Discover, rate, and verify biology preprints.

Missing by design: why genomic metadata must be captured at submission, not recovered from the literature

The paper highlights the lack of standardized genomic metadata in plant and metazoan genome assemblies and proposes making ploidy, cultivar, and subgenome structure mandatory metadata fields.

A Saliva-Inspired Model of Enzymatic Starch Hydrolysis by Alpha Amylase

This paper demonstrates how alpha-amylase hydrolyzes starch to generate reducing sugars, causing osmotic stress that remodels giant unilamellar vesicles.

Genome-scale metabolic models reveal phylogenetic conservation of amino acid fermentation-linked metabolic traits in soil bacteria

The paper constructs genome-scale metabolic models for soil bacteria to identify phylogenetically conserved fermentation traits and their metabolic fluxes.

KDM6A is enzymatically active at the Golgi apparatus where it is necessary for maintenance of Golgi apparatus morphology

This study shows KDM6A is enzymatically active at the Golgi apparatus and is necessary for maintaining its morphology, independent of its nuclear function.

Prediction of early Toxoplasma gondii infection during pregnancy combining host biomarkers and machine learning

This paper develops a machine learning model using serum biomarkers to predict early Toxoplasma gondii infection in pregnant sheep, achieving high accuracy and sensitivity for early diagnosis.

Massively parallel quantification and prediction of monomeric protein yield in Escherichia coli

The paper develops a scalable assay and a protein language model to predict monomeric yield of proteins in E. coli, showing it can be learned and designed.

Interpretable Machine Learning Links Group-Specific Plasma Proteomics to Regional Structural Neuroimaging in Alzheimer's Disease

The paper identifies group-specific plasma proteomic signatures in Alzheimer's disease stages and links them to regional brain structural changes using machine learning and neuroimaging.

AlphaFold 3 Prediction Accuracy and Reliability across RNA Structures and Protein-RNA Interfaces

This study evaluates AlphaFold 3's accuracy and reliability in predicting RNA structures and protein-RNA interfaces, finding that confidence scores do not always correlate with correct predictions.

The Application of 3D Cryo-Volume Electron Microscopy to Visualize and Quantify the Photosynthetic Filamentous Cyanobacterium Anabaena

This paper uses cryo-vEM to visualize and quantify ultrastructural features of two Anabaena species without chemical pre-treatment.

Predicting single-molecule chromatin distribution from DNA sequence

This paper introduces a sequence-to-distribution framework to predict single-molecule chromatin states from DNA sequence, revealing new regulatory mechanisms and variant effects.

Immersion as inference: An active inference account of induced realities and its relation to the two-competitor model

This paper develops an active inference framework to explain immersion in virtual and augmented realities by modeling induced realities as competing generative models.

IL-23 licenses the transition from preclinical autoimmunity to inflammatory arthritis through IL-17A-dependent mechanisms

This study shows IL-23 promotes the transition from preclinical autoimmunity to arthritis by enhancing IL-17A and IFN-gamma production, and identifies IL-23 pathway changes in at-risk individuals.

scPCIP: cross-species annotation of plant cell types with conserved gene programs

scPCIP annotates plant cell types across species using conserved gene programs, outperforming marker-based and deep-learning methods in held-out datasets.

brisc: a multithreaded CPU toolkit for single-cell analysis

brisc is a multithreaded CPU toolkit for single-cell analysis that is faster and more reproducible than existing tools like Scanpy and Seurat.

Single-cell transcriptomics of enriched rare neural lineages of Tribolium castaneum

The paper develops workflows for targeted single-cell and single-nucleus RNA sequencing of rare neural populations in Tribolium castaneum using reporter and antibody-based enrichment strategies.

Matching Corticospinal and Cortical Excitability along the motor cortex: TMS-EMG-EEG study

This study investigates the relationship between cortical and corticospinal excitability thresholds along the motor cortex using TMS-EMG-EEG in 24 subjects, finding strong correlations and site-specific differences.

High-throughput sequencing of unmethylated DNA (UMR-seq) reveals extensive epigenetic variation in the hypomethylome of diverse plant species

UMR-seq reveals epigenetic variation in plant hypomethylomes, showing UMRs are enriched in regulatory loci and improve genomic prediction and trait association mapping in wheat.

Cross-cancer knowledge transfer for lymph node metastasis prediction: Applicability of an axillary lymph node-based deep learning model

This paper evaluates a deep learning model trained on axillary lymph nodes for predicting metastasis in lymph nodes from different anatomical regions across cancers.

The collective effect of non-nicotine constituents on the reinforcing and neuropharmacological effects of comprehensive cigarette smoke and electronic nicotine delivery system (ENDS) aerosol extracts in rats.

This study compares the reinforcing and neuropharmacological effects of cigarette smoke and e-cigarette aerosol extracts with nicotine in rats, finding that non-nicotine constituents in cigarette smoke contribute to these effects.

Computational Analysis of Antioxidant Effects on Stress Response Mechanisms in Candida albicans

The paper uses computational methods to analyze antioxidant effects on stress response mechanisms in Candida albicans, identifying naringenin and quercetin as potential modulators of Sir2/SIRT3 pathways.