Antonio Gonzalez

Homology-aware average nucleotide identity estimation at scale with TurboANI

TurboANI is a fast, homology-aware ANI estimator with up to ~40,000x speedup over alignment-based methods and better accuracy than FastANI and skani.

Genome-resolved ecology and evolution of the microbiome enabled by quantitative long-read metagenomics

This paper introduces LRQ, a long-read metagenomics method that enables absolute strain abundance measurement and resolves microbial evolution in a Crohn's disease patient over eight years.

An expansive animal gut microbiome dataset elucidates major compositional shifts across bilaterian evolution

The paper presents a large-scale gut microbiome dataset across 1,553 host species and identifies major compositional shifts in gut microbiomes during animal evolution.

Pan-repository analysis reveals a drug-activating function of microbial bile acid conjugation

The paper identifies microbial bile acid conjugation as a drug-activating function for 5-ASA, revealing its therapeutic relevance through metabolomics analysis.

Enabling Megascale Microbiome Analysis with DartUniFrac

DartUniFrac is a fast, scalable algorithm for microbiome analysis that matches the statistical performance of exact UniFrac methods.

Community assembly modeling of microbial evolution within Barrett's esophagus and esophageal adenocarcinoma

The paper models microbial community assembly dynamics in Barrett's esophagus and esophageal adenocarcinoma, finding neutral dynamics in normal tissue and BE but not EAC, with H. pylori showing non-neutral behavior in BE non-cancer outcomes.

A searchable metadata network graph for microbiome metabolomics

The paper introduces microbiomeMASST, a metadata network graph linking metabolites across datasets, enabling cross-study analysis of microbial metabolites and their biological context.

Gut microbiome is associated with recurrence-free survival in patients with resected Stage IIIB-D or Stage IV melanoma treated with immune checkpoint inhibitors

The paper identifies gut microbiome taxonomic markers associated with recurrence in melanoma patients treated with immune checkpoint inhibitors, showing generalizability across regions when GMB composition is matched.

Integrating de novo and inherited variants in over 42,607 autism cases identifies mutations in new moderate risk genes

The paper identifies 60 new moderate risk genes for autism by integrating de novo and inherited variants across 42,607 cases and 236,000 controls.

OGUs enable effective, phylogeny-aware analysis of even shallow metagenome community structures

This paper introduces OGUs, a metagenome analysis method that uses sequence alignment hits to reference genomes for community analysis, showing better performance in predicting biological traits than taxonomic or 16S rRNA methods.