Vanessa R. Marcelino

StrainSpy fits zero-inflated beta mixed models to containment ANI, reaching >98% simulated sensitivity versus ~79% for logistic regression and detecting colorectal-cancer E. coli strain shifts.

Open plastid orthogroup resource for algae: 496 named orthogroups from 893 genomes, 224 core profile hidden Markov models with calibrated cutoffs, alignments, predicted structures, 859-genome phylogeny, CheckM-compatible marker sets.

The paper identifies metabolically flexible fermenters as drivers of increased intestinal gas production in Crohn's disease by analyzing microbial genomes and metagenomes.

This study identifies the group B [FeFe]-hydrogenase as the primary enzyme driving fermentative H2 production in the human gut, linking it to gut health and disease.

The paper integrates metagenomic and climatic data to model global picoplankton biogeography, identifying ten distinct groups and their environmental and functional features.

Metaphor is a fully-automated workflow for genome-resolved metagenomics that improves genome binning quality through flexible assembly strategies and combined binning algorithms.

The paper reports on 10 Ostreobium strains isolated from Great Barrier Reef corals, describing their phenotypic diversity, phylogenetic placement, and chloroplast genome structure.

The paper evaluates metagenomic software tools using realistic datasets, highlighting improvements in assembly and taxon profiling while identifying remaining challenges in virus/archaea detection and reproducibility.

This study presents the Ostreobium nuclear genome and metatranscriptomic analysis to understand its adaptations to the coral skeleton environment and its role in coral holobiont dynamics.

CCMetagen improves metagenomic classification by using weighted read mappings, outperforming existing tools in precision and F1 scores for species-level identification.

This study evaluates metatranscriptomics for identifying fungal species and subspecies in mixed communities using a mock community of 17 fungal isolates, showing high accuracy at species and strain levels when low-abundance taxa are excluded.

This study analyzes the chloroplast genomes of four green algae, finding that Ostreobium quekettii has a gene-dense, small chloroplast genome and slower molecular evolution rates, consistent with low light adaptation.