Caner Bağcı

BGC Atlas v2 expands the collection of predicted biosynthetic gene clusters to over 16 million, providing taxonomic and environmental context for natural product discovery.

metaSMASH improves BGC detection in large metagenomes by reducing computational cost while maintaining result accuracy.

The paper shows that cooperative siderophore exchange between Rhodotorula kratochvilovae and Pseudomonas species stabilizes the leaf microbiome and protects plants from pathogens.

This study uses ultra-deep metagenomic sequencing to analyze soil microbes, revealing extensive microbial diversity and biosynthetic potential previously unexplored.

PanBGC provides a framework to analyze biosynthetic gene clusters across microbial genomes, classifying genes into core, accessory, and unique categories and quantifying diversity through openness metrics.

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 investigates microbe-microbe interactions in a synthetic microbial community on Arabidopsis leaves, finding that in vitro pairwise interactions differ from in planta correlation networks, suggesting community-level synergism over competition.

The paper demonstrates that using AnnoTree improves speed and assignment rates in DIAMOND+MEGAN microbiome analysis compared to NCBI-nr.

The paper introduces an interactive tool using Mash sketches and SplitsTree5 to determine the phylogenetic context of draft genomes by displaying phylogenetic outlines.

The paper demonstrates obtaining whole bacterial chromosomes from metagenomic samples using long-read sequencing and presents a pipeline with frame-shift correction.

MEGAN-LR provides new algorithms for taxonomic and functional binning of long reads and contigs, with evaluation on simulated and real datasets.