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tilmweber.bsky.social
Tilmann Weber
@tilmweber.bsky.social
900 followers 1.4K following 21 posts
Professor at DTU NNF Center for Biosustainability with interest in bioactive compounds, comp. biol., WGS and much more; hobby photographer. Views are my own.
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Reposted by Tilmann Weber
nadineziemert.bsky.social
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 Tilmann Weber
natprodreports.rsc.org
Natural Product Reports @natprodreports.rsc.org · 12d
Be sure to read this review, part of our Industrial Perspective themed collection, by Stefano Donadio & co. from NAICONS Srl discussing the trends in metabolite discovery from Actinomycetes #secmet #natprod

Find it in full below👇
Trends in metabolite discovery from Actinomycetes
Covering: 2013 to 2023 In this review, we analyzed the scientific literature of the period 2013–2023 that reported novel specialized metabolites from the Actinomycetes, one of the most prolific…
pubs.rsc.org
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Reposted by Tilmann Weber
phypapers.bsky.social
phy_papers @phypapers.bsky.social · 12d
PhyloNaP: a user-friendly database of Phylogeny for Natural Product-producing enzymes https://www.biorxiv.org/content/10.1101/2025.09.23.677986v1
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Reposted by Tilmann Weber
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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Reposted by Tilmann Weber
evolvedbiofilm.bsky.social
Ákos T Kovács @evolvedbiofilm.bsky.social · Jul 4
Happy to share this detective work by Rune Overlund Stannius now published in #mSystems

phenotype+genomes▶️GWAS▶️gene cluster for pigment production

Identification of widely conserved biosynthetic gene cluster involved in pigment production of Bacillus subtilis
journals.asm.org/doi/10.1128/...
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Reposted by Tilmann Weber
kateduncan.bsky.social
Dr Katherine Duncan @kateduncan.bsky.social · Jun 17
After lunch at #ISBA2025: Keynote talk from Prof @lonegram.bsky.social (DTU) on ‘Tropodithietic acid - a multifunctional bacterial secondary metabolite’ #naturalproducts #specialisedmetabolites
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Reposted by Tilmann Weber
gillesvanwezel.bsky.social
Gilles van Wezel @gillesvanwezel.bsky.social · Jun 14
A key aspect of my @erc.europa.eu Advanced project 'Community' was to predict biosynthetic gene cluster (BGC) function entirely on how BGCs are controlled, without looking at predicted gene function or natural product. We show proof of concept for this idea in this paper in @plosbiology.org (1/2)
plosbiology.org
PLOS Biology @plosbiology.org · Jun 13
Most #biosynthetic gene clusters remain uncharacterized. @marnixmedema.bsky.social @gillesvanwezel.bsky.social &co integrate #GRN analysis & global expression data to identify desJGH as an operon essential for #biosynthesis of #desferrioxamineB in Streptomyces @plosbiology.org 🧪 plos.io/43UVUPB
Left: Predicted gene regulatory network of Streptomyces coelicolor based on 17 well-known regulators. Each node in the network represents a (regulatory) gene, and every edge represents a PWM predicted regulatory interaction between nodes. The edges colored in dark gray indicate strong PWM prediction scores, while the lighter gray shades represent weaker interactions. Matches within BGC regions are depicted as triangles. In six regions (black circled), the matches fall within a co-expressed region, highlighting their functional relation to these compounds. Right: Proposed biosynthetic pathway for assembly of desferrioxamines E and B. Main biosynthetic enzymes presented in bold face. DesG and DesH balance intracellular N-hydroxy-N-succinylcadaverine (HSC) and N-hydroxy-N-acetylcadaverine (HAC) concentrations by converting HSC to HAC. In the absence of DesG and/or DesH, the cells likely fail to produce sufficient levels of HAC, thereby strongly attenuating the production of DFOB. Although DesC has been shown to be able to catalyze the acetylation of N-hydroxycadaverine in vitro, the enzyme can only modestly compensate for the loss of DesH in vivo, underlining the important role played by DesG and DesH in DFOB production.
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Reposted by Tilmann Weber
kateduncan.bsky.social
Dr Katherine Duncan @kateduncan.bsky.social · Jun 15
Profs Gilles van Wezel and Eva Stegmann giving the Welcome Ceremony of the 20th International Symposium on the Biology of Actinomycetes in Edmond aan Zee (coastal Netherlands) #ISBA2025 #actinomycetes #streptomyces
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Reposted by Tilmann Weber
kateduncan.bsky.social
Dr Katherine Duncan @kateduncan.bsky.social · Jun 15
Wonderful to have Prof Pieter Dorrestein @pieterdorrestein.bsky.social giving the opening keynote talk of #ISBA2025 on ‘Scaling the discovery of new microbial natural products through data science of unused metabolomics data’ #naturalproducts #specializedmetabolites #secmet
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Reposted by Tilmann Weber
kblin.bsky.social
Kai Blin @kblin.bsky.social · May 26
We’ve just released #antiSMASH 8.0.1, a bug-fix release. Find the tarball and containers in the usual places, it’s also live on our website now. Bioconda containers aren’t built by us, they might take a while to update. We recommend installing deps via bioconda and then running from our releases.
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Reposted by Tilmann Weber
kblin.bsky.social
Kai Blin @kblin.bsky.social · Jun 11
Happy to contribute to a C&EN article on genome mining for antimicrobials cen.acs.org/pharmaceutic...
Great article by Max Barnhart, who’s not on BlueSky for all I can tell.
Bioprospectors mine microbial genomes for antibiotic gold
But turning what they find into drugs isn’t so easy
cen.acs.org
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Reposted by Tilmann Weber
magicmolfun.bsky.social
MAGic-MOLFUN @magicmolfun.bsky.social · Jun 12
Great start of our MAGic-MOLFUN Industrial Training Event at NAICONS Srl in Milano!
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Reposted by Tilmann Weber
cibiocm.bsky.social
Segata Lab @cibiocm.bsky.social · Jun 6
Join us at #EESMicrobiome!

