Satria Ardhe Kautsar

plantiSMASH 2.0: improvements to detection, annotation, and prioritization of plant biosynthetic gene clusters

plantiSMASH 2.0 improves detection, annotation, and prioritization of plant biosynthetic gene clusters by expanding BGC types and adding substrate prediction and regulatory analysis.

BiG-SCAPE 2.0 and BiG-SLiCE 2.0: scalable, accurate and interactive sequence clustering of metabolic gene clusters

The paper introduces updated versions of BiG-SCAPE and BiG-SLiCE for improved analysis of metabolic gene clusters, showing they provide consistent estimates of gene cluster diversity.

Uncovering the Genomic Manifold via Scalable Learning from the Global Microbiome

The paper introduces GenomeOcean, a large-scale generative model trained on metagenomic data, to explore the genomic manifold hypothesis and demonstrates its alignment with another model.

BGC Atlas: A Web Resource for Exploring the Global Chemical Diversity Encoded in Bacterial Genomes

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.

iPRESTO: automated discovery of biosynthetic sub-clusters linked to specific natural product substructures

iPRESTO detects sub-clusters in biosynthetic gene clusters to link natural product substructures to their genetic origins, improving annotation and discovery.

Compendium of secondary metabolite biosynthetic diversity encoded in bacterial genomes

The paper analyzes bacterial genomes and metagenome assembled genomes to assess the diversity of secondary metabolite biosynthesis, finding that only 3% of potential natural products are experimentally characterized.

BiG-SLiCE: A Highly Scalable Tool Maps the Diversity of 1.2 Million Biosynthetic Gene Clusters

BiG-SLiCE clusters 1.2 million biosynthetic gene clusters from microbial genomes and MAGs efficiently, enabling analysis of secondary metabolic diversity and novel chemistry.

A computational framework for systematic exploration of biosynthetic diversity from large-scale genomic data

The paper introduces two tools, BiG-SCAPE and CORASON, for analyzing biosynthetic gene clusters in large genomic datasets, demonstrating their utility through validation and discovery of new gene cluster families.

plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters

plantiSMASH identifies and analyzes plant biosynthetic gene clusters using genomic and transcriptomic data to prioritize candidates and study their evolutionary conservation.