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Reposted by Bas E. Dutilh

Ragnar {Groot Koerkamp} @curiouscoding.nl · Jul 18

Sassy is out now!

Ever need to search for approximate matches of short DNA strings?
Sassy is the tool to use!

Available now wherever you get your code

With @rickbitloo.bsky.social

curiouscoding.nl/papers/sassy...
github.com/ragnarGrootK...

Sassy solves approximate string matching: finding all matches of a pattern in a text.

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Reposted by Bas E. Dutilh

Xiu Jia @xiujia.bsky.social · 23d

💧🌊 What happens when freshwater bacteria meet their salty counterparts?
Our new preprint explores the ecological factors driving community coalescence 👉https://www.biorxiv.org/content/10.1101/2025.09.09.675091v1 @bedutilh.bsky.social @microverse.bsky.social

Bacterial community adaptation after freshwater and seawater coalescence

Microbial community coalescence, the merging of entire microbial communities, is common across ecosystems, particularly in estuaries where freshwater and seawater mix. The complexity of these habitats...

www.biorxiv.org

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Reposted by Bas E. Dutilh

Rob Edwards @linsalrob.bsky.social · Aug 22

New in @asm.org #MMBR Computational function prediction of bacteria and phage proteins. How to annotate your #phage and #bacteria genomes

by @susiegriggo.bsky.social @bedutilh.bsky.social @gbouras13.bsky.social and Bob

#phagesky #microsky

journals.asm.org/doi/epub/10....

Examples of protein annotations across functional classification schemes. Yellow: hierarchical classification schemes, red: orthologous/homologous groups, and blue: methods using protein domain information. Protein structures were generated using the ColabFold Alphafold MMseqs2 interactive notebook (version 1.5.2) (57) and visualized using ChimeraX (58). (A) Functional labels associated with the glycogen synthase protein in Escherichia coli (UniprotKB P0A6U8). (B) Functional labels associated with Kehishuvirus sp. tikala major capsid protein (NCBI WEU69752.1).

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Reposted by Bas E. Dutilh

Susie Grigson @susiegriggo.bsky.social · Aug 18

Thrilled to share our new review just published in Microbiology and Molecular Biology Reviews (@asm.org #MMBR):
“Computational Function Prediction of Bacteria and Phage Proteins”
with @gbouras13.bsky.social @linsalrob.bsky.social @bedutilh.bsky.social
🔗 journals.asm.org/doi/10.1128/...

Computational function prediction of bacteria and phage proteins | Microbiology and Molecular Biology Reviews

SUMMARYUnderstanding protein functions is crucial for interpreting microbial life; however, reliable function annotation remains a major challenge in computational biology. Despite significant advance...

journals.asm.org

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Reposted by Bas E. Dutilh

Balance of the Microverse @microverse.bsky.social · Jul 23

🎉 Roos Brouns (@bedutilh.bsky.social's #VEO-Group & @uni-jena.de) & Vikrant Minhas (mentee @kuesellab.bsky.social) won the ISME poster award at the AEM Gordon Conference! A great example of cross-institutional #excellence in microbial ecology. 👏 #Microbiology #ISME #AEMGordon #EarlyCareerResearchers

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Bas E. Dutilh @bedutilh.bsky.social · May 27

This paper is now published with @jcheminf.bsky.social : jcheminf.biomedcentral.com/articles/10....

Chemical characteristics vectors map the chemical space of natural biomes from untargeted mass spectrometry data - Journal of Cheminformatics

Untargeted metabolomics can comprehensively map the chemical space of a biome, but is limited by low annotation rates (< 10%). We used chemical characteristics vectors, consisting of molecular fingerp...

jcheminf.biomedcentral.com

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Reposted by Bas E. Dutilh

Universität Jena @uni-jena.de · May 21

Researchers led by @bedutilh.bsky.social at the Cluster of Excellence @microverse.bsky.social investigate #phages, showing how viruses not only cause harm but also create the basis for diversity & balance. Read more in the #UniJena research magazine.

➡️ www.lichtgedanken.uni-jena.de/en/3157/smal...

Angela Muraya (centre) examines her plants with Natia Geliashvili (left) and Bas E. Dutilh (right).

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Reposted by Bas E. Dutilh

Bram van Dijk 🏳️‍🌈 @bramvandijk.bsky.social · May 9

🧩 PhD Position – Origins of Darwinian Inheritance 🧩

This joint PhD project between the @rug.nl (Rampal Etienne & Martijn Egas) and @utrechtuniversity.bsky.social (Bram van Dijk) explores how simple prebiotic systems could evolve reliable information transfer.

