José D. D.Cediel-Becerra
@jcedielbecerra.bsky.social
Computational Biology | Genome mining | Structural Biology
Reposted by José D. D.Cediel-Becerra
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
MITE training session registration form
Registration form for mailing list
forms.gle
October 24, 2025 at 1:37 PM
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
Reposted by José D. D.Cediel-Becerra
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...
www.frontiersin.org/journals/mic...
September 30, 2025 at 8:54 PM
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...
www.frontiersin.org/journals/mic...
Reposted by José D. D.Cediel-Becerra
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/...
September 27, 2025 at 9:11 AM
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/...
Reposted by José D. D.Cediel-Becerra
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...
#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
September 27, 2025 at 9:32 AM
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...
#phylogeny #secmet #bioinformatics
www.biorxiv.org/content/10.1...
Reposted by José D. D.Cediel-Becerra
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
September 1, 2025 at 10:35 PM
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...
Reposted by José D. D.Cediel-Becerra
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!
Apply here: www.wur.nl/en/vacancy/p...
Please share!
www.wur.nl
September 8, 2025 at 9:07 AM
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!
Apply here: www.wur.nl/en/vacancy/p...
Please share!
Reposted by José D. D.Cediel-Becerra
⏰ 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
💡 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
September 8, 2025 at 12:14 PM
⏰ 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
💡 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
Reposted by José D. D.Cediel-Becerra
*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...
Come join the group! Informal enquires welcome!
Closing Date: 19 August 2025
jobs.ncl.ac.uk/job/Newcastl...
Research Associate - Microbial Metabolomic
Research Associate - Microbial Metabolomic
jobs.ncl.ac.uk
July 22, 2025 at 2:32 PM
*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...
Come join the group! Informal enquires welcome!
Closing Date: 19 August 2025
jobs.ncl.ac.uk/job/Newcastl...
Reposted by José D. D.Cediel-Becerra
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...
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
July 16, 2025 at 2:35 PM
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...
pubs.rsc.org/en/content/a...
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/...
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
July 8, 2025 at 12:04 PM
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/...
We uncover biosynthetic diversity missed by other genome mining tools
academic.oup.com/nar/article/...
Reposted by José D. D.Cediel-Becerra
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/
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/
April 11, 2025 at 3:01 PM
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/
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/
Reposted by José D. D.Cediel-Becerra
#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/...
April 30, 2025 at 12:05 AM
#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/...
Reposted by José D. D.Cediel-Becerra
Reposted by José D. D.Cediel-Becerra
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...
doi.org/10.1101/2025...
February 28, 2025 at 3:16 PM
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...
doi.org/10.1101/2025...
Reposted by José D. D.Cediel-Becerra
Our new review article "Microbial secondary metabolites: advancements to accelerate discovery towards application" in Nature Reviews Microbiology is now published!
rdcu.be/d6BHX
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
January 17, 2025 at 4:20 PM
Our new review article "Microbial secondary metabolites: advancements to accelerate discovery towards application" in Nature Reviews Microbiology is now published!
rdcu.be/d6BHX
rdcu.be/d6BHX
Reposted by José D. D.Cediel-Becerra
Reposted by José D. D.Cediel-Becerra
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
December 10, 2024 at 8:05 AM
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-...
Reposted by José D. D.Cediel-Becerra
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
-together with @tilmweber.bsky.social
Joint DTU-BGI PhD project and nice collaborative effort providing the isolates
www.nature.com/articles/s41...
#Bacillus
November 21, 2024 at 2:53 PM
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
-together with @tilmweber.bsky.social
Joint DTU-BGI PhD project and nice collaborative effort providing the isolates
www.nature.com/articles/s41...
#Bacillus
Reposted by José D. D.Cediel-Becerra
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
November 18, 2024 at 9:26 PM
Scripps Institution of Oceanography, UCSD is looking for an assistant prof in marine natural products / marine biotech apol-recruit.ucsd.edu/JPF04101 #naturalproducts
Reposted by José D. D.Cediel-Becerra
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.
November 19, 2024 at 4:27 PM
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.
Reposted by José D. D.Cediel-Becerra
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/...
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
November 14, 2024 at 5:31 PM
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/...
doi.org/10.1093/nar/...
Reposted by José D. D.Cediel-Becerra
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
November 16, 2024 at 6:42 PM
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
Reposted by José D. D.Cediel-Becerra
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
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
November 14, 2024 at 11:45 AM
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
Reposted by José D. D.Cediel-Becerra
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!
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
November 18, 2023 at 4:14 PM
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!
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!
Reposted by José D. D.Cediel-Becerra
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 🧪🧬🖥️
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 🧪🧬🖥️
November 17, 2023 at 4:56 PM
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 🧪🧬🖥️
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 🧪🧬🖥️