bioRxiv

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Multiplex design and discovery of proximity handles for programmable proteome editing

bioRxiv Jan 1, 2025
Although we now have a rich toolset for genome editing, an equivalent framework for manipulating the proteome with a comparable flexibility and specificity remains elusive. A promising strategy for “proteome editing” is to use bifunctional molecules ...
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D-LMBmapX: Generalised Deep Learning Pipeline for 5D Whole-brain Circuitry Profiling

bioRxiv Jan 1, 2025
Understanding whole-brain circuitry development is essential for uncovering the origins of disorders linked to abnormal neural wiring, yet progress has been limited by the lack of tools for accurate, comprehensive analysis. Brain development is highl...
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peleke-1: A Suite of Protein Language Models Fine-Tuned for Targeted Antibody Sequence Generation

bioRxiv Jan 1, 2025
The discovery of therapeutic antibodies is a traditionally arduous process. Today, the lab-based process of antibody discovery consists of several time-consuming steps that involve live animal immunization, B-cell harvesting, hybridoma creation, and ...
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Statistics of correlations in nonlinear recurrent neural networks

bioRxiv Jan 1, 2025
The statistics of correlations are central quantities characterizing the collective dynamics of recurrent neural networks. We derive exact expressions for the statistics of correlations of nonlinear recurrent networks in the limit of a large number N...
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CNValidatron: Accurate And Efficient Validation of PennCNV Calls Using Computer Vision

bioRxiv Jan 1, 2025
Large rare copy number variants (CNVs) are a main source of genetic variation in the genome and are important in both evolution and disease risk. CNVs can be detected using different data sources, including genome sequencing, genotyping arrays and qu...
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Evolutionary and geometric signatures reveal ligand-binding sites across proteomes

bioRxiv Jan 1, 2025
Identifying protein binding sites is central to drug discovery, yet many computational approaches still trade off precision, recall, or throughput when scaled. We introduce PickPocket, a deep learning model that fuses evolutionary information from pr...
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Dynamic and task-dependent decoding of the human attentional spotlight from MEG

bioRxiv Jan 1, 2025
Attention is a fundamental mechanism enabling the brain to overcome its limited capacity for parallel processing. In non-human primates, invasive electrophysiology has shown that attentional selection operates rhythmically, primarily within the alpha...
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Democratizing Protein Language Model Training, Sharing and Collaboration

bioRxiv Jan 1, 2025
Training and deploying large-scale protein language models typically requires deep machine learning expertise — a barrier for researchers outside this field. SaprotHub overcomes this challenge by offering an intuitive platform that facilitates traini...
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Mechanisms Driving Thoracic Aortic Aneurysm Stability

bioRxiv Jan 1, 2025
Thoracic aortic aneurysms (TAAs) arise from a combination of biological and mechanical factors. Current clinical guidelines use size and rate of expansion to stratify risk, but such metrics do not predict if an aneurysm will stabilize, grow, dissect,...
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Gradient-aware modeling advances AI-driven prediction of genetic perturbation effects

bioRxiv Jan 1, 2025
Predicting the transcriptional effects of genetic perturbations across diverse contexts is a central challenge in functional genomics. While single-cell perturbational assays such as Perturb-seq have generated valuable datasets, exhaustively profilin...
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