R. Maddamsetti

Circular RNA Obelisk-S.s is highly abundant in Streptococcus sanguinis SK36

The paper identifies a highly abundant circular RNA, Obelisk-S.s, in Streptococcus sanguinis SK36, despite its absence from the genome, and reports mutations in some samples.

Selection maintains protein interactome resilience in the long-term evolution experiment with Escherichia coli

The paper tests if natural selection maintains protein interactome resilience in Escherichia coli over 50,000 generations, finding evolved networks are more resilient than random ones.

Idiosyncratic purifying selection on metabolic enzymes in the long-term evolution experiment with Escherichia coli

The paper tests hypotheses about purifying selection on metabolic enzymes in Escherichia coli long-term evolution experiments and proposes the Jenga hypothesis to explain idiosyncratic patterns of selection.

Universal constraints on protein evolution in the long-term evolution experiment with Escherichia coli

The paper shows that abundant and highly interacting proteins evolve slowly in Escherichia coli over 60,000 generations, with mutation density anti-correlating with abundance and interaction.

Divergent evolution of mutation rates and biases in the long-term evolution experiment with Escherichia coli

The paper analyzes mutation rate and bias evolution in Escherichia coli populations from the LTEE, finding divergent mutation patterns and genetic loci affecting DNA topology.

Maintenance of metabolic plasticity despite relaxed selection in a long-term evolution experiment with Escherichia coli

The paper examines how relaxed selection affects metabolic plasticity in E. coli over 30 years, finding that anaerobic fitness is maintained despite relaxed selection.

Discovery of positive and purifying selection in metagenomic time series of hypermutator microbial populations

The paper introduces STIMS, a method to detect positive and purifying selection in metagenomic time series of hypermutator microbial populations, showing its effectiveness in real-time evolution studies.

Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment

This study examines the genomic and phenotypic evolution of Escherichia coli in a citrate-only environment, identifying copy-number variations and transposable elements as key factors, while noting persistent physiological mismatches.

Viral gain-of-function experiments uncover residues under diversifying selection in nature

The paper identifies two residues in bacteriophage λ that evolved under diversifying selection in nature, supporting host-shift evolution through experimental and genomic analysis.

Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection

The paper analyzes bacterial genomes from an evolution experiment with horizontal gene transfer, finding that recombination can overwhelm selection by driving donor alleles to fixation without providing selective advantage.

Core Genes Evolve Rapidly in the Long-term Evolution Experiment with Escherichia coli

The paper examines core gene evolution in E. coli, finding they accumulate more nonsynonymous mutations in lab experiments but are more conserved in nature.