A Hitchhiker's guide to RNA–RNA structure and interaction prediction tools
FYF Tieng, MR Abdullah-Zawawi… - Briefings in …, 2024 - academic.oup.com
RNA biology has risen to prominence after a remarkable discovery of diverse functions of
noncoding RNA (ncRNA). Most untranslated transcripts often exert their regulatory functions …
noncoding RNA (ncRNA). Most untranslated transcripts often exert their regulatory functions …
Bioinformatics tools for lncRNA research
Current experimental methods to identify the functions of a large number of the candidates of
long non-coding RNAs (lncRNAs) are limited in their throughput. Therefore, it is essential to …
long non-coding RNAs (lncRNAs) are limited in their throughput. Therefore, it is essential to …
De Novo RNA Tertiary Structure Prediction at Atomic Resolution Using Geometric Potentials from Deep Learning
Experimental characterization of RNA structure remains difficult, especially for non-coding
RNAs that are critical to many cellular activities. We developed DeepFoldRNA to predict …
RNAs that are critical to many cellular activities. We developed DeepFoldRNA to predict …
Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning
Motivation The recent discovery of numerous non-coding RNAs (long non-coding RNAs, in
particular) has transformed our perception about the roles of RNAs in living organisms. Our …
particular) has transformed our perception about the roles of RNAs in living organisms. Our …
CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction
T Puton, LP Kozlowski, KM Rother… - Nucleic acids …, 2013 - academic.oup.com
We present a continuous benchmarking approach for the assessment of RNA secondary
structure prediction methods implemented in the CompaRNA web server. As of 3 October …
structure prediction methods implemented in the CompaRNA web server. As of 3 October …
How the initiating ribosome copes with ppGpp to translate mRNAs
DS Vinogradova, V Zegarra, E Maksimova… - PLoS …, 2020 - journals.plos.org
During host colonization, bacteria use the alarmones (p) ppGpp to reshape their proteome
by acting pleiotropically on DNA, RNA, and protein synthesis. Here, we elucidate how the …
by acting pleiotropically on DNA, RNA, and protein synthesis. Here, we elucidate how the …
Bidirectional regulation between WDR83 and its natural antisense transcript DHPS in gastric cancer
WY Su, JT Li, Y Cui, J Hong, W Du, YC Wang, YW Lin… - Cell research, 2012 - nature.com
Natural antisense transcripts (NATs) exist ubiquitously in mammalian genomes and play
roles in the regulation of gene expression. However, both the existence of bidirectional …
roles in the regulation of gene expression. However, both the existence of bidirectional …
Ornithobacterium rhinotracheale: MALDI-TOF MS and Whole Genome Sequencing Confirm That Serotypes K, L and M Deviate from Well-Known Reference Strains …
M Alispahic, L Endler, M Hess, C Hess - Microorganisms, 2021 - mdpi.com
Ornithobacterium rhinotracheale is one of the most important bacterial agents of respiratory
diseases in poultry. For correct identification and characterization of this fastidious …
diseases in poultry. For correct identification and characterization of this fastidious …
RNA G-Quadruplex within the 5′-UTR of FEN1 Regulates mRNA Stability under Oxidative Stress
Y Ma, Y Yang, J Xin, L He, Z Hu, T Gao, F Pan, Z Guo - Antioxidants, 2023 - mdpi.com
Reactive oxygen species (ROS) are a group of highly oxidative molecules that induce DNA
damage, affecting DNA damage response (DDR) and gene expression. It is now recognized …
damage, affecting DNA damage response (DDR) and gene expression. It is now recognized …
Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain
A distance constrained secondary structural model of the≈ 10 kb RNA genome of the HIV-1
has been predicted but higher-order structures, involving long distance interactions, are …
has been predicted but higher-order structures, involving long distance interactions, are …