TDKC (Target Distilled K-mer Classifier): Ultrafast and Memory-Efficient Sequence Classification for Target Pathogen Diagnostics biorxiv.org 2026-06-06 Metagenomic sequencing can identify pathogens from clinical samples without prior knowledge of the causative agent.
Finetuning masking challenges narrow-task evaluation of cell foundation models biorxiv.org 2026-06-06 Single-cell foundation models are large, self-supervised deep learning networks pretrained on millions of cellular transcriptomes.
scMTG reconstructs single-cell temporal dynamics with Markov transition generators biorxiv.org 2026-06-06 Single-cell time-series data offer a unique opportunity to study how cell states emerge, evolve, and diversify over time.
Enformer-Based Phylogenetic Tree Reconstruction biorxiv.org 2026-06-06 Enformer is a deep learning model trained on human and mouse genomes to predict regulatory activity from 196,608 bp DNA windows.
VelOT: kinetic-free RNA velocity inference via optimal transport, flow-field smoothing, and VAMP coarse-graining of cellular dynamics biorxiv.org 2026-06-06 Inferring cellular dynamics from snapshot single-cell RNA sequencing remains difficult when spliced and unspliced counts are sparse or unreliable.
Automated Retinal Dysplasia Segmentation in Mouse Optical Coherence Tomography Scans Using a UNet-Based model biorxiv.org 2026-06-06 Optical coherence tomography (OCT) is the state-of-the-art non-invasive imaging technique for preclinical retinopathy studies.
Handshake: Partner-Specific Protein-Protein Binding Site Prediction at Scale Using ProstT5 and Cross-Chain Attention biorxiv.org 2026-06-06 Partner-specific protein-protein binding site prediction, identifying which residues of a protein form the interface when bound to a specific partner,
pLM-Guided Inverse Folding for Antibody Sequence Design biorxiv.org 2026-06-06 Inverse folding, predicting amino acid sequences from three-dimensional structures, is a foundational task in computational protein design, yet it is
Profiling Gingival Inflammation in a 3D Oral Tissue Model Reveals Early Features of Disease Progression biorxiv.org 2026-06-06 Gingival health depends on a balanced interplay among the gingival epithelium, immune system, and oral microbiome.
Discovery and characterization of a pigment produced by Streptococcus pyogenes biorxiv.org 2026-06-06 Streptococcus pyogenes is a major human-restricted pathogen capable of both localized and systemic diseases, as well as causing post-infectious acute
Top Model Decision Tree: Selecting Segmentation Models for Reliable Quantitative Analysis in Low- and Ultralow-Dose CryoEM biorxiv.org 2026-06-06 Deep learning neural networks provide a powerful approach for segmenting low-contrast cryogenic electron microscopy (cryoEM) images.
CascadeMAP: Autonomous Closed-loop Optimization of Enzyme Cascades via Microfluidics, Machine Learning and Agentic AI biorxiv.org 2026-06-07 Enzyme cascades enable complex biochemical transformations, but their optimization is resource-intensive, requiring navigation through high-dimensiona
Structural insights into the inhibition of sickle hemoglobin polymerization by asymmetric hemoglobin tetramer HbFS (α2γβS) biorxiv.org 2026-06-07 Sickle cell disease (SCD) is caused by a single amino acid substitution in the {beta}S globin chain at 6th position (6E[->]V).
Structure-guided compound prioritization strategy for virtual screening identifies putative binders for the nuclear receptor LRH-1 biorxiv.org 2026-06-07 Compound ranking in structure-based virtual screening notoriously yields highly ranked false positive binders due to variable poses or biases in scori
Learning quality scores for chromatin accessibility bigWig tracks using Machine Learning biorxiv.org 2026-06-07 High-throughput chromatin accessibility assays such as bulk and single-cell ATAC-seq have generated large collections of processed signal tracks in bi
CLASPP: A unified model for predicting post-translational modifications biorxiv.org 2026-06-07 Post-Translational Modifications (PTMs) are a fundamental mechanism for regulating cellular pathways and increasing the functional diversity of the pr
Ontologizer 3: a cross-platform desktop application for frequentist and Bayesian GO enrichment analysis biorxiv.org 2026-06-06 We present Ontologizer 3, an easy-to-use cross-platform desktop application for Gene Ontology (GO) overrepresentation analysis.
Using protein language models for pangenome construction biorxiv.org 2026-06-06 Current pangenome construction methods rely largely on nucleotide or protein sequence alignment, limiting their ability to detect remote orthologs and
Neural synchrony between prefrontal and visual cortex supports visual working memory biorxiv.org 2026-06-07 Working memory appears to depend on neural mechanisms that are distributed across the brain.
Neurophysiological Functional Connectivity Changes during Difficult Listening in Older and Younger Adults biorxiv.org 2026-06-07 Older adults often report increased difficulty understanding speech in noisy listening environments.
Cortical folding patterns are encoded in the geometry of the unfolded neocortex. biorxiv.org 2026-06-07 Cortical folding patterns are conserved across individuals of gyrencephalic species and are closely related to cytoarchitectural organisation, connect
Thalamic Nuclei Differentially Coordinate Propagation of Cortical Slow Oscillations biorxiv.org 2026-06-07 Sleep slow oscillations (SOs) vary in the spatial extent of their cortical propagation, ranging from widespread Global events to spatially restricted
Hippocampal CA2 modulates trace fear conditioning through circuit-specific control of CA1 biorxiv.org 2026-06-07 Forming associations between temporally separated events depends on pathways linking the CA1, the subiculum (SUB), and the entorhinal cortex.
Connectional neuroanatomy of U-fibers in the rhesus monkey brain biorxiv.org 2026-06-07 The superficial white matter (SWM), the region of white matter immediately beneath the gray matter-white matter (GM-WM) border, contains short cortico
Repurposing drugs to treat Amoebic Gill Disease in Atlantic Salmon biorxiv.org 2026-06-07 Neoparameoba perurans causes Amoebic Gill Disease (AGD), a major parasitic disease of marine-phase Atlantic salmon and rainbow trout worldwide.
The Sorghum Lipid Database (SoLD): population-scale lipidomics linking environmental and genetic variation in the Sorghum Association Panel biorxiv.org 2026-06-06 Sorghum (Sorghum bicolor ) is a climate-resilient crop whose acclimation to nutrient limitation and low temperature likely involves extensive lipidome
HOPE: Interpretable Histology Analysis with Spatial Omics-Derived Signatures for Precision Oncology biorxiv.org 2026-06-06 Hematoxylin and eosin (H&E) stained images are fundamental clinical tools for disease assessment.
Temporal Biodynamics: An AI Platform for Identification of Stage-Relevant Targets and Biomarkers biorxiv.org 2026-06-06 Temporal modeling of disease progression is poised to revolutionize the process of target identification, leading to better characterization of and in
EnzOracle: Mechanism-aware prediction of enzyme environmental adaptation via a classification-guided mixture-of-experts framework biorxiv.org 2026-06-06 Industrial biocatalysis increasingly requires enzymes capable of operating under extreme physicochemical conditions, yet most natural sequence data re
STITCH: Spatial Transcriptomics Imputation via Flow Matching with Internal Learning biorxiv.org 2026-06-06 Spatial transcriptomics datasets frequently suffer from spatial gaps and missing regions due to sectioning artifacts, tissue damage, and the high cost