EB, Koshal K, Kim K, Pröbstel AK, Banerji D, University of California, San Francisco MS-EPIC Team, Guo CY,…
• Killer Cell Immunoglobulin-like Receptor Variants Are Associated with Protection from Symptoms Associated with More Severe Course in Parkinson Disease.
  Journal of immunology (Baltimore, Md. : 1950) 2020 Anderson KM, Augusto DG, Dandekar R, Shams H, Zhao C, Yusufali T, Montero-Martín G, Marin WM, Nemat-Gorgani N, Creary LE, Caillier S, Mofrad MRK, Parham P, Fernández-Viña M, Oksenberg JR, Norman PJ, …
• Intrathecal B-cell activation in LGI1 antibody encephalitis.
  Neurology(R) neuroimmunology & neuroinflammation 2020 Lehmann-Horn K, Irani SR, Wang S, Palanichamy A, Jahn S, Greenfield AL, Dandekar R, Lepennetier G, Michael S, Gelfand JM, Geschwind MD, Wilson MR, Zamvil SS, von Büdingen HC
• Fluctuating and Geographically Specific Selection Characterize Rapid Evolution of the Human KIR Region.
  Frontiers in immunology 2019 Augusto DG, Norman PJ, Dandekar R, Hollenbach JA
• A specific amino acid motif of HLA-DRB1 mediates risk and interacts with smoking history in Parkinson's disease.
  Proceedings of the National Academy of Sciences of the United States of America 2019 Hollenbach JA, Norman PJ, Creary LE, Damotte V, Montero-Martin G, Caillier S, Anderson KM, Misra MK, Nemat-Gorgani N, Osoegawa K, Santaniello A, Renschen A, Marin WM, Dandekar R, Parham P, Tanner CM, …
• Longitudinally persistent cerebrospinal fluid B cells can resist treatment in multiple sclerosis.
  JCI insight 2019 Greenfield AL, Dandekar R, Ramesh A, Eggers EL, Wu H, Laurent S, Harkin W, Pierson NS, Weber MS, Henry RG, Bischof A, Cree BA, Hauser SL, Wilson MR, von Büdingen HC
• Allele-Level KIR Genotyping of More Than a Million Samples: Workflow, Algorithm, and Observations.
  Frontiers in immunology 2018 Wagner I, Schefzyk D, Pruschke J, Schöfl G, Schöne B, Gruber N, Lang K, Hofmann J, Gnahm C, Heyn B, Marin WM, Dandekar R, Hollenbach JA, Schetelig J, Pingel J, Norman PJ, Sauter J, Schmidt AH, Lange V
• Cost-effective and fast KIR gene-content genotyping by multiplex melting curve analysis.
  HLA 2018 Amorim LM, Santos THS, Hollenbach JA, Norman PJ, Marin WM, Dandekar R, Ribeiro EMSF, Petzl-Erler ML, Augusto DG
• Report from the Killer-cell Immunoglobulin-like Receptors (KIR) component of the 17th International HLA and Immunogenetics Workshop.
  Human immunology 2018 Misra MK, Augusto DG, Martin GM, Nemat-Gorgani N, Sauter J, Hofmann JA, Traherne JA, González-Quezada B, Gorodezky C, Bultitude WP, Marin W, Vierra-Green C, Anderson KM, Balas A, Caro-Oleas JL, …
• Decreased DGCR8 expression and miRNA dysregulation in individuals with 22q11.2 deletion syndrome.
  PloS one 2014 Sellier C, Hwang VJ, Dandekar R, Durbin-Johnson B, Charlet-Berguerand N, Ander BP, Sharp FR, Angkustsiri K, Simon TJ, Tassone F