1018 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 demonstrates that applying temperature scaling and epistemic neural networks significantly improves the reliability of transformer-based genomic language models when facing distribution shifts, such as noisy data or novel variants, across diverse genomic prediction tasks.
This study demonstrates that unsupervised embeddings from the pretrained Evo2 genome language model capture meaningful host-range signals for bacteriophages, achieving competitive retrieval performance that is further enhanced when combined with traditional alignment and k-mer-based methods in a hybrid pipeline.
PanXpress is a unified, efficient, and accurate framework for bacterial gene expression quantification that utilizes a pan-transcriptomic gapped k-mer index to overcome reference bias in mixed-strain samples by directly constructing references from genomic data and outperforming existing tools in precision, speed, and memory usage.
This study analyzes nucleic acid sequences from the Zag meteorite, revealing that they exhibit constrained complexity and low-dimensional structure distinct from both known biological patterns and random models, suggesting an unusual origin that warrants further independent investigation.
This study demonstrates that Large Language Models can accurately extract prognostic histologic features from unstructured pathology reports in Ewing sarcoma, revealing that Neuron-Specific Enolase (NSE) positivity and S100 negativity are significant independent predictors of inferior survival, particularly in non-metastatic patients.
The paper introduces FlashS, a scalable frequency-domain method that enables accurate, well-calibrated detection of spatially variable genes in atlas-scale spatial transcriptomics datasets by leveraging Random Fourier Features and sparse sketching to overcome the computational and expressiveness trade-offs of existing approaches.
This study presents the largest harmonized single-cell transcriptomic atlas of *Macaca fascicularis*, integrating over 2.5 million cells across 43 organs and leveraging a human foundation model to enable scalable cross-species comparisons that improve target qualification, mechanistic toxicity interpretation, and the reduction of non-human primate use in preclinical research.
The paper introduces evedesign, a unified open-source framework and web interface that overcomes current limitations in protein engineering by enabling flexible, method-agnostic, and iterative multi-objective biosequence design workflows accessible to both experts and non-experts.
StrucTTY is a self-contained, terminal-native tool that enables real-time, interactive visualization and comparative analysis of protein structures directly within text-only environments, addressing a critical gap in terminal-based structural biology workflows.
This study presents a structure-guided workflow that successfully identified, classified, and standardized the nomenclature of 1,513 Cytochrome P450 deposits in the Protein Data Bank, resulting in the first rigorously curated, structure-linked registry of these enzymes.