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Inferring tumour purity and stromal and immune cell admixture from expression data

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  1. Shen Zhao & De-Pin Chen & Tong Fu & Jing-Cheng Yang & Ding Ma & Xiu-Zhi Zhu & Xiang-Xue Wang & Yi-Ping Jiao & Xi Jin & Yi Xiao & Wen-Xuan Xiao & Hu-Yunlong Zhang & Hong Lv & Anant Madabhushi & Wen-Tao, 2023. "Single-cell morphological and topological atlas reveals the ecosystem diversity of human breast cancer," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
  2. Lucia Taraborrelli & Yasin Şenbabaoğlu & Lifen Wang & Junghyun Lim & Kerrigan Blake & Noelyn Kljavin & Sarah Gierke & Alexis Scherl & James Ziai & Erin McNamara & Mark Owyong & Shilpa Rao & Aslihan Ka, 2023. "Tumor-intrinsic expression of the autophagy gene Atg16l1 suppresses anti-tumor immunity in colorectal cancer," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  3. Xiaodong Liu & Ke Zhang & Neslihan A. Kaya & Zhe Jia & Dafei Wu & Tingting Chen & Zhiyuan Liu & Sinan Zhu & Axel M. Hillmer & Torsten Wuestefeld & Jin Liu & Yun Shen Chan & Zheng Hu & Liang Ma & Li Ji, 2024. "Tumor phylogeography reveals block-shaped spatial heterogeneity and the mode of evolution in Hepatocellular Carcinoma," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  4. Zhongqi Fan & Xinchen Zou & Guangyi Wang & Yahui Liu & Yanfang Jiang & Haoyan Wang & Ping Zhang & Feng Wei & Xiaohong Du & Meng Wang & Xiaodong Sun & Bai Ji & Xintong Hu & Liguo Chen & Peiwen Zhou & D, 2024. "A transcriptome based molecular classification scheme for cholangiocarcinoma and subtype-derived prognostic biomarker," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  5. Zhenmei Yao & Ning Xu & Guoguo Shang & Haixing Wang & Hui Tao & Yunzhi Wang & Zhaoyu Qin & Subei Tan & Jinwen Feng & Jiajun Zhu & Fahan Ma & Sha Tian & Qiao Zhang & Yuanyuan Qu & Jun Hou & Jianming Gu, 2023. "Proteogenomics of different urothelial bladder cancer stages reveals distinct molecular features for papillary cancer and carcinoma in situ," Nature Communications, Nature, vol. 14(1), pages 1-25, December.
  6. Qi Song & Ye Yang & Dongxian Jiang & Zhaoyu Qin & Chen Xu & Haixing Wang & Jie Huang & Lingli Chen & Rongkui Luo & Xiaolei Zhang & Yufeng Huang & Lei Xu & Zixiang Yu & Subei Tan & Minying Deng & Ruqun, 2022. "Proteomic analysis reveals key differences between squamous cell carcinomas and adenocarcinomas across multiple tissues," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
  7. Yafei Jiang & Jinzeng Wang & Mengxiong Sun & Dongqing Zuo & Hongsheng Wang & Jiakang Shen & Wenyan Jiang & Haoran Mu & Xiaojun Ma & Fei Yin & Jun Lin & Chongren Wang & Shuting Yu & Lu Jiang & Gang Lv , 2022. "Multi-omics analysis identifies osteosarcoma subtypes with distinct prognosis indicating stratified treatment," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  8. Hailiang Zhang & Lin Bai & Xin-Qiang Wu & Xi Tian & Jinwen Feng & Xiaohui Wu & Guo-Hai Shi & Xiaoru Pei & Jiacheng Lyu & Guojian Yang & Yang Liu & Wenhao Xu & Aihetaimujiang Anwaier & Yu Zhu & Da-Long, 2023. "Proteogenomics of clear cell renal cell carcinoma response to tyrosine kinase inhibitor," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
  9. Dongliang Bian & Liangdong Sun & Junjie Hu & Liang Duan & Haoran Xia & Xinsheng Zhu & Fenghuan Sun & Lele Zhang & Huansha Yu & Yicheng Xiong & Zhida Huang & Deping Zhao & Nan Song & Jie Yang & Xiao Ba, 2023. "Neoadjuvant Afatinib for stage III EGFR-mutant non-small cell lung cancer: a phase II study," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  10. Ming Chen & Runzhe Chen & Ying Jin & Jun Li & Xin Hu & Jiexin Zhang & Junya Fujimoto & Shawna M. Hubert & Carl M. Gay & Bo Zhu & Yanhua Tian & Nicholas McGranahan & Won-Chul Lee & Julie George & Xiao , 2021. "Cold and heterogeneous T cell repertoire is associated with copy number aberrations and loss of immune genes in small-cell lung cancer," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
  11. Bernardo P de Almeida & André F Vieira & Joana Paredes & Mónica Bettencourt-Dias & Nuno L Barbosa-Morais, 2019. "Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome," PLOS Computational Biology, Public Library of Science, vol. 15(3), pages 1-31, March.
