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

Mapping disease traits onto spatiotemporal domain landscapes through scalable multi-sample integration of spatial transcriptomics

STUltra is a scalable hypergraph-based framework that integrates large-scale spatial transcriptomics data to detect spatial domains and map disease-associated genetic traits across diverse tissue contexts, overcoming batch effects and enabling the discovery of molecular architectures underlying complex diseases like congenital heart disease and Alzheimer's.

Zhang, S., Luo, S., Luo, Y., Su, S., Shi, Y., Liu, L., Li, W., Tian, T., Li, J.2026-08-10

💻 bioinformatics

A Principled Statistical Framework for Analyzing Spatial Patterns in Spatially Resolved Multi-Omics

This paper introduces STORM, a principled statistical framework that unifies spatial hypothesis testing, effect size estimation, power analysis, and experimental design to rigorously analyze spatial patterns in multi-omics data.

Li, J., Raina, M., Wang, Y., Zeng, S., Yu, Y., Yu, X., Jin, X., Chang, Y., Feliciano, D., Himmelfarb, J., Ricardo, A. C. (…)2026-08-10

💻 bioinformatics

nf-cavalier: A Nextflow Pipeline for Rare Disease Variant Prioritization and Reporting

nf-cavalier is an open-source Nextflow pipeline that automates the annotation, filtering, and visual reporting of genomic variants to facilitate the identification of causal mutations in rare Mendelian diseases.

Munro, J. E., Reid, J., Bahlo, M. E., Bennett, M. F.2026-08-10

💻 bioinformatics

pysigscore: gene signatures scoring across bulk and single-cell transcriptomics

The paper introduces pysigscore, a versatile Python framework that integrates 18 gene set scoring methods with customizable options and reliability analyses to robustly quantify signature activity in both bulk and single-cell transcriptomics data.

Giacomello, T., Mazzara, S., Abbruzzese, G., Barberis, A., tangherloni, a., Buffa, F. M.2026-08-09

💻 bioinformatics

A Framework for Benchmarking Pathway Reconstruction Algorithms

This registered report introduces the Signaling Pathway Reconstruction Analysis Streamliner (SPRAS) framework to enable a large-scale, systematic benchmark of 14 pathway reconstruction algorithms across 822 datasets, aiming to resolve current heterogeneity challenges and guide optimal algorithm selection for specific biological contexts.

Talluri, N., Figueroa-Reid, T., Hiemstra, J., Magnano, C. S., Shedivy, A., Panda, N., Liu, Y., Sanjeev, S., Anderson, O. (…)2026-08-09

💻 bioinformatics

A generative model for dimensionality reduction with millions of features and few samples

This paper presents a deep generative decoder (DGD) capable of performing dimensionality reduction on datasets with millions of features and few samples, demonstrating that training requirements are largely independent of feature dimensionality and showing superior performance in tumor classification compared to PCA and VAE.

Pancotti, C., Fariselli, P., Meisner, J., Krogh, A.2026-08-09

💻 bioinformatics

Scop3P-Toolkit: executable structure-aware workflows linking PTMs, peptides, and mutations to protein function

Scop3P-Toolkit is an open-source, executable analytical environment that integrates diverse biological annotations with structural data to provide reproducible, interactive workflows for analyzing post-translational modifications, genetic variants, and proteomics-derived peptides within their three-dimensional context.

Diaz, A., Tichshenko, N., Depoortere, B. G. J., Andrade Buono, R., De Geest, P., Vranken, W. F., Martens, L., Ramasamy (…)2026-08-09

💻 bioinformatics

PanGBank: a large-scale resource of precomputed microbial pangenomes built with PPanGGOLiN

PanGBank is a comprehensive, open-access database that provides precomputed pangenomes for over 4,600 prokaryotic species using PPanGGOLiN, offering standardized, graph-based resources and multiple access tools to facilitate large-scale comparative genomics and the study of microbial evolution and adaptation.

Mainguy, J., Lemane, T., Bazin, A., Arnoux, J., Gautreau, G., Medigue, C., Calteau, A., Vallenet, D.2026-08-09

💻 bioinformatics

Move BeTween modAlities (MBTA) employs flow matching to predict single cell data modalities

The paper introduces Move BeTween modAlities (MBTA), a novel framework that utilizes flow matching to connect modality-specific latent spaces and address structural mismatch in single-cell data, thereby enabling accurate cross-modal translation while preserving the unique structural integrity of each molecular modality.

Xu, B., Zhang, Y., Michor, F.2026-08-09

💻 bioinformatics

Scalable Extraction of Information on Protein-Protein Interactions using Topological Data Analysis

This paper introduces a scalable Topological Data Analysis framework that significantly reduces the computational cost of predicting protein-protein interaction interfaces from surface patches while maintaining competitive accuracy compared to established geometric deep learning methods.

Mukherjee, A., Park, B., Malmstrom, A., Cisewski-Kehe, J., Van Lehn, R. C., Zavala, V. M.2026-08-09

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