Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions
Published 2017 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions
Authors
Keywords
-
Journal
NUCLEIC ACIDS RESEARCH
Volume 45, Issue 9, Pages 5523-5538
Publisher
Oxford University Press (OUP)
Online
2017-02-17
DOI
10.1093/nar/gkx115
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinkingin vivo
- (2016) Erik Holmqvist et al. EMBO JOURNAL
- Predicting RNA secondary structures from sequence and probing data
- (2016) Ronny Lorenz et al. METHODS
- Antagonistic control of the turnover pathway for the global regulatory sRNA CsrB by the CsrA and CsrD proteins
- (2016) Christopher A. Vakulskas et al. NUCLEIC ACIDS RESEARCH
- Bridging the gap between in vitro and in vivo RNA folding
- (2016) Kathleen A. Leamy et al. QUARTERLY REVIEWS OF BIOPHYSICS
- Development of Design Rules for Reliable Antisense RNA Behavior in E. coli
- (2016) Allison Hoynes-O’Connor et al. ACS Synthetic Biology
- AccessFold: predicting RNA–RNA interactions with consideration for competing self-structure
- (2015) Laura DiChiacchio et al. BIOINFORMATICS
- Rapid and high-throughput construction of microbial cell-factories with regulatory noncoding RNAs
- (2015) Amit Kumar Chaudhary et al. BIOTECHNOLOGY ADVANCES
- Ribozymes that can be regulated by external stimuli
- (2015) Jennifer Frommer et al. CURRENT OPINION IN BIOTECHNOLOGY
- Chaotropicity: a key factor in product tolerance of biofuel-producing microorganisms
- (2015) Jonathan A Cray et al. CURRENT OPINION IN BIOTECHNOLOGY
- Metabolic engineering of Escherichia coli for the production of 1,3-diaminopropane, a three carbon diamine
- (2015) Tong Un Chae et al. Scientific Reports
- Strain engineering via regulatory noncoding RNAs: not a one-blueprint-fits-all
- (2015) Seung Hee Cho et al. Current Opinion in Chemical Engineering
- Discovery of Ethanol-Responsive Small RNAs in Zymomonas mobilis
- (2014) Seung Hee Cho et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Ribonomic approaches to study the RNA-binding proteome
- (2014) Camilla Faoro et al. FEBS LETTERS
- Bacterial Cellular Engineering by Genome Editing and Gene Silencing
- (2014) Nobutaka Nakashima et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- An Immature Retroviral RNA Genome Resembles a Kinetically Trapped Intermediate State
- (2014) J. K. Grohman et al. JOURNAL OF VIROLOGY
- Landscape and variation of RNA secondary structure across the human transcriptome
- (2014) Yue Wan et al. NATURE
- Structural basis for activity of highly efficient RNA mimics of green fluorescent protein
- (2014) Katherine Deigan Warner et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Exploiting post-transcriptional regulation to probe RNA structures in vivo via fluorescence
- (2014) Steven W. Sowa et al. NUCLEIC ACIDS RESEARCH
- The Long-Range P3 Helix of the Tetrahymena Ribozyme Is Disrupted during Folding between the Native and Misfolded Conformations
- (2013) David Mitchell et al. JOURNAL OF MOLECULAR BIOLOGY
- Circular RNAs are a large class of animal RNAs with regulatory potency
- (2013) Sebastian Memczak et al. NATURE
- A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat–containing RNA
- (2013) Rita L Strack et al. NATURE METHODS
- Design and use of synthetic regulatory small RNAs to control gene expression in Escherichia coli
- (2013) Seung Min Yoo et al. Nature Protocols
- Regulatory RNAs
- (2013) Jorge Vazquez-Anderson et al. RNA Biology
- On the importance of cotranscriptional RNA structure formation
- (2013) D. Lai et al. RNA
- Post-transcriptional regulation on a global scale: form and function of Csr/Rsm systems
- (2012) Tony Romeo et al. ENVIRONMENTAL MICROBIOLOGY
- De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells
- (2012) G. Rodrigo et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- RNA Accessibility in cubic time
- (2011) Stephan H Bernhart et al. Algorithms for Molecular Biology
- Enhanced electrotransformation of the ethanologen Zymomonas mobilis ZM4 with plasmids
- (2011) Shao-lan Zou et al. ENGINEERING IN LIFE SCIENCES
- cis-Antisense RNA, Another Level of Gene Regulation in Bacteria
- (2011) J. Georg et al. MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
- Versatile RNA-sensing transcriptional regulators for engineering genetic networks
- (2011) J. B. Lucks et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- RNA Mimics of Green Fluorescent Protein
- (2011) J. S. Paige et al. SCIENCE
- RNA Targeting Therapeutics: Molecular Mechanisms of Antisense Oligonucleotides as a Therapeutic Platform
- (2010) C. Frank Bennett et al. Annual Review of Pharmacology and Toxicology
- RNAstructure: software for RNA secondary structure prediction and analysis
- (2010) Jessica S Reuter et al. BMC BIOINFORMATICS
- NUPACK: Analysis and design of nucleic acid systems
- (2010) Joseph N. Zadeh et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Multiple Unfolding Events during Native Folding of the Tetrahymena Group I Ribozyme
- (2010) Yaqi Wan et al. JOURNAL OF MOLECULAR BIOLOGY
- Genome-wide measurement of RNA secondary structure in yeast
- (2010) Michael Kertesz et al. NATURE
- Multiple small RNAs identified in Mycobacterium bovis BCG are also expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis
- (2010) J. M. DiChiara et al. NUCLEIC ACIDS RESEARCH
- Partition function and base pairing probabilities for RNA–RNA interaction prediction
- (2009) Fenix W. D. Huang et al. BIOINFORMATICS
- A partition function algorithm for interacting nucleic acid strands
- (2009) Hamidreza Chitsaz et al. BIOINFORMATICS
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- Conditional gene silencing of multiple genes with antisense RNAs and generation of a mutator strain of Escherichia coli
- (2009) Nobutaka Nakashima et al. NUCLEIC ACIDS RESEARCH
- In vivo expression and purification of aptamer-tagged small RNA regulators
- (2009) Nelly Said et al. NUCLEIC ACIDS RESEARCH
- IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
- (2008) Anke Busch et al. BIOINFORMATICS
- RNAplex: a fast tool for RNA–RNA interaction search
- (2008) Hakim Tafer et al. BIOINFORMATICS
- The Vienna RNA Websuite
- (2008) A. R. Gruber et al. NUCLEIC ACIDS RESEARCH
- High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis
- (2008) Somdeb Mitra et al. NUCLEIC ACIDS RESEARCH
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExplorePublish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn More