José D. D.Cediel-Becerra

Now out in @natcomms.nature.com :
versions 2.0 of both BiG-SCAPE and BiG-SLiCE! With significant speed and accuracy increases, as well as new interactive functionalities.
Read the full paper here #openaccess:
www.nature.com/articles/s41...

The MIBiG 5.0 Annotathon is coming soon, and registration is now open!

🧬 Does your research involve biosynthetic gene clusters? Do you love natural product biosynthesis? Do you have an interest in rare & exotic enzymes? We can use your help & expertise.

Register here 👉 forms.gle/C1cWcLHtrjT2...

Marnix Medema appointed chair of Bioinformatics at WUR Marnix Medema has been appointed Chair of the Bioinformatics Group at Wageningen University & Research as of 1 February. He aims to further strengthen bioinformatics as a connecting discipline within ...

I am delighted and feel honored to be appointed as chair of Bioinformatics at @w-u-r.bsky.social .
I look forward to working with the team and with our collaborators worldwide on keeping bioinformatics science and education flourishing at WUR and beyond.

www.wur.nl/en/news/marn...

EquilibraTor Streamlines Molecular Dynamics Simulations in a Single Execution Molecular dynamics (MD) simulations are powerful for investigating protein–ligand, protein–protein, and protein systems. However, manual setup remains time-consuming, error-prone for non-expert users,...

Excited to share EquilibraTor, our new pipeline that streamlines molecular dynamics simulations for proteins, protein–ligand, and protein–protein systems! Faster setups. Automated workflows. Useful from drug-discovery binding work to enzyme-mechanism insights.

www.csbj.org/article/S200...

MITE training session registration form Registration form for mailing list

Working on tailoring enzymes and want to learn more about the MITE database? We are organizing a hands-on training session on how use the DB and create new entries: October 30th and November 4th 10-11 am Amsterdam time. Sign up here: forms.gle/KHPqe9XV1RRg... See you there! #secmet #natprod

I’m excited to share the first paper from my lab that was led largely by undergraduate students at University of Wisconsin and Washington College! #secmet #natprod
www.frontiersin.org/journals/mic...

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/...

PhyloNaP: a user-friendly database of Phylogeny for Natural Product-producing enzymes Phylogenetic analysis is widely used to predict enzyme function, yet building annotated and reusable trees is labor-intensive and requires extensive knowledge about the specific enzymes. Existing reso...

Happy to share our newest preprint. PhyloNaP as a user friendly database of phylogeny for enzymes involved in natural product production and as public repository for well curated phylogenetic trees. Happy Tree Building!!!
#phylogeny #secmet #bioinformatics

www.biorxiv.org/content/10.1...

BiG-SCAPE 2.0 and BiG-SLiCE 2.0: scalable, accurate and interactive sequence clustering of metabolic gene clusters Microbial metabolic gene clusters encode the biosynthesis or catabolism of metabolites that facilitate ecological specialization, mediate microbiome interactions and constitute a major source of medic...

Now out as preprint: versions 2.0 of both BiG-SCAPE and BiG-SLiCE have been released! With significant speed and accuracy increases, as well as new interactive functionalities. www.biorxiv.org/content/10.1...

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!

Naming Challenge: Help Redefine the Glycopeptide Family! We are excited to launch a naming competition inspired by the recent preprint "Phylogenetic distance and structural diversity directing a reclassification of glycopeptide antibiotics" (https://www.bio...

⏰ Just 7 days left for our Glycopeptide Renaming Challenge!
💡 Share your best name idea and win 500€

👉 More info and submission here: docs.google.com/forms/d/1ym9...

#secmet #NaturalProducts #Antibiotics #NamingChallenge #Glycopeptides @gdwantibiotics.bsky.social @marghesosio.bsky.social

*JOB AD*: interested in doing a postdoc in microbial metabolomics? Passionate about natural products mass spec?

Come join the group! Informal enquires welcome!

Closing Date: 19 August 2025

jobs.ncl.ac.uk/job/Newcastl...

Green genes from blue greens: challenges and solutions to unlocking the potential of cyanobacteria in drug discovery Cyanobacteria are prolific producers of biologically active compounds that are important in influencing ecology, behavior of interacting organisms, and as leads in drug discovery efforts. Here we disc...

Here's a fun perspective piece on Cyanobacteria as prolific natural product producers with great potential for drug discovery. Thanks especially to @philmuslab.bsky.social for ringleading and letting us contribute!
pubs.rsc.org/en/content/a...

This is how we started implementing the similarity metric (GATOR Focal Scores) and how it actually turned out

Targeted genome mining with GATOR-GC maps the evolutionary landscape of biosynthetic diversity Abstract. Gene clusters, groups of physically adjacent genes that work collectively, are pivotal to bacterial fitness and valuable in biotechnology and med

GATOR-GC is out at @narjournal.bsky.social!! Check out our new targeted genome mining tool featuring a novel similarity metric to efficiently compare and deduplicate gene clusters.

