bioinformatics papers | Gist.Science

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.

💻 bioinformatics

Species-specific transformer models of bacterial gene order and content for genomic surveillance tasks

This study introduces PanBART, a species-specific transformer model trained on the gene content and order of *Escherichia coli* and *Streptococcus pneumoniae*, demonstrating its superior ability to unsupervisedly learn population structures, identify emergent lineages, predict antibiotic resistance gene uptake, and analyze gene co-selection for critical genomic surveillance tasks.

Horsfield, S. T., Wiatrak, M., McInerney, J. O., Bentley, S. D., Colijn, C., Lees, J. A.2026-04-30

💻 bioinformatics

A Conditional Variational Autoencoder with QSAR-Guided Surrogate-Weighted Fine-Tuning and Cross-Entropy Optimization for Targeted Antimicrobial Peptide Generation

This paper presents a conditional variational autoencoder pipeline that integrates QSAR-guided surrogate-weighted fine-tuning and cross-entropy optimization to overcome data scarcity and circular dependency challenges, successfully generating targeted antimicrobial peptides with high predicted efficacy and favorable structural properties.

Castanon, I., Wan, F., de la Fuente, C., Pini, A., Falciani, C.2026-04-30

💻 bioinformatics

Systems Pharmacology Reveals Type I Interferon and Myeloid-Like B Cell Reprogramming as Druggable Axes in Antiphospholipid Syndrome

This study employs an integrative systems pharmacology approach to characterize the molecular heterogeneity of antiphospholipid syndrome, identifying Type I interferon signaling and myeloid-like B cell reprogramming as key druggable axes that enable patient stratification and the repurposing of existing therapies for precision medicine.

Sun, B., Lu, Y., Liu, W., Wang, C.2026-04-30

💻 bioinformatics

Deterministic retrieval recovers biomedical associations lost by language models

The paper introduces BioChirp, an open-source framework that combines LLM-based query interpretation with deterministic graph-based retrieval to recover more biomedical associations with higher reproducibility than conventional LLM-based systems.

Halder, A., Singh, M., Kesarwani, R., Mathew, B., Bhattacharya, N., Chikhaliya, O., Motwani, D., Peela, S. C. M., Samant (…)2026-04-29

💻 bioinformatics

Explainable Prototype Booster: Enhancing Latent Representations of Foundation Models for Gene Expression Prediction

The paper introduces the Explainable Prototype Booster (EP-Booster), a method that integrates biological prior knowledge into foundation models to refine latent representations for accurate and interpretable gene expression prediction from histological images, thereby overcoming the cost and time limitations of spatial transcriptomics.

Li, C., Nguyen, Q.2026-04-29

💻 bioinformatics

PixelDeck: A local-first media library manager for biomedical imaging

PixelDeck is an open-source, local-first browser application that streamlines the organization, deduplication, and interactive browsing of large biomedical image and video collections on standard hardware through a modular architecture featuring recursive import, SHA-256 duplicate detection, and asynchronous processing.

Kidder, B. L.2026-04-28

💻 bioinformatics

Accurate ab initio gene prediction in eukaryotes with Tiberius in multiple clades

The paper introduces Tiberius, a deep learning-based ab initio gene predictor that achieves state-of-the-art accuracy and significantly faster runtimes across diverse eukaryotic clades by training lineage-specific models, effectively addressing current bottlenecks in genome annotation.

Gabriel, L., Bruna, T., Kaur, A., Krishnan, A., Ortmann, F., Salamov, A., Talbot, S., Becker, F., Krieg, R., Wheat, C. W (…)2026-04-28

💻 bioinformatics

Uniform pre-processing of bacterial single-cell RNA-seq

This paper adapts the kallisto-bustools suite to enable efficient, accurate, and uniform pre-processing of bacterial single-cell RNA-seq data, addressing challenges posed by operons and short gene lengths to establish a scalable foundation for microbial transcriptomics.

Oakes, C. G., Beilinson, V., McFall-Ngai, M. J., Pachter, L. G.2026-04-27

💻 bioinformatics

Modeling causal signal propagation in multi-omic factor space with COSMOS

The paper introduces COSMOS+, an interpretable framework that integrates data-driven multi-omics factor analysis with mechanistic prior knowledge to model causal signal propagation and generate actionable hypotheses about disease drivers, demonstrated through applications in breast cancer resistance models and patient cohorts.

Dugourd, A., Lafrenz, P., Mananes, D., Paton, V., Fallegger, R., Bai, Y., Kroger, A.-C., Turei, D., Li, Y., Trogdon, M. (…)2026-04-24

💻 bioinformatics

Verticall: A fast and robust tool for recombination detection in large-scale bacterial genomic datasets

Verticall is a fast, non-parametric, open-source tool designed to efficiently detect recombination and generate recombination-free phylogenies in large-scale bacterial genomic datasets (ranging from hundreds to thousands of genomes), demonstrating superior or comparable performance to existing methods like Gubbins and ClonalFrameML across diverse evolutionary scales.

Odih, E. E., Wick, R. R., Holt, K. E.2026-04-24

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