Results 31 to 40 of about 168,078 (169)

InspectorORF: a tool for visualizing Ribo-Seq and additional genomic or transcriptomic data. [PDF]

Bioinform Adv
Abstract Motivation The advent of ribosome profiling (an adaptation of RNA sequencing) to determine the translatome, has led to a huge improvement in our understanding of what parts of the transcriptome are translated. Many alternative open reading frames (ORFs) are now regularly being detected
Ward EL, Birds I, O'Connell MJ, Westhead DR, Aspden JL.   +4 more
europepmc   +4 more sources

Identifying and Visualizing Novel Small Open Reading Frames (sORFs) Via Ribo-Seq, Transcriptome Assembly, and ggRibo [PDF]

Methods in Molecular Biology
Polly Hsu
exaly   +2 more sources

Modernising the Ribo-Seq approach: a new gold standard

Controlled AccessRibosome profiling (Ribo-Seq) provides a genome-wide snapshot of protein synthesis by identifying the locations of translating ribosomes at single-nucleotide resolution via deep sequencing of ribosome protected mRNA fragments.
O'Connell, Aoife Myra
core   +2 more sources

The Translatome Map: RNC-Seq vs. Ribo-Seq for Profiling of HBE, A549, and MCF-7 Cell Lines [PDF]

International Journal of Molecular Sciences
Ekaterina Ilgisonis, Anna Kozlova, Elizaveta Sarygina   +2 more
exaly   +2 more sources

Variational inference for detecting differential translation in ribosome profiling studies

Frontiers in Genetics, 2023
Translational efficiency change is an important mechanism for regulating protein synthesis. Experiments with paired ribosome profiling (Ribo-seq) and mRNA-sequencing (RNA-seq) allow the study of translational efficiency by simultaneously quantifying the ...
David C. Walker, Zachary R. Lozier, Ran Bi, Pulkit Kanodia, W. Allen Miller, Peng Liu   +5 more
doaj   +1 more source

Improved Ribo-seq enables identification of cryptic translation events. [PDF]

Nat Methods, 2018
Ribosome profiling has been used to predict thousands of short open reading frames (sORFs) in eukaryotic cells, but it suffers from substantial levels of noise. PRICE (https://github.com/erhard-lab/price) is a computational method that models experimental noise to enable researchers to accurately resolve overlapping sORFs and noncanonical translation ...
Erhard F, Halenius A, Zimmermann C, L'Hernault A, Kowalewski DJ, Weekes MP, Stevanovic S, Zimmer R, Dölken L.   +8 more
europepmc   +5 more sources

Ribo-seq - more data

, 2022
Just a tad more ribo-seq data for Arabidopsis ...
Axel Thieffry (7510553)
core   +1 more source

Ribo-seq data

, 2022
Processed ribo-seq data from several public datasets, in bigwig format. List of dataset is as follow:├── Bazin_2017/│ ├── Bazin_wt_R1.bw│ └── Bazin_wt_R2.bw├── Hsu_2016/│ ├── Hsu_root_A.bw│ ├── Hsu_root_B.bw│ ├── Hsu_root_C.bw│ ├── Hsu_root_D.
Axel Thieffry (7510553)
core   +1 more source

Comparison of software packages for detecting unannotated translated small open reading frames by Ribo-seq [PDF]

, 2023
Accurate and comprehensive annotation of microprotein-coding small open reading frames (smORFs) is critical to our understanding of normal physiology and disease.
Tong, Gregory, Hah, Nasun, Martinez, Thomas F   +2 more
core   +1 more source

Accurate detection of short and long active ORFs using Ribo-seq data. [PDF]

Bioinformatics, 2020
Abstract Motivation Ribo-seq, a technique for deep-sequencing ribosome-protected mRNA fragments, has enabled transcriptome-wide monitoring of translation in vivo. It has opened avenues for re-evaluating the coding potential of open reading frames (ORFs), including many short ORFs that were previously ...
Choudhary S, Li W, D Smith A.
europepmc   +5 more sources