Marnix Medema

Sounds like a great opportunity for a professor position in computational biology in the Netherlands careers.universiteitleiden.nl/job/Assistan...

All in all, thanks to the engineering efforts of Arjan Draisma, @catarinacarolina.bsky.social, Nico Louwen, Satria Kautsar, @jorgenavarro.bsky.social and the rest of the author team, and shout-out to the
@jgi.doe.gov
and
@nigelmouncey.bsky.social .bsky.social
for a wonderful collaboration.

At the same time, for mid-size datasets (most frequent use case), BiG-SCAPE v2 approaches the speed of BiG-SLiCE. For larger datasets, BiG-SCAPE has become more resource-efficient, which now allowed us to analyse >250k BGCs (the antiSMASH database) with it in just a few days on a compute server.

Benchmarking on several different types of ground truth datasets shows the increases in accuracy, with BiG-SLiCE v2 often matching BiG-SCAPE v1 accuracy, and BiG-SCAPE v2 combining its speed increase with a small but notable accuracy gain as well.

BiG-SCAPE was completely rewritten from scratch over the past few years, and now features new alignment modes, a more prominent query mode (which allows you to search genomes from a single BGC query) and more scalable interactive visualizations and data selection/filtering.

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...

Make sure to join us in the MIBiG Annotathons! The MITE database (mite.bioinformatics.nl) will join the efforts! If you are interested in tailoring enzymes/maturases, make sure to join us!

Come join us again in a next round of this massive online open science community effort! 💪
Sign up using the link in the thread.
It’s great fun, and really helps the scientific community. What more can you ask? 🙂

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...

Come join us again in a next round of this massive online open science community effort! 💪
Sign up using the link in the thread.
It’s great fun, and really helps the scientific community. What more can you ask? 🙂

The students in my lab just started a Bluesky account 🦋 -- give them/us a follow to see events, scientist spotlights, and announcements!

Welcome to the Bluesky page for the Avalon Lab! Currently located at UC Irvine, we explore marine natural products in pursuit of discovering novel neurotherapeutics. Keep up with our lab through our social media posts!

Learn more about the Avalon Lab through the Linktree in our bio :)

#SynBYSS welcome Profs. Jae-Yean Kim at Gyeongsang National U., Pimchai Chaiyen, President of Vidyasirimedhi Institute of Science and Technology (VISTEC), Marnix Medema at Wageningen U. & Yajun Yan, an NAI fellow at U. Georgia as the 279th-282nd pioneer speakers! Thanks!
@marnixmedema.bsky.social

We have an open position for a bioinformatics/theoretical microbial ecology PhD student to study viral strategies in the global Microverse! Join us at the @microverse.bsky.social at @uni-jena.de, please apply through this link:
jobs.uni-jena.de/jobposting/9...

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...

Working in aquaculture, marine biotech, agrochemicals, biopharma or exploring marine natural products & blue‑biotech applications?

Then join us at the MARBLES Stakeholder Summit!

📅 26 March 2026
📍 Naturalis Biodiversity Center, Leiden
🌟 Register now: forms.office.com/e/y2kCNfH8BT 🌟

Full Professor and Chair Laboratory of Biophysics We are looking for a Full Professor in the Biophysics chair group, part of Wageningen University & Research (WUR)

www.wur.nl/en/vacancy/f...

Become our new colleague (and next door neighbor) and lead a chair/group/department of Biophysics at Wageningen University. Reach out to me for info and please spread!!!

In remembrance of Peer Bork  | EMBL EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General. 

We mourn the passing of Peer Bork, EMBO Member since 2000: https://www.embl.org/news/embl-announcements/in-remembrance-of-peer-bork/

Welcome to the SMASH family! Looking forward to using this wonderful new tool…

Paired-omics-based exploration and characterization of biosynthetic diversity in lichenized fungi The increasing demand for novel drug leads requires bioprospecting non-model taxa. Comparative genomics and correlative omics are a fast and efficient method for linking bioactive but genetically orph...

