Bas E. Dutilh
@bedutilh.bsky.social
📤 403
📥 107
📝 21
Try our new Nanopore barcode trimming and data cleaning tool Barbell & get insights into the structure of your reads! 👇
add a skeleton here at some point
18 days ago
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reposted by
Bas E. Dutilh
Ragnar {Groot Koerkamp}
4 months ago
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...
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reposted by
Bas E. Dutilh
Xiu Jia
about 2 months ago
💧🌊 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
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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...
https://www.biorxiv.org/content/10.1101/2025.09.09.675091v1
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reposted by
Bas E. Dutilh
Rob Edwards
3 months ago
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....
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reposted by
Bas E. Dutilh
Susie Grigson
3 months ago
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/...
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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...
https://journals.asm.org/doi/10.1128/mmbr.00022-25
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reposted by
Bas E. Dutilh
Balance of the Microverse
4 months ago
🎉 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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reposted by
Bas E. Dutilh
Universität Jena
6 months ago
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...
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reposted by
Bas E. Dutilh
Bram van Dijk 🏳️🌈
6 months ago
🧩 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 🏳️🌈
6 months ago
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...
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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!
https://www.uu.nl/en/organisation/working-at-utrecht-university/jobs/phd-position-in-modelling-regulation-of-plant-stress-responses-across-species
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reposted by
Bas E. Dutilh
Balance of the Microverse
6 months ago
🧬 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...
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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.
https://doi.org/10.1038/s41592-025-02701-7
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reposted by
Bas E. Dutilh
Nature Methods
6 months ago
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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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.
add a skeleton here at some point
6 months ago
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reposted by
Bas E. Dutilh
Tatiana Demina
8 months ago
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....
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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...
https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02053-6
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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...
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Postdoctoral Researcher experimental “Microverse-scale Viral and Microbial Ecology”
https://jobs.uni-jena.de/jobposting/1195fbd9dd79b09c67d0e3c4919b87a586d9c1b10
8 months ago
0
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reposted by
Bas E. Dutilh
Theoretical Biology & Bioinformatics @ UU
8 months ago
📣 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
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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
https://doi.org/10.1093/ismeco/ycaf036
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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...
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PhD student experimental “Mapping the Microverse: Everything is Everywhere?”
https://jobs.uni-jena.de/jobposting/dad48f4cff1ba66705a26ba197d15da015c176d60
8 months ago
0
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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...
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PhD student bioinformatics “Mapping the Microverse: Everything is Everywhere?”
https://jobs.uni-jena.de/jobposting/bc52cca96aa25f9bfc2a5442fd7f62a19b7591360
8 months ago
0
15
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reposted by
Bas E. Dutilh
Marnix Medema
8 months ago
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!
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Postdoc position on computational (meta)genome mining for natural products
https://www.wur.nl/en/vacancy/postdoc-position-on-computational-metagenome-mining-for-natural-products.htm
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🇩🇪 German speaker? Join us in Jena as a Professor of Bioinformatics and Digital Health:
stellenticket.eah-jena.de/de/offers/19...
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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)
https://stellenticket.eah-jena.de/de/offers/192006/?namespace=eahj_prof
9 months ago
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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
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https://www.biorxiv.org/content/10.1101/2025.01.22.634253
10 months ago
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One more week until the deadline!
add a skeleton here at some point
10 months ago
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Two weeks until the deadline! Please repost:
add a skeleton here at some point
11 months ago
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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...
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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!
https://www.uu.nl/en/organisation/working-at-utrecht-university/jobs/bioinformatics-postdoc-at-uuwur-map-metabolic-interactions-in-the-rhizosphere
11 months ago
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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
add a skeleton here at some point
12 months ago
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🚨🚨 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...
🦠🧬
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Why do we need a computational taxonomy?
A community challenge to evaluate and compare viral genome taxonomy classifiers
https://ictv-vbeg.github.io/ICTV-TaxonomyChallenge/
12 months ago
0
0
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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...
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Unveiling the Hidden World of Antarctic Marine Viruses
https://communities.springernature.com/posts/unveiling-the-hidden-world-of-antarctic-marine-viruses
about 1 year ago
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reposted by
Bas E. Dutilh
Amelia Barber
about 1 year ago
My 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
.
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reposted by
Bas E. Dutilh
Science Journal for Kids & Teens
about 1 year ago
Scientists 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
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reposted by
Bas E. Dutilh
Anna Heintz-Buschart
about 1 year ago
Is 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...
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Postdoctoral Researcher in Microbiome Analysis of the Soil-plant-gut-health Axis
Postdoctoral Researcher in Microbiome Analysis of the Soil-plant-gut-health Axis
https://vacatures.uva.nl/UvA/job/Postdoctoral-Researcher-in-Microbiome-Analysis-of-the-Soil-plant-gut-health-Axis/803607002/
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@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...
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Extreme diversity of phage amplification rates and phage-antibiotic interactions revealed by PHORCE
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
https://biorxiv.org/content/10.1101/2024.06.07.597930v1
about 1 year ago
0
2
4
reposted by
Bas E. Dutilh
bioRxiv Microbiology
over 1 year ago
Tunturi 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
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Tunturi 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
Acidobacteriota are phylogenetically and physiologically diverse soil bacteria that play important r
https://www.biorxiv.org/content/10.1101/2024.08.08.607240v1
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reposted by
Bas E. Dutilh
Britt Koskella
over 1 year ago
Job 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
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Assistant Professor - Global Change Biology- Department of Integrative Biology
University of California, Berkeley is hiring. Apply now!
https://aprecruit.berkeley.edu/JPF04476
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reposted by
Bas E. Dutilh
Theoretical Biology & Bioinformatics @ UU
over 1 year ago
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)
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Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes - Nature Communications
Metagenomic taxonomic profiling usually relies either on reads or assembled contigs/MAGs. Here, authors present RAT, a tool that integrates taxonomic signals from reads, contigs, and MAGs into one pro...
https://www.nature.com/articles/s41467-024-47155-1
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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!
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Why do we need a computational taxonomy?
A community challenge to evaluate and compare viral genome taxonomy classifiers
https://ictv-vbeg.github.io/ICTV-TaxonomyChallenge/
over 1 year ago
0
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reposted by
Bas E. Dutilh
Bram van Dijk 🏳️🌈
over 1 year ago
If 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. 🐀
add a skeleton here at some point
0
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reposted by
Bas E. Dutilh
Sean Meaden
over 1 year ago
I'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...
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Do you want to know which virus discovery tool to use? Check out
@lingyi.bsky.social
's new paper:
add a skeleton here at some point
over 1 year ago
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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
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Sign up
AMR forensics symposium, April 8th.
https://amrforensics.org/
over 1 year ago
0
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The VEO Group in
#Jena
is looking for a
#postdoc
with experience in
#bioinformatics
and
#phage
research
jobs.uni-jena.de/jobposting/2...
almost 2 years ago
0
3
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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
almost 2 years ago
0
6
4
reposted by
Bas E. Dutilh
Aldert Zomer
about 2 years ago
Interested 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...
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https://www.biorxiv.org/content/10.1101/2023.10.08.561343v1
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reposted by
Bas E. Dutilh
Detmer Sipkema
about 2 years ago
Hi 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...
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