Apply here: shorturl.at/WgYMF

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Reposted by Bas E. Dutilh

Bram van Dijk 🏳️‍🌈 @bramvandijk.bsky.social · May 12

PhD position available at @binfutrecht.bsky.social. Join us if you are interested in modelling how plants respond to stress!

www.uu.nl/en/organisat...

PhD Position in Modelling Regulation of Plant Stress Responses across Species

Join us to model plant stress responses and help breed climate-resilient crops in a collaborative, interdisciplinary research environment!

www.uu.nl

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Reposted by Bas E. Dutilh

Balance of the Microverse @microverse.bsky.social · May 16

🧬 New tool alert: Vclust helps researchers rapidly sort through millions of viral genomes—even fragmented ones.
@bedutilh.bsky.social co-developed Vclust, a tool for ultrafast clustering of viral genomes. It's open-source, web-accessible, and just published.
📄 doi.org/10.1038/s415...

Ultrafast and accurate sequence alignment and clustering of viral genomes - Nature Methods

Vclust generates fast and accurate estimation of average nucleotide identity for viral genomes, scaling clustering to millions of genomes.

doi.org

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Reposted by Bas E. Dutilh

Nature Methods @natmethods.nature.com · May 15

Vclust generates fast and accurate estimation of average nucleotide identity (ANI) for viral genomes, scaling clustering to millions of genomes. @sdeorowicz.bsky.social @bedutilh.bsky.social @prozwalak.bsky.social
@uni-jena.de @microverse.bsky.social

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

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Bas E. Dutilh @bedutilh.bsky.social · May 15

Faster && more accurate virus sequence clustering with Vclust! Thanks to Andrzej, Sebastian, et al. for the great collaboration. The author list also includes @prozwalak.bsky.social from the VEO Group.

Sebastian Deorowicz @sdeorowicz.bsky.social · May 15

Vclust (the ultra-fast, high-accuracy tool for viral genome comparison & clustering) is now published:
www.nature.com/articles/s41...
Great collaboration with A.Zielezinki, UAM guys and @bedutilh.bsky.social

Ultrafast and accurate sequence alignment and clustering of viral genomes - Nature Methods

Vclust generates fast and accurate estimation of average nucleotide identity for viral genomes, scaling clustering to millions of genomes.

www.nature.com

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Reposted by Bas E. Dutilh

Tatiana Demina @deminatanja.bsky.social · Mar 21

Interested in #soil #viruses? We are! Excited to share our study on #Acidobacteriota #phages in #Arctic #tundra #soils being now published together with an easy-to-follow video abstract: microbiomejournal.biomedcentral.com/articles/10....

Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils - Microbiome

Background Arctic soils are climate-critical areas, where microorganisms play crucial roles in nutrient cycling processes. Acidobacteriota are phylogenetically and physiologically diverse bacteria tha...

microbiomejournal.biomedcentral.com

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Bas E. Dutilh @bedutilh.bsky.social · Mar 17

We are looking for a #postdoc to join the VEO Group @microverse.bsky.social @uni-jena.de and build an experimental research line into the dynamics and functioning of microbial communities: jobs.uni-jena.de/jobposting/1...

Postdoctoral Researcher experimental “Microverse-scale Viral and Microbial Ecology”

jobs.uni-jena.de

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Reposted by Bas E. Dutilh

Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · Mar 14

📣 New, free webtool by the Snoek lab! Meet SpeSpeNet, an intuitive platform for automated network analysis of microbiomes to uncover complex interactions between microbes and their environments

@ismepublications.bsky.social @isme-microbes.bsky.social
doi.org/10.1093/isme...

#microsky #mevosky

SpeSpeNet: an interactive and user-friendly tool to create and explore microbial correlation networks

Abstract. Correlation networks are commonly used to explore microbiome data. In these networks, nodes are taxa and edges represent correlations between the

doi.org

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Bas E. Dutilh @bedutilh.bsky.social · Mar 17

Are you interested in the distribution of microbes, viruses, and #phages throughout the Microverse? Come and do a PhD with us in experimental microbial ecology @microverse.bsky.social @uni-jena.de: jobs.uni-jena.de/jobposting/d...

PhD student experimental “Mapping the Microverse: Everything is Everywhere?”

jobs.uni-jena.de

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Bas E. Dutilh @bedutilh.bsky.social · Mar 17

Are you interested in the distribution of microbes, viruses, and #phages throughout the Microverse? Come and do a #bioinformatics PhD with us @microverse.bsky.social @uni-jena.de: jobs.uni-jena.de/jobposting/b...

