Geometry of the Gene Expression Space of Individual Cells
Author
Abstract
Suggested Citation
DOI: 10.1371/journal.pcbi.1004224
Download full text from publisher
References listed on IDEAS
- Andrew McDavid & Lucas Dennis & Patrick Danaher & Greg Finak & Michael Krouse & Alice Wang & Philippa Webster & Joseph Beechem & Raphael Gottardo, 2014. "Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells," PLOS Computational Biology, Public Library of Science, vol. 10(7), pages 1-10, July.
- Jacques Banchereau & Ralph M. Steinman, 1998. "Dendritic cells and the control of immunity," Nature, Nature, vol. 392(6673), pages 245-252, March.
- Alex K. Shalek & Rahul Satija & Joe Shuga & John J. Trombetta & Dave Gennert & Diana Lu & Peilin Chen & Rona S. Gertner & Jellert T. Gaublomme & Nir Yosef & Schraga Schwartz & Brian Fowler & Suzanne W, 2014. "Single-cell RNA-seq reveals dynamic paracrine control of cellular variation," Nature, Nature, vol. 510(7505), pages 363-369, June.
- Thomas Gallagher & Theresa Bjorness & Robert Greene & Young-Jai You & Leon Avery, 2013. "The Geometry of Locomotive Behavioral States in C. elegans," PLOS ONE, Public Library of Science, vol. 8(3), pages 1-19, March.
- Ran Kafri & Jason Levy & Miriam B. Ginzberg & Seungeun Oh & Galit Lahav & Marc W. Kirschner, 2013. "Dynamics extracted from fixed cells reveal feedback linking cell growth to cell cycle," Nature, Nature, vol. 494(7438), pages 480-483, February.
- Nick Barker & Johan H. van Es & Jeroen Kuipers & Pekka Kujala & Maaike van den Born & Miranda Cozijnsen & Andrea Haegebarth & Jeroen Korving & Harry Begthel & Peter J. Peters & Hans Clevers, 2007. "Identification of stem cells in small intestine and colon by marker gene Lgr5," Nature, Nature, vol. 449(7165), pages 1003-1007, October.
- Alex K. Shalek & Rahul Satija & Xian Adiconis & Rona S. Gertner & Jellert T. Gaublomme & Raktima Raychowdhury & Schraga Schwartz & Nir Yosef & Christine Malboeuf & Diana Lu & John J. Trombetta & Dave , 2013. "Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells," Nature, Nature, vol. 498(7453), pages 236-240, June.
- Laila Ritsma & Saskia I. J. Ellenbroek & Anoek Zomer & Hugo J. Snippert & Frederic J. de Sauvage & Benjamin D. Simons & Hans Clevers & Jacco van Rheenen, 2014. "Intestinal crypt homeostasis revealed at single-stem-cell level by in vivo live imaging," Nature, Nature, vol. 507(7492), pages 362-365, March.
Citations
Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
Cited by:
- Aleix Alcacer & Irene Epifanio & M Victoria Ibáñez & Amelia Simó & Alfredo Ballester, 2020. "A data-driven classification of 3D foot types by archetypal shapes based on landmarks," PLOS ONE, Public Library of Science, vol. 15(1), pages 1-19, January.
- Ariel Madrigal & Tianyuan Lu & Larisa M. Soto & Hamed S. Najafabadi, 2024. "A unified model for interpretable latent embedding of multi-sample, multi-condition single-cell data," Nature Communications, Nature, vol. 15(1), pages 1-15, 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.- Shamir Montazid & Sheila Bandyopadhyay & Daniel W. Hart & Nan Gao & Brian Johnson & Sri G. Thrumurthy & Dustin J. Penn & Bettina Wernisch & Mukesh Bansal & Philipp M. Altrock & Fabian Rost & Patrycja , 2023. "Adult stem cell activity in naked mole rats for long-term tissue maintenance," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
- Sylvie Rato & Antonio Rausell & Miguel Muñoz & Amalio Telenti & Angela Ciuffi, 2017. "Single-cell analysis identifies cellular markers of the HIV permissive cell," PLOS Pathogens, Public Library of Science, vol. 13(10), pages 1-23, October.
- Philip S. Robinson & Laura E. Thomas & Federico Abascal & Hyunchul Jung & Luke M. R. Harvey & Hannah D. West & Sigurgeir Olafsson & Bernard C. H. Lee & Tim H. H. Coorens & Henry Lee-Six & Laura Butlin, 2022. "Inherited MUTYH mutations cause elevated somatic mutation rates and distinctive mutational signatures in normal human cells," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
- Manikandan Narayanan & Andrew J Martins & John S Tsang, 2016. "Robust Inference of Cell-to-Cell Expression Variations from Single- and K-Cell Profiling," PLOS Computational Biology, Public Library of Science, vol. 12(7), pages 1-33, July.
- Thanh Loc Nguyen & Youngjin Choi & Jihye Im & Hyunsu Shin & Ngoc Man Phan & Min Kyung Kim & Seung Woo Choi & Jaeyun Kim, 2022. "Immunosuppressive biomaterial-based therapeutic vaccine to treat multiple sclerosis via re-establishing immune tolerance," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
- Márton Demeter & Imre Derényi & Gergely J. Szöllősi, 2022. "Trade-off between reducing mutational accumulation and increasing commitment to differentiation determines tissue organization," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
- K. Brad Wray & Søren R. Paludan & Lutz Bornmann & Robin Haunschild, 2024. "Using Reference Publication Year Spectroscopy (RPYS) to analyze the research and publication culture in immunology," Scientometrics, Springer;Akadémiai Kiadó, vol. 129(6), pages 3271-3283, June.
