Jose Manuel Martí

Meta2DB: Curated Shotgun Metagenomic Feature Sets and Metadata for Health State Prediction

Meta2DB provides a curated metagenomic database with 13,897 samples across 84 studies for predicting human health states using ML models.

An Embeddings Fusion Approach Predicts Disease State from Microbiome Features

The paper introduces an embeddings fusion approach to predict disease state from microbiome features using visual representations of taxonomic data, achieving high classification accuracy across multiple factors.

Beyond Microbial Abundance: Metadata Integration Enhances Disease Prediction in Human Microbiome Studies

This study integrates host and sample metadata with microbiome abundance profiles to improve disease prediction models using machine learning.

Prediction of metabolic dynamics through deep learning and high-throughput multiomics data

This paper trains a deep learning model on multiomics data to predict metabolic dynamics in synthetic biology, achieving high accuracy in predicting product and metabolite levels.

Addressing the dynamic nature of reference data: a new nt database for robust metagenomic classification

The paper develops new Centrifuge-compatible nt databases to improve metagenomic classification accuracy by addressing reference database inconsistencies and growth challenges.

GENTANGLE: integrated computational design of gene entanglements

GENTANGLE is a computational tool for designing overlapping gene pairs in microbial genomes, enabling safer genetic engineering through gene entanglements.

Differential laboratory passaging of SARS-CoV-2 viral stocks impacts the in vitro assessment of neutralizing antibodies

The paper shows that passaging SARS-CoV-2 viral stocks under antiserum selection pressure increases genetic diversity and antibody escape mutations, making them more representative of circulating viruses.

Multiomics data collection, visualization, and utilization for guiding metabolic engineering

The paper presents tools for storing, visualizing, and leveraging multiomics data to predict outcomes of bioengineering efforts.

Metagenomic dynamics in Olea europaea after root damage and Verticillium dahliae infection

The paper analyzes metagenomic dynamics in olive trees after root damage and Verticillium dahliae infection, showing a polymicrobial community drives the infection rather than a single species.

Not just BLAST nt: WGS database joins the party

The paper argues for combining BLAST nt and WGS databases to improve taxonomic classification sensitivity in metagenomics and provides a script to facilitate this approach.

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

Recontrifuge removes contamination and enables comparative analysis in metagenomic data by providing confidence levels and shared/exclusive taxa per sample.