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Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease

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  1. Julia Paczkowska & Ming Tang & Kyle T. Wright & Li Song & Kelsey Luu & Vignesh Shanmugam & Emma L. Welsh & Jason L. Weirather & Naomi Besson & Harrison Olszewski & Billie A. Porter & Kathleen L. Pfaff, 2024. "Cancer-specific innate and adaptive immune rewiring drives resistance to PD-1 blockade in classic Hodgkin lymphoma," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  2. Qi Zhang & Rober Abdo & Cristiana Iosef & Tomonori Kaneko & Matthew Cecchini & Victor K. Han & Shawn Shun-Cheng Li, 2022. "The spatial transcriptomic landscape of non-small cell lung cancer brain metastasis," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
  3. Jeff DeMartino & Michael T. Meister & Lindy L. Visser & Mariël Brok & Marian J. A. Groot Koerkamp & Amber K. L. Wezenaar & Laura S. Hiemcke-Jiwa & Terezinha Souza & Johannes H. M. Merks & Anne C. Rios, 2023. "Single-cell transcriptomics reveals immune suppression and cell states predictive of patient outcomes in rhabdomyosarcoma," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  4. Karin D. Prummel & Kevin Woods & Maksim Kholmatov & Eric C. Schmitt & Evi P. Vlachou & Mayssa Labyadh & Rebekka Wehner & Gereon Poschmann & Kai Stühler & Susann Winter & Uta Oelschlaegel & Manja Wobus, 2025. "Inflammatory stromal and T cells mediate human bone marrow niche remodeling in clonal hematopoiesis and myelodysplasia," Nature Communications, Nature, vol. 16(1), pages 1-25, December.
  5. Khanyisile Kgoadi & Prashant Bajpai & Chris C. Ibegbu & Hedwin Kitdorlang Dkhar & Ana Beatriz Enriquez & Stanzin Dawa & Sushma K. Cribbs & Jyothi Rengarajan, 2025. "Alveolar macrophages from persons with HIV mount impaired TNF signaling networks to M. tuberculosis infection," Nature Communications, Nature, vol. 16(1), pages 1-20, December.
  6. Esra Güç & Agatha Treveil & Emma Leach & Anna Broomfield & Antonio Camera & James Clubley & Paula Nieto Garcia & Anastasiya Kazachenka & Rahul Khanolkar & Luis Carpio & Holger Heyn & Jessica C. Hassel, 2025. "Tebentafusp, a T cell engager, promotes macrophage reprogramming and in combination with IL-2 overcomes macrophage immunosuppression in cancer," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
  7. Jiashuo Chao & Yuan Liang & Hao Wang & Ziyu Xun & Shanshan Wang & Zhengfeng Xuan & Mingming Wang & Qiyuan Huang & Rui Zhang & Mu Liu & Lei Zhang & Bohang Shou & Yuhan Zhang & Feng Cheng & Haitao Zhao , 2025. "FAD synthase confers ferroptosis resistance and restrains CD8+ T cell recruitment in hepatocellular carcinoma," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
  8. Kaitlyn A. Lagattuta & Hannah L. Park & Laurie Rumker & Kazuyoshi Ishigaki & Aparna Nathan & Soumya Raychaudhuri, 2024. "The genetic basis of autoimmunity seen through the lens of T cell functional traits," Nature Communications, Nature, vol. 15(1), pages 1-6, December.
  9. Matthew P. Morrow & Elisabeth Gillespie & Albert Sylvester & Milan R. Amin & Peter C. Belafsky & Simon R. Best & Aaron D. Friedman & Adam M. Klein & David G. Lott & Ted Mau & Randal C. Paniello & Seth, 2025. "DNA immunotherapy for recurrent respiratory papillomatosis (RRP): phase 1/2 study assessing efficacy, safety, and immunogenicity of INO-3107," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
  10. Daphne Kolland & Miriam Kuhlmann & Gustavo P. Almeida & Amelie Köhler & Anela Arifovic & Alexandra Strempel & Mohsen Pourjam & Silvia Bolsega & Christine Wurmser & Katja Steiger & Marijana Basic & Kla, 2025. "A specific microbial consortium enhances Th1 immunity, improves LCMV viral clearance but aggravates LCMV disease pathology in mice," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
  11. Augusto Faria Andrade & Alva Annett & Elham Karimi & Danai Georgia Topouza & Morteza Rezanejad & Yitong Liu & Michael McNicholas & Eduardo G. Gonzalez Santiago & Dhana Llivichuzhca-Loja & Arne Gehlhaa, 2024. "Immune landscape of oncohistone-mutant gliomas reveals diverse myeloid populations and tumor-promoting function," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
  12. Tara Chari & Lior Pachter, 2023. "The specious art of single-cell genomics," PLOS Computational Biology, Public Library of Science, vol. 19(8), pages 1-20, August.
