Ulisses Nunes da Rocha

PhaGAMeToo: A semi-automated workflow for merging structural and functional annotation of phage genomes and generation of a GenBank file

PhaGAMeToo merges functional annotations from phage genomes and generates submission-ready GenBank files using Pharokka, VIBRANT, and BLASTP.

BioAutoML-FAST: an automated machine-learning platform for reusable and benchmarked biological sequence models

BioAutoML-FAST provides an automated ML platform for biological sequence analysis, offering reusable models and benchmarking across genomic, transcriptomic, and proteomic tasks.

BioPrediction-PPI: Simplifying the Prediction of Protein-Protein Interactions through Artificial Intelligence

BioPrediction-PPI is an end-to-end machine learning framework for predicting protein-protein interactions without deep learning, offering interpretability and competitive performance across multiple datasets.

Ecology of prophage-like elements in Bacillus subtilis at global and local geographical scale

This study investigates prophage-like elements in Bacillus subtilis across global and local scales, revealing their diversity, integration patterns, and potential impact on host evolution and physiology.

Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in Prokaryotic metagenome-assembled genome recovery

The paper simulates microbial communities to show sequencing depth and false positives significantly affect metagenome-assembled genome recovery accuracy.

MuDoGeR: Multi-Domain Genome Recovery from metagenomes made easy

MuDoGeR simplifies genome recovery from metagenomes for non-experts, demonstrating effectiveness across various sample sizes.

Recovery of 447 Eukaryotic bins reveals major challenges for Eukaryote genome reconstruction from metagenomes.

The paper recovers 447 eukaryotic bins from metagenomes, highlighting challenges in genome reconstruction and the need for improved methods and reference genomes.

OrtSuite - from genomes to prediction of microbial interactions within targeted ecosystem processes

OrtSuite predicts microbial interactions based on genomic content for specific ecosystem processes using ortholog clustering and user-defined functions.

PredicTF: a tool to predict bacterial transcription factors in complex microbial communities.

PredicTF predicts bacterial transcription factors in microbial communities using genomic and metagenomic data from environmental isolates and anammox bioreactors.

TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes

TerrestrialMetagenomeDB curates and standardizes metadata for terrestrial metagenomes to facilitate comparison and meta-analysis across datasets.