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NRDR specifications

Information


Unique identifier OMICS_29712
Name NRDR
Alternative name Non-coding RNA Databases Resource
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Version 2.0
Maintained Yes

Maintainer


  • person_outline Alan Mitchell Durham

Additional information


https://www.ncrnadatabases.org/about.php

Publication for Non-coding RNA Databases Resource

NRDR citations

 (11)
library_books

Long Non Coding RNAs Responsive to Salt and Boron Stress in the Hyper Arid Lluteño Maize from Atacama Desert

2018
Genes
PMCID: 5867891
PMID: 29558449
DOI: 10.3390/genes9030170

[…] As. To identify the lncRNAs as potential miRNA precursors, we performed sequence-similarity searches using Bowtie1 (version 1.1.1) [], allowing a unique mismatch. All miRNA sequences available on the Non-coding RNA Databases Resource [] were used and mapped against all Lluteño dataset of lncRNAs. […]

library_books

Monitoring global protein thiol oxidation and protein S mycothiolation in Mycobacterium smegmatis under hypochlorite stress

2017
Sci Rep
PMCID: 5430705
PMID: 28446771
DOI: 10.1038/s41598-017-01179-4

[…] The OxICAT results revealed an increased oxidation of many redox-sensitive transcriptional regulators under NaOCl stress, such as RseA, RshA, Zur and NrdR. Thiol-oxidation should lead to inactivation of these transcription factors resulting in transcriptional induction of the corresponding regulon members. To prove this hypothesis, we performed a R […]

library_books

Differential regulation of riboflavin supply genes in Vibrio cholerae

2017
PMCID: 5312566
PMID: 28239422
DOI: 10.1186/s13099-017-0159-z

[…] s (KEGG) [] for RBP genes and ribN. Results show that this strain conserves a cluster of contiguous ribD, ribE, ribA-COG3236 and ribH genes in chromosome 1 (Fig. a). This cluster is localized between nrdR and nusB. The ribA-COG3236 gene fusion encodes a protein with GTP cyclohydrolase II (RibA) activity fused to a protein domain belonging to the cluster of orthologous groups (COG) 3236. COG3236 mo […]

library_books

Performance comparison of two commercial human whole exome capture systems on formalin fixed paraffin embedded lung adenocarcinoma samples

2016
BMC Cancer
PMCID: 5004269
PMID: 27578032
DOI: 10.1186/s12885-016-2720-4

[…] ich requires higher coverage to accurately call InDels compared to SNVs, as suggested by Wong et al. []. Moreover, we determined the genotype concordance rate (CR) and non-reference discordance rate (NRDR) between each matched FF-FFPE pair at different coverage thresholds, for both exome capture systems. As shown in Additional file : Table S3a and in Fig. , for Agilent SureSelect kit the average C […]

library_books

Combining Metabolite Based Pharmacophores with Bayesian Machine Learning Models for Mycobacterium tuberculosis Drug Discovery

2015
PLoS One
PMCID: 4627656
PMID: 26517557
DOI: 10.1371/journal.pone.0141076

[…] nd/or microbiological studies. Using TB Mobile version 1.0 for BAS 04912643 the closest hit is pyrazinoic acid (), which is predicted to be similar to compounds that target DeaD, Mfd, RecG, DinG, and NrdR. PCA clustering also places this compound in a predominantly FabH cluster (). For BAS00623753 the closest hit targets the UDP-galactopyranose mutase Glf () while PCA clustering places it in a Mur […]

library_books

Genome Scale Co Expression Network Comparison across Escherichia coli and Salmonella enterica Serovar Typhimurium Reveals Significant Conservation at the Regulon Level of Local Regulators Despite Their Dissimilar Lifestyles

2014
PLoS One
PMCID: 4125155
PMID: 25101984
DOI: 10.1371/journal.pone.0102871

[…] in line with previous knowledge, as the conservation of the target of transcription factors and their upstream binding site motifs have been discussed in depth in separate focused papers for Fur , , NrdR , LexA , birA , ArgR/AhrC ). In addition, we could predict some regulatory network conservation just in E. coli and S. enterica (and not in B. subtilis). The observed conserved regulators were ba […]

Citations

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NRDR institution(s)
Engenharia da Computação, Universidade Tecnologica Federal do Paran - Campus Cornelio Procopio; Cornelio Procopio, Brazil; Programa Interunidades em Bioinformática, Instituto de Matemática e Estatistica, Universidade de São Paulo, São Paulo, Brazil; Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, São Paulo, Brazil; Departamento de Biologia, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil; Departamento de Ciência da Computação, Instituto de Matemática e Estatistica, Universidade de São Paulo, São Paulo, Brazil
NRDR funding source(s)
Supported in part by grants from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq); and from CNPq, Fundação de Amparo a Pesquisa do Estado de São Paulo (FAPESP), Financiadora de Estudos e Projetos (FINEP) and the FP-7 European Community SEtTReND grant agreement number 241865; by a fellowship from CAPES; and from FAPESP; and by an established investigator fellowship award from CNPq.

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