bioRxiv

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Designing proteins with reduced T-cell epitopes through policy optimization

bioRxiv Jan 1, 2025
Deep generative models for protein structure and sequence are increasingly used to design proteins with therapeutic and industrial applications, but the clinical success of designed therapeutics ultimately depends on their compatibility with the huma...
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Methane Cycling Microbes are Important Predictors of Methylmercury Accumulation in Rice Paddies

bioRxiv Jan 1, 2025
Microbial production of methylmercury from inorganic mercury in rice paddies poses health risks to consumers of this essential dietary staple. Although mercury-methylating communities are well characterized, the microbial guilds contributing to methy...
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Protein Language Models are Accidental Taxonomists

bioRxiv Jan 1, 2025
Protein-protein interactions (PPIs) are fundamental to nearly all biological processes, yet their experimental characterization remains costly and time-consuming. While computational methods, particularly those using protein language models (pLMs), o...
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Benchmarking Perturbation Tools for the Noncoding Genome

bioRxiv Jan 1, 2025
Deciphering the functionality of the noncoding genome which includes important cis-regulatory elements (CREs) and transcribed noncoding RNA genes remains technically challenging. Here, using massively parallel genetic screening, we systematically ben...
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RNAcomp2D: a visual tool to compare multiple predictions of RNA secondary structure

bioRxiv Jan 1, 2025
Ribonucleic acids (RNAs) are involved in many important biological processes. In particular, non-coding RNAs are crucial regulators of cellular processes, playing a significant role in gene expression. RNA secondary structure is key to infer their sp...
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The Impact of Stability Considerations on Genetic Fine-mapping

bioRxiv Jan 1, 2025
Fine-mapping methods, which aim to identify genetic variants responsible for complex traits following genetic association studies, typically assume that sufficient adjustments for confounding within the association study cohort have been made, e.g., ...
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Data Heterogeneity Limits the Scaling Effect of Pretraining Neural Data Transformers

bioRxiv Jan 1, 2025
A key challenge in analyzing neuroscience datasets is the profound variability they exhibit across sessions, animals, and data modalities–i.e., heterogeneity. Several recent studies have demonstrated performance gains from pretraining neural foundati...
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Multivariate analysis of glycogenes reveals coordinated regulation of immunoglobulin glycosylation in an immortalized human B cell system

bioRxiv Jan 1, 2025
While neutralizing ability has traditionally been considered the most important antibody function, appreciation has grown for Fc-mediated ‘extra-neutralizing’ functions, which are shaped by IgG glycosylation. However, there remain fundamental questio...
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Learning the Language of Phylogeny with MSA Transformer

bioRxiv Jan 1, 2025
Classical phylogenetics assumes site independence, potentially overlooking epistasis. Protein language models capture dependencies in conserved structural and functional domains across the protein universe. Here, we ask whether MSA Transformer, which...
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Histology and spatial transcriptomic integration revealed infiltration zone with specific cell composition as a prognostic hotspot in glioblastoma

bioRxiv Jan 1, 2025
Glioblastoma (GBM), the most aggressive primary brain tumor, has a median survival of approximately 15 months. Twenty percent of patients survive beyond three years, but known clinical factors like age, performance status, resection extent, and MGMT ...
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