💻 Category

bioinformatics

1182 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.

💻 bioinformatics

Human Intestinal Absorption Revisited: The 1998 Descriptors Survive, and the Method Extends to Permeability

This paper revisits a 1998 model for human intestinal absorption by demonstrating that its original performance relied on a fortunate data split, and subsequently establishes more robust, consensus-based predictive models for intestinal absorption and various permeability assays using genetic algorithm-selected descriptor sets and random forests across 250 stratified extractions.

Muskal, S. M., Wessel, M. D.2026-10-11
💻 bioinformatics

GenDiMug: a generic inclusive multigraph framework to analyze genomic organizations and -omics data at multiple scales

GenDiMug is a novel multigraph framework that overcomes the limitations of linear genome representations by using network models to integrate multi-omics data and analyze genomic organization across multiple scales, revealing structural patterns such as gene expression clumping and circadian regulation.

Teuliere, J., Lopez, P., Corel, E., Llorente, B., Bapteste, E.2026-10-11
💻 bioinformatics

In silico subtractive genomics and reverse vaccinology approach reveal outer membrane proteins OMP47 and LptD as dual-purpose drug and vaccine targets in Pasteurella multocida Pm70

This study employs an integrated *in silico* subtractive genomics and reverse vaccinology workflow to identify the outer membrane proteins OMP47 and LptD as dual-purpose drug and vaccine targets against *Pasteurella multocida* Pm70, culminating in the design of a safe, highly antigenic multi-epitope vaccine construct.

Khan Chowdhury, A. R., Islam, S., Farid, A., Lamia, F., Ahmad, T. F., Hossain, N. J., Paul, A. R., Afrin, T., Elias, S. (…)2026-10-11
💻 bioinformatics

kitAb: an automated framework for assay-specific antibody developability modeling and large-scale landscape analysis

The paper introduces kitAb, an open-source, computationally efficient framework that generates 59 interpretable descriptors for scalable, assay-specific antibody developability modeling and reveals systematic physicochemical differences across large-scale natural and therapeutic antibody repertoires.

Trofimova, E., Shaburova, E., Antonets, D., Ramensky, V.2026-10-11
💻 bioinformatics

Inferring ecDNA Evolution from Allele Frequency Spectra

This paper introduces ecEvol, a computational method that analyzes allele frequency spectra from bulk whole-genome sequencing to infer the timing, selection strength, and clonal dominance of extrachromosomal DNA (ecDNA) emergence, revealing that early ecDNA formation driven by oncogenes correlates with poorer patient survival and that ecDNA dynamics vary significantly between untreated and advanced tumors.

Dameracharla, B., Prasad, G., Luebeck, J., Amin, S., Kirkland, J., Chapman, O. S., Chavez, L., Verhaak, R., Huang, W., M (…)2026-10-11
💻 bioinformatics

Ab initio CryoEM maps minimizing preferred orientation problems in heterogeneous mixtures: ReconSIREN

ReconSIREN is a novel deep learning framework utilizing a Mixture-of-Experts architecture to perform fully \textit{ab initio} CryoEM single-particle analysis that simultaneously resolves preferred orientation artifacts, particle heterogeneity, and conformational flexibility without relying on traditional optimization methods.

Herreros, D., Sorzano, C. O. S., Carazo, J. M.2026-10-10
💻 bioinformatics

Proteome modulation by opposite inotropic drugs in human engineered cardiac tissue revealed by topology-driven cross-modal integration

This study introduces a topology-driven framework that successfully integrates proteomic and functional data from human engineered cardiac tissues to reveal how epinephrine and doxorubicin exert opposing inotropic effects by differentially modulating energy homeostasis, mitochondrial translation, and proteostasis.

Staykova, D. K., Snippert, D., Wessels, H. J. C. T., Passier, R., Conte, F.2026-10-08
💻 bioinformatics

KENT: Fast Pathogen Screening with NVIDIA Jetson Cluster in Resource-Constrained Areas

KENT is a portable, offline edge-computing framework utilizing a cluster of NVIDIA Jetson Nano modules to enable fast, GPU-accelerated metagenomic pathogen screening in resource-constrained environments, achieving significant speedups over CPU baselines while maintaining high classification accuracy and abundance estimation fidelity.

Icoz, A., Roman-Brenes, R., Bingöl, Z., Alkan, C.2026-10-08
💻 bioinformatics

FlyAnatoView: Visualization of Drosophila Single-cell RNA-seq Datasets on Anatomographs

FlyAnatoView is a resource that addresses the lack of spatial context in single-cell RNA sequencing data by projecting transcriptomic profiles onto anatomical diagrams of *Drosophila*, thereby restoring information about the specific tissue or organ locations of individual cells.

Hu, Y., Kalina, J., Veal, A., Ewen-Campen, B., Porter, T., Song, J., Luo, Y., Huang, K., Goutte-Gattat, D., Brown, N. H. (…)2026-10-08
💻 bioinformatics

FilAdh: degradation-aware analysis of focal adhesions and actin stress fibers

FilAdh is a unified, degradation-aware computational framework that simultaneously segments focal adhesions and reconstructs actin stress fibers to enable accurate morphometric analysis and spatial classification, outperforming existing methods in benchmark tests while explicitly characterizing how specific imaging imperfections affect structural measurements.

Rey-Paniagua, G., Garcia-Lopez-de-Haro, C., Hernandez-Martinez, M., Lachowski, D., Munoz-Barrutia, A.2026-10-08