bioRxiv

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Claustrum volume in humans – lifespan trajectory and effect of age, hemisphere, and sex

bioRxiv Jan 1, 2025
The human claustrum is a bilateral, thin, irregularly shaped gray matter structure located between the striatum and insula. While previous research demonstrated the effect of distinct medical conditions, such as prematurity, schizophrenia, and Alzhei...
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Generation of a global freshwater algal taxonomic database by application of PCR-free rbcL gene detection and machine-learning-based taxonomic classification to public metagenome datasets

bioRxiv Jan 1, 2025
While it has become increasingly evident that microalgae are critical components of aquatic ecosystems, comprehensive taxonomic analysis of the microalgal component of microbial communities has lagged behind recent innovations in prokaryotic sequenci...
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Combinatorial factorizable libraries outperform enumerated and random libraries for antibody discovery

bioRxiv Jan 1, 2025
The effective use of high-throughput functional assays to discover novel biological therapeutics requires a diverse library of desirable candidates. Here we design candidate antibody libraries using factorizable neural networks (FNNs) that permit the...
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CryoPhold: CryoEM meets AlphaFold and molecular simulation to reveal protein dynamics

bioRxiv Jan 1, 2025
Here we are introducing CryoPhold, a modular workflow that unifies AlphaFold-based ensemble generation, Bayesian reweighting against experimental cryo-EM maps, molecular simulation, and machine learning to quantify conformational populations and iden...
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PLiCat: Decoding protein-lipid interactions by large language model

bioRxiv Jan 1, 2025
Protein-lipid interactions are essential for many cellular processes, as proteins associate with diverse lipid molecules to exert distinct functions. However, existing approaches are limited in discriminating among lipid categories in these interacti...
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SPAGHETTI leverages massive H&E morphological models for phase contrast microscopy images with a generative deep learning approach

bioRxiv Jan 1, 2025
Phase contrast microscopy (PCM) is a powerful cell imaging method, one of the few technologies to delineate and track cell structure in live cells without staining. Despite PCM’s great potential and popularity in monitoring live-cell populations, the...
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Flexible navigation with neuromodulated cognitive maps

bioRxiv Jan 1, 2025
Animals develop specialized cognitive maps during navigation, constructing environmental representations that facilitate efficient exploration and goal-directed planning. The hippocampal CA1 region is implicated as the primary neural substrate for co...
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Sampling Protein Language Models for Functional Protein Design

bioRxiv Jan 1, 2025
Protein language models have emerged as powerful tools for learning rich protein representations, improving performance in tasks like structure prediction, mutation effect estimation, and homology detection. Their ability to model complex sequence di...
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DLC2Action: A Deep Learning-based Toolbox for Automated Behavior Segmentation

bioRxiv Jan 1, 2025
While expert biologists can annotate complex behaviors from video data, the process remains tedious and time-consuming, creating a bottleneck for efficient behavioral analysis. Here, we present DLC2Action, an open-source Python toolbox that enables a...
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Edit Distance Embedding with Genomic Large Language Model

bioRxiv Jan 1, 2025
Edit distance is a fundamental metric in genomic sequence analysis, yet it is computationally expensive to calculate. A practical approach for large-scale sequence analysis involves mapping sequences into a normed space and approximating the edit dis...
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