1197 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 study utilizes high-temporal-resolution RNA-Seq data from the aging male mouse colon to reveal that transcriptomic changes are dominated by complex, non-monotonic trajectories and a mid-to-late-life collapse of the unfolded protein response, while also enabling the construction of a compact, three-gene transcriptomic clock to accurately track chronological age.
MOSAIC is an unsupervised framework that learns graph node embeddings by analyzing the convergence behavior of accumulated diffusion operators via Krylov subspace analysis, achieving superior performance in node classification and link prediction tasks compared to existing methods like Node2Vec and GraphSAGE, as demonstrated on a large-scale biomedical knowledge graph.
The paper introduces "digestome," a commercially license-free marker-gene panel and scoring framework for functionally profiling anaerobic digestion microbiomes, which demonstrates high specificity in identifying methanogenesis and hydrolysis pathways while explicitly accounting for measurement biases to enable fee-for-service analysis for biogas operators.
Enrich.AI is an agentic AI platform that integrates statistical enrichment analysis with automated literature search and LLM-based reasoning to provide interactive, evidence-grounded biological interpretations of gene lists through a conversational interface.
This paper introduces a weighted pathway co-membership scoring method that incorporates Reactome's hierarchical and sequential pathway structures to generate biologically informed protein networks, demonstrating superior performance in cancer gene prioritization compared to state-of-the-art approaches.
The paper introduces pre-miRBench, a standardized multispecies benchmark and reference model designed to enable fair comparison of animal precursor microRNA predictors across diverse species and miRNA families, demonstrating that its ensemble model achieves superior overall performance while providing reproducible resources for future research.
By analyzing NOTCH3 sequences across 113 mammalian species, this study reveals rare evolutionary deviations that challenge strict conservation patterns and establish a context-dependent framework for interpreting CADASIL pathogenicity based on structural, disulfide, and proteolytic factors beyond simple cysteine count.
This paper demonstrates that genomic foundation models are highly susceptible to pervasive backdoor attacks via small-scale data poisoning with short DNA motifs during fine-tuning, while remaining robust in clean tasks, and proposes a novel two-stage auditing framework to detect such threats without prior knowledge of the triggers.
This study empirically characterizes the "verification debt" inherent in automated biological research workflows using the Biomni agentic platform, proposing a new VERIFY framework and a set of metrics to evaluate the traceability and validity of AI-driven scientific decisions across diverse biological domains.
The authors present methylTFR, an R package that quantifies transcription factor activity from DNA methylation data to identify cell-type-specific regulators and resolve developmental trajectories across bulk and single-cell immune cell methylomes.