Tilmann Weber

The paper develops a computational pipeline and database to annotate halogenating enzymes in genomic and metagenomic data, revealing underexplored clusters and improving predictions of microbial halogenated natural products.

The paper identifies a new PCR artifact called 'PCR leaping' and develops a DNA library screening method using it for natural product discovery.

This study analyzes 1432 transcriptomics datasets from 132 Actinomycetota strains to identify patterns of BGC expression and regulatory mechanisms.

RetroMol converts natural product structures and biosynthetic gene clusters into shared primary sequences to enable biosynthetic similarity comparisons.

PhyloNaP provides a database of phylogenetic trees for biosynthetic enzymes, enabling functional inference and community contributions.

geneML improves fungal gene prediction accuracy and recall using deep learning, outperforming existing tools and enabling faster, more comprehensive genome annotation.

epsSMASH identifies exopolysaccharide biosynthetic gene clusters in environmental and human microbiomes, revealing widespread uncharacterized clusters.

The paper develops Telomore to recover missing telomeres in Streptomycetaceae genomes, increasing detection from 0% to 37% and identifying a new telomere-related protein family.

StreptoCAD automates genome engineering workflows in Streptomyces, streamlining design, simulation, and documentation of CRISPR-based and overexpression strategies.

This study identifies lydicamycins as inducers of morphological differentiation in actinobacterial interactions using co-cultivation and multi-omics approaches.

The paper introduces a type I-C CRISPR system, pCRISPR-Cas3, for efficient genome engineering in streptomycetes, outperforming Cas9-based systems in deletion and substitution capabilities.

This paper introduces ActinoMation, a tool for automating Streptomyces conjugation, achieving varying conjugation efficiencies across strains and plasmids.

This study identifies 3,273 biosynthetic gene clusters in 284 Paenibacillus genomes, revealing extensive unknown clusters and clade-specific biosynthetic patterns.

getphylo automatically generates multi-locus phylogenetic trees from GenBank files, offering faster and more flexible analysis than existing tools.

This study presents 121 new Bacillales genomes, identifies 1,176 biosynthetic gene clusters, and provides open-access data to enhance research on secondary metabolite production.

This paper identifies alligamycin A, a novel antifungal compound from Streptomyces iranensis, and demonstrates its potent antifungal activity against clinically relevant fungi.

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.

The paper reports the discovery of maramycin, a novel isoquinolinequinone alkaloid produced through heterologous expression of a bifunctional enzyme in Streptomyces albidoflavus, showing moderate cytotoxicity against prostate cancer cells.

BGCFlow is a systematic workflow for analyzing biosynthetic gene clusters across large genomic datasets, demonstrating improved dereplication and comparative analysis of RiPPs in Saccharopolyspora genomes.

The paper analyzes 2,371 Streptomyces genomes to refine biosynthetic gene cluster (BGC) diversity using MASH-clusters and reveals conserved genomic structures suggesting vertical inheritance.

The paper introduces teemi, an open-source platform for bioengineering that supports simulation, data integration, and machine learning for metabolic pathway design under FAIR principles.

MassQL, an open-source query language, lets users search raw mass spectrometry data from any vendor for isotope, fragmentation and neutral-loss patterns, from one file to entire public repositories.

The paper analyzes enterobacterial genomes to identify secondary metabolite gene clusters, finding 8604 BGCs across 2627 genomes and associating some with specific biological functions.

The paper analyzes the phylogenetic distribution of biosynthetic gene clusters in the Bacillus subtilis group to understand secondary metabolite production patterns and conservation.

The paper develops CRISPR-BEST, a DSB-free base editing system for filamentous actinomycetes, achieving single-nucleotide resolution in Streptomyces species.

This paper introduces a yeast platform for producing bacterial aromatic polyketides using a synthetic polyketide synthase system.