Results 11 to 20 of about 2,190,860 (309)
Comprehensive benchmarking of large language models for RNA secondary structure prediction [PDF]
arXivInspired by the success of large language models (LLM) for DNA and proteins, several LLM for RNA have been developed recently. RNA-LLM uses large datasets of RNA sequences to learn, in a self-supervised way, how to represent each RNA base with a semantically rich numerical vector.
Zablocki LI +5 more
arxiv +2 more sources
iPseU-TWSVM: Identification of RNA pseudouridine sites based on TWSVM
Mathematical Biosciences and Engineering, 2022 Biological sequence analysis is an important basic research work in the field of bioinformatics. With the explosive growth of data, machine learning methods play an increasingly important role in biological sequence analysis. By constructing a classifier
Mingshuai Chen +4 more
doaj +1 more source
Structural Alignment and Covariation Analysis of RNA Sequences [PDF]
BIO-PROTOCOL, 2020 RNA molecules adopt defined structural conformations that are essential to exert their function. During the course of evolution, the structure of a given RNA can be maintained via compensatory base-pair changes that occur among covarying nucleotides in paired regions.
Nicolas J. Tourasse, Fabien Darfeuille
openaire +4 more sources
Deciphering the RRM-RNA recognition code: A computational analysis.
PLoS Computational Biology, 2023 RNA recognition motifs (RRM) are the most prevalent class of RNA binding domains in eucaryotes. Their RNA binding preferences have been investigated for almost two decades, and even though some RRM domains are now very well described, their RNA ...
Joel Roca-Martínez +3 more
doaj +1 more source
RNA Sequencing Analysis of Salivary Extracellular RNA [PDF]
, 2016 Salivary biomarkers for disease detection, diagnostic and prognostic assessments have become increasingly well established in recent years. In this chapter we explain the current leading technology that has been used to characterize salivary non-coding RNAs (ncRNAs) from the extracellular RNA (exRNA) fraction: HiSeq from Illumina® platform for RNA ...
Majem, Blanca +3 more
openaire +5 more sources
SePIA: RNA and small RNA sequence processing, integration, and analysis [PDF]
BioData Mining, 2016 Large-scale sequencing experiments are complex and require a wide spectrum of computational tools to extract and interpret relevant biological information. This is especially true in projects where individual processing and integrated analysis of both small RNA and complementary RNA data is needed.
Icay, Katherine +5 more
openaire +4 more sources
Towards Parsimonious Generative Modeling of RNA Families [PDF]
Nucleic Acids Research, gkae289 (2024), 2023 Generative probabilistic models emerge as a new paradigm in data-driven, evolution-informed design of biomolecular sequences. This paper introduces a novel approach, called Edge Activation Direct Coupling Analysis (eaDCA), tailored to the characteristics of RNA sequences, with a strong emphasis on simplicity, efficiency, and interpretability.
arxiv +1 more source
Big Data Analytics in RNA-sequencing
Korean Journal of Clinical Laboratory Science, 2023 As next-generation sequencing has been developed and used widely, RNA-sequencing (RNA-seq) has rapidly emerged as the first choice of tools to validate global transcriptome profiling.
Sung-Hun WOO, Byung Chul JUNG
doaj +1 more source
Power Analysis of Single Cell RNA-Sequencing Experiments [PDF]
Nature Methods, 2016 AbstractHigh-throughput single cell RNA sequencing (scRNA-seq) has become an established and powerful method to investigate transcriptomic cell-to-cell variation, and has revealed new cell types, and new insights into developmental process and stochasticity in gene expression.
Kedar Nath Natarajan +15 more
openaire +7 more sources
Circular RNA Expression Profiles in Nasopharyngeal Carcinoma by Sequence Analysis
Frontiers in Oncology, 2020 Circular RNAs (circRNAs), as a burgeoning sort of non-coding RNAs (ncRNAs), can regulate the expression of parental genes as miRNA sponges. This study was designed to explore the circRNA expression profile of nasopharyngeal carcinoma (NPC).
Jing Yang +7 more
doaj +1 more source