Rogier Braakman

Proteomes reflect size-based growth constraints across diverse microbes

The paper uses proteomic data to show that microbial growth rates are constrained by size-related factors, with intermediate-sized cells having the highest growth potential.

Characterization of Phytoplankton-Excreted Metabolites Mediating Carbon Flux through the Surface Ocean

This study quantifies amine- and alcohol-containing exometabolites from six phytoplankton species, revealing taxonomic variation in exometabolite composition and its impact on marine carbon cycling.

Simultaneous acclimation to nitrogen and iron scarcity in open ocean cyanobacteria revealed by sparse tensor decomposition of metatranscriptomes

The paper develops a sparse tensor decomposition method to analyze metatranscriptomes and identifies gene expression changes in marine cyanobacteria under nitrogen and iron scarcity.

Uptake of Prochlorococcus-derived metabolites by Alteromonas macleodii MIT1002 shows high levels of substrate specificity

This study shows that Alteromonas macleodii MIT1002 selectively uptakes specific metabolites from Prochlorococcus, highlighting the importance of transporter specificity in microbial interactions with dissolved organic matter.

Global niche partitioning of purine and pyrimidine cross-feeding among ocean microbes

The paper identifies purine and pyrimidine cross-feeding networks among ocean microbes, revealing niche partitioning and potential cryptic nitrogen cycles driven by Prochlorococcus and SAR11 interactions.

Digital Microbe: A Genome-Informed Data Integration Framework for Collaborative Research on Emerging Model Organisms

The paper introduces Digital Microbes, an integrative framework for collaborative research on microbes, demonstrating its application with two case studies involving genomic and transcriptomic data.

Emergence of metabolic coupling to the heterotroph Alteromonas promotes dark survival in Prochlorococcus

The paper shows that Prochlorococcus develops a dark-tolerant phenotype when co-cultured with Alteromonas, involving metabolic coupling and shifts in gene expression.