Organisers Mani Arumugam (#uni_copenhagen), Ami Bhatt (@stanfordpress.bsky.social), Peer Bork (@borklab.bsky.social) and Nicola Segata (#CIBIO_UniTrento) look forward to welcoming #microbiome scientists in September at @embl.org!

@events.embl.org
EESMicrobiome
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Reposted by Tilmann Weber
mkddueholm.bsky.social
Morten Kam Dahl Dueholm @mkddueholm.bsky.social · May 15
I can highly recommend you to try out this tool developed by my PhD student @andersohd.bsky.social and other members of our research group in collaboration with @tilmweber.bsky.social team. It is still a beta version, but we hope to finish it soon.
friendlymicrobe.bsky.social
Freya Harrison @friendlymicrobe.bsky.social · May 15
Now at #Biofilms11, @andersohd.bsky.social is introducing epssmash.secondarymetabolites.org - a tool for mining microbial genomes for exopolysaccharide biosynthetic gene clusters. Looks really valuable for finding new & different #biofilm producers #MicroSky
epsSMASH
epssmash.secondarymetabolites.org
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Reposted by Tilmann Weber
mingxunwang.bsky.social
Mingxun Wang @mingxunwang.bsky.social · May 12
I am thrilled to share after years of work/procrastination that the MassQL manuscript is finally published in @natmethods.nature.com - "A universal language for finding mass spectrometry data patterns". This was an team effort from all co-authors that helped shape MassQL and how it could be used.
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Reposted by Tilmann Weber
evolvedbiofilm.bsky.social
Ákos T Kovács @evolvedbiofilm.bsky.social · May 12
Congratulations to Dr Lijie Song for defending her PhD today 🎉 exploring Bacillales genome sequences & encoded BGCs.

