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Interpretation of T cell states from single-cell transcriptomics data using reference atlases

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  1. Jeffrey M. Grimes & Sadashib Ghosh & Shamza Manzoor & Li X. Li & Monica M. Moran & Jennifer C. Clements & Sherrie D. Alexander & James M. Markert & Jianmei W. Leavenworth, 2025. "Oncolytic reprogramming of tumor microenvironment shapes CD4 T-cell memory via the IL6ra-Bcl6 axis for targeted control of glioblastoma," Nature Communications, Nature, vol. 16(1), pages 1-20, December.
  2. Yinshen Wee & Junhua Wang & Emily C. Wilson & Coulson P. Rich & Aaron Rogers & Zongzhong Tong & Evelyn DeGroot & Y. N. Vashisht Gopal & Michael A. Davies & H. Atakan Ekiz & Joshua K. H. Tay & Chris St, 2024. "Tumour-intrinsic endomembrane trafficking by ARF6 shapes an immunosuppressive microenvironment that drives melanomagenesis and response to checkpoint blockade therapy," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  3. Nils-Petter Rudqvist & Maud Charpentier & Claire Lhuillier & Erik Wennerberg & Sheila Spada & Caroline Sheridan & Xi Kathy Zhou & Tuo Zhang & Silvia C. Formenti & Jennifer S. Sims & Alicia Alonso & Sa, 2023. "Immunotherapy targeting different immune compartments in combination with radiation therapy induces regression of resistant tumors," Nature Communications, Nature, vol. 14(1), pages 1-23, December.
  4. Joseph Zenga & Musaddiq J. Awan & Anne Frei & Jamie Foeckler & Rachel Kuehn & Julia Kasprzak & Becky Massey & Jennifer Bruening & Kenneth Akakpo & Monica Shukla & Stuart J. Wong & Angela J. Mathison &, 2025. "Radiation therapy results in preferential tumor antigen-specific lymphodepletion in head and neck cancer," Nature Communications, Nature, vol. 16(1), pages 1-20, December.
  5. Raphael Lutz & Florian Grünschläger & Malte Simon & Mohamed H. S. Awwad & Marcus Bauer & Schayan Yousefian & Niklas Beumer & Lea Jopp-Saile & Anastasia Sedlmeier & Llorenç Solé-Boldo & Bogdan Avanesya, 2024. "Multiple myeloma long-term survivors exhibit sustained immune alterations decades after first-line therapy," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  6. Marcel P. Trefny & Nicole Kirchhammer & Priska Auf der Maur & Marina Natoli & Dominic Schmid & Markus Germann & Laura Fernandez Rodriguez & Petra Herzig & Jonas Lötscher & Maryam Akrami & Jane C. Stin, 2023. "Deletion of SNX9 alleviates CD8 T cell exhaustion for effective cellular cancer immunotherapy," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
  7. Siqi Li & Kun Li & Kang Wang & Haoyuan Yu & Xiangyang Wang & Mengchen Shi & Zhixing Liang & Zhou Yang & Yongwei Hu & Yang Li & Wei Liu & Hua Li & Shuqun Cheng & Linsen Ye & Yang Yang, 2023. "Low-dose radiotherapy combined with dual PD-L1 and VEGFA blockade elicits antitumor response in hepatocellular carcinoma mediated by activated intratumoral CD8+ exhausted-like T cells," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
  8. Anneke L. Eerkens & Koen Brummel & Annegé Vledder & Sterre T. Paijens & Marta Requesens & Dominik Loiero & Nienke Rooij & Annechien Plat & Floris-Jan Haan & Patty Klok & Refika Yigit & Thijs Roelofsen, 2024. "Neoadjuvant immune checkpoint blockade in women with mismatch repair deficient endometrial cancer: a phase I study," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
  9. L. Llaó-Cid & JKL Wong & I. Fernandez Botana & Y. Paul & M. Wierz & L-M Pilger & A. Floerchinger & CL Tan & S. Gonder & G. Pagano & M. Chazotte & K. Bestak & C. Schifflers & M. Iskar & T. Roider & F. , 2025. "Integrative multi-omics reveals a regulatory and exhausted T-cell landscape in CLL and identifies galectin-9 as an immunotherapy target," Nature Communications, Nature, vol. 16(1), pages 1-22, December.