We uncover biosynthetic diversity missed by other genome mining tools

academic.oup.com/nar/article/...

A decade ago, we had thousands of bacterial genomes. Now, we have millions. How to scale computational methods?

Our paper in @naturemethods.bsky.social answers this: use evolutionary history to guide compression and search.

rdcu.be/eg4OA

w/ @baym.lol, @zaminiqbal.bsky.social et al. 🧵1/

#JNatProd celebrates inspiring contributions of early career researchers to the field of natural products. 20 authors from 12 countries across 5 continents are highlighted – learn about them and their research here pubs.acs.org/page/jnprdf/...

antiSMASH 8.0: extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation Abstract. Microorganisms synthesize small bioactive compounds through their secondary or specialized metabolism. Those compounds play an important role in

antiSMASH8: The Ocho

Manuscript is out!
doi.org/10.1093/nar/...

GATOR-GC preprint is live! If you haven't already, check out our new tool for targeted gene cluster mining. @jcedielbecerra.bsky.social

doi.org/10.1101/2025...

Microbial secondary metabolites: advancements to accelerate discovery towards application Nature Reviews Microbiology - In this Review, Dinglasan and colleagues explore innovations that facilitate rapid microbial secondary metabolite discovery, focusing on recent techniques for the...

Our new review article "Microbial secondary metabolites: advancements to accelerate discovery towards application" in Nature Reviews Microbiology is now published!

rdcu.be/d6BHX

PARAS: high-accuracy machine-learning of substrate specificities in nonribosomal peptide synthetases Nonribosomal peptides are chemically and functionally diverse natural products with important applications in medicine and agriculture. Bacterial and fungal genomes contain thousands of nonribosomal p...

www.biorxiv.org/content/10.1...

#secmet 🧪🖥️🧬

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration Abstract. Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in ag

Are you working on natural products? We’ve just released version 4.0 of the MIBiG data standard and repository! It now includes 3059 biosynthetic gene clusters, thanks to the combined efforts of 288 expert contributors. A thread: (1/8) academic.oup.com/nar/advance-...

Our new paper is published in Scientific Data describing the genome sequences of 121 Bacillales isolates from all around the world
-together with @tilmweber.bsky.social

Joint DTU-BGI PhD project and nice collaborative effort providing the isolates

www.nature.com/articles/s41...

#Bacillus

Marine Natural Products/Marine Biotechnology - Assistant Professor University of California, San Diego is hiring. Apply now!

Scripps Institution of Oceanography, UCSD is looking for an assistant prof in marine natural products / marine biotech apol-recruit.ucsd.edu/JPF04101 #naturalproducts

If you’re interested in Streptomyces, other filamentous actinomycete bacteria and their natural products follow @ActinoBase. Linked to our wiki at actinobase.org. Please share.

The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters Abstract. Secondary metabolites are small molecules produced by all corners of life, often with specialized bioactive functions with clinical and environme

Very pleased to announce that our manuscript describing @jgi.doe.gov 's Secondary Metabolism Collaboratory is now available! SMC has been up and active for a while now, but I'm really excited to start seeing more activity on here. Lots more to come.

doi.org/10.1093/nar/...

The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters Abstract. Secondary metabolites are small molecules produced by all corners of life, often with specialized bioactive functions with clinical and environme

Our paper introducing the Secondary Metabolism Collaboratory (SMC) containing 13M BGCs from >1.3M genomes is just out: doi.org/10.1093/nar/... Access SMC at smc.jgi.doe.gov

If you’re interested in microbial specialized metabolites #naturalproducts - we’ve compiled a list of useful bioinformatics / community resources - it’s not meant to be comprehensive- just somewhere to start - let us know if you find it useful 😊 #microsky #secmet

Natural Products Conferences, Symposia, and Workshops Upcoming events This is a list of upcoming conferences, symposia, and workshops that may be of interest to researchers working on natural products (particularly secondary/specialized metabolites) Sub...

Natural product researchers, do you first hear about conferences when your PI says "I'll be gone next week"?

Here's a list of upcoming events for those who work on secondary/specialized metabolites, along with their deadlines:
tinyurl.com/NP-events

Thanks to those who have submitted events!

The JGI’s Secondary Metabolism Collaboratory, SMC, version 1.0 is released!
This is JGI’s database of natural product BGCs. The current version contains BGC info from AntiSMASH 7 and EmeraldBGC for as many bacteria as we could find (~1.3M genomes).
smc.jgi.doe.gov or secondarymetabolism.com
1/n 🧪🧬🖥️