PhD student bioinformatics “Mapping the Microverse: Everything is Everywhere?”

jobs.uni-jena.de

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Reposted by Bas E. Dutilh

Marnix Medema @marnixmedema.bsky.social · Mar 3

Exciting opportunity to join our group as postdoc! Apply now for this project on computational (meta)genome mining as part of a collaborative European research consortium: www.wur.nl/en/vacancy/p...

Please share!

Postdoc position on computational (meta)genome mining for natural products

www.wur.nl

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Bas E. Dutilh @bedutilh.bsky.social · Feb 25

🇩🇪 German speaker? Join us in Jena as a Professor of Bioinformatics and Digital Health: stellenticket.eah-jena.de/de/offers/19...

Professur für Bioinformatik und Digital Health (ID: 192006, de) - Stellenangebote - Stellenticket Ernst-Abbe-Hochschule Jena

Stellenangebot: Ernst-Abbe-Hochschule Jena @ Stellenticket EAH Jena - Professur für Bioinformatik und Digital Health (ID: 192006, de)

stellenticket.eah-jena.de

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Bas E. Dutilh @bedutilh.bsky.social · Jan 27

Get a grasp of the chemistry of microbiomes! Check out Pilleriin Peets' preprint: she developed chemical characteristics vectors to reanalyze EMP's untargeted metabolomics data: www.biorxiv.org/content/10.1... with Aris Litos, Daniel Garza, Kai Dührkop, @jjjvanderhooft.bsky.social & Sebastian Böcker

www.biorxiv.org

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Bas E. Dutilh @bedutilh.bsky.social · Jan 7

One more week until the deadline!

Bas E. Dutilh @bedutilh.bsky.social · Dec 4

We have an opening for a 4-year postdoc position to study the #rhizosphere #microbiome in @utrechtuniversity.bsky.social @w-u-r.bsky.social, joint project with @marnixmedema.bsky.social in the context of MiCRop. Please tag/forward this to potential candidates and/or repost: www.uu.nl/en/organisat...

Bioinformatics Postdoc at UU/WUR: Map Metabolic Interactions in the Rhizosphere

Contribute to plant health and our understanding of the metabolic interactions between microbes and plants in the rhizosphere by computational modelling!

www.uu.nl

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Bas E. Dutilh @bedutilh.bsky.social · Dec 16

Two weeks until the deadline! Please repost:

Bas E. Dutilh @bedutilh.bsky.social · Nov 22

🚨🚨 Reminder: the deadline for ICTV's Computational Taxonomy Challenge is coming up! Remind your bioinformaticians and colleagues to submit: ictv-vbeg.github.io/ICTV-Taxonom... 🦠🧬

Why do we need a computational taxonomy?

A community challenge to evaluate and compare viral genome taxonomy classifiers

ictv-vbeg.github.io

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Bas E. Dutilh @bedutilh.bsky.social · Dec 4

We have an opening for a 4-year postdoc position to study the #rhizosphere #microbiome in @utrechtuniversity.bsky.social @w-u-r.bsky.social, joint project with @marnixmedema.bsky.social in the context of MiCRop. Please tag/forward this to potential candidates and/or repost: www.uu.nl/en/organisat...

Bioinformatics Postdoc at UU/WUR: Map Metabolic Interactions in the Rhizosphere

Contribute to plant health and our understanding of the metabolic interactions between microbes and plants in the rhizosphere by computational modelling!

www.uu.nl

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Bas E. Dutilh @bedutilh.bsky.social · Nov 26

Do you (plan to) use genome-scale metabolic models in your research? DNNGIOR facilitates model reconstruction from incomplete genomes and MAGs. See Meine Boer's new publication 👇 and the code on Github: github.com/MGXlab/DNNGIOR

mdboer.bsky.social @mdboer.bsky.social · Nov 26

Exciting news! 🎉 My article is out in iScience presenting DNNGIOR, a deep learning tool advancing gap-filling in metabolic models. Huge thanks to co-authors @cmelkonian.bsky.social, @hariszaf.bsky.social, Daniel Garza, Andreas Haas and @bedutilh.bsky.social. Read at shorturl.at/REOm8

Improving genome-scale metabolic models of incomplete genomes with deep learning

Microbial genomics; Biocomputational method; Computational bioinformatics; Genomic analysis.

shorturl.at

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