Some searches may not work properly. We apologize for the inconvenience.
My bibliography Save this articleGenome-wide promoter responses to CRISPR perturbations of regulators reveal regulatory networks in Escherichia coli
Author
Abstract
Suggested Citation
DOI: 10.1038/s41467-023-41572-4
Download full text from publisher
References listed on IDEAS
- Tianmin Wang & Changge Guan & Jiahui Guo & Bing Liu & Yinan Wu & Zhen Xie & Chong Zhang & Xin-Hui Xing, 2018. "Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance," Nature Communications, Nature, vol. 9(1), pages 1-15, December.
- Lun Cui & Antoine Vigouroux & François Rousset & Hugo Varet & Varun Khanna & David Bikard, 2018. "A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
- Jeremiah J Faith & Boris Hayete & Joshua T Thaden & Ilaria Mogno & Jamey Wierzbowski & Guillaume Cottarel & Simon Kasif & James J Collins & Timothy S Gardner, 2007. "Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles," PLOS Biology, Public Library of Science, vol. 5(1), pages 1-13, January.
- Rebecca Baumstark & Sonja Hänzelmann & Saburo Tsuru & Yolanda Schaerli & Mirko Francesconi & Francesco M. Mancuso & Robert Castelo & Mark Isalan, 2015. "The propagation of perturbations in rewired bacterial gene networks," Nature Communications, Nature, vol. 6(1), pages 1-11, December.
- Martin Lempp & Niklas Farke & Michelle Kuntz & Sven Andreas Freibert & Roland Lill & Hannes Link, 2019. "Systematic identification of metabolites controlling gene expression in E. coli," Nature Communications, Nature, vol. 10(1), pages 1-9, December.
- Sang Woo Seo & Donghyuk Kim & Edward J. O’Brien & Richard Szubin & Bernhard O. Palsson, 2015. "Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli," Nature Communications, Nature, vol. 6(1), pages 1-8, November.
- Mattias Rydenfelt & Hernan G Garcia & Robert Sidney Cox III & Rob Phillips, 2014. "The Influence of Promoter Architectures and Regulatory Motifs on Gene Expression in Escherichia coli," PLOS ONE, Public Library of Science, vol. 9(12), pages 1-31, December.
- Sang Woo Seo & Donghyuk Kim & Haythem Latif & Edward J. O’Brien & Richard Szubin & Bernhard O. Palsson, 2014. "Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli," Nature Communications, Nature, vol. 5(1), pages 1-10, December.
- Anand V. Sastry & Ye Gao & Richard Szubin & Ying Hefner & Sibei Xu & Donghyuk Kim & Kumari Sonal Choudhary & Laurence Yang & Zachary A. King & Bernhard O. Palsson, 2019. "The Escherichia coli transcriptome mostly consists of independently regulated modules," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
- Mark Isalan & Caroline Lemerle & Konstantinos Michalodimitrakis & Carsten Horn & Pedro Beltrao & Emanuele Raineri & Mireia Garriga-Canut & Luis Serrano, 2008. "Evolvability and hierarchy in rewired bacterial gene networks," Nature, Nature, vol. 452(7189), pages 840-845, April.
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.- Piaopiao Chen & Agnès H. Michel & Jianzhi Zhang, 2022. "Transposon insertional mutagenesis of diverse yeast strains suggests coordinated gene essentiality polymorphisms," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
- Ida Lauritsen & Pernille Ott Frendorf & Silvia Capucci & Sophia A. H. Heyde & Sarah D. Blomquist & Sofie Wendel & Emil C. Fischer & Agnieszka Sekowska & Antoine Danchin & Morten H. H. Nørholm, 2021. "Temporal evolution of master regulator Crp identifies pyrimidines as catabolite modulator factors," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
- Hossein Zare & Mostafa Kaveh & Arkady Khodursky, 2011. "Inferring a Transcriptional Regulatory Network from Gene Expression Data Using Nonlinear Manifold Embedding," PLOS ONE, Public Library of Science, vol. 6(8), pages 1-7, August.
- Diambra, L., 2011. "Coarse-grain reconstruction of genetic networks from expression levels," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 390(11), pages 2198-2207.
- Marco Grimaldi & Roberto Visintainer & Giuseppe Jurman, 2011. "RegnANN: Reverse Engineering Gene Networks Using Artificial Neural Networks," PLOS ONE, Public Library of Science, vol. 6(12), pages 1-19, December.
