Publications

2026

Spatially resolved host and microbiota RNA profiling in the mouse gut using microDBiT
Tao B, Song D, Dong M, Li G, Wang S, Wang D, Di X, Gao F, Lin L, Yu X, Xu J, Liu M, Zhang D, Kelley M, Feng A, Jin Y, Du J, Kluger Y, Palm N, Liu Y. Spatially resolved host and microbiota RNA profiling in the mouse gut using microDBiT. Nature Communications 2026 DOI: 10.1038/s41467-026-78852-8.
Peer-Reviewed Original Research
Spatial analysis reveals cellular microenvironments and mechanisms of inflammation and injury in acute interstitial nephritis
Baker M, Kakade V, Budiman T, Weiß M, Cunningham J, Sadarangani S, Lerner G, Moeckel G, Rosenberg A, Parikh C, Kluger Y, Moledina D, Cantley L. Spatial analysis reveals cellular microenvironments and mechanisms of inflammation and injury in acute interstitial nephritis. Nature Communications 2026, 17: 10262. PMID: 42802277, PMCID: PMC13616907, DOI: 10.1038/s41467-026-77210-y.
Peer-Reviewed Original Research
Sensitive detection of rare HIV-infected cells in the human brain by single-nucleus RNA sequencing
Cai Y, Jacobs N, Gabuzda D, Corley M, Herb B, Volsky D, Receveur J, Matkhanov D, White O, Spudich S, Kluger Y, Cheng C, Fox H, Niu M. Sensitive detection of rare HIV-infected cells in the human brain by single-nucleus RNA sequencing. Virology Journal 2026 DOI: 10.1186/s12985-026-03285-0.
Peer-Reviewed Original Research
A spatial multi-omics atlas of immunosenescence reveals germinal-center B cell alteration in human lymph nodes
Farzad N, Enninful A, Lu Y, Parisi F, Fung A, Kwon Y, Li Y, Labrosse M, Yang M, Strino F, Chen L, Yang J, Zhong M, Gao F, Tao B, Cunningham J, Bai Z, Li H, Wang F, Stankewich M, Kim D, Dong M, Bramer L, Li K, Bhat M, Loe E, Craft J, Pasa-Tolic L, Halene S, Shi L, Kluger Y, Xu M, Fan R. A spatial multi-omics atlas of immunosenescence reveals germinal-center B cell alteration in human lymph nodes. Cell Press Blue 2026, 1: 100053. PMID: 42519544, PMCID: PMC13384480, DOI: 10.1016/j.cpblue.2026.100053.
Peer-Reviewed Original Research
Immunometabolic resistors of aging in long-lived golden spiny mice
Kim H, Sagiv-Zangi T, Youm Y, Vardi-Naim H, Dlugos T, Strino F, Kazavchinsky-Bar M, Egulsky L, Bodogai M, Biragyn A, Kluger Y, Kronfeld-Schor N, Dixit V. Immunometabolic resistors of aging in long-lived golden spiny mice. Science Advances 2026, 12: eaec9991. PMID: 41739938, PMCID: PMC12935055, DOI: 10.1126/sciadv.aec9991.
Peer-Reviewed Original Research
AMULETY: A Python package to embed adaptive immune receptor sequences
Wang M, Jiang W, Kluger Y, Kleinstein S, Gabernet G. AMULETY: A Python package to embed adaptive immune receptor sequences. ImmunoInformatics 2026, 21: 100066. PMID: 42422552, PMCID: PMC13344335, DOI: 10.1016/j.immuno.2026.100066.
Peer-Reviewed Original Research
T cell receptors for antigen on intraepithelial cytolytic T lymphocytes in celiac disease engage enterocyte HLA-E and HLA-B
Johnson J, Agrawal K, Al-Lamki R, Zhang F, Wang X, Tobiasova Z, Taleb S, Liburd S, Rodriguez L, Martins A, Flavell R, Robert M, Sefik E, Pober J. T cell receptors for antigen on intraepithelial cytolytic T lymphocytes in celiac disease engage enterocyte HLA-E and HLA-B. Proceedings Of The National Academy Of Sciences Of The United States Of America 2026, 123: e2525433123. PMID: 41642982, PMCID: PMC12890992, DOI: 10.1073/pnas.2525433123.
Peer-Reviewed Original Research
MeSH Keywords

