Christian H. Ahrens

The paper combines experimental and bioinformatic methods to assess amino acid auxotrophy in 315 Pseudomonas isolates, finding most are prototrophic with few auxotrophs and multiple biosynthesis pathways.

GenomeCompendium is a database that integrates repeat, assembly quality, and functional content data from complete prokaryotic genomes to improve genome annotations and analyze taxonomic coverage.

This paper revises the genome annotation of Synechocystis using ribosome profiling and proteogenomics, identifying new genes and correcting existing annotations.

The paper uses long-read assemblies and proteogenomic analysis to discover novel small proteins in Mycobacterium tuberculosis strains.

This study uses Tn-seq to identify metal resistance genes in Pseudomonas putida, revealing both known and novel genes involved in cadmium, copper, and cobalt resistance.

The paper expands the known proteome of Sinorhizobium meliloti by identifying 48 novel small proteins using Ribo-seq and proteogenomics.

The paper validates a model system to identify genes involved in biofilm formation and antibiotic resistance in Pseudomonas aeruginosa MPAO1 using genomics and experimental approaches.

The paper sequences and analyzes the genome of M. enterolobii, revealing a polyploid structure and transposable element abundance similar to other mitotic parthenogenetic Meloidogyne species.

The paper presents a proteogenomics workflow to identify small proteins in Staphylococcus aureus, finding 185 SP100, 69 of which were previously unannotated.

The paper develops a proteogenomic resource for Listeria monocytogenes to analyze genotype-proteotype-phenotype relationships using proteotyping and genomic databases.

The paper uses long-read sequencing to assemble complete genomes from low-complexity microbial communities, revealing strain diversity and active phage systems.

The paper demonstrates that complex prokaryotic genomes with long, near-identical repeats require very long reads and specialized assemblers for accurate de novo assembly.

The paper develops an integrative proteogenomics strategy to improve prokaryotic genome annotation by combining multiple resources and experimental data, identifying novel ORFs and correcting errors.