  13. Alexandra Argyriou & Marc H. Wadsworth & Adrian Lendvai & Stephen M. Christensen & Aase H. Hensvold & Christina Gerstner & Annika Vollenhoven & Kellie Kravarik & Aaron Winkler & Vivianne Malmström & K, 2022. "Single cell sequencing identifies clonally expanded synovial CD4+ TPH cells expressing GPR56 in rheumatoid arthritis," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  14. Osama Al-Dalahmah & Michael G. Argenziano & Adithya Kannan & Aayushi Mahajan & Julia Furnari & Fahad Paryani & Deborah Boyett & Akshay Save & Nelson Humala & Fatima Khan & Juncheng Li & Hong Lu & Yu S, 2023. "Re-convolving the compositional landscape of primary and recurrent glioblastoma reveals prognostic and targetable tissue states," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
  15. Anna Schmidt & Jana Fuchs & Mark Dedden & Katharina Kocher & Christine Schülein & Julian Hübner & Ana Vieira Antão & Pascal Irrgang & Friederike Oltmanns & Vera Viherlehto & Natascha Leicht & Ralf Joa, 2025. "Inflammatory conditions shape phenotypic and functional characteristics of lung-resident memory T cells in mice," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
  16. Francesco Mazziotta & Lauren E. Martin & Daniel N. Egan & Merav Bar & Sinéad Kinsella & Kelly G. Paulson & Valentin Voillet & Miranda C. Lahman & Daniel Hunter & Thomas M. Schmitt & Natalie Duerkopp &, 2025. "A phase I/II trial of WT1-specific TCR gene therapy for patients with acute myeloid leukemia and active disease post-allogeneic hematopoietic cell transplantation: skewing towards NK-like phenotype im," Nature Communications, Nature, vol. 16(1), pages 1-20, December.
  17. Nader Atlasy & Anna Bujko & Espen S. Bækkevold & Peter Brazda & Eva Janssen-Megens & Knut E. A. Lundin & Jørgen Jahnsen & Frode L. Jahnsen & Hendrik G. Stunnenberg, 2022. "Single cell transcriptomic analysis of the immune cell compartment in the human small intestine and in Celiac disease," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  18. Dhiraj K. Singh & Mushtaq Ahmed & Sadia Akter & Vinay Shivanna & Allison N. Bucşan & Abhishek Mishra & Nadia A. Golden & Peter J. Didier & Lara A. Doyle & Shannan Hall-Ursone & Chad J. Roy & Garima Ar, 2025. "Prevention of tuberculosis in cynomolgus macaques by an attenuated Mycobacterium tuberculosis vaccine candidate," Nature Communications, Nature, vol. 16(1), pages 1-20, December.
  19. Xiaojian Lu & Yanwei Luo & Xichen Nie & Bailing Zhang & Xiaoyan Wang & Ran Li & Guangmin Liu & Qianyin Zhou & Zhizhong Liu & Liqing Fan & James M. Hotaling & Zhe Zhang & Hao Bo & Jingtao Guo, 2023. "Single-cell multi-omics analysis of human testicular germ cell tumor reveals its molecular features and microenvironment," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  20. Anja Fischer & Thomas K. Albert & Natalia Moreno & Marta Interlandi & Jana Mormann & Selina Glaser & Paurnima Patil & Flavia W. Faria & Mathis Richter & Archana Verma & Sebastian T. Balbach & Rabea Wa, 2024. "Lack of SMARCB1 expression characterizes a subset of human and murine peripheral T-cell lymphomas," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  21. Siwei Luo & Amber Notaro & Lan Lin, 2025. "ATLAS-seq: a microfluidic single-cell TCR screen for antigen-reactive TCRs," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
  22. Felix Drost & Yang An & Irene Bonafonte-Pardàs & Lisa M. Dratva & Rik G. H. Lindeboom & Muzlifah Haniffa & Sarah A. Teichmann & Fabian Theis & Mohammad Lotfollahi & Benjamin Schubert, 2024. "Multi-modal generative modeling for joint analysis of single-cell T cell receptor and gene expression data," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  23. Yingyi Huang & Xiang Liu & Shuo Li & Chen Li & Hong-Yan Wang & Qun Liu & Jian-Yang Chen & Yingying Zhang & Yanan Li & Xianghui Zhang & Qian Wang & Kaiqiang Liu & Yu-Yan Liu & Yue Pang & Shanshan Liu &, 2024. "Discovery of an unconventional lamprey lymphocyte lineage highlights divergent features in vertebrate adaptive immune system evolution," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  24. Jingyi Xie & Daniel G. Chen & William Chour & Rachel H. Ng & Rongyu Zhang & Dan Yuan & Jongchan Choi & Michaela McKasson & Pamela Troisch & Brett Smith & Lesley Jones & Andrew Webster & Yusuf Rasheed , 2025. "APMAT analysis reveals the association between CD8 T cell receptors, cognate antigen, and T cell phenotype and persistence," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
  25. E. Koncina & M. Nurmik & V. I. Pozdeev & C. Gilson & M. Tsenkova & R. Begaj & S. Stang & A. Gaigneaux & C. Weindorfer & F. Rodriguez & M. Schmoetten & E. Klein & J. Karta & V. S. Atanasova & K. Grzyb , 2023. "IL1R1+ cancer-associated fibroblasts drive tumor development and immunosuppression in colorectal cancer," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  26. Maxwell Ma & Fahad Paryani & Kelly Jakubiak & Shengnan Xia & Susumu Antoku & Adithya Kannan & Jaeseung Lee & Nacoya Madden & Shailesh Senthil Kumar & Juncheng Li & David Chen & Gunnar Hargus & Aayushi, 2025. "The spatial landscape of glial pathology and T cell response in Parkinson’s disease substantia nigra," Nature Communications, Nature, vol. 16(1), pages 1-24, December.
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