- Marco Del Giudice & Stefano Bo & Silvia Grigolon & Carla Bosia, 2018. "On the role of extrinsic noise in microRNA-mediated bimodal gene expression," PLOS Computational Biology, Public Library of Science, vol. 14(4), pages 1-26, April.
- Kulvinder Kochar Kaur & Gautam Allahbadia & Mandeep Singh, 2016. "Advances in the Therapy of Advanced Ovarian Cancer-Special Emphasis on the PD1/PDL1 Pathway," Current Trends in Biomedical Engineering & Biosciences, Juniper Publishers Inc., vol. 1(2), pages 32-40, December.
- Kalijn F. Bol & Gerty Schreibelt & Martine Bloemendal & Wouter W. Willigen & Simone Hins-de Bree & Anna L. Goede & Annemiek J. Boer & Kevin J. H. Bos & Tjitske Duiveman-de Boer & Michel A. M. Olde Nor, 2024. "Adjuvant dendritic cell therapy in stage IIIB/C melanoma: the MIND-DC randomized phase III trial," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
- Caroline Hoffmann & Floriane Noel & Maximilien Grandclaudon & Lucile Massenet-Regad & Paula Michea & Philemon Sirven & Lilith Faucheux & Aurore Surun & Olivier Lantz & Mylene Bohec & Jian Ye & Weihua , 2022. "PD-L1 and ICOSL discriminate human Secretory and Helper dendritic cells in cancer, allergy and autoimmunity," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
- Dominic Henn & Dehua Zhao & Dharshan Sivaraj & Artem Trotsyuk & Clark Andrew Bonham & Katharina S. Fischer & Tim Kehl & Tobias Fehlmann & Autumn H. Greco & Hudson C. Kussie & Sylvia E. Moortgat Illouz, 2023. "Cas9-mediated knockout of Ndrg2 enhances the regenerative potential of dendritic cells for wound healing," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
- Shuting Li & Chia-Wen Lu & Elia C. Diem & Wang Li & Melanie Guderian & Marc Lindenberg & Friederike Kruse & Manuela Buettner & Stefan Floess & Markus R. Winny & Robert Geffers & Hans-Hermann Richnow &, 2022. "Acetyl-CoA-Carboxylase 1-mediated de novo fatty acid synthesis sustains Lgr5+ intestinal stem cell function," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
- Qing Chen & Xin Zhang & Wei-Min Li & Yu-Qiang Ji & Hao-Zhe Cao & Pengsheng Zheng, 2014. "Prognostic Value of LGR5 in Colorectal Cancer: A Meta-Analysis," PLOS ONE, Public Library of Science, vol. 9(9), pages 1-9, September.
- Lana Kostic & Carly Leung & Katzrin Ahmad Murad & Snezhina Kancheva & Stefano Perna & Bernett Lee & Nick Barker, 2024. "Lgr5 marks stem/progenitor cells contributing to epithelial and muscle development in the mouse esophagus," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
- Adam E. Hall & Sebastian Öther-Gee Pohl & Patrizia Cammareri & Stuart Aitken & Nicholas T. Younger & Michela Raponi & Caroline V. Billard & Alfonso Bolado Carrancio & Aslihan Bastem & Paz Freile & Fio, 2022. "RNA splicing is a key mediator of tumour cell plasticity and a therapeutic vulnerability in colorectal cancer," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
- Seungjae Lee & Yen-Chung Chen & Austin E. Gillen & J. Matthew Taliaferro & Bart Deplancke & Hongjie Li & Eric C. Lai, 2022. "Diverse cell-specific patterns of alternative polyadenylation in Drosophila," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
- Md Tauhidul Islam & Jen-Yeu Wang & Hongyi Ren & Xiaomeng Li & Masoud Badiei Khuzani & Shengtian Sang & Lequan Yu & Liyue Shen & Wei Zhao & Lei Xing, 2022. "Leveraging data-driven self-consistency for high-fidelity gene expression recovery," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
- Angélique Richard & Loïs Boullu & Ulysse Herbach & Arnaud Bonnafoux & Valérie Morin & Elodie Vallin & Anissa Guillemin & Nan Papili Gao & Rudiyanto Gunawan & Jérémie Cosette & Ophélie Arnaud & Jean-Ja, 2016. "Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process," PLOS Biology, Public Library of Science, vol. 14(12), pages 1-35, December.
- Qi Liu & Charles A Herring & Quanhu Sheng & Jie Ping & Alan J Simmons & Bob Chen & Amrita Banerjee & Wei Li & Guoqiang Gu & Robert J Coffey & Yu Shyr & Ken S Lau, 2018. "Quantitative assessment of cell population diversity in single-cell landscapes," PLOS Biology, Public Library of Science, vol. 16(10), pages 1-29, October.
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:plo:pcbi00:1004224. 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: ploscompbiol (email available below). General contact details of provider: https://journals.plos.org/ploscompbiol/ .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.