bioRxiv

Showing 4741 to 4750 of 5021 articles

Enhanced sampling of protein conformations in AlphaFold3 with repulsive bias in the diffusion generative model

bioRxiv Jan 1, 2025
Conformational changes in proteins are vital to their function yet remain challenging for state-of-the-art artificial intelligence, such as AlphaFold3 (AF3), to predict. It has been observed that AF3 sometimes fails to capture ligand-induced conforma...
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Programmatic design and editing of cis-regulatory elements

bioRxiv Jan 1, 2025
The development of modern genome editing and DNA synthesis has enabled researchers to edit DNA sequences with high precision but has left unsolved the problem of designing these edits. We introduce Ledidi, a computational method that rephrases the di...
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Machine Learning-Augmented Analysis of Nano-electrochemical Sensor Data for Predictive and Quantitative Assays of Complex Biological Samples

bioRxiv Jan 1, 2025
Analytical chemistry provides the content of nearly every scientific, technical and business decision relating to what atoms, molecules and devices are and how they interact in their environment. Various workflows come together in describing those in...
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Spatially distinct chromatin compaction states predict neoadjuvant chemotherapy resistance in Triple Negative Breast Cancer

bioRxiv Jan 1, 2025
Organisation and dynamics of chromatin play a key role in regulation of cell state and function. In cancer, chromatin plasticity is known to be important in control of drug resistance, but the relationship between chromatin compaction and chemotherap...
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Genomic foundation models reveal RNA-binding proteins regulating translation and mRNA degradation during Drosophila development

bioRxiv Jan 1, 2025
The regulation of mRNA decay and translation is crucial for cellular function and development; however, the complex interplay of RNA-binding proteins (RBPs) regulating these processes remains incompletely understood. Recent advances in genomic founda...
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Cross-species etiologically informed stratification enables T cell receptor-based diagnosis of Parkinson’s Disease

bioRxiv Jan 1, 2025
Developing peripheral blood-based diagnostic models for idiopathic Parkinson’s disease (iPD), particularly those leveraging the T-cell receptor (TCR) repertoire, has long been considered infeasible because patient-derived TCRs appear to lack converge...
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An Explainable Knowledge Graph-Driven Approach to Decipher the Link Between Brain Disorders and the Gut Microbiome

bioRxiv Jan 1, 2025
The communication between the gut microbiome and the brain, known as the microbiome-gut-brain axis (MGBA), is emerging as a critical factor in neurological and psychiatric disorders. This communication involves complex pathways including neural, horm...
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Grid to Place Cell Connectivity in Eleven Different Rooms

bioRxiv Jan 1, 2025
To understand the grid to place cell connectivity, we took place cell firing data from the Moser lab. The data included single cell recordings from 342 CA3 neurons in 8 animals in 11 different rooms. Of these 342 cells, only 2 fired in all the 11 roo...
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Automated Seizure Detection in Animal EEG Signals

bioRxiv Jan 1, 2025
Automated seizure detection in animal electroencephalography (EEG) is crucial for accelerating epilepsy research. While machine learning (ML) and deep learning (DL) techniques have shown promise in seizure detection for human EEG and some rodent mode...
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MELO-ED: learning locality-sensitive multi-embeddings for edit distance

bioRxiv Jan 1, 2025
Edit distance is a fundamental metric for quantifying similarity between biological sequences, but its high computational cost limits large-scale applications. Previously, we proposed learned locality-sensitive bucketing (LSB) functions that achieved...
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