2025

CTLA-4 blockade shifts the B cell repertoire towards autoimmunity
Çakan E, Wang M, Dai Y, Mirouse A, Villanueva-Pachas C, Bouis D, Boeckers J, Gera R, Yraita S, Clapp L, Perdigoto A, Delmotte F, Massad C, Bacchiocchi A, Ring A, Kluger Y, Kluger H, Herold K, Meffre E. CTLA-4 blockade shifts the B cell repertoire towards autoimmunity. Journal Of Clinical Investigation 2025, 135: e189074. PMID: 41026527, PMCID: PMC12618075, DOI: 10.1172/jci189074.
Peer-Reviewed Original Research
MeSH Keywords
Sclerotic GVHD and scleroderma share dysregulated gene expression that is ameliorated by EREG therapeutic antibody
Newton N, Agrawal K, Odell A, Tracy T, Hacket C, Eldrup A, Whitfield M, Martyanov V, Girardi M, Sefik E, Flavell R, Odell I. Sclerotic GVHD and scleroderma share dysregulated gene expression that is ameliorated by EREG therapeutic antibody. Blood 2025, 146: 3201-3212. PMID: 40961242, PMCID: PMC12643462, DOI: 10.1182/blood.2025029836.
Peer-Reviewed Original Research
Humanization of CD47 enables development of functional human neutrophils via postirradiation remodeling of the bone marrow
Sefik E, Philbrick W, Zhang F, Agrawal K, Van Lee B, Sam J, Karatepe K, Zheng Y, Liang K, Peng S, Mirza H, Rangavajhula A, Simon P, Arun N, Babu P, Eynon E, Chiorazzi M, Shan L, Halene S, Luo H, Rongvaux A, Kluger Y, Flavell R. Humanization of CD47 enables development of functional human neutrophils via postirradiation remodeling of the bone marrow. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2426546122. PMID: 40956886, PMCID: PMC12478129, DOI: 10.1073/pnas.2426546122.
Peer-Reviewed Original Research
MeSH Keywords
Nerve-associated macrophages control adipose homeostasis across lifespan and restrain age-related inflammation
Gonzalez-Hurtado E, Leveau C, Li K, Mishra M, Qu R, Goldberg E, Sidorov S, Damani-Yokota P, Yeung S, Khairallah C, Gonzalez D, Shepard T, Camell C, Artyomov M, Kluger Y, Khanna K, Dixit V. Nerve-associated macrophages control adipose homeostasis across lifespan and restrain age-related inflammation. Nature Aging 2025, 5: 1828-1843. PMID: 40897908, PMCID: PMC12443591, DOI: 10.1038/s43587-025-00952-9.
Peer-Reviewed Original Research
MeSH Keywords
Humoral determinants of checkpoint immunotherapy
Dai Y, Aizenbud L, Qin K, Austin M, Jaycox J, Cunningham J, Wang E, Zhang L, Fischer S, Carroll S, van Aggelen H, Kluger Y, Herold K, Furchtgott L, Kluger H, Ring A. Humoral determinants of checkpoint immunotherapy. Nature 2025, 644: 527-536. PMID: 40702172, DOI: 10.1038/s41586-025-09188-4.
Peer-Reviewed Original Research
MeSH Keywords
Cluster-independent multiscale marker identification in single-cell RNA-seq data using localized marker detector (LMD)
Li R, Qu R, Parisi F, Strino F, Lam H, Stanley J, Cheng X, Myung P, Kluger Y. Cluster-independent multiscale marker identification in single-cell RNA-seq data using localized marker detector (LMD). Communications Biology 2025, 8: 1058. PMID: 40670619, PMCID: PMC12267854, DOI: 10.1038/s42003-025-08485-y.
Peer-Reviewed Original Research
MeSH Keywords
Dual Diffusion for Unified Image Generation and Understanding
Li Z, Li H, Shi Y, Farimani A, Kluger Y, Yang L, Wang P. Dual Diffusion for Unified Image Generation and Understanding. 2025, 00: 2779-2790. DOI: 10.1109/cvpr52734.2025.00265.
Peer-Reviewed Original Research
Tumor microenvironment of non-small cell lung cancer impairs immune cell function among people with HIV
Desai S, Salahuddin S, Yusuf R, Ranjan K, Gu J, Osmani L, Lin Y, Mehta S, Talmon R, Kang I, Kluger Y, Zhao H, Schalper K, Emu B. Tumor microenvironment of non-small cell lung cancer impairs immune cell function among people with HIV. Journal Of Clinical Investigation 2025, 135: e177310. PMID: 40459946, PMCID: PMC12259253, DOI: 10.1172/jci177310.
Peer-Reviewed Original Research
Medications for opioid use disorder shape immune responses during chronic HIV infection
Collora J, Steinhauser S, Davenport T, Lin D, Eshetu A, Zeidi S, Kim R, Frank C, Kluger Y, Springer S, Ho Y. Medications for opioid use disorder shape immune responses during chronic HIV infection. Cell Reports Medicine 2025, 6: 102159. PMID: 40460829, PMCID: PMC12208330, DOI: 10.1016/j.xcrm.2025.102159.
Peer-Reviewed Original Research
MeSH Keywords
Hormetic elevation of taurine restrains inflammaging by deactivating the NLRP3 inflammasome.
Guan C, Ryu S, Dong M, Youm YH, Mohanty S, Maeda R, Orliaguet L, Kim HH, Dlugos T, Smith SR, Ravussin E, Onyuru J, Wang A, Shaw AC, Hoffman HM, Kluger Y, Sugiura Y, Dixit VD. Hormetic elevation of taurine restrains inflammaging by deactivating the NLRP3 inflammasome. BioRxiv 2025 PMID: 40501605, DOI: 10.1101/2025.05.27.656381.
Publications for non-academic audiences
Supervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction
Wang M, Patsenker J, Li H, Kluger Y, Kleinstein S. Supervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction. PLOS Computational Biology 2025, 21: e1012153. PMID: 40163503, PMCID: PMC12013870, DOI: 10.1371/journal.pcbi.1012153.
Peer-Reviewed Original Research
MeSH Keywords
SIMVI disentangles intrinsic and spatial-induced cellular states in spatial omics data
Dong M, Su D, Kluger H, Fan R, Kluger Y. SIMVI disentangles intrinsic and spatial-induced cellular states in spatial omics data. Nature Communications 2025, 16: 2990. PMID: 40148341, PMCID: PMC11950362, DOI: 10.1038/s41467-025-58089-7.
Peer-Reviewed Original Research
MeSH Keywords
Engineering Mice to Study Human Immunity
Sefik E, Xiao T, Chiorazzi M, Odell I, Zhang F, Agrawal K, Micevic G, Flavell R. Engineering Mice to Study Human Immunity. Annual Review Of Immunology 2025, 43: 451-487. PMID: 40020225, DOI: 10.1146/annurev-immunol-082523-124415.
Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus Statements
The Dyson equalizer: adaptive noise stabilization for low-rank signal detection and recovery
Landa B, Kluger Y. The Dyson equalizer: adaptive noise stabilization for low-rank signal detection and recovery. Information And Inference A Journal Of The IMA 2025, 14: iaae036. PMID: 39830802, PMCID: PMC11735832, DOI: 10.1093/imaiai/iaae036.
Peer-Reviewed Original Research

