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Publications

From the Lab

Zdinak PM, Trivedi N, Grebinoski S, Torrey J, Martinez EZ, Martinez S, Hicks L, Ranjan R,Makani VKK, Roland MM, Kublo L, Arshad S, Anderson MS, Vignali DAA, Joglekar AV. “Denovo identification of CD4+ T cell epitopes”. Nature Methods. 2024 May;21(5):846-856. doi:10.1038/s41592-024-02255-0. https://pubmed.ncbi.nlm.nih.gov/38658646/

Rahimikollu J, Xiao H, Rosengart AE, Tabib T, Zdinak P, He K, Bing X, Bunea F, Wegkamp M,Poholek AC*, Joglekar AV*, Lafyatis RA*, Das J*. “SLIDE: Significant Latent Factor InteractionDiscovery and Exploration across biological domains”. Nature Methods. 2024 May;21(5):835-845. doi: 10.1038/s41592-024-02175-z. *Co-corresponding authors. https://pubmed.ncbi.nlm.nih.gov/38374265/

Omelchenko AA, Siwek JC, Chhibbar P, Arshad S, Nazarali I, Nazarali K, Rosengart A,Rahimikollu J, Tilstra J, Shlomchik MJ, Koes DR, Joglekar AV*, Das J*. “Sliding WindowINteraction Grammar (SWING): a generalized interaction language model for peptide andprotein interactions”. 2025. Nature Methods. 2025 Aug;22(8):1707-1719. doi: 10.1038/s41592-025-02723-1. *Co-corresponding authors. https://pubmed.ncbi.nlm.nih.gov/38746274/

Arshad S, Cameron B, Joglekar AV. “Immunopeptidomics for autoimmunity: unlocking the chamber of immune secrets.” NPJ Syst Biol Appl. 2025 Jan 17;11(1):10. doi: 10.1038/s41540-024-00482-x.

https://pubmed.ncbi.nlm.nih.gov/39833247/

James EA*, Joglekar AV*, Linnemann AK*, Russ HA*, Kent SC*. “The beta cell-immune cell interface in type 1 diabetes (T1D)”. Molecular Metabolism. 2023 Dec;78:101809. *All authors contributed equally https://pubmed.ncbi.nlm.nih.gov/37734713/

Collaborations

Srivastava N, Vomund AN, Yu R, Peterson OJ, Yang Y, Turicek DP, Abousaway O, Li T, Kain L, Stone P, Ansar A, Clement CC, Sharma S, Melhem R, Zhang B, Liu C, Joglekar AV, Hu H, Hsieh CS, Campisi L, Santambrogio L, Teyton L, Unanue ER, Arbelaez AM, Lichti CF, Wan X. "A microenvironment-driven HLA-II-associated insulin neoantigen elicits persistent memory T cell activation in diabetes". Nature Immunology. 2026 Jan;27(1):82-97. doi: 10.1038/s41590-025-02343-z. https://pubmed.ncbi.nlm.nih.gov/41315082/

Ramonell RP, Oriss TB, McCreary-Partyka JC, Kale SL, Brandon NR, Ross MA, Gauthier MC,Yue M, Nee TJ, Das S, Chen W, Joglekar AV, Ray P, St Croix CM, Rajasundaram D, WenzelSE, Ray A. “CD8+ TEMRAs in severe asthma associate with asthma symptom duration andescape proliferation arrest”. JCI Insight. 2025 Mar 6;10(8):e185061. doi:10.1172/jci.insight.185061

Vijay GKM, Zhou M, Thakkar K, Rothrauff A, Singh Chawla A, Chen D, Lau L, Habib Gerges P,Chetal K, Chhibbar P, Fan J, Das J, Joglekar A, Borghesi L, Salomonis N, Xu H, Singh H.“Temporal dynamics and genomic programming of plasma cell fates”. Nature Immunology.2024 Jun;25(6):1097-1109. https://pubmed.ncbi.nlm.nih.gov/38698087/

Bender MJ, McPherson AC, Phelps CM, Pandey SP, Laughlin CR, Shapira JH, MedinaSanchez L, Rana M, Richie TG, Mims TS, Gocher-Demske AM, Cervantes-Barragan L, MullettSJ, Gelhaus SL, Bruno TC, Cannon N, McCulloch JA, Vignali DAA, Hinterleitner R, JoglekarAV, Pierre JF, Lee STM, Davar D, Zarour HM, Meisel M. “Dietary tryptophan metabolitereleased by intratumoral Lactobacillus reuteri facilitates immune checkpoint inhibitor treatment”.Cell 2023 Apr 27;186(9):1846-1862.e26. https://pubmed.ncbi.nlm.nih.gov/37028428/

