bioRxiv

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Retrieval Augmented Protein Language Models for Protein Structure Prediction

bioRxiv Jan 1, 2025
The advent of advanced artificial intelligence technology has significantly accelerated progress in protein structure prediction, with AlphaFold2 setting a new benchmark for prediction accuracy by leveraging the Evoformer module to automatically extr...
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tangermeme: A toolkit for understanding cis-regulatory logic using deep learning models

bioRxiv Jan 1, 2025
Deep learning models have achieved state-of-the-art performance at predicting diverse genomic modalities, yet their promise for biological discovery lies in how they are used after demonstrating their predictive performance. Here, we describe the fun...
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Comparing Robotic and Computer Vision Assessments of Unilateral and Bilateral Reaching in Healthy Adults

bioRxiv Jan 1, 2025
Assessment of reaching is foundational to upper limb neurorehabilitation. Current neurorehabilitation needs have increased the demand for quantitative clinical assessments of bilateral coordination. Robotics and computer vision for motion tracking ar...
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Adjudicating competing theories of semantic representation with 7T-fMRI and multivariate decoding

bioRxiv Jan 1, 2025
Theories of semantic representation in the brain are numerous and contradictory and are supported by an equally contradictory literature of multivariate neuroimaging studies. Equipped with two pioneering tools – (1) a 7T-fMRI acquisition sequence cap...
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Integrative Analysis of the Mouse Cecal Microbiome Across Diet, Age, and Metabolic State in the Diverse BXD Population

bioRxiv Jan 1, 2025
The gut microbiota both adapts to, and shapes, the host’s metabolic state through metabolites and gene regulatory networks, influencing multiple organs via axes such as the gut–liver connection. While diet, age, and host genetics each modulate gut mi...
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Bursts of regional cortical inhibition during smartphone use

bioRxiv Jan 1, 2025
Transient burst of beta (β) oscillations – brief neural events lasting only a fraction of a second – are increasingly recognised for their role in functional inhibition that may support cognitive processes and motor timing underlying goal-directed be...
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Accessible and Robust Machine Learning Approaches to Improve the Opsin Genotype-Phenotype Map

bioRxiv Jan 1, 2025
Predicting phenotypes from genetic variation is a central challenge in biology. Linking genotypes and phenotypes using machine learning (ML) offers great promise, but its use is limited by poor accessibility, overestimated performance, and a “data-cl...
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stFormer: a foundation model for spatial transcriptomics

bioRxiv Jan 1, 2025
Recent foundation models for single-cell transcriptomics data generate informative, context-aware representations for genes and cells. The Spatial Transcriptomics (ST) data offer extra positional insights, which were not considered by these single-ce...
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From sequence to scaffold: computational design of protein nanoparticle vaccines from AlphaFold2-predicted building blocks

bioRxiv Jan 1, 2025
Self-assembling protein nanoparticles are being increasingly utilized in the design of next-generation vaccines due to their ability to induce antibody responses of superior magnitude, breadth, and durability. Computational protein design offers a ro...
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Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics

bioRxiv Jan 1, 2025
Data-independent acquisition (DIA)-based mass spectrometry is becoming an increasingly popular mass spectrometry acquisition strategy for carrying out quantitative proteomics experiments. Most of the popular DIA search engines make use of in silico g...
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