mmzdouc.bsky.social
Mitja M. Zdouc
@mmzdouc.bsky.social
290 followers 140 following 39 posts
Pharmacist from Austria, with a PhD in Natural Product Chemistry. PostDoc at Wageningen University. Really likes RiPPs and programming in Python, scuba diving, and hiking.
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mmzdouc.bsky.social
Mitja M. Zdouc @mmzdouc.bsky.social · 8d
Hopefully this will be a wakeup call for journals which still accept images of gels or western blots as experimental evidence 🙃
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Mitja M. Zdouc @mmzdouc.bsky.social · 11d
Typo: it should be mite.bioinformatics.nl
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Mitja M. Zdouc @mmzdouc.bsky.social · 11d
Great to see PhyloNaP out! Great tool, and it also connects to mite.bioinformatic.nl! #openscience #collaboration
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Mitja M. Zdouc @mmzdouc.bsky.social · 11d
Again, thanks a lot to all the contributors and especially @adafede.bsky.social @skepteis.bsky.social @jjjvanderhooft.bsky.social @marnixmedema.bsky.social @catarinacarolina.bsky.social @jorgenavarro.bsky.social @nadineziemert.bsky.social @tilmweber.bsky.social @kblin.bsky.social
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Mitja M. Zdouc @mmzdouc.bsky.social · 11d
MITE is created by the natural products community, for the community! If you are interested in learning more about using MITE or even contributing to it, make sure to sign up for the mailing list! We will organize a first training session for MITE soon-ish (mid-October)! forms.gle/9NUe2aovynTV...
MITE training session registration form
Registration form for mailing list
forms.gle
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mmzdouc.bsky.social
Mitja M. Zdouc @mmzdouc.bsky.social · 11d
MITE can be queried in various ways to get information about tailoring enzymes, their pathways, and associated organisms. Its already being used by @antismash.bsky.social and MIBiG, and we foresee its use in machine learning applications for enzyme reaction prediction and classification!
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Mitja M. Zdouc @mmzdouc.bsky.social · 11d
The MITE database is a curated, crowd-sourced, and expert-reviewed database of tailoring enzymes, capturing catalytic reactions, substrate specificities, genomic context, and cross-references to existing resources (e.g. MIBiG, Rhea, UniProt).
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mmzdouc.bsky.social
Mitja M. Zdouc @mmzdouc.bsky.social · 11d
Aaand it's out! Meet MITE - the natural product tailoring enzyme database, just published in @narjournal.bsky.social! MITE DB captures the substrate- and reaction-specificity of tailoring enzymes, allowing to capture this information in a human- and machine-readable way! doi.org/10.1093/nar/...
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Mitja M. Zdouc @mmzdouc.bsky.social · 13d
Next at @vaam-microbes.bsky.social Workshop, Leo Dumjahn talks about the opportunistic pathogen Chromobacterium haemolyticum and the cyclic lipopeptides it uses as virulence factors.
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Mitja M. Zdouc @mmzdouc.bsky.social · 13d
Next at the @vaam-microbes.bsky.social Workshop, Valerie Rebhahn is talking about the cyanobacterial aetokthonotoxin and its mode of action in uncoupling the oxidative phosphorylation in mitochondria.
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Mitja M. Zdouc @mmzdouc.bsky.social · 13d
In today's third talk at @vaam-microbes.bsky.social Workshop at @freieuniversitaet.bsky.social, Nico Brüssow talks about the lanthipeptide II RiPP nostolanthin A which apparently oligomerizes - a very unusual property in RiPPs.
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Mitja M. Zdouc @mmzdouc.bsky.social · 13d
Next at VAAM Workshop at @freieuniversitaet.bsky.social , Alexandra Eckart from HIPS talking about her discoveries of tenacious bacteria isolated from Hydractinia echinata hydroids.
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Mitja M. Zdouc @mmzdouc.bsky.social · 13d
@mitjare.bsky.social kicking off the second day of the VAAM Workshop at @freieuniversitaet.bsky.social talking about the phyllosphere, its bacterial inhabitants and the natural products they produce - including surfactants!
