Michael Baym

This study shows that prophage induction via SOS response limits resistance evolution to DNA-damaging antibiotics by eliminating mutants with high DNA damage.

The paper identifies deletion-born gene fusions as a mechanism for novel gene emergence in bacteria, demonstrating their prevalence across the bacterial tree of life.

This study measures within-cell plasmid fitness and shows that incompatible plasmids co-occur longer due to methylation-based eclipsing, with less transcriptionally active plasmids having a selective advantage.

This study analyzes historical microbial genomes to show that antibiotic resistance genes existed before antibiotics were introduced but became more frequent and mobile with antibiotic use.

Phage DisCo identifies phages that interact with specific bacterial traits by co-culturing strains with fluorescent tags and perturbations, using plaque morphology to detect infection inhibition.

This paper introduces phylogenetic compression to efficiently search large microbial genome collections, achieving significant compression improvements and enabling fast BLAST-like searches on desktop computers.

The paper demonstrates that RNA-guided nuclease TnpB enables gene drive in plasmids by biasing the inheritance of insertion sequences.

The paper evaluates nine computational tools for identifying SARS-CoV-2 lineages in wastewater sequencing data using simulated samples, finding most tools reliably detect lineages above 5% frequency.

The paper demonstrates a genetic code reassignment strategy that makes cells resistant to viral infections and prevents horizontal gene transfer by mistranslating viral proteins and relying on synthetic codons.

The paper identifies five genes essential for electron uptake from a cathode in Shewanella oneidensis, highlighting a distinct role in electron uptake compared to donation.

The paper introduces simplitigs, a compact and scalable representation of de Bruijn graphs, showing improved efficiency in sequence length and node count, especially with larger datasets.

This paper introduces a method to rapidly infer antibiotic resistance and susceptibility from bacterial genomes using genomic neighbor typing, achieving high sensitivity and specificity within minutes to hours.

The paper develops a model showing stronger gut microbiome connectivity increases resistance to invading bacteria and finds lower connectivity correlates with higher relapse rates after FMT.

This study shows that population diversity can reduce the effectiveness of antibiotic cycling strategies by enabling rare positive cross-resistant mutants to emerge.

This paper introduces Knockout Sudoku, a method to rapidly construct and curate a whole-genome transposon insertion collection for Shewanella oneidensis, enabling high-throughput analysis of gene function.