Sitemap
A list of all the posts and pages found on the site. For you robots out there, there is an XML version available for digesting as well.
Pages
Posts
Modern Python Project GitHub Template
Published:
TL;DR: I created a freely available template to facilitate setting up “modern” Python projects.
Fixing Persistence Issues with Git Inside Docker Containers
Published:
TL;DR: Cloned Git directories inside Docker containers can persist across builds or runs, causing branching and committing issues. Explicitly removing the directory before cloning prevents these errors.
portfolio
Portfolio item number 1
Published:
Short description of portfolio item number 1
Portfolio item number 2
Published:
Short description of portfolio item number 2
publications
Discovery of Mycobacterium tuberculosis InhA Inhibitors by Binding Sites Comparison and Ligands Prediction
Published in Journal of medicinal chemistry, 2016
Creation of the ProBiS plugin for PyMol and Chimera, a protein binding site alignment tool, and its use in the discovery of novel Mycobacterium tuberculosis InhA Inhibitors.
Docking study with biological validation on bacterial enzyme MurD
Published in Chemical Data Collections, 2018
Rational investigation of the bacterial cell-wall forming enzyme MurD for novel inhibitory binding sites, using molecular docking with experimental validation.
Planomonospora: a Metabolomics Perspective on an Underexplored Actinobacteria Genus
Published in bioRxiv, 2020
In-depth investigation of 74 strain of the bacterial genus Planomonospora using mass spectrometry-based metabolomics and genomics, with the discovery of novel congeners of the antibiotic siomycin.
A biaryl-linked tripeptide from Planomonospora leads to widespread class of minimal RiPP gene clusters
Published in bioRxiv, 2020
Discovery of the biarylitide class of natural products, encoded by the shortest known coding gene bytA of only 18 base pairs.
A biaryl-linked tripeptide from Planomonospora reveals a widespread class of minimal RiPP gene clusters
Published in Cell Chemical Biology, 2020
Discovery of the biarylitide class of natural products, encoded by the shortest known coding gene bytA of only 18 base pairs.
MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters
Published in Nucleic Acids Research, 2021
Update of the MIBiG database of biosynthetic gene clusters, with a focus on expanding non-ribosomal peptide synthetases.
Planomonospora: A Metabolomics Perspective on an Underexplored Actinobacteria Genus
Published in Journal of Natural Products, 2021
In-depth investigation of 74 strain of the bacterial genus Planomonospora using mass spectrometry-based metabolomics and genomics, with the discovery of novel congeners of the antibiotic siomycin.
Effective approaches to discover new microbial metabolites in a large strain library
Published in Journal of Industrial Microbiology and Biotechnology, 2021
Perspective article on approaches for the natural product drug discovery from microbes in an industrial setting.
Blocks in the pseudouridimycin pathway unlock hidden metabolites in the Streptomyces producer strain
Published in Scientific Reports, 2021
Analysis of the biosynthetic capacity of Streptomyces sp. ID38640, the producer of the bacterial RNA polymerase inhibitor pseudouridimycin, using paired metabolomics and genomics analysis.
Feature-Based Molecular Networking for the Targeted Identification of Gq-Inhibiting FR900359 Derivatives
Published in Journal of Natural Products, 2021
Discovery of congeners of the Gq-inhibitor FR900359 using mass spectrometry-based metabolomics.
FERMO: a Dashboard for Streamlined Rationalized Prioritization of Molecular Features from Mass Spectrometry Data
Published in bioRxiv, 2022
Reports the prototype of a metabolomics dashboard for facilitating the prioritization of bioactive metabolite by integrating orthogonal data.
Metabolome-guided genome mining of RiPP natural products
Published in Trends in Pharmacological Sciences, 2023
Review on genome- and metabolome-mining strategies for the investigation of ribosomally synthesized and post-translationally modified peptides (RiPPs).
Olive mill solid waste induces beneficial mushroom-specialized metabolite diversity: a computational metabolomics study
Published in bioRxiv, 2024
Investigation of the impact of olive mill solid waste on the metabolic profile of medicinal fungi Hericium erinaceus and Pleurotus eryngii, using metabolome mining.
The Minimum Information about a Tailoring Enzyme/Maturase data standard for capturing natural product biosynthesis
Published in chemRxiv, 2024
Whitepaper for a data standard/repository for natural product-acting tailoring enzymes, which are essential for the biological activities of many specialized metabolites.
Non-targeted metabolomics-based molecular networking enables the chemical characterization of Rumex sanguineus
Published in chemRxiv, 2024
In-depth metabolomics profiling of the plant Rumex sanguineus for food safety.
MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration
Published in Nucleic Acids Research, 2025
Update of the MIBiG database of biosynthetic gene clusters, with participation of 267 contributors in a global, collaborative effort.
Non-targeted metabolomics-based molecular networking enables the chemical characterization of Rumex sanguineus, a wild edible plant
Published in Springer Metabolomics, 2025
In-depth metabolomics profiling of the plant Rumex sanguineus for food safety.
Paired-omics-based exploration and characterisation of biosynthetic diversity in lichenized fungi
Published in Research Square, 2025
Investigation of the biosynthetic diversity of 111 lichen-associated fungi using genome and metabolome mining.
antiSMASH 8.0: extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation
Published in Nucleic Acids Research, 2025
Update of the genome mining platform antiSMASH, with a focus on tailoring enzymes and terpenoids.
Olive mill solid waste induces beneficial mushroom-specialized metabolite diversity revealed by computational metabolomics strategies
Published in Springer Metabolomics, 2025
Investigation of the impact of olive mill solid waste on the metabolic profile of medicinal fungi Hericium erinaceus and Pleurotus eryngii, using metabolome mining.
FERMO: a Dashboard for Automated Prioritization of Molecular Features from Mass Spectral Data
Published in bioRxiv, 2025
A free online dashboard for mining of mass spectrometry metabolomics data, automatically integrating orthogonal data on biological activity, sample metadata, and genomic information.
Multilaboratory Untargeted Mass Spectrometry Metabolomics Collaboration to Identify Bottlenecks and Comprehensively Annotate A Single Dataset
Published in Analytical Chemistry, 2025
Comparative study on differences in metabolome mining strategies and annotation performance between different laboratories on the same dataset.
MITE: the Minimum Information about a Tailoring Enzyme database for capturing specialized metabolite biosynthesis
Published in chemRxiv, 2025
Database on natural product-acting tailoring enzymes, which are essential for the biological activities of many specialized metabolites.
MITE: the Minimum Information about a Tailoring Enzyme database for capturing specialized metabolite biosynthesis
Published in Nucleic Acids Research, 2025
Database on natural product-acting tailoring enzymes, which are essential for the biological activities of many specialized metabolites.
talks
Talk 1 on Relevant Topic in Your Field
Published:
This is a description of your talk, which is a markdown file that can be all markdown-ified like any other post. Yay markdown!
Conference Proceeding talk 3 on Relevant Topic in Your Field
Published:
This is a description of your conference proceedings talk, note the different field in type. You can put anything in this field.
teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
This is a description of a teaching experience. You can use markdown like any other post.
Teaching experience 2
Workshop, University 1, Department, 2015
This is a description of a teaching experience. You can use markdown like any other post.