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 👇
- 📣Excited to share our (first) VirJenDB publication! 🎁Check it out to see how your #virus database supports #metadata #biocuration and #bioinformatics integration. 🎶Stay tuned for collaboration opportunities in 2026, including a hackathon at #ViBioM2026! 📃 doi.org/10.1093/nar/... 💻 www.virjendb.org
- Reposted by Bas E. Dutilh🚨 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! 👇
- 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...
- Reposted by Bas E. DutilhSassy 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...
- Reposted by Bas E. Dutilh💧🌊 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
- Reposted by Bas E. DutilhNew 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....
- Reposted by Bas E. DutilhThrilled 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/...
- Reposted by Bas E. Dutilh🎉 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
- 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
- This paper is now published with @jcheminf.bsky.social : jcheminf.biomedcentral.com/articles/10....
- Reposted by Bas E. DutilhResearchers 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...
- Reposted by Bas E. Dutilh🧩 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
- Reposted by Bas E. DutilhPhD position available at @binfutrecht.bsky.social. Join us if you are interested in modelling how plants respond to stress! www.uu.nl/en/organisat...
- Reposted by Bas E. Dutilh🧬 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...
- Reposted by Bas E. DutilhVclust 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.
- 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
- Reposted by Bas E. DutilhInterested 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...
- Reposted by Bas E. Dutilh📣 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...
- Reposted by Bas E. DutilhExciting 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!
- 🇩🇪 German speaker? Join us in Jena as a Professor of Bioinformatics and Digital Health: stellenticket.eah-jena.de/de/offers/19...
- Reposted by Bas E. Dutilh
[Not loaded yet] - One more week until the deadline!
- 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...
- Two weeks until the deadline! Please repost:
- 🚨🚨 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... 🦠🧬
- 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
- 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
- 🚨🚨 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... 🦠🧬
- We found new #Crassvirales clades on #Antarctica (prospective families): @goncalopiedade.bsky.social's new paper on the viruses in Antarctic waters is out! Check out the manuscript (www.nature.com/articles/s41...) and Gonçalo's "Behind the Paper": communities.springernature.com/posts/unveil...
- Reposted by Bas E. DutilhMy group is recruiting a postdoc to study how environmental interactions shape the virulence of human fungal pathogens. Please share! Full job description and how to apply at barber-lab.com/join.
- Reposted by Bas E. DutilhScientists at Adam Mickiewicz University turned to poop to learn about how bacteria-killing viruses found in the human gut have changed over time, including 1 from 5,300 yr old Ötzi the Iceman! Learn more in our new adapted article: www.sciencejournalforkids.org/articles/how... @bedutilh.bsky.social
- Reposted by Bas E. DutilhIs there a link between the microbes in your food and your gut microbiome? and how about the soil that your food grew on? join us for a postdoc to find out: vacatures.uva.nl/UvA/job/Post...
- @lingyi.bsky.social and @ehauptfeld.bsky.social from the MGX Group are organizing a hybrid workshop in Utrecht, supported by NL Association of Virus Ecology. @yuvalmulla.bsky.social will explain how to measure phage parameters for quantitative viral ecology. Register: docs.google.com/forms/d/e/1F...
- Reposted by Bas E. DutilhTunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils https://www.biorxiv.org/content/10.1101/2024.08.08.607240v1
- Reposted by Bas E. DutilhJob alert!! Join Integrative Biology at UC Berkeley. We are hiring an Assistant Professor in the area of global change biology with emphasis on the Ecology and Evolution of Host-Microbe Interactions (pathogens, mutualists, microbiomes). aprecruit.berkeley.edu/JPF04476
- Reposted by Bas E. DutilhThe RAT is out! 🐀 Our new Read Annotation Tool integrates taxonomic signals from MAGs, contigs, and reads from #metagenomics 🧬 into one microbial community profile with great sensitivity and precision. Read the article at www.nature.com/articles/s41.... 🧵 (1/5)
- We finally put it together! The first ICTV #Virus #Taxonomy Challenge provides a dataset of thousands of contigs from diverse viruses, asking bioinformaticians to classify them in an automated, reproducible way. See: ictv-vbeg.github.io/ICTV-Taxonom... - tell your bioinformaticians and colleagues!
- Reposted by Bas E. DutilhIf you want more reliable annotation of your reads, try RAT. I have very good experiences with RAT, and it performs very well in the benchmarks! Also, can we all just appreciate that @bedutilh.bsky.social now published a bin-, contig-, and a read annotation tool. Bat. 🦇 Cat. 🐈⬛ Rat. 🐀
- The RAT is out! 🐀 Our new Read Annotation Tool integrates taxonomic signals from MAGs, contigs, and reads from #metagenomics 🧬 into one microbial community profile with great sensitivity and precision. Read the article at www.nature.com/articles/s41.... 🧵 (1/5)
- Reposted by Bas E. DutilhI've got a fully funded, 4-year PhD position available to work on virus-bacteria interactions in soils. Part of the GenerationResearch scheme at York aimed at widening access to postgrad research. Please share! generationresearch.ac.uk/phd_proposal...
- Do you want to know which virus discovery tool to use? Check out @lingyi.bsky.social 's new paper:
- #Viromics #VirusDiscovery 🦠 by #Metagenomics 🧬! We used real metagenomic data from diverse biomes to #benchmark state-of-the-art #bioinformatics virus identification tools: genomebiology.biomedcentral.com/articles/10.... @goncalopiedade.bsky.social @bedutilh.bsky.social 🧵 (1/4)
- Symposium "AMR Forensics" - Global tracking of antimicrobial resistance genes. Co-organized by @aldertzomer.bsky.social, @bedutilh.bsky.social, Utrecht University and KNVM Section Microbial Bioinformatics, and supported by ZonMw. For program & registration see: amrforensics.org
- The VEO Group in #Jena is looking for a #postdoc with experience in #bioinformatics and #phage research jobs.uni-jena.de/jobposting/2...
- Standardization of metagenomics is (not) required! Join the symposium on 2 February in Utrecht: www.knvm.org/activities/6... with @cmelkonian.bsky.social @annecmg.bsky.social @aldertzomer.bsky.social and many more
- Reposted by Bas E. DutilhInterested in finding the maximum overlap between (meta)genomes, eg for HGT? Rick Beeloo, from @BEDutilh lab, has developed Graphite which makes this possible for 1000s of genomes. Graphite: painting genomes using a colored De Bruijn graph www.biorxiv.org/content/10.1...
- Reposted by Bas E. DutilhHi all, I have a postdoc position (3 years) in my group on a very challenging topic: co-cultivation of sponge cells and bacterial symbionts. Looking for someone with experience with marine invertebrate cells AND bacteria. Thanks for sharing! www.wur.nl/en/vacancy/p...