2024

Circulating tumor-reactive KIR+CD8+ T cells suppress anti-tumor immunity in patients with melanoma
Lu B, Lucca L, Lewis W, Wang J, Nogueira C, Heer S, Rayon-Estrada V, Axisa P, Reeves S, Buitrago-Pocasangre N, Pham G, Kojima M, Wei W, Aizenbud L, Bacchiocchi A, Zhang L, Walewski J, Chiang V, Olino K, Clune J, Halaban R, Kluger Y, Coyle A, Kisielow J, Obermair F, Kluger H, Hafler D. Circulating tumor-reactive KIR+CD8+ T cells suppress anti-tumor immunity in patients with melanoma. Nature Immunology 2024, 26: 82-91. PMID: 39609626, PMCID: PMC12285569, DOI: 10.1038/s41590-024-02023-4.
Peer-Reviewed Original Research
Bi-stochastically normalized graph Laplacian: convergence to manifold Laplacian and robustness to outlier noise
Cheng X, Landa B. Bi-stochastically normalized graph Laplacian: convergence to manifold Laplacian and robustness to outlier noise. Information And Inference A Journal Of The IMA 2024, 13: iaae026. PMID: 39309272, PMCID: PMC11415053, DOI: 10.1093/imaiai/iaae026.
Peer-Reviewed Original Research
The single-cell opioid responses in the context of HIV (SCORCH) consortium
Ament S, Campbell R, Lobo M, Receveur J, Agrawal K, Borjabad A, Byrareddy S, Chang L, Clarke D, Emani P, Gabuzda D, Gaulton K, Giglio M, Giorgi F, Gok B, Guda C, Hadas E, Herb B, Hu W, Huttner A, Ishmam M, Jacobs M, Kelschenbach J, Kim D, Lee C, Liu S, Liu X, Madras B, Mahurkar A, Mash D, Mukamel E, Niu M, O’Connor R, Pagan C, Pang A, Pillai P, Repunte-Canonigo V, Ruzicka W, Stanley J, Tickle T, Tsai S, Wang A, Wills L, Wilson A, Wright S, Xu S, Yang J, Zand M, Zhang L, Zhang J, Akbarian S, Buch S, Cheng C, Corley M, Fox H, Gerstein M, Gummuluru S, Heiman M, Ho Y, Kellis M, Kenny P, Kluger Y, Milner T, Moore D, Morgello S, Ndhlovu L, Rana T, Sanna P, Satterlee J, Sestan N, Spector S, Spudich S, Tilgner H, Volsky D, White O, Williams D, Zeng H. The single-cell opioid responses in the context of HIV (SCORCH) consortium. Molecular Psychiatry 2024, 29: 3950-3961. PMID: 38879719, PMCID: PMC11609103, DOI: 10.1038/s41380-024-02620-7.
Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus Statements
Hyperbolic Diffusion Procrustes Analysis for Intrinsic Representation of Hierarchical Data Sets
Lin Y, Kluger Y, Talmon R. Hyperbolic Diffusion Procrustes Analysis for Intrinsic Representation of Hierarchical Data Sets. 2024, 00: 6325-6329. DOI: 10.1109/icassp48485.2024.10446370.
Peer-Reviewed Original Research

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