Christian von Mering

This study shows AI-2 functions as both a quorum sensing and metabolic signal in E. coli, linking nutrient sensing to population-level signaling through CRP and the lsr operon.

Susagi is a permutation-invariant denoising transformer that models microbial community stability from bacterial SSU rRNA gene embeddings, showing reliable predictions and capturing biological structure.

The paper evaluates WISH-barcoding in Salmonella Typhimurium for in vivo population dynamics, finding wild-type strains prone to fitness-altering mutations during in vitro construction.

This study identifies D-gluconate as a key nutrient source for Salmonella during both acute and chronic infection, supporting its growth in the inflamed gut.

MicrobeAtlas unifies over two million microbiome samples to enable cross-technology insights into microbial ecosystems and their global patterns.

The paper develops CRISPR-PAMdb and CICERO to uncover PAM diversity in Cas9 proteins, enabling better CRISPR tool design.

The paper investigates community conservatism in microorganisms, finding it普遍存在 across environments and phyla, with specialized taxa showing stronger signals.

This paper uses large language models to automate the annotation of microbiome sequencing records, achieving better performance than a keyword-based approach.

The paper develops cross-species protein embeddings using network data and shows they improve subcellular localization and function prediction when combined with sequence embeddings.

The paper analyzes the pan-genome of nearly 20,000 Enterobacteriaceae genomes to identify core and accessory metabolic genes, revealing core genes for mixed acid fermentation and accessory genes for anaerobic respiration and carbohydrate utilization.

This study analyzes microbiome data from multiple OA cohorts and finds no significant differences between OA patients and controls, attributing microbiome changes to age and BMI instead of OA.

This study identifies context-dependent and -independent carbohydrates used by Salmonella Typhimurium for gut colonization in mice, highlighting D-glucose, D-fructose, and D-galactose as key substrates.

The paper investigates how microbiota origin affects transplant outcomes in soil, finding that habitat filtering, not origin, determines success.

The paper introduces the BGC Atlas, a web resource that explores BGC diversity in metagenomes, identifying nearly 1.8 million BGCs and showing RiPPs as the most abundant compound class.

This study uses single-cell long-read sequencing to analyze transcriptomes of ccRCC organoids, identifying novel transcripts and highlighting cell-specific alternative splicing events.

The paper identifies theta ribozymes in gut phages that associate with suppressor tRNAs, suggesting a role in regulating phage assembly through RNA-based mechanisms.

PaxDB 5.0 provides updated protein abundance data across species, highlighting expanded coverage and comparative analysis with existing resources.

The paper improves protein-protein interaction prediction by integrating clade-wise alignments, enhancing co-evolutionary signals and reducing false positives for genome-wide scans.

CanIsoNet is a database that integrates isoform expression data with interaction networks and ClinVar annotations to predict the pathogenic impact of isoform switching events in diseases.

treeclimbR identifies optimal hierarchical resolutions for detecting entities associated with phenotypes in multi-resolution data.

The paper analyzes pan-genomes of 155 prokaryotic species to assess how environmental and phylogenetic factors influence strain diversity and pan-genome features.

The paper assesses the value and sustainability of ELIXIR Core Data Resources, showing their critical role in preserving biological data and highlighting funding challenges.

FlashWeave infers direct microbial interactions from large-scale metagenomic data, outperforming existing methods in speed and accuracy across diverse benchmarks.

The paper improves the inference of orthologous group hierarchies by combining tree reconciliation with subsampling, showing comparable or better performance than previous methods.

The paper introduces Viruses.STRING, a database of virus-host protein-protein interactions combining experimental and text-mining evidence.

The paper analyzes non-coding mutations across 2,583 cancer genomes to identify genes and pathways affected, finding clusters of interacting proteins and insights into cancer mechanisms.

The paper analyzes the human kinome and phosphatome to identify signaling networks altered by protein overexpression, revealing novel relationships and mechanisms of cancer progression.

MAPseq improves speed and accuracy of rRNA metagenomic analysis by providing faster and more consistent taxonomy classifications and OTU mappings.

The paper introduces eggNOG-mapper, a tool for fast genome-wide functional annotation through orthology assignment, showing improved accuracy and efficiency compared to BLAST and InterProScan.