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Long-Read Metagenome-Assembled Genomes Improve Identification of Novel Complete Biosynthetic Gene Clusters in a Complex Microbial Activated Sludge Ecosystem

Published in Msystems, 2022

Genome mining of high-quality metagenome-assembled genomes (MAGs) from wastewater treatment plants using long-read sequencing revealed over 4,000 mostly novel and complete biosynthetic gene clusters, highlighting the significant biosynthetic potential and secondary metabolite diversity in this ecosystem.

Recommended citation: Sánchez-Navarro R, Nuhamunada M, et. al. 2022. mSystems 7:e00632-22.
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BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets

Published in Nucleic Acids Research, 2024

BGCFlow is a workflow integrating multiple genome analytics tools to facilitate large-scale genome mining and analysis of bacterial pangenomes, enhancing the discovery and comparative analysis of biosynthetic gene clusters, demonstrated through its application on mining Saccharopolyspora genomes.

Recommended citation: Nuhamunada, M., O.S. Mohite et. al. 2024. Nucleic Acids Research. Volume 52, Issue 10, 10 June 2024, Pages 5478–5495.
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A treasure trove of 1034 actinomycete genomes

Published in Nucleic Acids Research, 2024

We report the whole genome sequencing of 1034 Actinomycetia strains from the New Bioactive Compounds (NBC) Collection of the Novo Nordisk Foundation Center for Biosustainability at the Technical University of Denmark; 881 strains with complete genomes and 153 near-complete genomes.

Recommended citation: TS Jørgensen, OS Mohite, EB Sterndorff, M Alvarez-Arevalo, K Blin, TJ Booth, P Charusanti, D Faurdal, TØ Hansen, **M Nuhamunada**, A Mourched, BØ Palsson, T Weber, A treasure trove of 1034 actinomycete genomes, Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7487–7503.
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BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes

Published in Nucleic Acids Research, 2024

Here, we present the BGC Atlas (https://bgc-atlas.cs.uni-tuebingen.de), a web resource that facilitates the exploration and analysis of BGC diversity in metagenomes. The BGC Atlas identifies and clusters BGCs from publicly available datasets, offering a centralized database and a web interface for metadata-aware exploration of BGCs and gene cluster families (GCFs).

Recommended citation: C Bağcı, **M Nuhamunada**, H Goyat, C Ladanyi, L Sehnal, K Blin, SA Kautsar, A Tagirdzhanov, A Gurevich, S Mantri, C von Mering, D Udwary, MH Medema, T Weber, N Ziemert. 2024. BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes, Nucleic Acids Research, gkae953
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Leveraging Modern Data Stack in Box for Natural Product Genome Mining in Small-Scale and Private Strain Collection

Published: June 10, 2024

This talk is about giving solutions to small and private labs to help them perform, manage, and explore genomics information from their strain collection to look for interesting BGCS. This talk offers more of the data management vibe from our published workflow.

27255 - Advanced Experimental Prokaryotic Molecular Biology and Ecology (Spring 2023)

MSc course, DTU Bioengineering, 2023

This is the bioinformatic tutorial for week 11 of the course 27255 - Advanced Experimental Prokaryotic Molecular Biology and Ecology (Spring 2023) held at DTU Bioengineering. I was helping Prof. Lars Jelsbak on the final part of the course where we sequence and analyze the genome information from the strain isolated by the students. The course material is available online here.