Results 41 to 50 of about 185,351 (165)

Differential analysis of Ribo-seq and RNA-seq read counts by genomic feature.

, 2023
Differential analysis of Ribo-seq and RNA-seq read counts by genomic feature.
Andrew A. Smith (17041553), Sujatha Jagannathan (294058), Chao-Jen Wong (2743033), Amy E. Campbell (3820846), Danielle C. Hamm (4693915), Sean R. Bennett (17041550), Cynthia L. Wladyka (16011824), Stephen J. Tapscott (10287250), Andrew C. Hsieh (16011836), Ellen M. Paatela (17041547)   +9 more
core   +1 more source

Integrated workflow for discovery of microprotein-coding small open reading frames

STAR Protocols, 2023
Summary: Small open reading frame (smORF)-encoded microproteins, proteins containing less than 100–150 amino acids, are an emerging class of functional biomolecules.
Kevin Cao, Yasamin Hajy Heydary, Gregory Tong, Thomas Farid Martinez   +3 more
doaj   +1 more source

Fig1C GlnRS ribo-seq reads in WT and dfrq.csv

, 2023
 Fig1C GlnRS ribo-seq reads in WT and ...
Kathrina Castillo (13712005)
core   +1 more source

Reliable detection of translational regulation with Ribo-seq [PDF]

, 2017
Ribosome profiling (Ribo-Seq) reveals genome-wide translation rates via the quantification of ribosome protected fragments (RPFs) of mRNAs. Several methods have recently been developed to detect differentially translated genes (DTGs) using Ribo-seq: Xtail, Ribodiff and Riborex. At their core, all of these approaches either utilize existing differential
Chothani, Sonia P, Adami, Eleonora, Viswanathan, Sivakumar, Hubner, Norbert, Cook, Stuart, Schafer, Sebastian, Rackham, Owen J L   +6 more
openaire   +1 more source

Fig1B AspRS ribo-seq reads in WT and dfrq

, 2023
 Fig1B AspRS ribo-seq reads in WT and dfrq 
Kathrina Castillo (13712005)
core   +1 more source

Visualizing the periodic Ribo-seq reads with RiboPlotR [PDF]

, 2019
ABSTRACT Background Ribo-seq has revolutionized the study of mRNA translation in a genome-wide scale. High-quality Ribo-seq data display strong 3-nucleotide (nt) periodicity, which corresponds to translating ribosomes decipher three nucleotides each time.
Wu, Hsin-Yen Larry, Hsu, Polly Yingshan
openaire   +1 more source

Fig1A WT and dfrq ribo-seq data for heatmaps

, 2023
Fig1A WT and dfrq ribo-seq data for heatmaps 
Kathrina Castillo (13712005), Deborah Bell-Pedersen (197589)   +1 more
core   +1 more source

GWIPS-viz: development of a ribo-seq genome browser

Nucleic Acids Research, 2013
We describe the development of GWIPS-viz (http://gwips.ucc.ie), an online genome browser for viewing ribosome profiling data. Ribosome profiling (ribo-seq) is a recently developed technique that provides genome-wide information on protein synthesis (GWIPS) in vivo. It is based on the deep sequencing of ribosome-protected messenger RNA (mRNA) fragments,
Audrey M. Michel, Gearoid Fox, Anmol M. Kiran, Christof De Bo, Patrick B. F. O'Connor, Stephen M. Heaphy, James P. A. Mullan, Claire A. Donohue, Desmond G. Higgins, Pavel V. Baranov   +9 more
openaire   +3 more sources

Data-driven design of LNA-blockers for efficient contaminant removal in Ribo-Seq libraries. [PDF]

Sci Rep
Abstract Ribo-Seq libraries often contain highly abundant non-coding RNA contaminants, which are challenging to remove due to their high sequence variability and diverse fragmentation patterns. We present an organism-independent computational pipeline that identifies experiment-specific target sequences and enables their efficient ...
Ricciardi DA, Peter FE, Böhmer M.
europepmc   +4 more sources

Repurposing Ribo-Seq to provide insights into structured RNAs [PDF]

, 2020
Abstract Ribosome profiling (Ribo-Seq) is a powerful method to study translation in bacteria. However, this method can enrich RNAs that are not bound by ribosomes, but rather, are protected from degradation in another way.
Brayon J. Fremin, Ami S. Bhatt
openaire   +1 more source