As (deep) generative chemistry rapidly enters the landscape of drug discovery, evaluating the models and their structural output relevance, tractability, and innovation potential becomes both a...

Single-cell RNA sequencing (scRNA-seq) enables high-resolution characterization of cellular heterogeneity, but its rich, complementary structure across cells and genes remains underexploited,...

Extracting meaningful biological signals from Cytometry by time-of-flight (CyTOF) data remains challenging due to heterogeneity, data characteristics, and the presence of various technical artifacts....

Motivation: X chromosome inactivation (XCI) is an epigenetic process that equalizes X-linked gene dosage between females (XX) and males (XY). During early development, one X chromosome in each cell...

Bacteria are highly heterogeneous, even under controlled conditions, making single-cell RNA sequencing (scRNA-seq) essential for studying microbial diversity and symbiosis. Since its first applicat...

Protein–protein interactions (PPIs) play a central role in elucidating cellular mechanisms. However, a substantial gap remains in current prediction models, as they frequently overlook the structural...

Background The regulation of mRNA decay and translation is crucial for cellular function and development; however, the complex interplay of RNA-binding proteins (RBPs) regulating these processes...

Metagenomic taxonomic profiling is essential for characterizing microbial community composition in both environmental and clinical contexts. Existing profilers have greatly advanced community...

Gaining structural insights into the interactions between antibodies and their corresponding antigens is essential for understanding immune recognition and for guiding therapeutic antibody design....

Fungi represent less than 1% of the gut microbiota; However, their importance in host homeostasis and disease is increasingly recognized. Accurate characterization of the gut mycobiome from metagen...

The human microbiome is widely recognized as a key determinant of health and disease, yet most reported links between observed microbial features and clinical outcomes remain descriptive and lack an...

Single-cell RNA sequencing (scRNA-seq) has significantly advanced our understanding of Alzheimer's disease and aging by revealing cellular heterogeneity and shifts in cell-type composition between...

The role of gut microbiome in predicting diet response and developing personalized dietary recommendations has been increasingly recognized. Yet, we still lack comprehensive, genome-based insights...

Spatial transcriptomics captures neighborhood–dependent gene expression, but existing workflows do not always fully account for measurement scale and often treat space implicitly. We present geneSC...

The General Feature Format (GFF) is widely used to represent genomic annotations, but its hierarchical, multi-attribute structure makes manual querying and analysis challenging. Existing libraries...

Agent systems powered by large language models (LLMs) are increasingly applied in computational biology to automate analysis, integrate data, and accelerate discovery. Here, we investigate the...

Single–nucleus RNA sequencing (snRNA–seq) provides a powerful tool to profile cell–type–specific transcriptional programs in woody fruit trees. Yet its application in Malus domestica has been limited...

Background: Many clinically important antimicrobial resistance (AMR) phenotypes such as fluoroquinolones and rifamycins are driven by antimicrobial resistance-conferring mutations (ARMs) in conserved...

We present a deep-learning based pipeline for generating high-quality synthetic instance-segmentation datasets of tissues undergoing early gastrulation in chick embryo. We create point-clouds using...

Background: The increased demand for genomic sequencing has consequently led to a rise in the number of Variants of Uncertain Significance (VUS), which are classified as such due to insufficient...