bioRxiv

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The olfactory bulb reflects structural plasticity within a genetically stable olfactory network

bioRxiv Jan 1, 2025
The olfactory bulb (OB), the first central relay of the olfactory pathway, plays a critical role in odor perception and exhibits remarkable structural plasticity shaped by environmental influences. This raises a fundamental question about the extent ...
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Enhancing Missense Variant Classification in Predicted Intrinsically Disordered Regions

bioRxiv Jan 1, 2025
The accurate classification of missense variants is a fundamental challenge in genomics, particularly for those within intrinsically disordered regions (IDRs) where the performance of existing computational predictors is suboptimal. To address this, ...
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ViralQuest: A user-friendly interactive pipeline for viral-sequences analysis and curation

bioRxiv Jan 1, 2025
High-throughput sequencing (HTS) has become an essential, unbiased tool in virology for identifying known and novel viruses. However, analyzing the large and complex datasets generated by HTS presents significant bioinformatics challenges. The proces...
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NucEL: Single-Nucleotide ELECTRA-Style Genomic Pre-training for Efficient and Interpretable Representations

bioRxiv Jan 1, 2025
Pre-training large language models on genomic sequences has become a powerful approach for learning biologically meaningful representations. While masked language modeling (MLM)-based approaches, such as DNABERT and Nucleotide Transformer (NT), achie...
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Developing inhibitors of the guanosine triphosphate hydrolysis accelerating activity of Regulator of G protein Signaling-14

bioRxiv Jan 1, 2025
Regulator of G protein Signaling-14 (RGS14), an intracellular inactivator of G protein-coupled receptor (GPCR) signaling, is considered an undruggable protein given its shallow and relatively featureless protein-protein interaction interface combined...
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A contextualised protein language model reveals the functional syntax of bacterial evolution

bioRxiv Jan 1, 2025
Bacteria have evolved a vast diversity of functions and behaviours which are currently incompletely understood and poorly predicted from DNA sequence alone. To understand the syntax of bacterial evolution and discover genome-to-phenotype relationship...
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Design of Orthogonal Far-Red, Orange and Green Fluorophore-binding Proteins for Multiplex Imaging

bioRxiv Jan 1, 2025
Fluorescent proteins have transformed biological imaging, yet their limited photostability and brightness restrict their applications. We used deep learning-based de novo protein design methods to design binders to three bright, stable and cell-perme...
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Advancing Luciferase Activity and Stability beyond Directed Evolution and Rational Design through Expert Guided Deep Learning

bioRxiv Jan 1, 2025
Engineered luciferases have transformed biological imaging and sensing, yet optimizing NanoLuc luciferase (NLuc) remains challenging due to the inherent stability-activity trade-off and its limited sequence homology with characterized proteins. We re...
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Improving RNA Secondary Structure Prediction Through Expanded Training Data

bioRxiv Jan 1, 2025
In recent years, deep learning has revolutionized protein structure prediction, achieving remarkable speed and accuracy. RNA structure prediction, however, has lagged behind. Although several methods have shown some success in predicting RNA secondar...
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Protein folding stability estimation with explicit consideration of unfolded states

bioRxiv Jan 1, 2025
Folding stability is a critical requirement for the vast majority of proteins. Computational methods suggested to date for the absolute folding stability (ΔG) prediction – including those driven from protein structure prediction AIs – show clear limi...
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