  12. Shixiang Wang & Chen-Yi Wu & Ming-Ming He & Jia-Xin Yong & Yan-Xing Chen & Li-Mei Qian & Jin-Ling Zhang & Zhao-Lei Zeng & Rui-Hua Xu & Feng Wang & Qi Zhao, 2024. "Machine learning-based extrachromosomal DNA identification in large-scale cohorts reveals its clinical implications in cancer," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
  13. Shaoshuai Tang & Yunzhi Wang & Rongkui Luo & Rundong Fang & Yufeng Liu & Hang Xiang & Peng Ran & Yexin Tong & Mingjun Sun & Subei Tan & Wen Huang & Jie Huang & Jiacheng Lv & Ning Xu & Zhenmei Yao & Qi, 2024. "Proteomic characterization identifies clinically relevant subgroups of soft tissue sarcoma," Nature Communications, Nature, vol. 15(1), pages 1-24, December.
  14. Jennifer G. Abelin & Erik J. Bergstrom & Keith D. Rivera & Hannah B. Taylor & Susan Klaeger & Charles Xu & Eva K. Verzani & C. Jackson White & Hilina B. Woldemichael & Maya Virshup & Meagan E. Olive &, 2023. "Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
  15. Bruna Calsina & Elena Piñeiro-Yáñez & Ángel M. Martínez-Montes & Eduardo Caleiras & Ángel Fernández-Sanromán & María Monteagudo & Rafael Torres-Pérez & Coral Fustero-Torre & Marta Pulgarín-Alfaro & Ed, 2023. "Genomic and immune landscape Of metastatic pheochromocytoma and paraganglioma," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
  16. Fatima Khan & Yiyun Lin & Heba Ali & Lizhi Pang & Madeline Dunterman & Wen-Hao Hsu & Katie Frenis & R. Grant Rowe & Derek A. Wainwright & Kathleen McCortney & Leah K. Billingham & Jason Miska & Craig , 2024. "Lactate dehydrogenase A regulates tumor-macrophage symbiosis to promote glioblastoma progression," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
  17. Yuanyuan Qu & Jinwen Feng & Xiaohui Wu & Lin Bai & Wenhao Xu & Lingli Zhu & Yang Liu & Fujiang Xu & Xuan Zhang & Guojian Yang & Jiacheng Lv & Xiuping Chen & Guo-Hai Shi & Hong-Kai Wang & Da-Long Cao &, 2022. "A proteogenomic analysis of clear cell renal cell carcinoma in a Chinese population," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
  18. Funan He & Abhik M. Bandyopadhyay & Laura J. Klesse & Anna Rogojina & Sang H. Chun & Erin Butler & Taylor Hartshorne & Trevor Holland & Dawn Garcia & Korri Weldon & Luz-Nereida Perez Prado & Anne-Mari, 2023. "Genomic profiling of subcutaneous patient-derived xenografts reveals immune constraints on tumor evolution in childhood solid cancer," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  19. David J. Klinke & Audry Fernandez & Wentao Deng & Atefeh Razazan & Habibolla Latifizadeh & Anika C. Pirkey, 2022. "Data-driven learning how oncogenic gene expression locally alters heterocellular networks," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  20. Xiaoyu Song & Jiayi Ji & Joseph H. Rothstein & Stacey E. Alexeeff & Lori C. Sakoda & Adriana Sistig & Ninah Achacoso & Eric Jorgenson & Alice S. Whittemore & Robert J. Klein & Laurel A. Habel & Pei Wa, 2023. "MiXcan: a framework for cell-type-aware transcriptome-wide association studies with an application to breast cancer," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  21. Wanzun Lin & Li Chen & Haojiong Zhang & Xianxin Qiu & Qingting Huang & Fangzhu Wan & Ziyu Le & Shikai Geng & Anlan Zhang & Sufang Qiu & Long Chen & Lin Kong & Jiade J. Lu, 2023. "Tumor-intrinsic YTHDF1 drives immune evasion and resistance to immune checkpoint inhibitors via promoting MHC-I degradation," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
  22. Zheqi Li & Olivia McGinn & Yang Wu & Amir Bahreini & Nolan M. Priedigkeit & Kai Ding & Sayali Onkar & Caleb Lampenfeld & Carol A. Sartorius & Lori Miller & Margaret Rosenzweig & Ofir Cohen & Nikhil Wa, 2022. "ESR1 mutant breast cancers show elevated basal cytokeratins and immune activation," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  23. Xiaoping Su & Xiaofan Lu & Sehrish Khan Bazai & Linda Dainese & Arnauld Verschuur & Benoit Dumont & Roger Mouawad & Li Xu & Wenxuan Cheng & Fangrong Yan & Sabine Irtan & Véronique Lindner & Catherine , 2023. "Delineating the interplay between oncogenic pathways and immunity in anaplastic Wilms tumors," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  24. Yin Li & Manling Jiang & Ling Aye & Li Luo & Yong Zhang & Fengkai Xu & Yongqi Wei & Dan Peng & Xiang He & Jie Gu & Xiaofang Yu & Guoping Li & Di Ge & Chunlai Lu, 2024. "UPP1 promotes lung adenocarcinoma progression through the induction of an immunosuppressive microenvironment," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
  25. Kang Wang & Ioannis Zerdes & Henrik J. Johansson & Dhifaf Sarhan & Yizhe Sun & Dimitris C. Kanellis & Emmanouil G. Sifakis & Artur Mezheyeuski & Xingrong Liu & Niklas Loman & Ingrid Hedenfalk & Jonas , 2024. "Longitudinal molecular profiling elucidates immunometabolism dynamics in breast cancer," Nature Communications, Nature, vol. 15(1), pages 1-24, December.
