AIMC Topic: Software
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Reliable protein-protein docking with AlphaFold, Rosetta, and replica exchange.
eLife
May 27, 2025
Despite the recent breakthrough of AlphaFold (AF) in the field of protein sequence-to-structure prediction, modeling protein interfaces and predicting protein complex structures remains challenging, especially when there is a significant conformation...
MultiOmicsAgent: Guided Extreme Gradient-Boosted Decision Trees-Based Approaches for Biomarker-Candidate Discovery in Multiomics Data.
Journal of proteome research
May 25, 2025
MultiOmicsAgent (MOAgent) is an innovative, Python-based open-source tool for biomarker discovery, utilizing machine learning techniques, specifically extreme gradient-boosted decision trees, to process multiomics data. With its cross-platform compat...
A standardized framework for robust fragmentomic feature extraction from cell-free DNA sequencing data.
Genome biology
May 23, 2025
Fragmentomics features of cell-free DNA represent promising non-invasive biomarkers for cancer diagnosis. A lack of systematic evaluation of biases in feature quantification hinders the adoption of such applications. We compare features derived from ...
RNAcare: integrating clinical data with transcriptomic evidence using rheumatoid arthritis as a case study.
BMC medical genomics
May 21, 2025
BACKGROUND: Gene expression analysis is a crucial tool for uncovering the biological mechanisms that underlie differences between patient subgroups, offering insights that can inform clinical decisions. However, despite its potential, gene expression...
CMImpute: cross-species and tissue imputation of species-level DNA methylation samples across mammalian species.
Genome biology
May 20, 2025
The large-scale application of the mammalian methylation array has substantially expanded the availability of DNA methylation data in mammalian species. However, this data captures only a small portion of species-tissue combinations. To address this,...
ADEPT: An advanced data exploration and processing tool for clinical data insights.
Computer methods and programs in biomedicine
May 17, 2025
BACKGROUND AND OBJECTIVE: The rapid growth of clinical data creates challenges in analysis and interpretation for medical professionals. To address these issues, we developed the Advanced Data Exploration and Processing Tool (ADEPT), integrating data...
Flexible imputation toolkit for electronic health records.
Scientific reports
May 17, 2025
Missing data in electronic health records (EHRs) poses a significant challenge for analysis. This study introduces Pympute, a comprehensive Python package designed for efficient and robust missing value imputation for EHRs. Pympute's core algorithm, ...
ConsensuSV-ONT - A modern method for accurate structural variant calling.
Scientific reports
May 17, 2025
Improvements in sequencing technology make the development of new tools for detection of structural variance more and more common. However, since the tools available for the long-read Oxford Nanopore sequencing are limited, and the selection of the o...
Deep learning-assisted analysis of single-particle tracking for automated correlation between diffusion and function.
Nature methods
May 8, 2025
Subcellular diffusion in living systems reflects cellular processes and interactions. Recent advances in optical microscopy allow the tracking of this nanoscale diffusion of individual objects with unprecedented precision. However, the agnostic and a...
AgeML: Age Modeling With Machine Learning.
IEEE journal of biomedical and health informatics
May 6, 2025
An approach to age modeling involves the supervised prediction of age using machine learning from subject features. The derived age metrics are used to study the relationship between healthy and pathological aging in multiple body systems, as well as...
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