Targeting and engineering long non-coding RNAs for cancer therapy
RNA therapeutics (RNATx) aim to treat diseases, including cancer, by targeting or
employing RNA molecules for therapeutic purposes. Amongst the most promising targets …
employing RNA molecules for therapeutic purposes. Amongst the most promising targets …
RNA design via structure-aware multifrontier ensemble optimization
Motivation RNA design is the search for a sequence or set of sequences that will fold to
desired structure, also known as the inverse problem of RNA folding. However, the …
desired structure, also known as the inverse problem of RNA folding. However, the …
Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition
RNA design is the search for a sequence or set of sequences that will fold into predefined
structures, also known as the inverse problem of RNA folding. While numerous RNA design …
structures, also known as the inverse problem of RNA folding. While numerous RNA design …
Differentiable partition function calculation for RNA
MC Matthies, R Krueger, AE Torda… - Nucleic Acids …, 2024 - academic.oup.com
Ribonucleic acid (RNA) is an essential molecule in a wide range of biological functions. In
1990, McCaskill introduced a dynamic programming algorithm for computing the partition …
1990, McCaskill introduced a dynamic programming algorithm for computing the partition …
gRNAde: Geometric Deep Learning for 3D RNA inverse design
Computational RNA design tasks are often posed as inverse problems, where sequences
are designed based on adopting a single desired secondary structure without considering …
are designed based on adopting a single desired secondary structure without considering …
DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters
TM Pham, T Miffin, H Sun, KK Sharp, X Wang… - ACS Synthetic …, 2023 - ACS Publications
We show that in silico design of DNA secondary structures is improved by extending the
base pairing alphabet beyond A–T and G–C to include the pair between 2-amino-8-(1′-β-d …
base pairing alphabet beyond A–T and G–C to include the pair between 2-amino-8-(1′-β-d …
Scalable Identification of Minimum Undesignable RNA Motifs on Loop-Pair Graphs
T Zhou, WY Tang, DH Mathews, L Huang - arXiv preprint arXiv …, 2024 - arxiv.org
Motivation: RNA design aims to find at least one sequence that folds with the highest
probability into a designated target structure, but some structures are undesignable in the …
probability into a designated target structure, but some structures are undesignable in the …
Context-dependent structure formation of RNA hairpin motifs
V Bukina, A Bozic - bioRxiv, 2024 - biorxiv.org
Many functions of ribonucleic acid (RNA) rely on its ability to assume specific sequence-
structure motifs. Packaging signals of some RNA viruses-hairpin motifs that interact with …
structure motifs. Packaging signals of some RNA viruses-hairpin motifs that interact with …
Scalable Differentiable for mRNA Design
mRNA is an emerging therapeutic platform with applications ranging from vaccines to
genome editing. However, there are an exponential number of mRNA sequences to deliver …
genome editing. However, there are an exponential number of mRNA sequences to deliver …