Advances and opportunities in RNA structure experimental determination and computational modeling
Beyond transferring genetic information, RNAs are molecules with diverse functions that
include catalyzing biochemical reactions and regulating gene expression. Most of these …
include catalyzing biochemical reactions and regulating gene expression. Most of these …
Tailor made: the art of therapeutic mRNA design
Abstract mRNA medicine is a new and rapidly developing field in which the delivery of
genetic information in the form of mRNA is used to direct therapeutic protein production in …
genetic information in the form of mRNA is used to direct therapeutic protein production in …
Multiple sequence alignment-based RNA language model and its application to structural inference
Compared with proteins, DNA and RNA are more difficult languages to interpret because
four-letter coded DNA/RNA sequences have less information content than 20-letter coded …
four-letter coded DNA/RNA sequences have less information content than 20-letter coded …
Challenges and best practices in omics benchmarking
TG Brooks, NF Lahens, A Mrčela, GR Grant - Nature Reviews Genetics, 2024 - nature.com
Technological advances enabling massively parallel measurement of biological features—
such as microarrays, high-throughput sequencing and mass spectrometry—have ushered in …
such as microarrays, high-throughput sequencing and mass spectrometry—have ushered in …
Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery
Computational analysis of RNA sequences constitutes a crucial step in the field of RNA
biology. As in other domains of the life sciences, the incorporation of artificial intelligence …
biology. As in other domains of the life sciences, the incorporation of artificial intelligence …
Machine learning for RNA 2D structure prediction benchmarked on experimental data
Since the 1980s, dozens of computational methods have addressed the problem of
predicting RNA secondary structure. Among them are those that follow standard optimization …
predicting RNA secondary structure. Among them are those that follow standard optimization …
Machine learning modeling of RNA structures: methods, challenges and future perspectives
The three-dimensional structure of RNA molecules plays a critical role in a wide range of
cellular processes encompassing functions from riboswitches to epigenetic regulation …
cellular processes encompassing functions from riboswitches to epigenetic regulation …
Scalable deep learning for RNA secondary structure prediction
The field of RNA secondary structure prediction has made significant progress with the
adoption of deep learning techniques. In this work, we present the RNAformer, a lean deep …
adoption of deep learning techniques. In this work, we present the RNAformer, a lean deep …
Advances in RNA 3D structure prediction
X Ou, Y Zhang, Y Xiong, Y Xiao - Journal of Chemical Information …, 2022 - ACS Publications
RNA molecules carry out various cellular functions, and understanding the mechanisms
behind their functions requires the knowledge of their 3D structures. Different types of …
behind their functions requires the knowledge of their 3D structures. Different types of …
MARS and RNAcmap3: The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search
Recent success of AlphaFold2 in protein structure prediction relied heavily on co-
evolutionary information derived from homologous protein sequences found in the huge …
evolutionary information derived from homologous protein sequences found in the huge …