Ever wondered about the funny moss growing on trees? Chances were good that you were looking at #lichen! These hybrid fungal-algae/cyanobacterial colonies are biosynthetically surprisingly diverse, as we show in our newest publication led by @garimasingh-gs.bsky.social doi.org/10.1099/mgen... (1/5)

Of course I see your general point. Admiring something does not mean I suggest mindlessly emulating it, although it would be arrogant to deny there is a lot we can learn from how people do things in other corners of the world, like China; see e.g. also the speed of transport electrification there.

Grab the chance to already pre-register for the MIBiG 5.0 annotathons that we plan to organize in spring 2026!

Kudos to #yijunzhu #hannahaugustijn and #victoriapascal for getting this out, and thanks to @gillesvanwezel.bsky.social #dylandodd and #michaelfischbach for the collaboration!
Try it out now on gutsmash.bioinformatics.nl

gutSMASH 2.0: Extended Identification of Primary Metabolic Gene Clusters From the Human Gut Microbiota Microbiota-derived metabolites serve as key messengers mediating host–microbe and microbe–microbe interactions, often through specialized primary meta…

Now available online: the new 2.0 version of gutSMASH, with capabilities to detect 12 new types of catabolic gene clusters relevant to gut microbiome ecology, as well as predictions of their regulation through transcription factor binding site detection. www.sciencedirect.com/science/arti...

Strategies for community-sourced biocuration in bioinformatics: a case study on MIBiG 4.0 Abstract. Biocuration is essential to transform molecular sequence data into standardized, machine-readable resources. Such curated datasets enable compara

Have you ever used a #bioinformatics #database and were frustrated by its lack of coverage? Did you ever think about starting your own resource? We just published a new strategy for community-driven #biocuration, based on our experiences with the #MIBiG database (1/8)! doi.org/10.1093/bib/...

Impressed by the hyper modern campus of Shenzhen University of Advanced Technology. All built in just over one year... 😮

Now out in @asm.org #mSystems! journals.asm.org/doi/10.1128/...
Congratulations to Robert and thanks to all collaborators. See thread below for a summary of the work, exploring the use of cross-species coexpression analyses to predict primary and secondary metabolic interactions in microbiomes.

Discovery and Heterologous Expression of the Soil Metagenome-Derived Lasso Peptide Metanodin with an Unprecedented Ring Structure Culture-independent metagenomic approaches have proven to be effective tools for identifying previously hidden biosynthetic gene clusters (BGCs) encoding novel natural products with potential medical relevance. However, producing these compounds remains challenging as metagenomic BGCs often originate from organisms phylogenetically distant from available heterologous hosts. Lasso peptides, a subclass of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products, exhibit diverse bioactivities, yet no lasso peptide has previously been discovered directly from a metagenome. Here, we report the discovery and heterologous expression of the first soil metagenome-derived lasso peptide. Expression of its biosynthetic gene cluster in Escherichia coli, followed by mass spectrometry analysis, strongly supported the predicted amino acid sequence and lasso structure of the peptide. Notably, this lasso peptide is the first to feature asparagine as the ring-forming residue at position one. Taxonomic analysis of the corresponding BGC identified an uncultivated member of the Steroidobacterales family (Gammaproteobacteria) as the closest known relative of the potential native host. These findings underscore the potential of metagenomic genome mining to reveal structurally novel RiPPs and to expand our understanding of the natural diversity of lasso peptides.

Happy to share our newest manuscript about the discovery and hererologous expression of metanodin, a new lassopeptide with unprecedented structural features directly from soil metagenomes. pubs.acs.org/doi/full/10....
#secmet #lassopeptides #syntheticbiology

Kudos to @elenadelpup.bsky.social for this significant update to plantiSMASH! Try it out now...

Charting the biosynthetic landscape of hybrid polyketide-nonribosomal peptide-specialized lipids Polyunsaturated fatty acid (PUFA) synthase-like enzymes are best known for their role in membrane lipid biosynthesis in marine bacteria, but have also been repurposed for the assembly of specialized l...

Polyunsaturated fatty acid (PUFA) synthase enzymes turn out to be far more versatile than we ever imagined! In our new preprint, we reveal a largely untapped biosynthetic space where they team up with PKSs and NRPSs to create new types of bioactive amphiphilic metabolites.
👉http://bit.ly/4hzUUak