Bulk tissue cell type deconvolution with multi-subject single-cell expression reference

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1. Bryce Rowland & Ruth Huh & Zoey Hou & Cheynna Crowley & Jia Wen & Yin Shen & Ming Hu & Paola Giusti-Rodríguez & Patrick F Sullivan & Yun Li, 2022. "THUNDER: A reference-free deconvolution method to infer cell type proportions from bulk Hi-C data," PLOS Genetics, Public Library of Science, vol. 18(3), pages 1-18, March.
2. Zhiyuan Liu & Dafei Wu & Weiwei Zhai & Liang Ma, 2023. "SONAR enables cell type deconvolution with spatially weighted Poisson-Gamma model for spatial transcriptomics," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
3. Kobe Ridder & Huiwen Che & Kaat Leroy & Bernard Thienpont, 2024. "Benchmarking of methods for DNA methylome deconvolution," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
4. Gavin J. Sutton & Daniel Poppe & Rebecca K. Simmons & Kieran Walsh & Urwah Nawaz & Ryan Lister & Johann A. Gagnon-Bartsch & Irina Voineagu, 2022. "Comprehensive evaluation of deconvolution methods for human brain gene expression," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
5. Raúl F. Pérez & Patricia Tezanos & Alfonso Peñarroya & Alejandro González-Ramón & Rocío G. Urdinguio & Javier Gancedo-Verdejo & Juan Ramón Tejedor & Pablo Santamarina-Ojeda & Juan José Alba-Linares & , 2024. "A multiomic atlas of the aging hippocampus reveals molecular changes in response to environmental enrichment," Nature Communications, Nature, vol. 15(1), pages 1-26, December.
6. Yi Xu & Michael H. Nipper & Angel A. Dominguez & Zhenqing Ye & Naoki Akanuma & Kevin Lopez & Janice J. Deng & Destiny Arenas & Ava Sanchez & Francis E. Sharkey & Colin M. Court & Aatur D. Singhi & Hua, 2024. "Reconstitution of human PDAC using primary cells reveals oncogenic transcriptomic features at tumor onset," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
7. Joschka Hey & Michelle Paulsen & Reka Toth & Dieter Weichenhan & Simone Butz & Jolanthe Schatterny & Reinhard Liebers & Pavlo Lutsik & Christoph Plass & Marcus A. Mall, 2021. "Epigenetic reprogramming of airway macrophages promotes polarization and inflammation in muco-obstructive lung disease," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
8. Jakob Hartmann & Thomas Bajaj & Joy Otten & Claudia Klengel & Tim Ebert & Anne-Kathrin Gellner & Ellen Junglas & Kathrin Hafner & Elmira A. Anderzhanova & Fiona Tang & Galen Missig & Lindsay Rexrode &, 2024. "SKA2 regulated hyperactive secretory autophagy drives neuroinflammation-induced neurodegeneration," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
9. Yanshuo Chen & Yixuan Wang & Yuelong Chen & Yuqi Cheng & Yumeng Wei & Yunxiang Li & Jiuming Wang & Yingying Wei & Ting-Fung Chan & Yu Li, 2022. "Deep autoencoder for interpretable tissue-adaptive deconvolution and cell-type-specific gene analysis," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
10. Xiaoguang Xu & Chachrit Khunsriraksakul & James M. Eales & Sebastien Rubin & David Scannali & Sushant Saluja & David Talavera & Havell Markus & Lida Wang & Maciej Drzal & Akhlaq Maan & Abigail C. Lay , 2024. "Genetic imputation of kidney transcriptome, proteome and multi-omics illuminates new blood pressure and hypertension targets," Nature Communications, Nature, vol. 15(1), pages 1-29, December.
11. Zhenzhen Xun & Xinyu Ding & Yao Zhang & Benyan Zhang & Shujing Lai & Duowu Zou & Junke Zheng & Guoqiang Chen & Bing Su & Leng Han & Youqiong Ye, 2023. "Reconstruction of the tumor spatial microenvironment along the malignant-boundary-nonmalignant axis," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
12. Jie Liao & Jingyang Qian & Yin Fang & Zhuo Chen & Xiang Zhuang & Ningyu Zhang & Xin Shao & Yining Hu & Penghui Yang & Junyun Cheng & Yang Hu & Lingqi Yu & Haihong Yang & Jinlu Zhang & Xiaoyan Lu & Li , 2022. "De novo analysis of bulk RNA-seq data at spatially resolved single-cell resolution," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
13. Zehua Zeng & Yuqing Ma & Lei Hu & Bowen Tan & Peng Liu & Yixuan Wang & Cencan Xing & Yuanyan Xiong & Hongwu Du, 2024. "OmicVerse: a framework for bridging and deepening insights across bulk and single-cell sequencing," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
14. Bárbara Andrade Barbosa & Saskia D. Asten & Ji Won Oh & Arantza Farina-Sarasqueta & Joanne Verheij & Frederike Dijk & Hanneke W. M. Laarhoven & Bauke Ylstra & Juan J. Garcia Vallejo & Mark A. Wiel & Y, 2021. "Bayesian log-normal deconvolution for enhanced in silico microdissection of bulk gene expression data," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
15. Stefano Berto & Alex H. Treacher & Emre Caglayan & Danni Luo & Jillian R. Haney & Michael J. Gandal & Daniel H. Geschwind & Albert A. Montillo & Genevieve Konopka, 2022. "Association between resting-state functional brain connectivity and gene expression is altered in autism spectrum disorder," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
16. Michael T. H. Ng & Rowie Borst & Hamez Gacaferi & Sarah Davidson & Jessica E. Ackerman & Peter A. Johnson & Caio C. Machado & Ian Reekie & Moustafa Attar & Dylan Windell & Mariola Kurowska-Stolarska &, 2024. "A single cell atlas of frozen shoulder capsule identifies features associated with inflammatory fibrosis resolution," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
17. Xiao Zhou & Zhen Cheng & Mingyu Dong & Qi Liu & Weiyang Yang & Min Liu & Junzhang Tian & Weibin Cheng, 2022. "Tumor fractions deciphered from circulating cell-free DNA methylation for cancer early diagnosis," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
18. Matteo D’Antonio & Jennifer P. Nguyen & Timothy D. Arthur & Hiroko Matsui & Agnieszka D’Antonio-Chronowska & Kelly A. Frazer, 2023. "Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
19. 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.
