Bas E. Dutilh
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bedutilh.bsky.social
Bas E. Dutilh
@bedutilh.bsky.social
400 followers 110 following 21 posts
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bedutilh.bsky.social
Try our new Nanopore barcode trimming and data cleaning tool Barbell & get insights into the structure of your reads! 👇
rickbitloo.bsky.social Rick Beeloo @rickbitloo.bsky.social · Oct 23
Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it:

www.biorxiv.org/content/10.1...

Want to get started? github.com/rickbeeloo/b...
October 24, 2025 at 12:26 PM
Reposted by Bas E. Dutilh
curiouscoding.nl
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.
July 18, 2025 at 8:20 PM
Reposted by Bas E. Dutilh
xiujia.bsky.social
💧🌊 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
September 15, 2025 at 9:37 PM
Reposted by Bas E. Dutilh
linsalrob.bsky.social
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).
August 22, 2025 at 4:00 AM
Reposted by Bas E. Dutilh
susiegriggo.bsky.social
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
August 18, 2025 at 1:19 PM
Reposted by Bas E. Dutilh
microverse.bsky.social
🎉 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
July 23, 2025 at 8:03 AM
Reposted by Bas E. Dutilh
uni-jena.de
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).
May 21, 2025 at 8:14 AM
Reposted by Bas E. Dutilh
bramvandijk.bsky.social
🧩 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
May 9, 2025 at 2:55 PM
Reposted by Bas E. Dutilh
bramvandijk.bsky.social
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
May 12, 2025 at 6:11 PM
Reposted by Bas E. Dutilh
microverse.bsky.social
🧬 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
May 16, 2025 at 6:09 AM
Reposted by Bas E. Dutilh
natmethods.nature.com
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...
May 15, 2025 at 4:30 PM
bedutilh.bsky.social
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.
May 15, 2025 at 3:07 PM
Reposted by Bas E. Dutilh
deminatanja.bsky.social
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
March 21, 2025 at 12:11 PM
bedutilh.bsky.social
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
March 17, 2025 at 8:12 PM
Reposted by Bas E. Dutilh
binfutrecht.bsky.social
📣 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
March 14, 2025 at 2:15 PM
bedutilh.bsky.social
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
March 17, 2025 at 8:00 PM
bedutilh.bsky.social
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
March 17, 2025 at 7:58 PM
Reposted by Bas E. Dutilh
marnixmedema.bsky.social
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
March 3, 2025 at 10:44 PM
bedutilh.bsky.social
🇩🇪 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
February 25, 2025 at 11:53 AM
bedutilh.bsky.social
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
January 27, 2025 at 1:25 PM
bedutilh.bsky.social
One more week until the deadline!
January 7, 2025 at 7:55 PM
bedutilh.bsky.social
Two weeks until the deadline! Please repost:
bedutilh.bsky.social 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
December 16, 2024 at 1:29 PM
bedutilh.bsky.social
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
December 4, 2024 at 4:09 PM
bedutilh.bsky.social
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 @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
November 26, 2024 at 9:56 PM