bioRxiv

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NucGen3D: a Synthetic Framework for Large-Scale 3D Nuclear Segmentation with Open-Source Training Data AND Models

bioRxiv Jan 1, 2025
Robust nuclear segmentation in 3D microscopy images is a critical yet unresolved challenge in quantitative cell biology, hindered by the scarcity and variability of annotated volumetric datasets. Because such data are difficult to obtain, most state-...
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BERT-T6: Towards High-accuracy T6SS Bacterial Toxin Identification Using Protein Language Model

bioRxiv Jan 1, 2025
Type VI secretion system effectors target the cell wall, membranes and nucleic acids, leading to the killing of bacteria or impairment of host cell defense mechanisms. Accurate identification of T6SEs will be beneficial to understand the virulence of...
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Evaluating peer-to-peer bioinformatics education: a case study of student learning outcomes and community impact in an undergraduate multi-omic data analysis course

bioRxiv Jan 1, 2025
Computational methodology has become ubiquitous in biomedical research with the rise of big data analysis and popularity of artificial intelligence and machine learning. However, undergraduate bioinformatics education has largely struggled to keep pa...
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Robust and accurate diagnosis of infectious skin diseases from histopathology images by integrating deep learning and explainable AI

bioRxiv Jan 1, 2025
Accurate diagnosis of infectious skin diseases remains a major challenge, particularly for neglected tropical diseases such as mycetoma, where precise pathogen identification is crucial for effective treatment. Histopathology imaging is the diagnosti...
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Slow Transition to Low-Dimensional Chaos in Heavy-Tailed Recurrent Neural Networks

bioRxiv Jan 1, 2025
Growing evidence suggests that synaptic weights in the brain follow heavy-tailed distributions, yet most theoretical analyses of recurrent neural networks (RNNs) assume Gaussian connectivity. We systematically study the activity of RNNs with random w...
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Hippocampal grey matter changes across scales in Alzheimer’s Disease

bioRxiv Jan 1, 2025
Alzheimer’s disease (AD) is a progressive and debilitating neurodegenerative disease of the central nervous system, characterized by deterioration in cognitive function including extensive memory impairment. The hippocampus, a medial temporal lobe re...
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Quantifying the impact of genetic mutations on enhancer dynamics

bioRxiv Jan 1, 2025
Transcriptional regulation is mediated by enhancers, yet how genetic perturbations alter enhancer activity and gene expression remains poorly understood. We developed UDI-UMI-STARR-seq, which integrates dual indexes and unique molecular identifiers, ...
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Ascending propriospinal modulation of thoracic sympathetic preganglionic neurons during lumbar locomotor activity

bioRxiv Jan 1, 2025
Although the autonomic sympathetic system is activated in parallel with locomotion, the underlying neural mechanisms mediating this coordination are not completely understood. Descending exercise or ‘central command’ signals from hypothalamic and bra...
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TRANCERs: Engineering enhancers into autonomous tissue-specific expression cassettes

bioRxiv Jan 1, 2025
The process by which a foreign gene is introduced into a cell and translated into a functional protein is referred to as transgene expression. Understanding and optimising transgene expression is crucial for a wide variety of applications which range...
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Fingerprint-Based Explainable Machine Learning for Predicting Blood–Brain Barrier Permeability

bioRxiv Jan 1, 2025
Predicting blood–brain barrier (BBB) permeability is essential for early central nervous system (CNS) drug discovery, yet reliable computational screening remains challenging. This study presents a gradient-boosted ensemble framework trained on preco...
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