Cargando…

dStruct: identifying differentially reactive regions from RNA structurome profiling data

RNA biology is revolutionized by recent developments of diverse high-throughput technologies for transcriptome-wide profiling of molecular RNA structures. RNA structurome profiling data can be used to identify differentially structured regions between groups of samples. Existing methods are limited...

Descripción completa

Detalles Bibliográficos
Autores principales:	Choudhary, Krishna, Lai, Yu-Hsuan, Tran, Elizabeth J., Aviran, Sharon
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2019
Materias:	Method
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6385470/ https://www.ncbi.nlm.nih.gov/pubmed/30791935 http://dx.doi.org/10.1186/s13059-019-1641-3

Ejemplares similares

Accurate detection of RNA stem-loops in structurome data reveals widespread association with protein binding sites
por: Radecki, Pierce, et al.
Publicado: (2021)

Recent advances in RNA structurome
por: Xu, Bingbing, et al.
Publicado: (2022)

PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures
por: Ledda, Mirko, et al.
Publicado: (2018)

Probing the dynamic RNA structurome and its functions
por: Spitale, Robert C., et al.
Publicado: (2022)

3DStructGen: an interactive web-based 3D structure generation for non-periodic molecule and crystal
por: Chen, Pin, et al.
Publicado: (2020)

An in silico map of the SARS-CoV-2 RNA Structurome
por: Andrews, Ryan J., et al.
Publicado: (2020)

RNA Secondary Structurome Revealed Distinct Thermoregulation in Plasmodium falciparum
por: Qi, Yanwei, et al.
Publicado: (2022)

A map of the SARS-CoV-2 RNA structurome
por: Andrews, Ryan J, et al.
Publicado: (2021)

Tissue-specific changes in the RNA structurome mediate salinity response in Arabidopsis
por: Tack, David C., et al.
Publicado: (2020)

ConStruct: Improved construction of RNA consensus structures
por: Wilm, Andreas, et al.
Publicado: (2008)

Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis
por: Ferrero-Serrano, Ángel, et al.
Publicado: (2022)

Rice In Vivo RNA Structurome Reveals RNA Secondary Structure Conservation and Divergence in Plants
por: Deng, Hongjing, et al.
Publicado: (2018)

Pan-cancer structurome reveals overrepresentation of beta sandwiches and underrepresentation of alpha helical domains
por: Medvedev, Kirill E., et al.
Publicado: (2023)

StructMAn: annotation of single-nucleotide polymorphisms in the structural context
por: Gress, Alexander, et al.
Publicado: (2016)

EvolStruct-Phogly: incorporating structural properties and evolutionary information from profile bigrams for the phosphoglycerylation prediction
por: Chandra, Abel Avitesh, et al.
Publicado: (2019)

Optimized photochemistry enables efficient analysis of dynamic RNA structuromes and interactomes in genetic and infectious diseases
por: Zhang, Minjie, et al.
Publicado: (2021)

In vivo nuclear RNA structurome reveals RNA-structure regulation of mRNA processing in plants
por: Liu, Zhenshan, et al.
Publicado: (2021)

deconSTRUCT: general purpose protein database search on the substructure level
por: Zhang, Zong Hong, et al.
Publicado: (2010)

Simulation of the ILC Collimation System using BDSIM, MARS15 and STRUCT
por: Carter, John, et al.
Publicado: (2006)

StructRNAfinder: an automated pipeline and web server for RNA families prediction
por: Arias-Carrasco, Raúl, et al.
Publicado: (2018)

ObStruct: A Method to Objectively Analyse Factors Driving Population Structure Using Bayesian Ancestry Profiles
por: Gayevskiy, Velimir, et al.
Publicado: (2014)

Genome-wide RNA structurome reprogramming by acute heat shock globally regulates mRNA abundance
por: Su, Zhao, et al.
Publicado: (2018)

Intact RNA structurome reveals mRNA structure-mediated regulation of miRNA cleavage in vivo
por: Yang, Minglei, et al.
Publicado: (2020)

The in vivo RNA structurome of the malaria parasite Plasmodium falciparum, a protozoan with an A/U-rich transcriptome
por: Dumetz, Franck, et al.
Publicado: (2022)

Are we conSTRucting the best treatment regimens for all patients with HIV infection?
por: Friday, D, et al.
Publicado: (2012)

GlyStruct: glycation prediction using structural properties of amino acid residues
por: Reddy, Hamendra Manhar, et al.
Publicado: (2019)

struct: an R/Bioconductor-based framework for standardized metabolomics data analysis and beyond
por: Lloyd, Gavin Rhys, et al.
Publicado: (2020)

Struct-f4: a Rcpp package for ancestry profile and population structure inference from f(4)-statistics
por: Librado, Pablo, et al.
Publicado: (2022)

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
por: Rashid, Naim U, et al.
Publicado: (2011)

ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data
por: Videm, Pavankumar, et al.
Publicado: (2021)

Observation of dually decoded regions of the human genome using ribosome profiling data
por: Michel, Audrey M., et al.
Publicado: (2012)

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions
por: Hansen, Kasper D, et al.
Publicado: (2012)

A statistical approach for identifying differential distributions in single-cell RNA-seq experiments
por: Korthauer, Keegan D., et al.
Publicado: (2016)

PhoglyStruct: Prediction of phosphoglycerylated lysine residues using structural properties of amino acids
por: Chandra, Abel, et al.
Publicado: (2018)

PupStruct: Prediction of Pupylated Lysine Residues Using Structural Properties of Amino Acids
por: Singh, Vineet, et al.
Publicado: (2020)

Integration of Multiple Resolution Data in 3D Chromatin Reconstruction Using ChromStruct
por: Caudai, Claudia, et al.
Publicado: (2021)

OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations
por: Mularoni, Loris, et al.
Publicado: (2016)

metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data
por: Jühling, Frank, et al.
Publicado: (2016)

A distance difference matrix approach to identifying transcription factors that regulate differential gene expression
por: De Bleser, Pieter, et al.
Publicado: (2007)

Use of differential scanning fluorimetry as a high-throughput assay to identify nuclear receptor ligands
por: DeSantis, Kara, et al.
Publicado: (2012)

Cannot write session to /tmp/vufind_sessions/sess_aslqvprocd4v3ll4hlmdr8okkb