JL Weissman

Aquatic bacterial metabolic rates from RNA quantitative stable isotope probing (RNA-qSIP) depend on experimental design

This study shows that experimental design affects qSIP-derived metabolic activity estimates in aquatic bacteria, with chemostats reducing the competitive advantage of fast-growing taxa.

Growth Optimization Predicts Microbial Success in a Permafrost Thaw Experiment

The paper develops a genomic index to predict microbial success in permafrost thaw by analyzing growth optimization and validates it with incubation experiments.

Emergent Metabolic Niches for Marine Heterotrophs

This study identifies metabolic niches in marine heterotrophs using global metagenomic data and models, linking microbial diversity to carbon cycling rates.

Assembly-Free Short-Read Metagenomic Maximum Growth Rate Prediction

The paper develops gene-length specific models to predict community average maximum growth rates from soil metagenomes without requiring assembly.

On Copiotrophy and Temperature: Controls on Microbial Maximum Growth Rate Versus Translation Rate Optimization

The paper examines how temperature affects microbial growth optimization and shows that genomic signatures of growth optimization better predict ecological roles than maximum growth rates.

Metagenomes and Metagenome-Assembled Genomes from Tidal Lagoons at a New York City Waterfront Park

The paper sequences and analyzes 15 shotgun metagenomes from tidal lagoons, reconstructing 129 high-quality metagenome-assembled genomes to provide a baseline for microbial community studies in public waterfront areas.

Oxygen intrusions sustain aerobic nitrite-oxidizing bacteria in anoxic marine zones

The paper shows how periodic oxygen intrusions sustain aerobic nitrite-oxidizing bacteria in anoxic marine zones, increasing microbial diversity and altering biogeochemical cycling.

Improved maximum growth rate prediction from microbial genomes by integrating phylogenetic information

The paper improves maximum growth rate prediction for microbes by integrating phylogenetic information with codon statistics, using a large database of temperature-corrected growth rates.

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.

Ecological drivers of CRISPR immune systems

This study investigates how ecological factors like prokaryotic density and diversity influence the distribution of CRISPR-Cas immune systems in different environments.

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.