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Mitja M. Zdouc @mmzdouc.bsky.social · 26d
Super interesting perspective!
mmzdouc.bsky.social
Mitja M. Zdouc @mmzdouc.bsky.social · Sep 8
If you are interested, make sure to apply! I have been working with Marnix, Justin, and Daniel over the last few years and they are awesome!
marnixmedema.bsky.social
Marnix Medema @marnixmedema.bsky.social · Sep 8
We are looking for a 3-year postdoc to work with Daniel Probst, Justin van der Hooft and myself on an exciting project involving federated learning and integrative omics for discovery of new antibiotics from natural products.
Apply here: www.wur.nl/en/vacancy/p...
Please share!
www.wur.nl
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Reposted by Mitja M. Zdouc
marnixmedema.bsky.social
Marnix Medema @marnixmedema.bsky.social · Sep 8
We are looking for a 3-year postdoc to work with Daniel Probst, Justin van der Hooft and myself on an exciting project involving federated learning and integrative omics for discovery of new antibiotics from natural products.
Apply here: www.wur.nl/en/vacancy/p...
Please share!
www.wur.nl
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Mitja M. Zdouc @mmzdouc.bsky.social · Aug 21
This work would have not been possible without the contributions of our many data submitters, reviewers, and collaborators, especially @adafede.bsky.social , @skepteis.bsky.social , @kblin.bsky.social , @jjjvanderhooft.bsky.social, @marnixmedema.bsky.social! Many thanks! (8/8)
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Mitja M. Zdouc @mmzdouc.bsky.social · Aug 21
If you want to get involved, make sure to contact us, either via email, or using our Discussion forum at the MITE Standard GitHub Organization (github.com/mite-standard)! (7/8)
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Mitja M. Zdouc @mmzdouc.bsky.social · Aug 21
As a crowd-sources database, MITE lives from community contributions! Data submission happens via the webpage and undergoes expert review. With its rolling release system, approved entries go live quickly and contributors become eligible as co-authors of the next update manuscript! (6/8)
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mmzdouc.bsky.social
Mitja M. Zdouc @mmzdouc.bsky.social · Aug 21
Besides as a knowledge base, MITE can be used as an reference database (already used by antiSMASH), input for in silico biosynthesis simulations, and as training dataset for machine learning. The MITE database is free open source and can be either downloaded or accessed via its API (5/8).
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Mitja M. Zdouc @mmzdouc.bsky.social · Aug 21
In microcin J25 biosynthesis, the macrolactam-synthase McjC acts on diverse peptides with only a few essential residues. Instead of listing every possible variant, MITE encodes this neatly in one SMARTS statement – comprehensive and clean (see it here: mite.bioinformatics.nl/repository/M...). (4/8)
Minimum Information about a Tailoring Enzyme Repository
mite.bioinformatics.nl
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Mitja M. Zdouc @mmzdouc.bsky.social · Aug 21
To summarize the catalytic function of tailoring enzymes, MITE uses reaction SMARTS, a chemical pattern language. This abstracts reaction- and substrate-specificity beyond individual substrate-product pairs. – here an example (3/8).
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Mitja M. Zdouc @mmzdouc.bsky.social · Aug 21
The MITE (Minimum Information about a Tailoring Enzyme) database is a curated, crowd-sourced, and expert-reviewed database of tailoring enzymes, currently containing 202 enzymes. Each entry contains catalytic reactions, substrate specificity, genomic context, and cross-reference (e.g. MIBiG). (2/8)
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mmzdouc.bsky.social
Mitja M. Zdouc @mmzdouc.bsky.social · Aug 21
Into natural product biosynthesis & tailoring enzymes? Frustrated by the lack of a dedicated resource to explore their functions? Tired of endless literature searches for reaction info? Meet the MITE database, freely available at mite.bioinformatics.nl. Preprint: doi.org/10.26434/che... (1/8)
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Mitja M. Zdouc @mmzdouc.bsky.social · Jun 4
Great to see it out @georgelund.bsky.social! Congrats!
georgelund.bsky.social
George Lund @georgelund.bsky.social · Jun 3
🚨 New preprint!
We've developed a bioassay-guided genome mining approach to identify bacterial secondary metabolites that inhibit Zymoseptoria tritici — a major fungal pathogen of wheat.
Available now on bioRxiv: doi.org/10.1101/2025...
Development of a bioassay guided genome mining approach for antifungal natural product discovery from pseudomonads
Zymoseptoria tritici causes Septoria Leaf Blotch disease of wheat and has evolved to overcome most chemical and genetic control methods. As such, new tools are required for future disease control. We...
doi.org
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