bioRxiv

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Brain-like variability in convolutional neural networks reveals evidence-, uncertainty- and bias-driven decision-making

bioRxiv Jan 1, 2025
Even when stimuli and tasks are held constant, brain activity fluctuates markedly across trials, yet it is not well understood how these fluctuations affect decision-making and behavior. Here we address this gap in knowledge using a convolutional neu...
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GlycoEnzDB: A database of enzymes involved in human glycosylation

bioRxiv Jan 1, 2025
The glycan distribution on cells is governed by the stochastic activity of different families of enzymes that are together called ‘glycoEnzymes’. These include ~400 gene products or 2% of the proteome, that have recently been curated in an ontology c...
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Frequency-Aware Interpretable Deep Learning Framework for Alzheimer’s Disease Classification Using rs-fMRI

bioRxiv Jan 1, 2025
Gaining insight into the spectral and temporal alterations in brain connectivity associated with Alzheimer’s disease (AD) may offer pathways toward more informative biomarkers and a deeper understanding of disease mechanisms. We propose FINE (Frequen...
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Efficiently finding activity cliffs

bioRxiv Jan 1, 2025
Activity cliffs remain a key challenge in computational drug design, defying even modern machine learning approaches. Here, we present a dual approach that allows either navigating a structure-activity landscape to quickly identify activity cliffs, o...
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Identification and classification of ion-channels across the tree of life provide functional insights into understudied CALHM channels

bioRxiv Jan 1, 2025
The ion channel (IC) genes encoded in the human genome play fundamental roles in cellular functions and disease and are one of the largest classes of druggable proteins. However, limited knowledge of the diverse molecular and cellular functions carri...
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Intracellular acidification by bacteria-derived valeric acid is a mechanism of trans-kingdom ecology against Candida parapsilosis colonization

bioRxiv Jan 1, 2025
In hematopoietic cell transplant patients, intestinal Candida parapsilosis expansion and translocation cause life-threatening candidemia, yet how commensal intestinal bacteria prevent Candida expansion remains incompletely defined. Here, we trained a...
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JAX Animal Behavior System (JABS): A genetics informed, end-to-end advanced behavioral phenotyping platform for the laboratory mouse

bioRxiv Jan 1, 2025
Automated detection of complex animal behavior remains a challenge in neuroscience. Developments in computer vision have greatly advanced automated behavior detection and allow high-throughput preclinical and mechanistic studies. An integrated hardwa...
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CDCA7 facilitates MET1-mediated CG DNA methylation maintenance in centromeric heterochromatin via histone H1

bioRxiv Jan 1, 2025
DNA methylation is a conserved epigenetic modification essential for maintaining genome stability. However, how methyltransferases maintain CG methylation within compact chromatin, including centromeres, remains unclear. In humans, CDCA7 is necessary...
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Shared texture-like representations, not global form, underlie deep neural network alignment with human visual processing

bioRxiv Jan 1, 2025
Deep neural networks (DNNs) are a leading computational framework for understanding neural visual processing. A standard approach for evaluating their similarity to brain function uses DNN activations to predict human neural responses to the same ima...
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Predicting microbial community responses to disturbance using genome-resolved trait-based life-history strategies

bioRxiv Jan 1, 2025
Understanding how microbial communities respond to disturbance remains a fundamental question in ecology, with broad implications for biodiversity, ecosystem function, and biotechnology. Trait-based approaches offer general rules to predict community...
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