bioRxiv

Showing 4921 to 4930 of 5021 articles

Different data analysis models for detecting miRNAs using nanopores

bioRxiv Jan 1, 2025
Nanopore sensors generate complex ionic current traces that encode rich molecular information, making them well-suited for computational signal analysis. Building on previous work in which DNA-barcoded probes were developed for the multiplexed detect...
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Incorporating Large Language Model-Derived Information into Hypothesis Testing for Genomics

bioRxiv Jan 1, 2025
We propose strategies for incorporating the information in large language models (LLMs) into statistical hypothesis tests in genomics studies. Using gene embeddings derived from text inputs to OpenAI’s GPT-3.5 model, we show that biological signals i...
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Integrated Cross-Organ Transcriptomic Analysis Uncovers Conserved Gene Signatures Predictive of Allograft Rejection

bioRxiv Jan 1, 2025
Long-term transplant success is limited by allograft rejection, a complex process traditionally studied on an organ-specific basis. To establish a unified framework beyond organ-specific studies, we performed a network-based systems biology analysis ...
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Pervasive binding of the stem cell transcription factor SALL4 shapes the chromatin landscape

bioRxiv Jan 1, 2025
Mechanistic understanding of how gene activity is regulated has focussed on the roles of transcription factors at promoters and enhancers, whereas mechanisms capable of globally fine-tuning gene expression through dispersed binding across large genom...
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Individual and social contributions to learning of mice in Intellicages: the general framework and mean field theory

bioRxiv Jan 1, 2025
Reinforcement learning enables the adaptation of behaviors to changes in the environment. Models of reinforcement learning based on using previous experience to guide future choices enable balancing exploitation of opportunities and exploring the opt...
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Pro4S: prediction of protein solubility by fusing sequence, structure, and surface

bioRxiv Jan 1, 2025
Protein solubility is a critical physicochemical property influencing protein stability, therapeutic efficacy, and overall developability in drug discovery. However, traditional experimental methods for assessing solubility are often resource-intensi...
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Topological basal ganglia model with dopamine-modulated spike-timing-dependent plasticity reproduces reinforcement learning, discriminatory learning, and neuropsychiatric disorders

bioRxiv Jan 1, 2025
The basal ganglia (BG) are central to action selection and reinforcement learning, yet how the topological organization of the BG circuit with dopamine (DA) D1- and D2-receptors shape learning remains unclear. We present a topologically organized spi...
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Deep learning-driven characterization of single cell tuning in primate visual area V4 supports topological organization

bioRxiv Jan 1, 2025
Deciphering the brain’s structure-function relationship is key to understanding the neuronal mechanisms underlying perception and cognition. The cortical column, a vertical organization of neurons with similar functions, is a classic example of prima...
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Multiplex imaging combined to machine learning enable automated profiling of cortical malformations: applications in tuberous sclerosis complex

bioRxiv Jan 1, 2025
Malformations of cortical development such as tuberous sclerosis complex arise within a heterogeneous cellular landscape that conventional histopathology only partially resolves. Here, we combined a 19-marker multiplex immunofluorescence panel with a...
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Machine learning informs mitigation strategies for nitrous oxide emissions from wastewater operations

bioRxiv Jan 1, 2025
This study focused on the development of machine-learning- (ML) based strategies for mitigating nitrous oxide (N2O) emissions from various wastewater treatment systems in the United States measured using a benchmark USEPA-endorsed protocol. Results r...
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