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Predicting RNA secondary structures from sequence and probing data

Methods (San Diego, Calif.), 2016-07, Vol.103, p.86-98

2016

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SHAPE directed RNA folding

Bioinformatics, 2016-01, Vol.32 (1), p.145-147

2016

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Interplay between the catabolite repression control protein Crc, Hfq and RNA in Hfq-dependent translational regulation in Pseudomonas aeruginosa

Nucleic acids research, 2018-02, Vol.46 (3), p.1470

2018

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Functional RNA Structures in the 3′UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses

Viruses, 2019-03, Vol.11 (3), p.298

2019

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Theoretical studies on RNA recognition by Musashi 1 RNA-binding protein

Scientific reports, 2022-07, Vol.12 (1), p.12137-12137, Article 12137

2022

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Musashi binding elements in Zika and related Flavivirus 3′UTRs: A comparative study in silico

Scientific reports, 2019-05, Vol.9 (1), Article 6911

2019

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Distinctive Regulation of Carbapenem Susceptibility in Pseudomonas aeruginosa by Hfq

Frontiers in microbiology, 2020-05, Vol.11, p.1001-1001

2020

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General and MicroRNA-Mediated mRNA Degradation Occurs on Ribosome Complexes in Drosophila Cells

Molecular and cellular biology, 2015-07, Vol.35 (13), p.2309-2320

2015

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Investigating RNA-RNA interactions through computational and biophysical analysis

Nucleic acids research, 2023-05, Vol.51 (9), p.4588

2023

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Cross-regulation by CrcZ RNA controls anoxic biofilm formation in Pseudomonas aeruginosa

Scientific reports, 2016-12, Vol.6 (1), p.39621-39621, Article 39621

2016

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Rewiring of Gene Expression in Pseudomonas aeruginosa During Diauxic Growth Reveals an Indirect Regulation of the MexGHI-OpmD Efflux Pump by Hfq

Frontiers in microbiology, 2022-06, Vol.13, p.919539-919539

2022

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Efficient computation of co-transcriptional RNA-ligand interaction dynamics

Methods (San Diego, Calif.), 2018-07, Vol.143, p.70-76

2018

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Harnessing Metabolic Regulation to Increase Hfq-Dependent Antibiotic Susceptibility in Pseudomonas aeruginosa

Frontiers in microbiology, 2018-11, Vol.9, p.2709-2709

2018

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Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture

Viruses, 2019-08, Vol.11 (9), p.798

2019

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Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site

RNA biology, 2022-12, Vol.19 (1), p.496-506

2022

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Gene Expression Profiling of Pseudomonas aeruginosa Upon Exposure to Colistin and Tobramycin

Frontiers in microbiology, 2021-04, Vol.12, p.626715-626715

2021

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Discoveries of Exoribonuclease-Resistant Structures of Insect-Specific Flaviviruses Isolated in Zambia

Viruses, 2020-09, Vol.12 (9), p.1017

2020

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Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction

Frontiers in bioinformatics, 2022-07, Vol.2, p.835422-835422

2022

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The Anaerobically Induced sRNA PaiI Affects Denitrification in Pseudomonas aeruginosa PA14

Frontiers in microbiology, 2017-11, Vol.8, p.2312-2312

2017

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An African tick flavivirus forming an independent clade exhibits unique exoribonuclease-resistant RNA structures in the genomic 3'-untranslated region

Scientific reports, 2021-03, Vol.11 (1), p.4883-4883, Article 4883

2021

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Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter RNA Structure in Chikungunya Virus

Genes, 2021-02, Vol.12 (2), p.239

2021

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Memory-efficient RNA energy landscape exploration

Bioinformatics (Oxford, England), 2014-09, Vol.30 (18), p.2584-2591

2014

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BarMap: RNA folding on dynamic energy landscapes

RNA (Cambridge), 2010-07, Vol.16 (7), p.1308-1316

2010

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RNASeq Based Transcriptional Profiling of Pseudomonas aeruginosa PA14 after Short- and Long-Term Anoxic Cultivation in Synthetic Cystic Fibrosis Sputum Medium

PloS one, 2016, Vol.11 (1), p.e0147811-e0147811

2016

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ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines [version 2; peer review: 1 approved, 2 approved with reservations]

F1000 research, 2015-01, Vol.4, p.50-50

2015

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Predicting RNA secondary structures from sequence and probing data

SHAPE directed RNA folding

Interplay between the catabolite repression control protein Crc, Hfq and RNA in Hfq-dependent translational regulation in Pseudomonas aeruginosa

Functional RNA Structures in the 3′UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses

Theoretical studies on RNA recognition by Musashi 1 RNA-binding protein

Musashi binding elements in Zika and related Flavivirus 3′UTRs: A comparative study in silico

Distinctive Regulation of Carbapenem Susceptibility in Pseudomonas aeruginosa by Hfq

General and MicroRNA-Mediated mRNA Degradation Occurs on Ribosome Complexes in Drosophila Cells

Investigating RNA-RNA interactions through computational and biophysical analysis

Cross-regulation by CrcZ RNA controls anoxic biofilm formation in Pseudomonas aeruginosa

Rewiring of Gene Expression in Pseudomonas aeruginosa During Diauxic Growth Reveals an Indirect Regulation of the MexGHI-OpmD Efflux Pump by Hfq

Efficient computation of co-transcriptional RNA-ligand interaction dynamics

Harnessing Metabolic Regulation to Increase Hfq-Dependent Antibiotic Susceptibility in Pseudomonas aeruginosa

Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture

Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site

Gene Expression Profiling of Pseudomonas aeruginosa Upon Exposure to Colistin and Tobramycin

Discoveries of Exoribonuclease-Resistant Structures of Insect-Specific Flaviviruses Isolated in Zambia

Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction

The Anaerobically Induced sRNA PaiI Affects Denitrification in Pseudomonas aeruginosa PA14

An African tick flavivirus forming an independent clade exhibits unique exoribonuclease-resistant RNA structures in the genomic 3'-untranslated region

Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter RNA Structure in Chikungunya Virus

Memory-efficient RNA energy landscape exploration

BarMap: RNA folding on dynamic energy landscapes

RNASeq Based Transcriptional Profiling of Pseudomonas aeruginosa PA14 after Short- and Long-Term Anoxic Cultivation in Synthetic Cystic Fibrosis Sputum Medium

ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines [version 2; peer review: 1 approved, 2 approved with reservations]

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