Cillo AR, Somasundaram A, Shan F, Cardello C, Workman CJ, Kitsios GD, Ruffin AT, Kunning
S, Lampenfeld C, Onkar S, Grebinoski S, Deshmukh G, Methe B, Liu C, Nambulli S, Andrews
LP, Duprex WP, Joglekar AV, Benos PV, Ray P, Ray A, McVerry BJ, Zhang Y, Lee JS, Das J,
Singh H, Morris A, Bruno TC, Vignali DAA. “People critically ill with COVID-19 exhibit peripheral
immune profiles predictive of mortality and reflective of SARS-CoV-2 lung viral burden”. Cell
Reports Medicine 2021 Dec 21;2(12):100476. https://pubmed.ncbi.nlm.nih.gov/34873589/

Past Publications

Joglekar AV, Leonard MT, Jeppson JD, Swift M, Li G, Wong S, Peng S, Zaretsky J, Heath Jr, Ribas A, Bethune MT, Baltimore D. “T cell antigen discovery via Signaling and Antigen presenting Bifunctional Receptors.” Nature Methods. 2019 16:191–198.

Joglekar AV, Swift M, Leonard MT, Jeppson JD, Sandoval S, Baltimore D. “T cell receptor immunotherapy drives viral evolution in humanized mice”. BioRxiv: https://doi.org/10.1101/574608

Li G*, Bethune MT*, Wong S, Joglekar AV, Leonard MT, Wang J, Kim J, Cheng D, Peng S, Zaretsky J, Su Y, Ribas A, Witte O, Heath JR, Baltimore D. “T cell antigen discovery via trogocytosis.” Nature Methods. 2019 16:183-190. *Equal contribution.

Kuo CY, Long JD, Campo-Fernandez B, de Oliveira S, Cooper AR, Romero Z, Hoban MD, Joglekar AV, Lill GR, Kaufman ML, Fitz-Gibbon S, Wang X, Hollis RP, Kohn DB. “Site-Specific Gene Editing of Human Hematopoietic Stem Cells for X-Linked Hyper-IgM Syndrome.” Cell Rep. 2018 May 29;23(9):2606-2616.

Joglekar AV, Liu Z, Weber JK, Ouyang Y, Jeppson J, Noh W, Lamothe-Molina PA, Chen H, Kang S, Bethune MT, Zhou R, Walker BD, Baltimore D. “T cell receptors for the HIV KK10 epitope from patients with differential immunologic control are functionally indistinguishable” Proc Natl Acad Sci U S A. 2018 Feb 20;115(8):1877-1882.

Joglekar AV, Sandoval S. “Pseudotyped lentiviral vectors: one vector, many guises”. Hum Gene Ther Methods. 2017 Dec;28(6):291-301.

Bethune MT, Joglekar AV. “Personalized T cell-mediated cancer immunotherapy: progress and challenges”. Current Opinion in Biotechnology, 48:142–152.

Hoban MD, Cost GJ, Mendel MC, Romero Z, Kaufman ML, Joglekar AV, Ho M, Lumaquin D, Gray D, Lill GR, Cooper AR, Urbinati F, Senadheera S, Zhu A, Liu P, Paschon DE, Zhang L, Rebar EJ, Wilber A, Wang X, Gregory PD, Holmes MC, Reik A, Hollis RP, Kohn DB “Correction of the sickle-cell disease mutation in human hematopoietic stem/progenitor cells” Blood. 2015 Apr 23; 125(17):2597-604.

Joglekar AV, Stein L, Ho M, Hoban MD, Hollis RP, Kohn DB “Dissecting the mechanism of histone deacetylase inhibitors to enhance the activity of zinc finger nucleases delivered by integrase-defective lentiviral vectors.” Hum Gene Ther. 2014 Jul; 25(7):599-608.

Joglekar AV, Hollis RP, Kuftinec G, Senadheera S, Chan R, Kohn DB “Integrase-defective lentiviral vectors as a delivery platform for targeted modification of adenosine deaminase locus” Mol Ther. 2013 Sep; 21(9):1705-17.

Kurrey NK, Jalgaonkar SP, Joglekar AV, Ghanate AD, Chaskar PD, Doiphode RY, Bapat SA “Snail and slug mediate radioresistance and chemoresistance by antagonizing p53-mediated apoptosis and acquiring a stem-like phenotype in ovarian cancer cells” Stem Cells. 2009 Sep;27(9):2059-68.