Jed A. Fuhrman

Estimating Gene Prevalence with Incomplete Genomes: Application to the Prochlorococcus Pangenome

The paper develops a maximum-likelihood framework to estimate gene prevalence from incomplete genomes and applies it to Prochlorococcus, revealing a pangenome dominated by rare genes.

Estimating absolute microbial abundances from metabarcoding anchored to cytometry data

This paper calibrates metabarcoding data using flow cytometry to estimate absolute microbial abundances and gene concentrations in oceanic samples.

Expansive Diversity and Temporal Dynamics of Emerging Polinton-like Viruses in a Marine Ecosystem

This study identifies 2,355 PLV populations in marine viromes, revealing their seasonal dynamics and functional roles in coastal ecosystems.

A Multidomain Lens on the Temporal Dynamics of Surface Microbial Communities in the Southern Ocean (2013-2019)

The paper analyzes microbial community dynamics in the Northwestern Antarctic Peninsula over six years, revealing seasonal and yearly changes in eukaryotic phytoplankton and stability in prokaryotic communities, particularly Nitrincolaceae.

Induced pathogenicity toward open-ocean diatoms by a newly isolated filterable bacterium Ekhidna algicida sp. nov.

A newly isolated bacterium from the Pacific Ocean kills diatoms, suggesting a pathogenic role in open-ocean ecosystems.

A roadmap for fair reuse of public microbiome data

The paper proposes a roadmap for fair reuse of public microbiome data by introducing a Data Reuse Information tag (DRI) to facilitate communication between data creators and consumers.

The JEDI marker as a universal measure of planetary biodiversity

The paper introduces the JEDI marker as a universal biodiversity measure, demonstrating its applicability across ecological scales and providing an automated bioinformatic workflow for standardized analysis.

Characterizing organisms from three domains of life with universal primers from throughout the global ocean

The paper introduces GRUMP, a database of global ocean microbial communities using universal primers, enabling direct comparison of taxonomic ratios across samples and domains.

Functional biogeography of marine microbial heterotrophs

The paper synthesizes genetic data with a marine ecosystem model to analyze functional biogeography of marine heteroprokaryotes, identifying key ecological factors shaping their distribution.

Variational inference for microbiome survey data with application to global ocean data

The paper introduces VI-MIDAS, a probabilistic framework for analyzing microbiome data, and applies it to Tara Ocean data to identify microbial community modules and associations.

Phylogenetic proximity drives temporal succession of marine giant viruses in a five-year metagenomic time-series

The paper analyzes a five-year metagenomic time-series to study temporal dynamics of marine giant viruses, finding that phylogenetic proximity influences their seasonal abundance and ecological interactions.

DeepMicroClass sorts metagenomes into prokaryotes, eukaryotes and viruses, with marine applications

DeepMicroClass classifies metagenomic contigs into five sequence classes with high accuracy, outperforming existing methods in marine metagenomic analysis.

Benchmarking community-wide estimates of growth potential from metagenomes using codon usage statistics

The paper benchmarks an improved metagenomic growth rate predictor, showing better performance on mixed-species communities and providing guidelines for data preprocessing.

HiCzin: Normalizing metagenomic Hi-C data and detecting spurious contacts using zero-inflated negative binomial regression

HiCzin normalizes metagenomic Hi-C data and detects spurious contacts using zero-inflated negative binomial regression, improving bias correction and contig clustering.

A network-based integrated framework for predicting virus-host interactions

The paper introduces a network-based framework to predict virus-host interactions, achieving higher accuracy than previous methods and expanding known interactions across diverse datasets.

Dynamic marine viral infections and major contribution to photosynthetic processes shown by regional and seasonal picoplankton metatranscriptomes

The paper uses metatranscriptomics to study viral infections in coastal California, showing viruses contribute significantly to photosynthesis through psbA expression.