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Biology subjects

Patrick, M. T.

Publications and source records attributed to Patrick, M. T..

2 recordsLinked to original sources

Accelerating Insight Discovery in Large Biomedical Text with Scalable Processing Framework

Large language models are increasingly being used by dermatology professionals to support diagnostic investigation, patient education, and medical research. While these models can help manage information overload and improve efficiency, concerns persist regarding their accuracy and potential reliance on dubious sources. We introduce Quanta, a hybrid system that combines large language models with established evaluation metrics, such as cosine similarity, to enable efficient summarization and interpretation of curated research corpora. This methodology ensures that synthesized insights remain domain-specific and contextually relevant, thereby supporting clinicians and researchers in navigating the expanding digital landscape of dermatology literature. Deployed within an interactive chatbot, the tool delivers direct answers to user queries, provides cross-publication insights, and can suggest new directions for research. Comparative evaluations on benchmark datasets demonstrate improvements in accuracy, efficiency, and computational cost, with the curated document approach enhancing reliability and reducing misinformation risk.

bioinformatics↗

Loopsim: Enrichment Analysis of ChromosomeConformation Capture with Fast EmpiricalDistribution Simulation

SummaryGene regulation is intricately influenced by the three-dimensional organization of the genome. In particular, chromatin can exist in loop structures that enable long-range regulatory interactions. By utilizing chromosome conformation capture techniques such as Hi-C, valuable information regarding the organization of these loop structures in 3D space can be obtained. While functional/feature enrichment has become a standard downstream analysis for different genomic data to provide biological context, tools that developed specifically for high throughput assays capturing chromosome conformation are relatively limited. Here, we present Loopsim, a command-line application that performs enrichment analysis on Hi-C loop profiles against user-defined regions. Loopsim efficiently simulates a background distribution using a distinctive sampling approach that considers loop size, intervals, loop-loop distances, and structure; it then computes loop-level statistics based on the empirical null distribution. AvailabilityLoopsim is a Python package available via PyPI (https://pypi.org/project/loopsim) and the source code is available on GitHub (https://github.com/CutaneousBioinf/Loopsim) under the MIT license.

bioinformatics↗