Alexander Goesmann

The paper uses R-DeeP to show stress-induced compartment-specific RNA buffering of protein aggregation in yeast, with nuclear RNA retention protecting nuclear proteins from aggregation.

This study compares deep learning models for generating antimicrobial peptides, finding that auto-encoders, especially Wasserstein auto-encoders, produce more diverse sequences than other models.

Baktfold improves protein functional annotation for microbial genomes using structural information, achieving higher annotation rates than existing tools for bacteria and archaea.

This study analyzes 37970 Streptococcus agalactiae genomes from BakRep to map population trends and identify metadata gaps in serotypes, lineage-specific genes, and AMR profiles.

The paper identifies uORFs in bacterial mRNAs using bioinformatics and experimental validation, revealing translational coupling and ribosome-mediated RBS occlusion as regulatory mechanisms.

This paper shows that phosphorylated EpsW activates exopolysaccharide biosynthesis by promoting EpsZ dimerization in Myxococcus xanthus.

This study identifies a novel sublineage of Streptococcus agalactiae in German zoo elephants through whole-genome sequencing, showing phylogenetic divergence and clustering by zoo and genotype.

sORFdb is a database for small proteins and sORFs in bacteria, addressing gaps in detection and functional annotation through curated data and family classification.

The paper investigates the role of RNA interference in Arabidopsis by analyzing AGO and DCL mutants against various pathogens and a mutualist, revealing both positive and neutral effects on immunity and colonization.

BakRep provides a searchable web repository of 661,405 bacterial genomes with consistent characterizations and metadata, enabling flexible querying and offline analysis.

MGX 2.0 provides a modular tool for analyzing metagenome and metatranscriptome data using both shotgun and assembly-based approaches.

This paper identifies evolutionarily stable gene clusters in Acinetobacter species that reveal genetic features associated with pathogenicity and host interaction.

Bakta annotates bacterial genomes with one taxon-independent database, uses MD5-hash protein lookups to skip alignments and assign cross-references, detects small proteins, and lowers hypothetical-protein rates versus Prokka/DFAST.

This paper demonstrates how software engineering techniques improve reproducibility of a mathematical model of the atrioventricular node by implementing automated testing, version control, and modular design.

This paper introduces Swarm Learning, a decentralized machine learning approach for disease classification using transcriptomic data, demonstrating its effectiveness in developing classifiers for COVID-19, tuberculosis, and leukemias while preserving privacy.

The paper expands and reclassifies the ECF σ factor family by analyzing NCBI data, identifying 157 phylogenetic groups and significantly increasing the number of classified sequences.

Platon identifies and characterizes plasmid contigs in bacterial draft assemblies using a replicon distribution score, achieving high accuracy and balanced performance across bacterial taxa.

ASA3P automates and scales bacterial genome assembly, annotation, and analysis, enabling rapid processing of hundreds of genomes.

ReferenceSeeker identifies appropriate reference genomes by combining kmer profiling and ANI calculations for microbial genomics analyses.