1210 papers
Bioinformatics sits at the exciting intersection where biology meets data science, using powerful computer tools to decode the vast complexity of living systems. From mapping the human genome to tracking how viruses evolve, this field transforms raw biological information into actionable insights that drive modern medicine and research forward without requiring a supercomputer to understand the basics.
On Gist.Science, we ensure you never miss a breakthrough by processing every new preprint in this category directly from bioRxiv. Our team provides both plain-language explanations and detailed technical summaries for each paper, making cutting-edge discoveries accessible to everyone regardless of their background.
Below are the latest bioinformatics papers added from bioRxiv, ready for you to explore with clarity and depth.
This paper introduces APEX, an explainable AI framework that integrates evolutionary embeddings and graph attention networks to enable cross-species pathogen target discovery and pocket-guided molecular design, successfully identifying novel drug targets and generating specific inhibitor candidates for antimicrobial development.
The paper introduces scDynOmics, a scalable and interpretable transformer model that leverages gene regulatory networks and Linformer-style attention to learn compact multimodal single-cell representations, which are then efficiently adapted via low-rank modules to achieve state-of-the-art performance in cellular classification and trajectory analysis.
This study integrates network pharmacology with experimental verification to demonstrate that Panax notoginseng accelerates skin wound healing in rats by modulating key inflammatory cytokines (TNF-α, IL-6, IL-10) through multi-component, multi-target regulation of NF-κB, MAPK, and JAK-STAT signaling pathways.
SpatialCompassV (SCOMV) is a novel computational tool that enables de novo classification of cell and gene spatial patterns and the identification of spatially differential genes by quantifying vectorial relationships between transcript locations and regions of interest without relying on prior biological annotations.
This study demonstrates that recent improvements in Oxford Nanopore Technologies (ONT) sequencing accuracy now enable the direct generation of error-free amplicon sequence variants (ASVs) from raw reads across a wide range of amplicon lengths, allowing for high-resolution microbial community profiling without reliance on reference databases, although achieving full resolution for very long amplicons in complex samples currently requires significantly higher sequencing depth compared to PacBio.
This study employs in silico systems biology approaches to identify shared molecular biomarkers, regulatory networks, and therapeutic targets involving autoimmune inflammation and infectious disease pathways across Post-Traumatic Stress Disorder, Schizophrenia, and Bipolar Disorder.
This paper presents a comprehensive benchmarking framework that evaluates computational tools for locus-specific transposable element analysis in single-cell RNA-seq data, revealing that while older insertions can be accurately quantified, young TEs remain difficult to resolve due to mapping ambiguities and recommending unique-mapper strategies or subfamily aggregation as best practices.
Using agent-based simulations, this study on Caribbean *Acropora* restoration concludes that while hybridization poses a low risk of genetic swamping, it offers limited potential for beneficial adaptive introgression, suggesting that hybrid-mediated genetic exchange is unlikely to significantly aid coral recovery within relevant management timescales.
The paper introduces DeepAllele, a novel deep learning framework that leverages paired allele-specific input from unambiguously phased datasets to predict subtle regulatory changes and uncover functionally relevant cis-regulatory motifs with greater accuracy than existing statistical methods.
EGGS is a C-based software tool designed to generalize empirical genotype data with missing sites across replicates while offering diverse functionalities such as format conversion, phase removal, and the simulation of sequencing errors and deamination.