20. Chang Su & Zichun Xu & Xinning Shan & Biao Cai & Hongyu Zhao & Jingfei Zhang, 2023. "Cell-type-specific co-expression inference from single cell RNA-sequencing data," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
21. Keyong Sun & Runda Xu & Fuhai Ma & Naixue Yang & Yang Li & Xiaofeng Sun & Peng Jin & Wenzhe Kang & Lemei Jia & Jianping Xiong & Haitao Hu & Yantao Tian & Xun Lan, 2022. "scRNA-seq of gastric tumor shows complex intercellular interaction with an alternative T cell exhaustion trajectory," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
22. Benjamin Villalard & Arjan Boltjes & Florie Reynaud & Olivier Imbaud & Karine Thoinet & Ilse Timmerman & Séverine Croze & Emy Theoulle & Gianluigi Atzeni & Joël Lachuer & Jan J. Molenaar & Godelieve A, 2024. "Neuroblastoma plasticity during metastatic progression stems from the dynamics of an early sympathetic transcriptomic trajectory," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
23. Daniel Charytonowicz & Rachel Brody & Robert Sebra, 2023. "Interpretable and context-free deconvolution of multi-scale whole transcriptomic data with UniCell deconvolve," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
24. Yusuke Adachi & Kazutaka Ueda & Seitaro Nomura & Kaoru Ito & Manami Katoh & Mikako Katagiri & Shintaro Yamada & Masaki Hashimoto & Bowen Zhai & Genri Numata & Akira Otani & Munetoshi Hinata & Yuta Hir, 2022. "Beiging of perivascular adipose tissue regulates its inflammation and vascular remodeling," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
25. Maja Olecka & Alena Bömmel & Lena Best & Madlen Haase & Silke Foerste & Konstantin Riege & Thomas Dost & Stefano Flor & Otto W. Witte & Sören Franzenburg & Marco Groth & Björn Eyss & Christoph Kaleta , 2024. "Nonlinear DNA methylation trajectories in aging male mice," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
26. Beibei Ru & Jinlin Huang & Yu Zhang & Kenneth Aldape & Peng Jiang, 2023. "Estimation of cell lineages in tumors from spatial transcriptomics data," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
27. Seoyeon Lee & Mohammad Naimul Islam & Kaveh Boostanpour & Dvir Aran & Guangchun Jin & Stephanie Christenson & Michael A. Matthay & Walter L. Eckalbar & Daryle J. DePianto & Joseph R. Arron & Liam Mage, 2021. "Molecular programs of fibrotic change in aging human lung," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
28. Nelson Johansen & Hongru Hu & Gerald Quon, 2023. "Projecting RNA measurements onto single cell atlases to extract cell type-specific expression profiles using scProjection," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
29. Kai Kang & Qian Meng & Igor Shats & David M Umbach & Melissa Li & Yuanyuan Li & Xiaoling Li & Leping Li, 2019. "CDSeq: A novel complete deconvolution method for dissecting heterogeneous samples using gene expression data," PLOS Computational Biology, Public Library of Science, vol. 15(12), pages 1-18, December.
30. 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.
31. 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.
32. Michael S. Balzer & Tomohito Doke & Ya-Wen Yang & Daniel L. Aldridge & Hailong Hu & Hung Mai & Dhanunjay Mukhi & Ziyuan Ma & Rojesh Shrestha & Matthew B. Palmer & Christopher A. Hunter & Katalin Suszt, 2022. "Single-cell analysis highlights differences in druggable pathways underlying adaptive or fibrotic kidney regeneration," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
33. David R. Ghasemi & Konstantin Okonechnikov & Anne Rademacher & Stephan Tirier & Kendra K. Maass & Hanna Schumacher & Piyush Joshi & Maxwell P. Gold & Julia Sundheimer & Britta Statz & Ahmet S. Rifaiog, 2024. "Compartments in medulloblastoma with extensive nodularity are connected through differentiation along the granular precursor lineage," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
34. Jingtao Wang & Gregory J. Fonseca & Jun Ding, 2024. "scSemiProfiler: Advancing large-scale single-cell studies through semi-profiling with deep generative models and active learning," Nature Communications, Nature, vol. 15(1), pages 1-27, December.