  10. Xiaofeng Liao & Wenxue Li & Hongyue Zhou & Barani Kumar Rajendran & Ao Li & Jingjing Ren & Yi Luan & David A. Calderwood & Benjamin Turk & Wenwen Tang & Yansheng Liu & Dianqing Wu, 2024. "The CUL5 E3 ligase complex negatively regulates central signaling pathways in CD8+ T cells," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
  11. Isabelle Damei & Aziza Caidi & Edouard Auclin & Julien Adam & Sébastien Mella & Milena Hasan & Eric Tartour & Caroline Robert & Stéphanie Corgnac & Fathia Mami-Chouaib, 2025. "Different tumour-resident memory T-cell subsets regulate responses to anti-PD-1 and anti-CTLA-4 cancer immunotherapies," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
  12. Matthew A. Cottam & Heather L. Caslin & Nathan C. Winn & Alyssa H. Hasty, 2022. "Multiomics reveals persistence of obesity-associated immune cell phenotypes in adipose tissue during weight loss and weight regain in mice," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  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. Ahmed E. I. Hamouda & Jessica Filtjens & Elisabeth Brabants & Daliya Kancheva & Ayla Debraekeleer & Jan Brughmans & Lotte Jacobs & Pauline M. R. Bardet & Elisabeth Knetemann & Pierre Lefesvre & Lize A, 2024. "Intratumoral delivery of lipid nanoparticle-formulated mRNA encoding IL-21, IL-7, and 4-1BBL induces systemic anti-tumor immunity," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
  15. Alessandra Castiglioni & Yagai Yang & Katherine Williams & Alvin Gogineni & Ryan S. Lane & Amber W. Wang & Justin A. Shyer & Zhe Zhang & Stephanie Mittman & Alan Gutierrez & Jillian L. Astarita & Minh, 2023. "Combined PD-L1/TGFβ blockade allows expansion and differentiation of stem cell-like CD8 T cells in immune excluded tumors," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
  16. Joyce B. Kang & Aparna Nathan & Kathryn Weinand & Fan Zhang & Nghia Millard & Laurie Rumker & D. Branch Moody & Ilya Korsunsky & Soumya Raychaudhuri, 2021. "Efficient and precise single-cell reference atlas mapping with Symphony," Nature Communications, Nature, vol. 12(1), pages 1-21, December.
  17. Marina T. Broz & Emily Y. Ko & Kristin Ishaya & Jinfen Xiao & Marco Simone & Xen Ping Hoi & Roberta Piras & Basia Gala & Fernando H. G. Tessaro & Anja Karlstaedt & Sandra Orsulic & Amanda W. Lund & Ke, 2024. "Metabolic targeting of cancer associated fibroblasts overcomes T-cell exclusion and chemoresistance in soft-tissue sarcomas," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  18. Carmen Oi Ning Leung & Yang Yang & Rainbow Wing Hei Leung & Karl Kam Hei So & Hai Jun Guo & Martina Mang Leng Lei & Gregory Kenneth Muliawan & Yuan Gao & Qian Qian Yu & Jing Ping Yun & Stephanie Ma & , 2023. "Broad-spectrum kinome profiling identifies CDK6 upregulation as a driver of lenvatinib resistance in hepatocellular carcinoma," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
  19. 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.
  20. Binbin Wang & Robert Saddawi-Konefka & Lauren M. Clubb & Shiqi Tang & Di Wu & Sumit Mukherjee & Sahil Sahni & Saugato Rahman Dhruba & Xinping Yang & Sumeet Patiyal & Chi-Ping Day & Parth A. Desai & Cl, 2025. "Longitudinal liquid biopsy identifies an early predictive biomarker of immune checkpoint blockade response in head and neck squamous cell carcinoma," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
  21. 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.
  22. 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.
  23. Michal Polonsky & Louisa M. S. Gerhardt & Jina Yun & Kari Koppitch & Katsuya Lex Colón & Henry Amrhein & Barbara Wold & Shiwei Zheng & Guo-Cheng Yuan & Matt Thomson & Long Cai & Andrew P. McMahon, 2024. "Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and disease," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  24. Lulu Ren & Jianqin Wan & Xiaoyan Li & Jie Yao & Yan Ma & Fanchao Meng & Shusen Zheng & Weidong Han & Hangxiang Wang, 2024. "Mitochondrial rewiring with small-molecule drug-free nanoassemblies unleashes anticancer immunity," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
  25. Yi Zhang & Guanjue Xiang & Alva Yijia Jiang & Allen Lynch & Zexian Zeng & Chenfei Wang & Wubing Zhang & Jingyu Fan & Jiajinlong Kang & Shengqing Stan Gu & Changxin Wan & Boning Zhang & X. Shirley Liu , 2023. "MetaTiME integrates single-cell gene expression to characterize the meta-components of the tumor immune microenvironment," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
  26. Massimo Andreatta & Léonard Hérault & Paul Gueguen & David Gfeller & Ariel J. Berenstein & Santiago J. Carmona, 2024. "Semi-supervised integration of single-cell transcriptomics data," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
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