DELVE: feature selection for preserving biological trajectories in single-cell data
Author
Abstract
Suggested Citation
DOI: 10.1038/s41467-024-46773-z
Download full text from publisher
References listed on IDEAS
- Gioele La Manno & Ruslan Soldatov & Amit Zeisel & Emelie Braun & Hannah Hochgerner & Viktor Petukhov & Katja Lidschreiber & Maria E. Kastriti & Peter Lönnerberg & Alessandro Furlan & Jean Fan & Lars E, 2018. "RNA velocity of single cells," Nature, Nature, vol. 560(7719), pages 494-498, August.
- Phipson Belinda & Smyth Gordon K, 2010. "Permutation P-values Should Never Be Zero: Calculating Exact P-values When Permutations Are Randomly Drawn," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 9(1), pages 1-16, October.
- Shobana V. Stassen & Gwinky G. K. Yip & Kenneth K. Y. Wong & Joshua W. K. Ho & Kevin K. Tsia, 2021. "Generalized and scalable trajectory inference in single-cell omics data with VIA," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
- Peijie Zhou & Shuxiong Wang & Tiejun Li & Qing Nie, 2021. "Dissecting transition cells from single-cell transcriptome data through multiscale stochastic dynamics," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
- Xiuwei Zhang & Chenling Xu & Nir Yosef, 2019. "Simulating multiple faceted variability in single cell RNA sequencing," Nature Communications, Nature, vol. 10(1), pages 1-16, December.
- Wenpin Hou & Zhicheng Ji & Zeyu Chen & E. John Wherry & Stephanie C. Hicks & Hongkai Ji, 2023. "A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
- Junyue Cao & Malte Spielmann & Xiaojie Qiu & Xingfan Huang & Daniel M. Ibrahim & Andrew J. Hill & Fan Zhang & Stefan Mundlos & Lena Christiansen & Frank J. Steemers & Cole Trapnell & Jay Shendure, 2019. "The single-cell transcriptional landscape of mammalian organogenesis," Nature, Nature, vol. 566(7745), pages 496-502, February.
- Kieran R Campbell & Christopher Yau, 2018. "Uncovering pseudotemporal trajectories with covariates from single cell and bulk expression data," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
- Koen Van den Berge & Hector Roux de Bézieux & Kelly Street & Wouter Saelens & Robrecht Cannoodt & Yvan Saeys & Sandrine Dudoit & Lieven Clement, 2020. "Trajectory-based differential expression analysis for single-cell sequencing data," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
- Yue Cao & Pengyi Yang & Jean Yee Hwa Yang, 2021. "A benchmark study of simulation methods for single-cell RNA sequencing data," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
- Reiichi Sugihara & Yuki Kato & Tomoya Mori & Yukio Kawahara, 2022. "Alignment of single-cell trajectory trees with CAPITAL," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
- Miloš Daković & Ljubiša Stanković & Ervin Sejdić, 2019. "Local Smoothness of Graph Signals," Mathematical Problems in Engineering, Hindawi, vol. 2019, pages 1-14, April.
- Mladen Jergović & Christopher P. Coplen & Jennifer L. Uhrlaub & David G. Besselsen & Shu Cheng & Megan J. Smithey & Janko Nikolich-Žugich, 2021. "Infection-induced type I interferons critically modulate the homeostasis and function of CD8+ naïve T cells," Nature Communications, Nature, vol. 12(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.- Wenpin Hou & Zhicheng Ji & Zeyu Chen & E. John Wherry & Stephanie C. Hicks & Hongkai Ji, 2023. "A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
- Gaofei Li & Yicong Sun & Immanuel Kwok & Liting Yang & Wanying Wen & Peixian Huang & Mei Wu & Jing Li & Zhibin Huang & Zhaoyuan Liu & Shuai He & Wan Peng & Jin-Xin Bei & Florent Ginhoux & Lai Guan Ng , 2024. "Cebp1 and Cebpβ transcriptional axis controls eosinophilopoiesis in zebrafish," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
- Zhixin Li & Kathy Nga-Chu Lui & Sin-Ting Lau & Frank Pui-Ling Lai & Peng Li & Patrick Ho-Yu Chung & Kenneth Kak-Yuen Wong & Paul Kwong-Hing Tam & Maria-Mercedes Garica-Barcelo & Chi-Chung Hui & Pak Ch, 2023. "Transcriptomics of Hirschsprung disease patient-derived enteric neural crest cells reveals a role for oxidative phosphorylation," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
- Z. L. Liu & X. Y. Meng & R. J. Bao & M. Y. Shen & J. J. Sun & W. D. Chen & F. Liu & Y. He, 2024. "Single cell deciphering of progression trajectories of the tumor ecosystem in head and neck cancer," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
