Ribosome profiling
Ribosome profiling reveals resemblance between long non coding RNAs and 5′ leaders of coding RNAs
... the ribosome profiling dataset for the classification of ORFs, we developed a random forest classifier (Breiman, ...whether ribosome profiles over RNA subregions might reliably distinguish CDSs from ...
7
SPECtre: a spectral coherence based classifier of actively translated transcripts from ribosome profiling sequence data
... We assessed the sensitivity and specificity of each classi- fication algorithm using recently published ribosome profiling and mRNA-Seq data derived from HEK293 cells [4]. For the comparative analysis of ...
6
Ribosome profiling reveals the what, when, where and how of protein synthesis
... A ribosome subunit is fused to a biotin-acceptor (AVI) tag and BirA biotin ligase is fused to a localization element that spatially restricts its activity, for example, to the ...collected. Ribosome ...
15
PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration
... a ribosome profiling experiment are first checked for their quality and subsequently mapped to the appropriate genome, using the STAR or TopHat transcriptome mapper and different species-specific annotation ...
10
Estimation of ribosome profiling performance and reproducibility at various levels of resolution
... One possible approach to alleviate the issues discussed here is to conduct larger/high-coverage experiments, as we show that reproducibility is strongly correlated with depth and coverage. Sequencing depth can also be ...
12
Ligation free ribosome profiling of cell type specific translation in the brain
... of ribosome profil- ing studies in eukaryotes is the prevalence of unanno- tated uORFs which manifest as ribosomal density in the 5′ UTRs of mRNAs ...ligation-free ribosome profiling, we have ...
15
REPARATION : ribosome profiling assisted (re-)annotation of bacterial genomes
... RibosomeE Profiling Assisted (re- )AnnotaTION (REPARATION), a de novo machine learning algorithm that takes advantage of exper- imental protein synthesis evidence from ribosome profiling (Ribo-seq) ...
13
Ribosome profiling uncovers selective mRNA translation associated with eIF2 phosphorylation in erythroid progenitors
... Several ribosome profiling datasets were published that address the ISR, but the data are diffi- cult to ...increased ribosome density in response to arsenite treatment of HEK293 cell ...differential ...
24
An update on sORFs.org : a repository of small ORFs identified by ribosome profiling
... sORFs.org (http://www.sorfs.org) is a public repos- itory of small open reading frames (sORFs) identi- fied by ribosome profiling (RIBO-seq). This update elaborates on the major improvements implemented ...
6
Deciphering Poxvirus Gene Expression by RNA Sequencing and Ribosome Profiling
... scanning past earlier start codons or from shorter mRNAs as we previously reported evidence for pervasive transcription initiation (10). The presence of noncoded A residues preceding many of the novel translation ...
13
Survey of the translation shifts in hepatocellular carcinoma with ribosome profiling
... There are many other examples showing different patterns of associations between translation of the uORFs with their main CDS regions. The potential underlying mechanisms are certainly worth further investigations. ...
15
Ribosome profiling of the retrovirus murine leukemia virus
... tandem ribosome profiling (RiboSeq) and RNA sequencing (RNASeq) of MuLV-infected ...Results: Ribosome profiling of MuLV-infected cells was performed, using the translational inhibitors ...
8
sORFs.org : a repository of small ORFs identified by ribosome profiling
... of ribosome profiling (2,3), a next generation sequencing ...technique. Ribosome profiling (RIBO-seq) recovers and subsequently sequences the ±30 nt RNA fragments captured within translating ...
6
Ribosome Profiling of Synechocystis Reveals Altered Ribosome Allocation at Carbon Starvation
... the ribosome profiling and mRNA sequencing data set, ...the ribosome profiling and RNA sequencing (RNA-seq) data set, ...for ribosome profiling or the whole genome for RNA-seq and the length (in ...
12
Ribosome Profiling Reveals HSP90 Inhibitor Effects on Stage-Specific Protein Synthesis in Leishmania donovani
... of ribosome- protected mRNA ...from ribosome-protected mRNA fragments and the total mRNA from a cell allows distin- guishing mRNA that is actively translated at a given time point in the cell, but also the ...
18
Ribosome Profiling Reveals Translational Upregulation of Cellular Oxidative Phosphorylation mRNAs during Vaccinia Virus-Induced Host Shutoff
... and ribosome profiling, two techniques quantifying genome-wide levels of mRNA and active protein translation, respectively, we analyzed the responses of host cells to vaccinia virus infection at both the tran- ...
17
Identifying Small Proteins by Ribosome Profiling with Stalled Initiation Complexes
... for ribosome density at start codons in ribosome profiling ...performed ribosome profiling on an untreated ...1a, ribosome density on the highly expressed lpp gene is spread across the coding ...
21
Simultaneous Ribosome Profiling of Human Host Cells Infected with Toxoplasma gondii
... ABSTRACT Toxoplasma gondii is a ubiquitous obligate intracellular parasite that in- fects the nucleated cells of warm-blooded animals. From within the parasitophorous vacuole in which they reside, Toxoplasma tachyzoites ...
15
2A induced ribosome stalling
... the ribosome A site ...a ribosome profiling study carried out on mouse stem cells, it was reported that stalling sequences in the eukaryotic proteome is also ...a ribosome residue within the ...
183
Involvement of the bacterial ribosome in response to stress
... de Ribosome profiling que se realizaron (lisis, cuantificación del RNA, digestión, ultracentrifugación, extracción del RNA, precipitación, obtención de los fragmentos de interés, extracción del RNA del gel, ...
42