Mutations in the SOD1 gene are among the most significant genetic contributors to amyotrophic lateral sclerosis (ALS), with different variants linked to varying disease severity. To investigate the...

The process of lead optimization in drug discovery is a complex, multi-objective challenge that remains a major bottleneck in the development of new therapeutics. Traditional approaches often...

Codon sequence design is crucial for generating mRNA sequences with desired functional properties for tasks such as creating novel mRNA vaccines or gene editing therapies. Yet existing methods lack...

A growing body of empirical research shows that interspecific gene flow is a widespread biological force that shapes evolutionary histories across the Tree of Life. Computational approaches designed...

This paper presents a novel, physiologically inspired framework for reconstructing missing pupil data during blink-induced interruptions. Pupillometry has become integral to studies of cognition,...

Summary: The functional annotation of microbial genes lags far behind genome sequencing, leaving critical gaps in our knowledge of metabolic pathways. While integrating genetic manipulation with...

Variational Autoencoders (VAEs) are a widely used framework to integrate diverse biomedical data modalities, create representations that capture the underlying structure of the datasets, and obtain...

Multi-copy gene families evolve through dynamic processes of duplication, loss, and sequence divergence, often exhibiting complex paralogy and orthology relationships that complicate the detection of...

Diabetic cardiomyopathy (DbCM) is a condition characterized by myocardial dysfunction in diabetes. Although the clinical recognition of DbCM is increasing, its underlying molecular mechanisms remain...

A patient with a medical condition can have medical tests or symptoms scored that generate numerical results before a treatment, during a treatment or after a treatment, usually over several days, to...

We present FeatureDCA, a statistical framework for protein sequence modeling and generation that extends Direct Coupling Analysis (DCA) with biologically meaningful conditioning. The method can...

Many single-cell transcriptomics datasets are stored in the HDF5-backed AnnData (H5AD) file format, as popularised by the Python scverse ecosystem. However, accessing these datasets from R, allowing...

In every region of the world, antibiotic resistance is increasing to dangerously high levels. Our ability to cure widespread infectious diseases is being threatened by the emergence of new resistance...

Two types of experiments are used to study RNA-chromatin interactions: a search for the interactome of individual RNAs ("one-to-all" or OTA) and a genome-wide search for contacts of all RNAs ("all-...

Background: Alternative promoter usage regulates isoform diversity in mammals, playing critical roles in development, disease, and cellular reprogramming. While Cap Analysis of Gene Expression (CAGE)...

The success of COVID-19 mRNA vaccines has made optimizing mRNAs for in-vial stability a key objective. However, we still lack a complete understanding of the sequence metrics that influence mRNA...

Single-cell omics technologies enable the dissection of cellular heterogeneity, yet the high dimensionality, inherent noise, and sparsity present significant analytical challenges. As the technolog...

Single-nucleus RNA sequencing (snRNA-seq) generates single cell data from nuclei. It provides valuable compatibility with frozen or difficult-to-dissociate tissues while avoiding stress responses in...

Sequencing an entire spatial transcriptomics slide can cost thousands of dollars per assay, making routine use impractical. Focusing on smaller regions of interest (ROIs) based on adjacent routine...

Live biotherapeutic products (LBPs) deliver microbial strains to modulate the host microbiota in order to promote health or treat and prevent disease. Since endogenous strains are already present,...