bioRxiv

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A high-throughput platform for biophysical antibody developability assessment to enable AI/ML model training

bioRxiv Jan 1, 2025
Antibodies must bind their targets with high affinity and specificity to achieve useful therapeutic activity. They must also possess suitable developability properties (e.g., thermostability, solubility, viscosity, polyreactivity) to ensure favorable...
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Characterizing spatial functional microniches with SpaceTravLR

bioRxiv Jan 1, 2025
The advent of spatial omics has revolutionized our understanding of tissue biology; however, these technologies remain largely descriptive and do not capture how changes in gene regulation propagate across spatial neighborhoods. While in-silico pertu...
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Automatic measurement of temporalis muscle thickness from CT head scans using deep learning

bioRxiv Jan 1, 2025
To construct and validate a deep-learning (DL) model for the automatic quantification of temporalis muscle thickness (TMT) in CT head scans. We developed and evaluated the performance of a DL-based method for the measurement of temporalis muscle thic...
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RNA–X: Modeling RNA interactions to design binder RNA and simultaneously target multiple molecules of different types

bioRxiv Jan 1, 2025
RNA interactions with proteins, other RNA molecules, and DNA play essential roles in numerous cellular processes and underpin a wide range of therapeutic mechanisms. Consequently, modeling these interactions is critical for understanding biological s...
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Bridging Language Markers and Pathology: Correlations Between Digital Speech Measures and Surrogate CSF Biomarkers in Alzheimer’s Disease

bioRxiv Jan 1, 2025
Digital language markers show promise in detecting early cognitive impairment related to Alzheimer’s disease (AD), yet their relationship with cerebrospinal fluid (CSF) biomarkers of AD pathology remains unclear mainly due to the lack of data with bo...
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Cognitive and brain function enhancement in Gen X group after personalized, AI supervised EEG-neurofeedback training

bioRxiv Jan 1, 2025
Interventions supporting medical care and enhancing quality of life in neurodegenerative or age-related cognitive decline are strongly needed. Electroencephalographic (EEG) neurofeedback can enable users to modulate their brain activity through real-...
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Stable Somatotopy in Chronic Low Back Pain: Is Cortical Map Reorganization a Myth?

bioRxiv Jan 1, 2025
Chronic low back pain (CLBP) has been linked to maladaptive cortical plasticity in sensorimotor regions, which may contribute to pain persistence through less distinct (“smudged”) somatotopic maps of afferent input from the back. However, empirical s...
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Fix or Freeze? Spectral Differences Arising from Tissue Preparation in Chemical Imaging

bioRxiv Jan 1, 2025
Spectrochemical imaging has emerged as a powerful, label-free modality for visualizing the bio-chemical composition of tissues based on intrinsic vibrational signatures. Specifically, mid-infrared spectrochemical imaging (MIRSI) is becoming essential...
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Squidly: Enzyme Catalytic Residue Prediction Harnessing a Biology-Informed Contrastive Learning Framework

bioRxiv Jan 1, 2025
Enzymes present a sustainable alternative to traditional chemical industries, drug synthesis, and bioremediation applications. Because catalytic residues are the key amino acids that drive enzyme function, their accurate prediction facilitates enzyme...
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From bench assays to bedside: a context-embedding transformer predicts monoclonal antibody viscosity, clearance, and regulatory success

bioRxiv Jan 1, 2025
Late-stage failures of monoclonal antibody (mAb) programs often reflect developability liabilities, including high-concentration viscosity and rapid clearance, that standard early screens only partially capture. We introduce ACeT, an attention-based ...
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