bioRxiv

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Chromatin and gene-regulatory dynamics of human pulmogenesis by single cell multiomic sequencing

bioRxiv Jan 1, 2025
Human lung development is governed by complex gene regulatory networks that orchestrate cellular differentiation and organogenesis. We present a single cell multiomic atlas of human pulmogenesis, simultaneously capturing both the chromatin accessibil...
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Virtual Brain Inference (VBI): A flexible and integrative toolkit for efficient probabilistic inference on virtual brain models

bioRxiv Jan 1, 2025
Network neuroscience has proven essential for understanding the principles and mechanisms underlying complex brain (dys)function and cognition. In this context, whole-brain network modeling–also known as virtual brain modeling–combines computational ...
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Passive Acoustic Monitoring within the Northwest Forest Plan Area: 2023 Annual Report

bioRxiv Jan 1, 2025
Here we document progress in implementing large-scale passive acoustic monitoring across the Northwest Forest Plan area to track population trends of northern spotted owls (Strix occidentalis caurina), barred owls (S. varia), marbled murrelets (Brach...
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Comparative Machine Learning Analysis of Saliva and Plaque Microbiomes in Children with Type 1 Diabetes

bioRxiv Jan 1, 2025
Type 1 diabetes (T1D) is associated with microbial dysbiosis. While most research has focused on the gut microbiome, limited data address the role of the oral microbiome in T1D. The oral and gut microbiomes overlap substantially, and the oral cavity ...
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Fourier transform infrared spectroscopy enables rapid species discrimination across Malassezia and strain-level typing in M. pachydermatis

bioRxiv Jan 1, 2025
Malassezia pachydermatis is a zoophilic yeast found on the skin and in the outer ear canal of many mammals. It normally maintains a commensal lifestyle but can cause dermatitis and otitis in predisposed hosts, particularly in atopic dogs. M. pachyder...
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Prediction of TdP Arrhythmia Risk Through Molecular Simulations of Conformation-specific Drug Interactions with the hERG K+, NaV1.5, and CaV1.2 Channels

bioRxiv Jan 1, 2025
Unintended block of cardiac ion channels, particularly hERG (KV11.1), remains a key concern in drug development as disruption of ion channel function can lead to deadly arrhythmia. To assess proarrhythmic risk, we investigated how drugs interact with...
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Bridging Evolution and Design: Mapping the Diversity of LOV Photosensors

bioRxiv Jan 1, 2025
Light-sensitive proteins allow organisms to perceive and respond to their environment, and have diversified over billions of years. Among these, Light–Oxygen–Voltage (LOV) domains are widely distributed photosensors that control diverse physiological...
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Large-language-model-based antibiotic resistance gene prediction and resistomes mining in cyanobacterial blooms

bioRxiv Jan 1, 2025
The rapid spread of antibiotic resistance genes (ARGs) in aquatic ecosystems poses a serious public health threat. Conventional ARG detection methods, including sequence-alignment and machine learning, are limited by high false-negative or false-posi...
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Deep Learning-Based Segmentation of 2D Projection-Derived Overlapping Prospore Membrane in Yeast

bioRxiv Jan 1, 2025
Quantitative morphological analysis is crucial for understanding cellular processes. While 3D Z-stack imaging offers high-resolution data, the complexity of 3D structures makes direct interpretation and manual annotation challenging and time-consumin...
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Flippable Siamese Differential Neural Network for Differential Graph Inference

bioRxiv Jan 1, 2025
Differential graph inference is a critical analytical technique that enables researchers to accurately identify the variables and their interactions that change under different conditions. By comparing two conditions, researchers can gain a deeper un...
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