bioRxiv

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Multiplex mapping of protein-protein interaction interfaces

bioRxiv Jan 1, 2025
We describe peptide mapping through Split Antibiotic Resistance Complementation (SpARC-map), a method to identify the probable interface between two interacting proteins. Our method is based on in vivo affinity selection inside a bacterial host, and ...
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A General Transformer-Based Multi-Task Learning Framework for Predicting Interaction Types between Enzyme and Small Molecule

bioRxiv Jan 1, 2025
Predicting enzyme–small molecule interactions is critical for drug discovery and generally understanding the biochemical processes of life. While recent deep learning approaches have shown promising results, several challenges remain: the lack of a c...
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A universal model for drug-receptor interactions

bioRxiv Jan 1, 2025
The modern AI models promise decoding of the genomic landscape that holds, in principle, the information required for rational therapeutic design. Genes encode proteins whose functions are mediated by their three-dimensional structures via bonded and...
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Temperature is the key weather determinant of Aedes albopictus seasonal activity in southern France

bioRxiv Jan 1, 2025
The presence and the activity of Aedes albopictus are a growing concern for nuisance and public health in Europe. Vector control operators, public health officers, and communities look for weather-based decision support systems to inform mosquito man...
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A blueprint for mutation-defined hallmark vulnerabilities across human cancers

bioRxiv Jan 1, 2025
Hallmark gene mutations shape cancer cell vulnerabilities and inform drug discovery1–3. A systematic map of hallmark gene mutation-defined cancer dependencies and therapeutic responses is essential to uncover novel targets and refine therapeutic stra...
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Theta and gamma transcranial alternating current stimulation modulate Mandarin consonant and lexical tone perception

bioRxiv Jan 1, 2025
A theta/gamma oscillatory neural mechanism has been postulated to explain the auditory sampling of hierarchical syllable-phoneme structure with corresponding speech rates or linguistic hierarchies (theta for syllable and gamma for phoneme). Yet, whet...
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Computer Vision Methods for Spatial Transcriptomics: A Survey

bioRxiv Jan 1, 2025
Spatial transcriptomics (ST) enables the simultaneous measurement of gene expression and spatial localization within tissue sections, providing unprecedented opportunities to dissect tissue architecture and functional organization. As a relatively ne...
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DNACSE: Enhancing Genomic LLMs with Contrastive Learning for DNA Barcode Identification †

bioRxiv Jan 1, 2025
DNA barcoding is a powerful tool for exploring biodiversity, and DNA language models have significantly facilitated its construction and identification. However, since DNA barcodes come from a specific region of mitochondrial DNA and there are struct...
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Hybrid deep learning–mechanistic modeling of cellular dynamics from a spatiotemporal single-cell atlas

bioRxiv Jan 1, 2025
Single-cell measurement technologies provide a powerful framework for studying cellular heterogeneity, transitions, and regulatory networks, yet reconstructing the underlying dynamical processes governing these transitions remains a major challenge d...
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Deep learning models reading clinical data and liver omics strongly distinguish NASH from steatosis and suggest new genes involved in liver disease severity

bioRxiv Jan 1, 2025
Metabolic dysfunction-associated steatotic liver disease (MASLD, previously NAFLD) is a frequent co-morbidity of obesity and diabetes, with prevalence increasing worldwide in all age groups and both sexes. Only early stages of the disease are fully r...
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