Cutting edge deep-learning based tools for metagenomic research

EL Karin, M Steinegger - National Science Review, 2025 - academic.oup.com
Recent years have seen incredible progress in the development of deep-learning (DL) tools
for the analysis of biological data, with the most prominent example being AlphaFold2 for …

Deep learning in microbiome analysis: a comprehensive review of neural network models

P Przymus, K Rykaczewski, A Martín-Segura… - Frontiers in …, 2025 - frontiersin.org
Microbiome research, the study of microbial communities in diverse environments, has seen
significant advances due to the integration of deep learning (DL) methods. These …

[HTML][HTML] BIOFILM DAIRY FOODS REVIEW: Microbial Community Tracking from Dairy Farm to Factory: Insights on Biofilm Management for Enhanced Food Safety and …

G LaPointe, T Wilson, A Tarrah, M Gagnon… - Journal of Dairy Science, 2025 - Elsevier
This review aimed to assess the scope of the literature on tracking the microbial community
of biofilms, focusing on the dairy farm and processing environments. The majority of studies …

MetaBakery: a Singularity implementation of bioBakery tools as a skeleton application for efficient HPC deconvolution of microbiome metagenomic sequencing data to …

B Murovec, L Deutsch, D Osredkar, B Stres - Frontiers in microbiology, 2024 - frontiersin.org
In this study, we present MetaBakery (http://metabakery. fe. uni-lj. si), an integrated
application designed as a framework for synergistically executing the bioBakery workflow …

Prediction of colorectal cancer based on taxonomic levels of microorganisms and discovery of taxonomic biomarkers using the Grou**-Scoring-Modeling (GSM) …

B Bakir-Gungor, M Temiz, B Canakcimaksutoglu… - Computers in Biology …, 2025 - Elsevier
Colorectal cancer (CRC) is one of the most prevalent forms of cancer globally. The human
gut microbiome plays an important role in the development of CRC and serves as a …

Multi-class boosting for the analysis of multiple incomplete views on microbiome data

A Simeon, R Kapçiu, B Preni, E Kalluçi - Transdisciplinary Journal of Engineering …, 2024 - atlas-tjes.org
Acquiring a profound comprehension of the complex correlation between genes is essential
for progressing treatment and diagnostics in acute leukemia research. This work utilizes …

The Use of Machine Learning and Explainable Artificial Intelligence in Gut Microbiome Research: A Sco** Review

H Tourab, LL Pérez, P Arroyo-Gallego, E Georga… - Authorea …, 2024 - techrxiv.org
Gut microbiome research has made tremendous progress, especially with the integration of
machine learning and artificial intelligence that can provide new insights from complex …