- P. Bielefeld & A. Martirosyan & S. Martín-Suárez & A. Apresyan & G. F. Meerhoff & F. Pestana & S. Poovathingal & N. Reijner & W. Koning & R. A. Clement & I. Veen & E. M. Toledo & O. Polzer & I. Durá &, 2024. "Traumatic brain injury promotes neurogenesis at the cost of astrogliogenesis in the adult hippocampus of male mice," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
- Stefanie Kirchberger & Mohamed R. Shoeb & Daria Lazic & Andrea Wenninger-Weinzierl & Kristin Fischer & Lisa E. Shaw & Filomena Nogueira & Fikret Rifatbegovic & Eva Bozsaky & Ruth Ladenstein & Bernd Bo, 2024. "Comparative transcriptomics coupled to developmental grading via transgenic zebrafish reporter strains identifies conserved features in neutrophil maturation," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
- Xiaohang Fu & Yingxin Lin & David M. Lin & Daniel Mechtersheimer & Chuhan Wang & Farhan Ameen & Shila Ghazanfar & Ellis Patrick & Jinman Kim & Jean Y. H. Yang, 2024. "BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
- Mattia Zaghi & Federica Banfi & Luca Massimino & Monica Volpin & Edoardo Bellini & Simone Brusco & Ivan Merelli & Cristiana Barone & Michela Bruni & Linda Bossini & Luigi Antonio Lamparelli & Laura Pi, 2023. "Balanced SET levels favor the correct enhancer repertoire during cell fate acquisition," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
- 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.
- Joachim Jonghe & Tomasz S. Kaminski & David B. Morse & Marcin Tabaka & Anna L. Ellermann & Timo N. Kohler & Gianluca Amadei & Charlotte E. Handford & Gregory M. Findlay & Magdalena Zernicka-Goetz & Sa, 2023. "spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
- Angeles Arzalluz-Luque & Pedro Salguero & Sonia Tarazona & Ana Conesa, 2022. "acorde unravels functionally interpretable networks of isoform co-usage from single cell data," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
- Zhen Zuo & Xuesen Cheng & Salma Ferdous & Jianming Shao & Jin Li & Yourong Bao & Jean Li & Jiaxiong Lu & Antonio Jacobo Lopez & Juliette Wohlschlegel & Aric Prieve & Mervyn G. Thomas & Thomas A. Reh &, 2024. "Single cell dual-omic atlas of the human developing retina," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
- Christopher W. Murray & Jennifer J. Brady & Mingqi Han & Hongchen Cai & Min K. Tsai & Sarah E. Pierce & Ran Cheng & Janos Demeter & David M. Feldser & Peter K. Jackson & David B. Shackelford & Monte M, 2022. "LKB1 drives stasis and C/EBP-mediated reprogramming to an alveolar type II fate in lung cancer," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
- Kun Yin & Yiling Xu & Ye Guo & Zhong Zheng & Xinrui Lin & Meijuan Zhao & He Dong & Dianyi Liang & Zhi Zhu & Junhua Zheng & Shichao Lin & Jia Song & Chaoyong Yang, 2024. "Dyna-vivo-seq unveils cellular RNA dynamics during acute kidney injury via in vivo metabolic RNA labeling-based scRNA-seq," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
- Rong Li & Tianyuan Wang & Ryan M. Marquardt & John P. Lydon & San-Pin Wu & Francesco J. DeMayo, 2023. "TRIM28 modulates nuclear receptor signaling to regulate uterine function," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
- Gennady Gorin & John J. Vastola & Meichen Fang & Lior Pachter, 2022. "Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
- 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.
- Yichi Niu & Jiayi Luo & Chenghang Zong, 2024. "Single-cell total-RNA profiling unveils regulatory hubs of transcription factors," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
- Lee E. Korshoj & Tammy Kielian, 2024. "Bacterial single-cell RNA sequencing captures biofilm transcriptional heterogeneity and differential responses to immune pressure," Nature Communications, Nature, vol. 15(1), pages 1-25, December.
- Zhuo Ma & Xiaofei Zhang & Wen Zhong & Hongyan Yi & Xiaowei Chen & Yinsuo Zhao & Yanlin Ma & Eli Song & Tao Xu, 2023. "Deciphering early human pancreas development at the single-cell level," Nature Communications, Nature, vol. 14(1), pages 1-17, 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:15:y:2024:i:1:d:10.1038_s41467-024-46773-z. 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.