  26. Khoa A. Tran & Venkateswar Addala & Rebecca L. Johnston & David Lovell & Andrew Bradley & Lambros T. Koufariotis & Scott Wood & Sunny Z. Wu & Daniel Roden & Ghamdan Al-Eryani & Alexander Swarbrick & E, 2023. "Performance of tumour microenvironment deconvolution methods in breast cancer using single-cell simulated bulk mixtures," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  27. Elisa I. Rivas & Jenniffer Linares & Melissa Zwick & Andrea Gómez-Llonin & Marc Guiu & Anna Labernadie & Jordi Badia-Ramentol & Anna Lladó & Lídia Bardia & Iván Pérez-Núñez & Carolina Martínez-Ciarpag, 2022. "Targeted immunotherapy against distinct cancer-associated fibroblasts overcomes treatment resistance in refractory HER2+ breast tumors," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  28. 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.
  29. Romain Sigaud & Thomas K. Albert & Caroline Hess & Thomas Hielscher & Nadine Winkler & Daniela Kocher & Carolin Walter & Daniel Münter & Florian Selt & Diren Usta & Jonas Ecker & Angela Brentrup & Mar, 2023. "MAPK inhibitor sensitivity scores predict sensitivity driven by the immune infiltration in pediatric low-grade gliomas," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
  30. Antonio De Falco & Francesca Caruso & Xiao-Dong Su & Antonio Iavarone & Michele Ceccarelli, 2023. "A variational algorithm to detect the clonal copy number substructure of tumors from scRNA-seq data," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  31. Yuanyuan Qu & Xiaohui Wu & Aihetaimujiang Anwaier & Jinwen Feng & Wenhao Xu & Xiaoru Pei & Yu Zhu & Yang Liu & Lin Bai & Guojian Yang & Xi Tian & Jiaqi Su & Guo-Hai Shi & Da-Long Cao & Fujiang Xu & Yu, 2022. "Proteogenomic characterization of MiT family translocation renal cell carcinoma," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  32. A. Gordon Robertson & Khyati Meghani & Lauren Folgosa Cooley & Kimberly A. McLaughlin & Leigh Ann Fall & Yanni Yu & Mauro A. A. Castro & Clarice S. Groeneveld & Aurélien Reyniès & Vadim I. Nazarov & V, 2023. "Expression-based subtypes define pathologic response to neoadjuvant immune-checkpoint inhibitors in muscle-invasive bladder cancer," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
  33. María-Jesús Lobón-Iglesias & Mamy Andrianteranagna & Zhi-Yan Han & Céline Chauvin & Julien Masliah-Planchon & Valeria Manriquez & Arnault Tauziede-Espariat & Sandrina Turczynski & Rachida Bouarich-Bou, 2023. "Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
  34. Brian D. Lehmann & Antonio Colaprico & Tiago C. Silva & Jianjiao Chen & Hanbing An & Yuguang Ban & Hanchen Huang & Lily Wang & Jamaal L. James & Justin M. Balko & Paula I. Gonzalez-Ericsson & Melinda , 2021. "Multi-omics analysis identifies therapeutic vulnerabilities in triple-negative breast cancer subtypes," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
  35. Han Jin & Cheng Zhang & Martin Zwahlen & Kalle Feilitzen & Max Karlsson & Mengnan Shi & Meng Yuan & Xiya Song & Xiangyu Li & Hong Yang & Hasan Turkez & Linn Fagerberg & Mathias Uhlén & Adil Mardinoglu, 2023. "Systematic transcriptional analysis of human cell lines for gene expression landscape and tumor representation," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
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