Project was jointly supervised by @tilmweber.bsky.social - my first PhD graduate where co-supervision truly meant equal supervision, for which I am thankfull to Tilmann!
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Reposted by Tilmann Weber
ioannachatzig.bsky.social
Ioanna Chatzigiannidou @ioannachatzig.bsky.social · May 7
Time for our yearly #DTU microbes conference and we have a great program this year! 🦠🎤 #microbiology
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Reposted by Tilmann Weber
natprodreports.rsc.org
Natural Product Reports @natprodreports.rsc.org · Apr 29
🔓Don't miss this #OpenAccess Viewpoint by @jjjvanderhooft.bsky.social @marnixmedema.bsky.social Adam Skiredj & co at @w-u-r.bsky.social @univparissaclay.bsky.social @mit.edu on empowering natural product science with AI #natprod #chemsky

Check it out here🔽
pubs.rsc.org/en/content/a...
Empowering natural product science with AI: leveraging multimodal data and knowledge graphs
Artificial intelligence (AI) is accelerating how we conduct science, from folding proteins with AlphaFold and summarizing literature findings with large language models, to annotating genomes and…
pubs.rsc.org
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tilmweber.bsky.social
Tilmann Weber @tilmweber.bsky.social · Apr 28
Many thanks to the funding agencies supporting the scientists contributing to #antiSMASH. At @dtu.dk, the #antiSMASH team would like to thank the Novo Nordisk Foundation, Danmarks Grundforskningsfond @dg.dk (@cemist.bsky.social), and the EU MSCA DN @magicmolfun.bsky.social. #dkforsk
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tilmweber.bsky.social
Tilmann Weber @tilmweber.bsky.social · Apr 28
We're happy to announce that the #antiSMASH v8 paper is out in @narjournal.bsky.social: academic.oup.com/nar/advance-...
Many thanks to @kblin.bsky.social, @marnixmedema.bsky.social and many international collaborators!
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
academic.oup.com
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Reposted by Tilmann Weber
cemist.bsky.social
cemist.bsky.social @cemist.bsky.social · Mar 25
Forskningens døgn/Science Fair - www.Forsk.dk
Come get inspired!
The Centers of Excellence at DTU invites everyone to come see our work on Thursday 24th of April at 10-13, Building 202, Anker Engelunds Vej 1

Contact @cemist.bsky.social for more info.
@dg.dk Danmarks Grundforskningsfond
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tilmweber.bsky.social
Tilmann Weber @tilmweber.bsky.social · Apr 5
Many thanks to Tenna A. Møller, @thombooth.bsky.social, Simon Shaw from DTU Biosustain and Vilhelm K. Møller and Rasmussen JN Frandsen from DTU Bioengineering
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tilmweber.bsky.social
Tilmann Weber @tilmweber.bsky.social · Apr 5
Have a look at our latest tool: ActinoMation - a toolkit for automated E. coli – Streptomyces conjugation on Opentron laboratory automation systems: www.sciencedirect.com/science/arti...
ActinoMation: A literate programming approach for medium-throughput robotic conjugation of Streptomyces spp
The genus Streptomyces are valuable producers of antibiotics and other pharmaceutically important bioactive compounds. Advances in molecular engineeri…
www.sciencedirect.com
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Reposted by Tilmann Weber
chriiswh.bsky.social
Christopher Whitford @chriiswh.bsky.social · Mar 27
8/8 Finally, a big thank you to all co-authors - Peter, David, Renata, Tetiana, and @tilmweber.bsky.social ! This has been a fun collaboration!
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Reposted by Tilmann Weber
chriiswh.bsky.social
Christopher Whitford @chriiswh.bsky.social · Mar 27
7/8 We further further sequenced hosts after BAC integration and verified multicopy integrations, and showed that the genomes remain stable, even in non-selective medium.

If your are engineering streptomycetes, please give it a try and let us know how it goes! All plasmids are on Addgene!
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