Inferring TF activation order in time series scRNA-Seq studies
Author
Abstract
Suggested Citation
DOI: 10.1371/journal.pcbi.1007644
Download full text from publisher
References listed on IDEAS
- Edroaldo Lummertz da Rocha & R. Grant Rowe & Vanessa Lundin & Mohan Malleshaiah & Deepak Kumar Jha & Carlos R. Rambo & Hu Li & Trista E. North & James J. Collins & George Q. Daley, 2018. "Reconstruction of complex single-cell trajectories using CellRouter," Nature Communications, Nature, vol. 9(1), pages 1-13, December.
- Kieran R Campbell & Christopher Yau, 2016. "Order Under Uncertainty: Robust Differential Expression Analysis Using Probabilistic Models for Pseudotime Inference," PLOS Computational Biology, Public Library of Science, vol. 12(11), pages 1-20, November.
- Barbara Treutlein & Qian Yi Lee & J. Gray Camp & Moritz Mall & Winston Koh & Seyed Ali Mohammad Shariati & Sopheak Sim & Norma F. Neff & Jan M. Skotheim & Marius Wernig & Stephen R. Quake, 2016. "Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq," Nature, Nature, vol. 534(7607), pages 391-395, June.
- J. Gray Camp & Keisuke Sekine & Tobias Gerber & Henry Loeffler-Wirth & Hans Binder & Malgorzata Gac & Sabina Kanton & Jorge Kageyama & Georg Damm & Daniel Seehofer & Lenka Belicova & Marc Bickle & Ric, 2017. "Multilineage communication regulates human liver bud development from pluripotency," Nature, Nature, vol. 546(7659), pages 533-538, June.
- Christian Mayer & Christoph Hafemeister & Rachel C. Bandler & Robert Machold & Renata Batista Brito & Xavier Jaglin & Kathryn Allaway & Andrew Butler & Gord Fishell & Rahul Satija, 2018. "Developmental diversification of cortical inhibitory interneurons," Nature, Nature, vol. 555(7697), pages 457-462, March.
- 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.
- Barbara Treutlein & Doug G. Brownfield & Angela R. Wu & Norma F. Neff & Gary L. Mantalas & F. Hernan Espinoza & Tushar J. Desai & Mark A. Krasnow & Stephen R. Quake, 2014. "Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq," Nature, Nature, vol. 509(7500), pages 371-375, May.
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.- 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.
- 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.
- Peizhuo Wang & Xiao Wen & Han Li & Peng Lang & Shuya Li & Yipin Lei & Hantao Shu & Lin Gao & Dan Zhao & Jianyang Zeng, 2023. "Deciphering driver regulators of cell fate decisions from single-cell transcriptomics data with CEFCON," Nature Communications, Nature, vol. 14(1), pages 1-16, 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.
- Rohith Palli & Mukta G Palshikar & Juilee Thakar, 2019. "Executable pathway analysis using ensemble discrete-state modeling for large-scale data," PLOS Computational Biology, Public Library of Science, vol. 15(9), pages 1-21, September.
- 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.
- Maria E. Monberg & Heather Geiger & Jaewon J. Lee & Roshan Sharma & Alexander Semaan & Vincent Bernard & Justin Wong & Fang Wang & Shaoheng Liang & Daniel B. Swartzlander & Bret M. Stephens & Matthew , 2022. "Occult polyclonality of preclinical pancreatic cancer models drives in vitro evolution," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
- 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.
- Ming-Wen Hu & Dong Won Kim & Sheng Liu & Donald J Zack & Seth Blackshaw & Jiang Qian, 2019. "PanoView: An iterative clustering method for single-cell RNA sequencing data," PLOS Computational Biology, Public Library of Science, vol. 15(8), pages 1-17, August.
- Cornelia Fuetterer & Thomas Augustin & Christiane Fuchs, 2020. "Adapted single-cell consensus clustering (adaSC3)," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 14(4), pages 885-896, December.
- Ran Wang & Xianfa Yang & Jiehui Chen & Lin Zhang & Jonathan A. Griffiths & Guizhong Cui & Yingying Chen & Yun Qian & Guangdun Peng & Jinsong Li & Liantang Wang & John C. Marioni & Patrick P. L. Tam & , 2023. "Time space and single-cell resolved tissue lineage trajectories and laterality of body plan at gastrulation," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
- Jia-Ru Wei & Zhao-Zhe Hao & Chuan Xu & Mengyao Huang & Lei Tang & Nana Xu & Ruifeng Liu & Yuhui Shen & Sarah A. Teichmann & Zhichao Miao & Sheng Liu, 2022. "Identification of visual cortex cell types and species differences using single-cell RNA sequencing," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
- Kieran R Campbell & Christopher Yau, 2016. "Order Under Uncertainty: Robust Differential Expression Analysis Using Probabilistic Models for Pseudotime Inference," PLOS Computational Biology, Public Library of Science, vol. 12(11), pages 1-20, November.
- Erica Carolina & Yoshiki Kuse & Ayumu Okumura & Kenji Aoshima & Tomomi Tadokoro & Shinya Matsumoto & Eriko Kanai & Takashi Okumura & Toshiharu Kasai & Souichiro Yamabe & Yuji Nishikawa & Kiyoshi Yamag, 2024. "Generation of human iPSC-derived 3D bile duct within liver organoid by incorporating human iPSC-derived blood vessel," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
- Yael Korem & Pablo Szekely & Yuval Hart & Hila Sheftel & Jean Hausser & Avi Mayo & Michael E Rothenberg & Tomer Kalisky & Uri Alon, 2015. "Geometry of the Gene Expression Space of Individual Cells," PLOS Computational Biology, Public Library of Science, vol. 11(7), pages 1-27, July.
- Jing Qi & Yang Zhou & Zicen Zhao & Shuilin Jin, 2021. "SDImpute: A statistical block imputation method based on cell-level and gene-level information for dropouts in single-cell RNA-seq data," PLOS Computational Biology, Public Library of Science, vol. 17(6), pages 1-20, June.
- Wenwei Sun & Meimei Wang & Jun Zhao & Shuang Zhao & Wenchao Zhu & Xiaoting Wu & Feifei Li & Wei Liu & Zhuo Wang & Meng Gao & Yiyue Zhang & Jin Xu & Meijia Zhang & Qiang Wang & Zilong Wen & Juan Shen &, 2023. "Sulindac selectively induces autophagic apoptosis of GABAergic neurons and alters motor behaviour in zebrafish," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
- Jingyu Zhang & Hengyu Chen & Ruoyan Li & David A Taft & Guang Yao & Fan Bai & Jianhua Xing, 2019. "Spatial clustering and common regulatory elements correlate with coordinated gene expression," PLOS Computational Biology, Public Library of Science, vol. 15(3), pages 1-16, March.
- Zhoufeng Wang & Zhe Li & Kun Zhou & Chengdi Wang & Lili Jiang & Li Zhang & Ying Yang & Wenxin Luo & Wenliang Qiao & Gang Wang & Yinyun Ni & Shuiping Dai & Tingting Guo & Guiyi Ji & Minjie Xu & Yiying , 2021. "Deciphering cell lineage specification of human lung adenocarcinoma with single-cell RNA sequencing," Nature Communications, Nature, vol. 12(1), pages 1-15, 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:plo:pcbi00:1007644. 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.