AIMC Topic: RNA, Ribosomal
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TwinCons: Conservation score for uncovering deep sequence similarity and divergence.
PLoS computational biology
Oct 29, 2021
We have developed the program TwinCons, to detect noisy signals of deep ancestry of proteins or nucleic acids. As input, the program uses a composite alignment containing pre-defined groups, and mathematically determines a 'cost' of transforming one ...
Identification of RNA pseudouridine sites using deep learning approaches.
PloS one
Feb 23, 2021
Pseudouridine(Ψ) is widely popular among various RNA modifications which have been confirmed to occur in rRNA, mRNA, tRNA, and nuclear/nucleolar RNA. Hence, identifying them has vital significance in academic research, drug development and gene thera...
Supervised machine learning outperforms taxonomy-based environmental DNA metabarcoding applied to biomonitoring.
Molecular ecology resources
Aug 3, 2018
Biodiversity monitoring is the standard for environmental impact assessment of anthropogenic activities. Several recent studies showed that high-throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) could overcome many limitations ...
The first two mitochondrial genomes from Taeniopterygidae (Insecta: Plecoptera): Structural features and phylogenetic implications.
International journal of biological macromolecules
Dec 29, 2017
The complete mitochondrial genomes (mitogenomes) of Taeniopteryx ugola and Doddsia occidentalis (Plecoptera: Taeniopterygidae) were firstly sequenced from the family Taeniopterygidae. The 15,353-bp long mitogenome of T. ugola and the 16,020-bp long m...
B-factor profile prediction for RNA flexibility using support vector machines.
Journal of computational chemistry
Nov 21, 2017
Determining the flexibility of structured biomolecules is important for understanding their biological functions. One quantitative measurement of flexibility is the atomic Debye-Waller factor or temperature B-factor. Most existing studies are limited...
Loss of the integral nuclear envelope protein SUN1 induces alteration of nucleoli.
Nucleus (Austin, Tex.)
Mar 10, 2016
A supervised machine learning algorithm, which is qualified for image classification and analyzing similarities, is based on multiple discriminative morphological features that are automatically assembled during the learning processes. The algorithm ...
A novel representation of genomic sequences for taxonomic clustering and visualization by means of self-organizing maps.
Bioinformatics (Oxford, England)
Oct 24, 2014
MOTIVATION: Self-organizing maps (SOMs) are readily available bioinformatics methods for clustering and visualizing high-dimensional data, provided that such biological information is previously transformed to fixed-size, metric-based vectors. To inc...
Rapid and accurate identification of ribosomal RNA sequences via deep learning.
Nucleic acids research
Jun 10, 2022
Advances in transcriptomic and translatomic techniques enable in-depth studies of RNA activity profiles and RNA-based regulatory mechanisms. Ribosomal RNA (rRNA) sequences are highly abundant among cellular RNA, but if the target sequences do not inc...
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