bioRxiv

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Non-destructive label-free automated identification of bacterial colonies at the species level directly on agar media using digital holography and convolutional neural network algorithms

bioRxiv Jan 1, 2025
this study aimed to develop a fully automated, non-destructive and label-free identification method of bacterial colonies, directly on agar plates, using a combination of digital holography and artificial intelligence and to evaluate its performances...
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KeySDL: Sparse Dictionary Learning for Keystone Microbe Identification

bioRxiv Jan 1, 2025
Identification of microbes with large impacts on their microbial communities, known as keystone microbes, is a topic of long-standing interest in microbiome research. However, many approaches to identify keystone microbes are limited by the inherent ...
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Out-of-the-box bioinformatics capabilities of large language models (LLMs)

bioRxiv Jan 1, 2025
Large Language Models (LLMs), AI agents and co-scientists promise to accelerate scientific discovery across fields ranging from chemistry to biology. Bioinformatics- the analysis of DNA, RNA and protein sequences plays a crucial role in biological re...
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Deep learning-based joint sequence–structure de novo membrane protein design

bioRxiv Jan 1, 2025
Deep learning has revolutionized soluble protein design, yet de novo transmembrane (TM) protein engineering remains hindered by scarce structural data, complex membrane-specific interactions and conformational dynamics. We developed TMDiffusion (TMDF...
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Independence and Coherence in Temporal Sequence Computation across the Fronto-Parietal Network

bioRxiv Jan 1, 2025
Time processing requires distributed and coordinated cortical dynamics. Flexible yet robust temporal representations can arise from two distinct computational modes: a coherence mode, where multiple cortical areas hold the same elapsed-time estimate,...
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WITHDRAWN: Using Machine Learning to Improve Cancer Diagnosis Accuracy Through Genetic Data Analysis

bioRxiv Jan 1, 2025
The authors have withdrawn this manuscript because : 1-After careful consideration, my co-authors and I have decided to pursue significant revisions that fundamentally change the scope of the study. 2-Due to unforeseen circumstances, we are unable t...
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“Frustratingly easy” domain adaptation for cross-species transcription factor binding prediction

bioRxiv Jan 1, 2025
Understanding how DNA sequence encodes gene regulation remains a central challenge in genomics. While deep learning models can predict regulatory activity from sequence with high accuracy, their generalizability across species—and thus their ability ...
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BioTransformer4.0 a comprehensive computational tool for small molecule metabolism prediction

bioRxiv Jan 1, 2025
BioTransformer 4.0, the successor to BioTransformer 3.0, is a freely available in silico metabolism prediction tool. It integrates both knowledgebased and machine learning approaches to predict metabolites for small molecules using one of seven modul...
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Mapping antigenic evolution of influenza A virus using deep learning-based prediction of hemagglutination inhibition titers

bioRxiv Jan 1, 2025
Seasonal influenza remains a significant public health challenge through unpredictable antigenic drift, where accumulated mutations enable immune evasion and necessitate vaccine updates. Comprehensive antigenic characterization has been hindered by t...
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Photoacoustics-guided Real-Time Closed-loop Control of Magnetic Microrobots through Deep Learning

bioRxiv Jan 1, 2025
Medical microrobots promise to increase the efficacy and reduce the invasiveness of certain medical procedures in the future. Real-time tracking of the microrobot, actuation, and closed-loop control of its position under in vivo conditions is crucial...
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