Results 61 to 70 of about 1,212,393 (317)

A twist in the tail : SHAPE mapping of long-range interactions and structural rearrangements of RNA elements involved in HCV replication [PDF]

, 2011
The RNA structure and long-range interactions of the SL9266 cis-acting replication element located within the NS5B coding region of hepatitis C virus (HCV) were determined using selective 2′-hydroxyl acylation analysed by primer extension.
Tuplin, Andrew, Struthers, Madeleine, Struthers, M., Andrew Tuplin, Tuplin, A., Struthers, M, Madeleine Struthers, Simmonds, Peter, David J. Evans, Tuplin, A, Evans, DJ, Peter Simmonds, Evans, David J., Simmonds, P., Evans, D. J., Simmonds, P   +15 more
core   +1 more source

RNA sequence analysis using covariance models

Nucleic Acids Research, 1994
We describe a general approach to several RNA sequence analysis problems using probabilistic models that flexibly describe the secondary structure and primary sequence consensus of an RNA sequence family. We call these models 'covariance models'. A covariance model of tRNA sequences is an extremely sensitive and discriminative tool for searching for ...
S R, Eddy, R, Durbin
openaire   +3 more sources

The hitchhikers’ guide to RNA sequencing and functional analysis

Briefings in Bioinformatics, 2023
Abstract DNA and RNA sequencing technologies have revolutionized biology and biomedical sciences, sequencing full genomes and transcriptomes at very high speeds and reasonably low costs. RNA sequencing (RNA-Seq) enables transcript identification and quantification, but once sequencing has concluded researchers can be easily overwhelmed ...
Jiung-Wen Chen, Lisa Shrestha, George Green, André Leier, Tatiana T. Marquez-Lago   +4 more
openaire   +2 more sources

Tau acetylation at K331 has limited impact on tau pathology in vivo

FEBS Letters, EarlyView.
We mapped tau post‐translational modifications in humanized MAPT knock‐in mice and in amyloid‐bearing double knock‐in mice. Acetylation within the repeat domain, particularly around K331, showed modest increases under amyloid pathology. To test functional relevance, we generated MAPTK331Q knock‐in mice.
Shoko Hashimoto, Yukio Matsuba, Mika Takahashi, Takaomi C. Saido   +3 more
wiley   +1 more source

Valosin‐containing protein counteracts ATP‐driven dissolution of FUS condensates through its ATPase activity in vitro

FEBS Letters, EarlyView.
Biomolecular condensates formed by fused in sarcoma (FUS) are dissolved by high ATP concentrations yet persist in cells. Using a reconstituted system, we demonstrate that valosin‐containing protein (VCP), an AAA+ ATPase, counteracts ATP‐driven dissolution of FUS condensates through its D2 ATPase activity.
Hitomi Kimura, Shin‐ichi Tate, Kyota Yasuda   +2 more
wiley   +1 more source

Transcriptome Analysis May Be Beneficial for Identification of Specific Pathways in Host Cell-Leishmania major Interactions(letter to editor)

Medical Laboratory Journal, 2022
Dear Editor, There are several reports about the modulatory effects of intracellular pathogens, such as Leishmania spp., to help survival and replication inside host cells.
Khodaberdi Kalavi, Mohammad Ali Faghihi, Ogholniaz Jorjani, Zolikha Tatari   +3 more
doaj  

Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-seq and ESTs [PDF]

, 2014
The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct and complete annotation in addition to the underlying genomic sequence is particularly important when interpreting the results ...
Junfang Song, Geoffrey J Barton, Schurch Nicholas J., Brown, Sara J., Gordon G Simpson, Nicholas J Schurch, McLean, W. H. Irwin, Song Junfang, Simpson Gordon G., Sherstnev, Alexander, Brown Sara J., Alexander Sherstnev, Song, Junfang, McLean W. H. Irwin, Duc, Celine, Kate G Storey, Storey, Kate G., Schurch, Nicholas J., Cole Christian, Sherstnev Alexander, Simpson, Gordon G., Céline Duc, W H Irwin McLean, Cole, Christian; id_orcid, Christian Cole, Barton Geoffrey J., Sara J Brown, Duc Céline, Barton, Geoffrey J.; id_orcid, Storey Kate G.   +29 more
core   +1 more source

Diversity and complexity in neural organoids

FEBS Letters, EarlyView.
Neural organoid research aims to expand genetic diversity on one side and increase tissue complexity on the other. Chimeroids integrate multiple donor genomes within single organoids. Self‐organising multi‐identity organoids, exogenous cell seeding, or enforced assembly of region‐specific organoids contribute to tissue complexity.
Ilaria Chiaradia, Madeline A. Lancaster
wiley   +1 more source

Dynamic changes in RNA–protein interactions and RNA secondary structure in mammalian erythropoiesis

Life Science Alliance, 2021
Analysis of PIP-seq data from a model of erythropoiesis reveals dynamics of RBP–RNA interaction and changes in RNA secondary structure throughout red blood cell development.
Mengge Shan, Xinjun Ji, Kevin Janssen, Ian M Silverman, Jesse Humenik, Ben A Garcia, Stephen A Liebhaber, Brian D Gregory   +7 more
doaj   +1 more source

PRADA: pipeline for RNA sequencing data analysis [PDF]

Bioinformatics, 2014
Abstract Summary:  Technological advances in high-throughput sequencing necessitate improved computational tools for processing and analyzing large-scale datasets in a systematic automated manner. For that purpose, we have developed PRADA (Pipeline for RNA-Sequencing Data Analysis), a flexible, modular and highly scalable software ...
Wandaliz Torres-García, Siyuan Zheng, Andrey Sivachenko, Rahulsimham Vegesna, Qianghu Wang, Rong Yao, Michael F. Berger, John N. Weinstein, Gad Getz, Roel G. W. Verhaak   +9 more
openaire   +2 more sources