Bas E. Dutilh

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...

PhD position in Jena! Unique German-French collaboration to work on integrating phage genomic modules into VirJenDB.org - make sense of #phages, #big_data, #front_end, #back_end, #database. Please apply here 👇
jobs.uni-jena.de/jobposting/c...

VirJenDB.org: the database for all virus sequence- and curated metadata with API access, and version control 👇

🚨 A quick reminder: the PhD and postdoc positions within the ERC project #BindingShadows are still open!

We’ve just moved into a brand-new building, and during the transition our servers and website were occasionally down, meaning we might not have received some applications.

Try our new Nanopore barcode trimming and data cleaning tool Barbell & get insights into the structure of your reads! 👇

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

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...

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...

💧🌊 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

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).

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....

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...

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/...

🎉 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

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...

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

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

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...

🧩 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

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!

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...

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.

🧬 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...

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...

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.

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...

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....

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...

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

📣 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

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...

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...

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

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!

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)

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

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

One more week until the deadline!

Two weeks until the deadline! Please repost:

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!

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...

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