Daan Speth
Computational microbiologist. Senior scientist at @cemess.bsky.social, @univie.ac.at.
Microbial ecology, mostly of nitrogen cycle microbes, and data driven physiology.
Maintainer of the GlobDB genome database https://globdb.org
- Reposted by Daan SpethDo you have experience in bioinformatics and are looking for a new challenge? To immerse yourself in a group and institute doing highly diverse research? Then come and join our group !
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- Reposted by Daan SpethNew research published! I wanted to write about this, because I think the DE-Score *might* be the thing I'm proudest of so far! All my career I have dreamt of finding something so clean. The DE-Score is a way to tell when amino acid data stops being informative. 1/7 academic.oup.com/sysbio/advan...
- Reposted by Daan SpethWe are hiring for group leaders again — EBI is a great place to start your research group! embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
- Reposted by Daan SpethWe 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...
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- Calling all OrthoFinder users! We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny. GLADE runs directly on OrthoFinder results. www.biorxiv.org/content/10.6... github.com/lauriebelch/... (1/10)
- Reposted by Daan SpethCalling all OrthoFinder users! We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny. GLADE runs directly on OrthoFinder results. www.biorxiv.org/content/10.6... github.com/lauriebelch/... (1/10)
- Reposted by Daan SpethJoin us at the Evolutionary Biology Centre at Uppsala University. We’re searching for an Assistant Professor in Biology. www.uu.se/en/about-uu/...
- Reposted by Daan Speth🚨 Hiring Alert! 🚨My lab at Institut Pasteur is recruiting several Postdocs! We have exciting open projects in: 🦠 Synthetic Biology and🛡️ Bacterial Immunity. Come do great science with us in the middle of Paris! 🇫🇷🥐 research.pasteur.fr/en/job/postd...
- Reposted by Daan Spethwww.wur.nl/en/vacancy/f... Become our new colleague (and next door neighbor) and lead a chair/group/department of Biophysics at Wageningen University. Reach out to me for info and please spread!!!
- Reposted by Daan SpethWe have two funded postdoctoral positions available. Topics encompass: -Next gen light-sheet fluorescence microscopy instrumentation -Structured illumination microscopy and other approaches to extend the resolution limit. -Nonlinear microscopy combined with adaptive optics / phase conjugation
- Reposted by Daan SpethOn the importance of preprints, regardless of whether you are Team Sponge or Team Jelly: 'King says that she wishes she had posted the study as a preprint so that the errors could have been caught sooner.' www.nature.com/articles/d41...
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- With the release of anvi'o v9, the 300k+ contigs databases available for download on the GlobDB website are now compatible with both the development version and the latest stable release (v9) of anvi'o. More info: globdb.org/news Thanks #anvio team! 🖥️🧬🦠
- We just released #anvio v9, "eunice" 🎉 This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176. Read the release notes: github.com/merenlab/anv... Visit our up-to-date web page: anvio.org
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- Reposted by Daan SpethOur latest. Led by the very talented @ahoiching.bsky.social Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.nature.com/articles/s41... #jcampubs 🌊
- Reposted by Daan SpethEMBL is deeply saddened by the passing of our Interim Director General Peer Bork, a pioneering scientist who left an indelible imprint on life science research in Europe and beyond. We extend our deepest condolences to his family, friends, and colleagues. www.embl.org/news/people-...
- Reposted by Daan Speth🗜️⚡ If you use gzip/gunzip a lot in your pipelines, switch to the faster"libdeflate" versions instead! They use modern CPU capabilities to achieve a 2-3x speedup. libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix github.com/ebiggers/lib...
- Reposted by Daan SpethMy time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring! mirdita.org
- Reposted by Daan SpethWe just released #anvio v9, "eunice" 🎉 This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176. Read the release notes: github.com/merenlab/anv... Visit our up-to-date web page: anvio.org
- Reposted by Daan SpethMany Americans are terrible neighbors to each other, and that is why MN is striking everyone as extraordinary activism... when they are telling us that it is not. They're good neighbors! It's no wonder that "being a shitty neighbor" is the hallmark of our domestic politics and our foreign policy.
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- Reposted by Daan Spethvery sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
- Reposted by Daan SpethLove this from @stephenbheard.bsky.social on how to prioritize learning and useful discussion over tearing apart papers, and look forward to using some of these question prompts in future lab meetings: scientistseessquirrel.wordpress.com/2026/01/13/h...
- Reposted by Daan SpethAn interesting way to look at encoded structural characters to build alignments and trees downstream. This takes structural phylogenetics one step further in the post-AlphaFold era. #Evolution #Science #StrPhy On Confidence Assessment in Structure-Aware Alignments doi.org/10.1093/gbe/...
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- Reposted by Daan SpethPIs & Group Leaders, do your trainees need to learn light microscopy and image analysis? Send them to us! Financial aid is available! Applications due Friday 1/30. meetings.cshl.edu/courses.aspx...
- Reposted by Daan SpethThey also use medical illustrators to create accurate graphics I keep a bit of a list: scidraw.io - high-quality graphics for free download and use (all images under CC-BY licensing) bioicons.com - free science illustrations healthicons.org - simple icons covering a range of health contexts
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- Reposted by Daan Speth⚡️Fully funded #PhD position in my lab at Stockholm University / SciLifeLab! If you’re interested in #lichens, #symbiosis, fungal biology, or meta-omics, please apply. Deadline Feb 1. Read more here: su.varbi.com/en/what:job/...
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- Reposted by Daan SpethTwo fantastic papers published back-to-back in @natmicrobiol.nature.com show that strictly lytic phages can persist intracellularly for long periods of time. Very much in line with ideas we had suggested in a recent study. Highly recommended reads 👇 www.nature.com/articles/s41...
- Reposted by Daan SpethThe cost of sequencing a human genome has fallen over 100,000 fold in nominal terms since 2001. In a new visualization, I've added some of the key advances in sequencing during that timeline:
- Reposted by Daan SpethNew paper up on bioRxiv! This is my third and hopefully final paper on rarefaction. It's still better than the other available methods. www.biorxiv.org/content/10.6...
- Reposted by Daan SpethCongrats to the 14 researchers with proposals accepted for our 2026 Large Scale call! These projects accelerate bioenergy innovation through genomic discovery across diverse organisms and ecosystems. 🖥️🧬🦠🌱🧪🍄 More: jgi.doe.gov/user-science... @berkeleylab.lbl.gov @axelvisel.bsky.social
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- Reposted by Daan Speth"The changing roles of Escherichia coli" -- a short essay by yours truly. rdcu.be/eVtXT
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- Reposted by Daan SpethA free, open-access library of high-quality organism illustrations for science communication
- Reposted by Daan SpethI'm reviewing abstracts for an upcoming scientific conference, helping the planning team to select which attendees get a chance to present their work. Some are amazingly good. Some suggest that the applicant has not ever been taught how to write an abstract. Here are some basic tips: 🧪
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- Useful discussion on circular contigs in metagenome assembly
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- Reposted by Daan SpethI am interested in working with an artist on a graphic novel on soil and/ or global environmental change. The lab would have money to fund this. Do you know of any graphic artists that would be interested?
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- Reposted by Daan Speth💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to. #bioinformatics #microbiology #genomics github.com/tseemann/pro...
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