Related papers: Bridging Sequence-Structure Alignment in RNA Found…
Alignment-free sequence analysis approaches provide important alternatives over multiple sequence alignment (MSA) in biological sequence analysis because alignment-free approaches have low computation complexity and are not dependent on…
Many computerized methods for RNA-RNA interaction structure prediction have been developed. Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA…
Deep learning has made significant progress in protein structure prediction, advancing the development of computational biology. However, despite the high accuracy achieved in predicting single-chain structures, a significant number of…
Recent advances in AI foundation models have significant potential for lightening the clinical workload by mimicking the comprehensive and multi-faceted approaches used by medical professionals. In the field of radiation oncology, the…
Background: Genotype-phenotype maps provide a meaningful filtration of sequence space and RNA secondary structures are particular such phenotypes. Compatible sequences i.e.~sequences that satisfy the base pairing constraints of a given RNA…
Biological sequences encode fundamental instructions for the building blocks of life, in the form of DNA, RNA, and proteins. Modeling these sequences is key to understand disease mechanisms and is an active research area in computational…
Analysis of the sequence-structure relationship in RNA molecules are essential to evolutionary studies but also to concrete applications such as error-correction methodologies in sequencing technologies. The prohibitive sizes of the…
The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
The transformer architecture has revolutionized bioinformatics and driven progress in the understanding and prediction of the properties of biomolecules. To date, most biosequence transformers have been trained on single-omic data - either…
Sequence alignments are fundamental to bioinformatics which has resulted in a variety of optimized implementations. Unfortunately, the vast majority of them are hand-tuned and specific to certain architectures and execution models. This not…
Structural prediction has long been considered critical in RNA research, especially following the success of AlphaFold2 in protein studies, which has drawn significant attention to the field. While recent advances in machine learning and…
Recurrent Neural Networks (RNNs) laid the foundation for sequence modeling, but their intrinsic sequential nature restricts parallel computation, creating a fundamental barrier to scaling. This has led to the dominance of parallelizable…
RNA co-transcriptional folding has long been suspected to play an active role in helping proper native folding of ribozymes and structured regulatory motifs in mRNA untranslated regions. Yet, the underlying mechanisms and coding…
The Genomic Foundation Model (GFM) paradigm is expected to facilitate the extraction of generalizable representations from massive genomic data, thereby enabling their application across a spectrum of downstream applications. Despite…
Emerging integrative analysis of genomic and anatomical imaging data which has not been well developed, provides invaluable information for the holistic discovery of the genomic structure of disease and has the potential to open a new…
Designing RNA molecules has garnered recent interest in medicine, synthetic biology, biotechnology and bioinformatics since many functional RNA molecules were shown to be involved in regulatory processes for transcription, epigenetics and…
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…
RNA function is tied to secondary structure, operating through dynamic and heterogeneous structural ensembles. While current analysis tools typically output single static structures or averaged contact maps, chemical probing methods like…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…