A variational algorithm to detect the clonal copy number substructure of tumors from scRNA-seq data
Author
Abstract
Suggested Citation
DOI: 10.1038/s41467-023-36790-9
Download full text from publisher
References listed on IDEAS
- Véronique Frattini & Stefano M. Pagnotta & Tala & Jerry J. Fan & Marco V. Russo & Sang Bae Lee & Luciano Garofano & Jing Zhang & Peiguo Shi & Genevieve Lewis & Heloise Sanson & Vanessa Frederick & Ang, 2018. "A metabolic function of FGFR3-TACC3 gene fusions in cancer," Nature, Nature, vol. 553(7687), pages 222-227, January.
- Kosuke Yoshihara & Maria Shahmoradgoli & Emmanuel Martínez & Rahulsimham Vegesna & Hoon Kim & Wandaliz Torres-Garcia & Victor Treviño & Hui Shen & Peter W. Laird & Douglas A. Levine & Scott L. Carter , 2013. "Inferring tumour purity and stromal and immune cell admixture from expression data," Nature Communications, Nature, vol. 4(1), pages 1-11, December.
- Itay Tirosh & Andrew S. Venteicher & Christine Hebert & Leah E. Escalante & Anoop P. Patel & Keren Yizhak & Jonathan M. Fisher & Christopher Rodman & Christopher Mount & Mariella G. Filbin & Cyril Nef, 2016. "Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma," Nature, Nature, vol. 539(7628), pages 309-313, November.
- Ruiyang Liu & Qingsong Gao & Steven M. Foltz & Jared S. Fowles & Lijun Yao & Julia Tianjiao Wang & Song Cao & Hua Sun & Michael C. Wendl & Sunantha Sethuraman & Amila Weerasinghe & Michael P. Rettig &, 2021. "Co-evolution of tumor and immune cells during progression of multiple myeloma," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
Citations
Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
Cited by:
- Kaichen Xu & Yan Lu & Suyang Hou & Kainan Liu & Yihang Du & Mengqian Huang & Hao Feng & Hao Wu & Xiaobo Sun, 2024. "Detecting anomalous anatomic regions in spatial transcriptomics with STANDS," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
- Zhixing Zhong & Junchen Hou & Zhixian Yao & Lei Dong & Feng Liu & Junqiu Yue & Tiantian Wu & Junhua Zheng & Gaoliang Ouyang & Chaoyong Yang & Jia Song, 2024. "Domain generalization enables general cancer cell annotation in single-cell and spatial transcriptomics," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
- Aleksandr Ianevski & Kristen Nader & Kyriaki Driva & Wojciech Senkowski & Daria Bulanova & Lidia Moyano-Galceran & Tanja Ruokoranta & Heikki Kuusanmäki & Nemo Ikonen & Philipp Sergeev & Markus Vähä-Ko, 2024. "Single-cell transcriptomes identify patient-tailored therapies for selective co-inhibition of cancer clones," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- 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.
- 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.
- 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.
- Teresa Maria Rosaria Noviello & Anna Maria Giacomo & Francesca Pia Caruso & Alessia Covre & Roberta Mortarini & Giovanni Scala & Maria Claudia Costa & Sandra Coral & Wolf H. Fridman & Catherine Sautès, 2023. "Guadecitabine plus ipilimumab in unresectable melanoma: five-year follow-up and integrated multi-omic analysis in the phase 1b NIBIT-M4 trial," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
- Michael J. Geuenich & Dae-won Gong & Kieran R. Campbell, 2024. "The impacts of active and self-supervised learning on efficient annotation of single-cell expression data," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
- Wei Cheng & Hao-Long Li & Shao-Yan Xi & Xiao-Feng Zhang & Yun Zhu & Le Xing & Yan-Xuan Mo & Mei-Mei Li & Fan-En Kong & Wen-Jie Zhu & Xiao-Gang Chen & Hui-Qing Cui & Zhi-Ming Cao & Yuan-Feng Gong & Yun, 2021. "Growth differentiation factor 1-induced tumour plasticity provides a therapeutic window for immunotherapy in hepatocellular carcinoma," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
- 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.
- 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.
- Hyeon-Jin Kim & Greg Booth & Lauren Saunders & Sanjay Srivatsan & José L. McFaline-Figueroa & Cole Trapnell, 2022. "Nuclear oligo hashing improves differential analysis of single-cell RNA-seq," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
- 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.
- Boshu Ouyang & Caihua Shan & Shun Shen & Xinnan Dai & Qingwang Chen & Xiaomin Su & Yongbin Cao & Xifeng Qin & Ying He & Siyu Wang & Ruizhe Xu & Ruining Hu & Leming Shi & Tun Lu & Wuli Yang & Shaojun P, 2024. "AI-powered omics-based drug pair discovery for pyroptosis therapy targeting triple-negative breast cancer," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
- 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.
- 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.
- Yuanli Zhen & Kai Liu & Lei Shi & Simran Shah & Qin Xu & Haley Ellis & Eranga R. Balasooriya & Johannes Kreuzer & Robert Morris & Albert S. Baldwin & Dejan Juric & Wilhelm Haas & Nabeel Bardeesy, 2024. "FGFR inhibition blocks NF-ĸB-dependent glucose metabolism and confers metabolic vulnerabilities in cholangiocarcinoma," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
- 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.
- Sang Bae Lee & Luciano Garofano & Aram Ko & Fulvio D’Angelo & Brulinda Frangaj & Danika Sommer & Qiwen Gan & KyeongJin Kim & Timothy Cardozo & Antonio Iavarone & Anna Lasorella, 2022. "Regulated interaction of ID2 with the anaphase-promoting complex links progression through mitosis with reactivation of cell-type-specific transcription," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
- 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.
- 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.
- Vidhya M. Ravi & Nicolas Neidert & Paulina Will & Kevin Joseph & Julian P. Maier & Jan Kückelhaus & Lea Vollmer & Jonathan M. Goeldner & Simon P. Behringer & Florian Scherer & Melanie Boerries & Marie, 2022. "T-cell dysfunction in the glioblastoma microenvironment is mediated by myeloid cells releasing interleukin-10," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
- 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.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-36790-9. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.