Matthew B. Sullivan

CheckAMG identifies auxiliary viral genes by combining annotation-based prediction with a genome-language model, improving accuracy and uncovering novel genes with no sequence similarity to references.

The paper investigates how viral dynamics influence carbon metabolism in peat microcosms amended with catechin, showing that viral lysis redistributes intermediates to sustain methane suppression.

The paper predicts microbial ecosystem impact on host metabolism using genome-resolved metagenomics, identifying key species and pathways involved in nitrogen balance and host health.

This study identifies 42 bacterial genes involved in Klebsiella phage infection using RB-TnSeq, revealing cross-family resistance and genus-specific gene dependencies.

This paper organizes a community challenge to develop automated virus taxonomy classification tools and evaluates their performance on a combined dataset of expert-curated and metagenomic sequences.

The paper analyzes mobile genetic elements in thawing permafrost soils to assess their impact on microbial diversity and function using meta-omic data.

This study shows that disrupting the spinal cord-gut axis alters gut microbial dynamics and carbohydrate cross-feeding, with interventions restoring health.

CRESSENT is a bioinformatic toolkit for ssDNA virus annotation that addresses challenges in identification, classification, and decontamination of metagenomic datasets.

This study shows that higher-order interactions and density-dependent feedback stabilize phage-bacteria communities, challenging pairwise model predictions of population collapse.

The paper identifies viral shunt activity as a driver of seasonal subsurface oxygen maxima in the Sargasso Sea by linking elevated cyanophage activity and bacterial catabolism.

The paper introduces vConTACT3, a machine learning tool that improves virus taxonomy classification, scalability, and accuracy, and identifies taxonomic issues across the virosphere.

The paper samples and analyzes viruses in the Bermuda Atlantic Time Series to reveal population-level dynamics and functional differences, but not community-level changes over short timeframes.

This study examines the cervicovaginal microbiome of HIV-positive pregnant people in the DRC, finding taxonomic and functional differences compared to HIV-negative individuals and linking microbiome features to adverse pregnancy outcomes.

The paper analyzes groundwater viromes to show viruses influence microbial metabolism and nutrient cycling through auxiliary metabolic genes and host-targeting mechanisms.

This study analyzes diatom diversity and abundance in the global ocean using Tara Oceans data, identifying key environmental drivers and community patterns.

This study investigates how plant-bacteria-phage interactions affect nitrogen acquisition and exometabolite composition by comparing phage-lysed and uninfected bacterial necromass.

The paper develops a genome-scale metabolic model for ocean microbial communities to infer metabolic processes and viral impacts on biogeochemical cycles.

The paper identifies and characterizes RNA viruses in permafrost soil over four years, showing their diversity is structured by habitat and linked to greenhouse gas emissions.

The paper benchmarks Hi-C for virus-host linkage detection using synthetic communities and applies optimized protocols to soil samples, revealing new interactions and establishing performance metrics.

This study shows that catechin reduces methane emissions in peatlands by altering microbial metabolism and depriving methanogens of substrates.

The paper quantifies plankton community structure globally, revealing inverted biomass pyramids dominated by gelatinous organisms and predicting future shifts in oceanic carbon cycles.

The paper identifies four new 7-deazaguanine derivatives in phages and characterizes enzymes involved in their biosynthesis and insertion into DNA.

kb_DRAM integrates DRAM tools into KBase for microbial and viral genome annotation and metabolic modeling through a user-friendly interface.

MetaboDirect is an open-source pipeline for processing FTICR-MS metabolomics data, offering automated analysis, visualization, and biochemical network generation.

The paper analyzes genetic divergence in three coral species across a Pacific environmental gradient, showing species-specific evolutionary patterns despite similar environments.

The paper expands the global RNA virome by five-fold, identifying new clades of RNA bacteriophages and revealing novel virus-host interactions.

The paper develops a platform using proximity-ligation sequencing to reconstruct viral genomes and assign hosts from metagenomic data, showing high accuracy and efficiency.

MetaPop analyzes and visualizes microbial and viral metagenome-derived populations at macro- and micro-diversity levels, revealing lower viral nucleotide diversity in autistic children.

A human gut virome reference catalog compiled from 648 metagenomes identifies 13,203 viral populations across 702 previously uncharacterized genera, boosting viral detection nearly 60-fold over NCBI viral RefSeq.

The paper introduces VirION, a long-read sequencing method for viral metagenomics that improves genome assembly and captures microdiverse viral populations and genomic islands.