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Reposted by José D. D.Cediel-Becerra

Dan May @dansmay.bsky.social · 8d

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...

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Reposted by José D. D.Cediel-Becerra

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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Reposted by José D. D.Cediel-Becerra

Nadine Ziemert @nadineziemert.bsky.social · 11d

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...

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...

www.biorxiv.org

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Reposted by José D. D.Cediel-Becerra

Marnix Medema @marnixmedema.bsky.social · Sep 1

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...

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...

www.biorxiv.org

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Reposted by José D. D.Cediel-Becerra

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 José D. D.Cediel-Becerra

Nadine Ziemert @nadineziemert.bsky.social · Sep 8

⏰ 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

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...

docs.google.com

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Reposted by José D. D.Cediel-Becerra

Dr Katherine Duncan @kateduncan.bsky.social · Jul 22

*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...

Research Associate - Microbial Metabolomic

jobs.ncl.ac.uk

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Reposted by José D. D.Cediel-Becerra

Dan Udwary @danudwary.secondarymetabolism.com · Jul 16

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...

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...

pubs.rsc.org

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José D. D.Cediel-Becerra @jcedielbecerra.bsky.social · Jul 8

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

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José D. D.Cediel-Becerra @jcedielbecerra.bsky.social · Jul 8

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/...

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

academic.oup.com

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Reposted by José D. D.Cediel-Becerra

Karel Břinda @brinda.eu · Apr 11

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/

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Reposted by José D. D.Cediel-Becerra

Katherine Maloney @katherinem.bsky.social · Apr 30

#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/...

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Reposted by José D. D.Cediel-Becerra

Marc Chevrette @wildtypemc.bsky.social · Apr 27

antiSMASH8: The Ocho

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

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

doi.org

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Reposted by José D. D.Cediel-Becerra

Marc Chevrette @wildtypemc.bsky.social · Feb 28

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...

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Reposted by José D. D.Cediel-Becerra

Nigel Mouncey @nigelmouncey.bsky.social · Jan 17

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

rdcu.be/d6BHX

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...

rdcu.be

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Reposted by José D. D.Cediel-Becerra

Dan Udwary @danudwary.secondarymetabolism.com · Jan 13

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

#secmet 🧪🖥️🧬

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

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Reposted by José D. D.Cediel-Becerra

Mitja M. Zdouc @mmzdouc.bsky.social · Dec 10

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-...

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

academic.oup.com

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Reposted by José D. D.Cediel-Becerra

Ákos T Kovács @evolvedbiofilm.bsky.social · Nov 21

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

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Reposted by José D. D.Cediel-Becerra

Dr Katherine Duncan @kateduncan.bsky.social · Nov 18

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

Marine Natural Products/Marine Biotechnology - Assistant Professor

University of California, San Diego is hiring. Apply now!

apol-recruit.ucsd.edu

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Reposted by José D. D.Cediel-Becerra

Matt Hutchings @matthutchings.bsky.social · Nov 19

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.

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Reposted by José D. D.Cediel-Becerra

Dan Udwary @danudwary.secondarymetabolism.com · Nov 14

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

doi.org

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Reposted by José D. D.Cediel-Becerra

Nigel Mouncey @nigelmouncey.bsky.social · Nov 16

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

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

doi.org

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Reposted by José D. D.Cediel-Becerra

Dr Katherine Duncan @kateduncan.bsky.social · Nov 14

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

ActinoBase @actinobase.bsky.social · Nov 14

We’ve just published a comprehensive list of bioinformatics resources. Thanks to @kateduncan.bsky.social and @andytruman4.bsky.social for compiling this list: actinobase.org/index.php?ti...

Bioinformatics - ActinoBase

actinobase.org

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Reposted by José D. D.Cediel-Becerra

Zach Reitz @zachreitz.bsky.social · Nov 18

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!

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...

tinyurl.com

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Reposted by José D. D.Cediel-Becerra

Dan Udwary @danudwary.secondarymetabolism.com · Nov 17

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 🧪🧬🖥️

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