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

scDRP: Disentangled representation learning for predicting single-cell responses to perturbations and estimating individual treatment effects

The paper introduces scDRP, a generative framework utilizing disentangled representation learning and conditional optimal transport to accurately estimate individualized treatment effects and infer counterfactual cell states from unmatched single-cell perturbation data, thereby revealing heterogeneous biological mechanisms across diverse cell types and conditions.

Sun, J., Stojanov, P., Zhang, K.2026-08-13

💻 bioinformatics

ASPIRE: the Amplicon Sequencing Profiler for Investigating Respiratory Ecosystems

This paper introduces ASPIRE, an accessible Nextflow workflow designed to process, analyze, and interpret linked amplicon sequence variant (ASV) and volatile organic compound (VOC) data to investigate respiratory microbial ecosystems and their relationship to health.

McLaughlin, R. J., Chen, S., Nag, A., Noonan, A. J. C., Bartolomeu, C., Borden, S. A., Lam, S., Myers, R., Hallam, S. J.2026-08-12

💻 bioinformatics

megaMine: a scalable, rule-based framework for mining gene-cancer-drug evidence from biomedical literature

The paper introduces megaMine, a transparent and scalable rule-based framework that effectively extracts structured gene-cancer-drug evidence from biomedical literature, demonstrating high accuracy in distinguishing therapeutic efficacy and generating interpretable data for downstream knowledge synthesis.

JUNAID, M., Prazanowska, K. H., Jeong, H.-E., Ryu, Y., Choi, J., An, J.-Y., Lim, S. B.2026-08-12

💻 bioinformatics

DuplexFM: Transferable small-RNA target representations link miRNA interactions to siRNA efficacy prediction

DuplexFM is a biologically grounded framework that leverages transferable miRNA-derived representations and experimentally grounded accessibility features to significantly improve the prediction of siRNA efficacy, offering a parameter-efficient approach to unified modeling of Argonaute-mediated RNA regulation.

Chen, B., Yin, J., Fei, J., Yang, M.2026-08-12

💻 bioinformatics

STR-PG: A Topology-decoupled Pangenome Framework for Scalable Short-read Genotyping of Short Tandem Repeats

STR-PG introduces a topology-decoupled pangenome framework that separates stable locus representation from dynamic allele content via an external registry, enabling scalable and accurate short-read genotyping of short tandem repeats without requiring graph reconstruction when new alleles are added.

YUAN, J., XUE, Z., TANG, H., LIU, Y., WANG, J.2026-08-12

💻 bioinformatics

SeqDesk: a sequencing-facility management system for standards-compliant and FAIR (meta)data submission

SeqDesk is an open-source, FAIR-compliant data management system designed for sequencing facilities to streamline the collection of standardized metadata, automate bioinformatics analysis, and facilitate direct submission to the European Nucleotide Archive by embedding these processes into routine operational workflows rather than treating them as retrospective tasks.

Muench, P. C., Robertson, G., McHardy, A. C.2026-08-11

💻 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