Cargando…

Ribosome elongating footprints denoised by wavelet transform comprehensively characterize dynamic cellular translation events

Translation is dynamically regulated during cell development and stress response. In order to detect actively translated open reading frames (ORFs) and dynamic cellular translation events, we have developed a computational method, RiboWave, to process ribosome profiling data. RiboWave utilizes wavel...

Descripción completa

Detalles Bibliográficos
Autores principales:	Xu, Zhiyu, Hu, Long, Shi, Binbin, Geng, SiSi, Xu, Longchen, Wang, Dong, Lu, Zhi J
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2018
Materias:	Methods Online
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6182183/ https://www.ncbi.nlm.nih.gov/pubmed/29945224 http://dx.doi.org/10.1093/nar/gky533

Ejemplares similares

Real time determination of bacterial in vivo ribosome translation elongation speed based on LacZα complementation system
por: Zhu, Manlu, et al.
Publicado: (2016)

Evaluating data integrity in ribosome footprinting datasets through modelled polysome profiles
por: Hedayioglu, Fabio, et al.
Publicado: (2022)

Luciferase-based reporter system for in vitro evaluation of elongation rate and processivity of ribosomes
por: Kisly, Ivan, et al.
Publicado: (2021)

Long-read amplicon denoising
por: Kumar, Venkatesh, et al.
Publicado: (2019)

Translation elongation rate varies among organs and decreases with age
por: Gerashchenko, Maxim V, et al.
Publicado: (2020)

Translation inhibitors cause abnormalities in ribosome profiling experiments
por: Gerashchenko, Maxim V., et al.
Publicado: (2014)

De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles
por: Chen, Yong, et al.
Publicado: (2016)

Application of translation wavelet transform with new threshold function in pulse wave signal denoising
por: Zhang, Jun, et al.
Publicado: (2023)

Quantitative analysis of ribosome–mRNA complexes at different translation stages
por: Shirokikh, Nikolay E., et al.
Publicado: (2010)

Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data
por: Sievers, Cem, et al.
Publicado: (2012)

Identifying ribosome heterogeneity using ribosome profiling
por: Alkan, Ferhat, et al.
Publicado: (2022)

RiboAbacus: a model trained on polyribosome images predicts ribosome density and translational efficiency from mammalian transcriptomes
por: Lauria, Fabio, et al.
Publicado: (2015)

Hydroxyl radical footprinting in vivo: mapping macromolecular structures with synchrotron radiation
por: Adilakshmi, Tadepalli, et al.
Publicado: (2006)

Nuclease-mediated depletion biases in ribosome footprint profiling libraries
por: Zinshteyn, Boris, et al.
Publicado: (2020)

Dual transcriptional-translational cascade permits cellular level tuneable expression control
por: Morra, Rosa, et al.
Publicado: (2016)

High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis
por: Mitra, Somdeb, et al.
Publicado: (2008)

A 96-well DNase I footprinting screen for drug–DNA interactions
por: Ellis, Tom, et al.
Publicado: (2007)

Following the footprints of polymorphic inversions on SNP data: from detection to association tests
por: Cáceres, Alejandro, et al.
Publicado: (2015)

BiFET: sequencing Bias-free transcription factor Footprint Enrichment Test
por: Youn, Ahrim, et al.
Publicado: (2019)

In situ visualization of telomere elongation patterns in human cells
por: Diolaiti, Morgan E., et al.
Publicado: (2013)

PAP-LMPCR for improved, allele-specific footprinting and automated chromatin fine structure analysis
por: Ingram, R., et al.
Publicado: (2008)

A highly sensitive in vivo footprinting technique for condition-dependent identification of cis elements
por: Gorsche, Rita, et al.
Publicado: (2014)

Ribonuclease selection for ribosome profiling
por: Gerashchenko, Maxim V., et al.
Publicado: (2017)

Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins
por: Shcherbakova, Inna, et al.
Publicado: (2006)

Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data
por: Piper, Jason, et al.
Publicado: (2013)

Purification, characterization and crystallization of the human 80S ribosome
por: Khatter, Heena, et al.
Publicado: (2014)

Finding 3D motifs in ribosomal RNA structures
por: Apostolico, Alberto, et al.
Publicado: (2009)

Footprinting of mammalian promoters: use of a CpG DNA methyltransferase revealing nucleosome positions at a single molecule level
por: Fatemi, Mehrnaz, et al.
Publicado: (2005)

Single-molecule imaging of full protein synthesis by immobilized ribosomes
por: Uemura, Sotaro, et al.
Publicado: (2008)

REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes
por: Ndah, Elvis, et al.
Publicado: (2017)

De novo annotation and characterization of the translatome with ribosome profiling data
por: Xiao, Zhengtao, et al.
Publicado: (2018)

A rapid protocol for ribosome profiling of low input samples
por: Meindl, Andreas, et al.
Publicado: (2023)

Birdsong Denoising Using Wavelets
por: Priyadarshani, Nirosha, et al.
Publicado: (2016)

Site-specific labeling of Saccharomyces cerevisiae ribosomes for single-molecule manipulations
por: Petrov, Alexey, et al.
Publicado: (2010)

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration
por: Crappé, Jeroen, et al.
Publicado: (2015)

Rapid and accurate identification of ribosomal RNA sequences via deep learning
por: Deng, Zhi-Luo, et al.
Publicado: (2022)

Spanning high-dimensional expression space using ribosome-binding site combinatorics
por: Zelcbuch, Lior, et al.
Publicado: (2013)

riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions
por: Waters, Nicholas R, et al.
Publicado: (2018)

Analysis of factor interactions with RNA polymerase II elongation complexes using a new electrophoretic mobility shift assay
por: Cheng, Bo, et al.
Publicado: (2008)

Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation
por: Li, Qianru, et al.
Publicado: (2022)

Cannot write session to /tmp/vufind_sessions/sess_j2gguhl71nv2n601mu2l48kn15