- Javier Santos-Moreno & Eve Tasiudi & Hadiastri Kusumawardhani & Joerg Stelling & Yolanda Schaerli, 2023. "Robustness and innovation in synthetic genotype networks," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
- Jian Wang & Yuxi Teng & Ruihua Zhang & Yifei Wu & Lei Lou & Yusong Zou & Michelle Li & Zhong-Ru Xie & Yajun Yan, 2021. "Engineering a PAM-flexible SpdCas9 variant as a universal gene repressor," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
- Payne, Joshua L., 2016. "No tradeoff between versatility and robustness in gene circuit motifs," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 449(C), pages 192-199.
- Ruonan Wu & Michelle R. Davison & William C. Nelson & Montana L. Smith & Mary S. Lipton & Janet K. Jansson & Ryan S. McClure & Jason E. McDermott & Kirsten S. Hofmockel, 2023. "Hi-C metagenome sequencing reveals soil phage–host interactions," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
- Arianna Miano & Kevin Rychel & Andrew Lezia & Anand Sastry & Bernhard Palsson & Jeff Hasty, 2023. "High-resolution temporal profiling of E. coli transcriptional response," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
- Muir Morrison & Manuel Razo-Mejia & Rob Phillips, 2021. "Reconciling kinetic and thermodynamic models of bacterial transcription," PLOS Computational Biology, Public Library of Science, vol. 17(1), pages 1-30, January.
- repec:jss:jstsof:37:i01 is not listed on IDEAS
- Joeri Ruyssinck & Vân Anh Huynh-Thu & Pierre Geurts & Tom Dhaene & Piet Demeester & Yvan Saeys, 2014. "NIMEFI: Gene Regulatory Network Inference using Multiple Ensemble Feature Importance Algorithms," PLOS ONE, Public Library of Science, vol. 9(3), pages 1-13, March.
- Cheemeng Tan & Robert Phillip Smith & Ming-Chi Tsai & Russell Schwartz & Lingchong You, 2014. "Phenotypic Signatures Arising from Unbalanced Bacterial Growth," PLOS Computational Biology, Public Library of Science, vol. 10(8), pages 1-10, August.
- Jae Sung Cho & Dongsoo Yang & Cindy Pricilia Surya Prabowo & Mohammad Rifqi Ghiffary & Taehee Han & Kyeong Rok Choi & Cheon Woo Moon & Hengrui Zhou & Jae Yong Ryu & Hyun Uk Kim & Sang Yup Lee, 2023. "Targeted and high-throughput gene knockdown in diverse bacteria using synthetic sRNAs," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
- Enrico Orsi & Pablo Ivan Nikel & Lars Keld Nielsen & Stefano Donati, 2023. "Synergistic investigation of natural and synthetic C1-trophic microorganisms to foster a circular carbon economy," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
- Tom Wilderjans & Dirk Depril & Iven Van Mechelen, 2013. "Additive Biclustering: A Comparison of One New and Two Existing ALS Algorithms," Journal of Classification, Springer;The Classification Society, vol. 30(1), pages 56-74, April.
- Shuhei Kimura & Masanao Sato & Mariko Okada-Hatakeyama, 2013. "Inference of Vohradský's Models of Genetic Networks by Solving Two-Dimensional Function Optimization Problems," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-11, December.
- Xiaomeng Zhang & Bin Shao & Yangle Wu & Ouyang Qi, 2013. "A Reverse Engineering Approach to Optimize Experiments for the Construction of Biological Regulatory Networks," PLOS ONE, Public Library of Science, vol. 8(9), pages 1-9, September.
- Takanori Hasegawa & Rui Yamaguchi & Masao Nagasaki & Satoru Miyano & Seiya Imoto, 2014. "Inference of Gene Regulatory Networks Incorporating Multi-Source Biological Knowledge via a State Space Model with L1 Regularization," PLOS ONE, Public Library of Science, vol. 9(8), pages 1-19, August.
- Jiao Liu & Moshi Liu & Tuo Shi & Guannan Sun & Ning Gao & Xiaojia Zhao & Xuan Guo & Xiaomeng Ni & Qianqian Yuan & Jinhui Feng & Zhemin Liu & Yanmei Guo & Jiuzhou Chen & Yu Wang & Ping Zheng & Jibin Su, 2022. "CRISPR-assisted rational flux-tuning and arrayed CRISPRi screening of an l-proline exporter for l-proline hyperproduction," Nature Communications, Nature, vol. 13(1), pages 1-16, 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_s41467-023-41572-4. 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.