bioRxiv

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Cumulative microscopy reveals cellular states in fibroblasts from patients with genetic disorders

bioRxiv Jan 1, 2025
Analysis of cellular states and signaling trajectories can provide insights into causes of disease. We developed cumulative microscopy, a method to perform cyclical imaging without elution or quenching steps. Cumulative microscopy computationally ext...
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Modeling differences in neurodevelopmental maturity of the reading network using support vector regression on functional connectivity data

bioRxiv Jan 1, 2025
The construction of growth charts trained to predict age or developmental deviation (the ‘brain-age index’) based on structural/functional properties of the brain may be informative of children’s neurodevelopmental trajectories. When applied to both ...
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ICEPIC: A Toolkit to Discover Ice Binding Proteins from Sequence

bioRxiv Jan 1, 2025
Ice binding proteins, such as antifreeze proteins (AFPs) and ice nucleation proteins (INPs), are critical for survival in subzero environments and have wide-ranging applications in biotechnology, agriculture, and materials science. Current discovery ...
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BioScientist Agent: Designing LLM-Biomedical Agents with KG-Augmented RL Reasoning Modules for Drug Repurposing and Mechanistic of Action Elucidation

bioRxiv Jan 1, 2025
Drug discovery is protracted, resource-intensive, and afflicted by attrition rates exceeding 90 %, which leaves most diseases, particularly rare or neglected indications, without effective therapies. Drug repurposing offers a cost effective alternati...
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Uncovering Developmental Lineages from Single-cell Data with Contrastive Poincaré Maps

bioRxiv Jan 1, 2025
Single-cell RNA-sequencing (scRNA-seq) enables the study of hierarchical and branching patterns in organismic development at high resolution. Analyzing such data requires visualization and analysis tools that faithfully represent the deep, tree-like ...
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Social Decision Preferences for Close Others are Embedded in Neural and Linguistic Representations

bioRxiv Jan 1, 2025
Humans frequently make decisions that impact close others. Prior research has shown that people have stable preferences regarding such decisions and maintain rich, nuanced mental representations of their close social partners. Yet, if and how such me...
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Inferences from epigenetic information in an ecological context: a case study of early-life environmental effects on DNA methylation in zebra finches

bioRxiv Jan 1, 2025
DNA methylation (DNAm) plays a key role in mediating phenotypic responses to environmental variation. Various approaches exist to link DNAm variation to phenotypes, ranging from single nucleotide resolution to the development of composite indexes. We...
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Reading specific memories from human neurons before and after sleep

bioRxiv Jan 1, 2025
The ability to retrieve a single episode encountered just once is a hallmark of human intelligence and episodic memory[1]. Yet, decoding a specific memory from neuronal activity in the human brain remains a formidable challenge. Here, we develop a tr...
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Machine Learning–Guided Structure–Activity Discovery of Polymer Configurations in Lipid Nanoparticles for Kiss-and-Run Endosomal Escape

bioRxiv Jan 1, 2025
Endosomal escape remains a major barrier to effective nucleic acid delivery via lipid nanoparticles (LNPs). Here, we address this challenge by incorporating a pH-sensitive polymer, polyhistidine, into LNPs (pLNPs) to facilitate endosomal escape, with...
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Antibody immunogenicity prediction and optimization with ImmunoSeq

bioRxiv Jan 1, 2025
Therapeutic antibody development faces persistent immunogenicity challenges from anti-drug antibodies (ADA). Identifying peptide fragments presented by major histocompatibility complex is the central challenge in predicting immunogenicity. Here, we p...
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