Daan Speth
@daanspeth.bsky.social
1.5K followers 1.6K following 170 posts
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
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daanspeth.bsky.social
I'm happy to announce the latest release of the GlobDB, available at globdb.org.

The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
home | GlobDB
globdb.org
Reposted by Daan Speth
Reposted by Daan Speth
ameliarandich.bsky.social
Interested in a tenure track position teaching and doing research with undergrads at a PUI? We are looking for a broadly-defined microbiologist who can teach Med Micro and Immunology. Apply at universityofscrantonjobs.com/postings/8308. Pls share widely to feeds (& on twitter if you still tweet)! 🦠
Reposted by Daan Speth
astrobiomike.org
To maybe spare someone else the headache I just went through trying to figure out why I couldn’t find any NCBI assembly tables letting me parse by “representative” genomes, they purged the term last year and solely use “reference” now. #MicroSky
Updated Genomes Terminology! “Representative Genome” is Replaced with “Reference Genome” - NCBI Insights
NCBI is streamlining the terminology around our reference genomes. We currently have a small set of genomes collectively called representatives and an even smaller set called references. We have slowl...
ncbiinsights.ncbi.nlm.nih.gov
Reposted by Daan Speth
couchmicroscopy.bsky.social
Rutgers Newark is hiring multiple new profs who work in microbial pathogenesis, structural bio, human/microbial genetics, genomics, biochemistry, or computational biophysics. I loved doing my PhD at Rutgers and I LOVE New Jersey. Reach out if you’re applying and have questions about the school/area.
Open Rank Faculty Position on the Tenure Track - Newark, New Jersey (US) job with Rutgers | 12844885
MULTIPLE TENURE-TRACK FACULTY POSITIONS AVAILABLE The Dept. of Microbiology, Biochemistry, and Molecular Genetics at Rutgers New Jersey Medical School
www.nature.com
Reposted by Daan Speth
cellarchlab.com
EXCITING NEWS!! We're searching for a new professor colleague at the Biozentrum🇨🇭. Ideal candidates are exploring novel biological questions with structure, biophysics, or high-resolution imaging. 🧪 🧶🧬 🔬

The call closes Nov 3. Please get in touch if you would like more information. Come join us! 👩‍🔬🤓
Reposted by Daan Speth
alexjprobst.bsky.social
New article on equitable reuse of public sequencing data, published in @natmicrobiol.nature.com!
Led by the Data reuse core team @lhug.bsky.social @environmicrobio.bsky.social Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and with Anke Heyer and The Data Reuse Consotrium!
Reposted by Daan Speth
wkhuber.bsky.social
Do you like theoretical biology, mathematical&conceptual modelling and want to apply yourself to cutting-edge research at all levels of biology, from molecules to ecosystems?

Come to EMBL! Scope includes physics-based models, emergence, statistics, ML/AI
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Reposted by Daan Speth
jbdsf.bsky.social
Our Department of Microbiology & Immunology at UCSF is running a faculty search this year for a new Assistant Professor! Please see the ad below for details. Searching for a great colleague, mentor, and scientist!
aprecruit.ucsf.edu/JPF05807
Microbiology and Immunology – Faculty Position (Ladder Rank) – Assistant Professor
University of California, San Francisco is hiring. Apply now!
aprecruit.ucsf.edu
Reposted by Daan Speth
jomcinerney.bsky.social
OK, here it is. Come work with me at the University of Liverpool making ALL THE AI models from ALL THE prokaryote pangenome data. Heck, we will make models from ALL the pangenomes, even eukaryotes!!! (link below👇) 1/4
Reposted by Daan Speth
jlsteenwyk.bsky.social
#PhyKIT now supports Python 3.12 and 3.13.

#Optimizations are also included in the latest release -- more details to come :)
Reposted by Daan Speth
vscooper.micropopbio.org
🚨 Microbiologists! We are recruiting Assistant / Associate Professors in 3 collaborative areas of our U. Pittsburgh School of Medicine.
1) MMG (my dept): fundamental research in med micro
2) Peds ID / I4Kids institute
3) Center for Vaccine Research
🔗 to all 3 w/info: www.linkedin.com/posts/vaughn...
Faculty Professor Associate - Full-Time | Vaughn Cooper
We are recruiting Faculty microbiologists in three (3) different, complementary, and collaborative areas at the University of Pittsburgh associated with the School of Medicine. 1) Fundamental researc...
www.linkedin.com
Reposted by Daan Speth
ashish-malik.bsky.social
📢 Funded PhD opportunities for UK candidates in beautiful Edinburgh. Get in touch if you're interested in a PhD on understanding the mechanisms of soil carbon cycling and the role of microbes. We work in different ecosystems: peatlands, forests and agricultural soils. Please repost/spread the word.
Poster showing the following text: PhD in microbial mechanisms of soil carbon cycling. Soil microbes shape the global carbon cycle in life and death. We study the effect of aboveground land management on belowground soil carbon cycling processes. We aim create a scalable understanding of microbial processes from single cells to populations to communities to ecosystems. Pictures with text: peatland restoration, sustainable agriculture and woodland regeneration.
Reposted by Daan Speth
rrwick.bsky.social
New blog post!

metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper:
rrwick.github.io/2025/09/23/a...

Both tools improved considerably! Time to update your conda environments 😄
Benchmark update: metaMDBG and Myloasm
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
Reposted by Daan Speth
harmitmalik.bsky.social
Any academic folks on H1B visas (even with stamps in passports) please get legal advice from your University attorneys before leaving the US.
Reposted by Daan Speth
sazanovlab.bsky.social
How the twin-arginine translocase (Tat) system manages to transport folded proteins across membranes without any leaks? To answer this fundamental question we solved the first structure of TatB3C3 complex with bound cargo. Please check out new preprint!
t.co/962Kj9pt6F
https://www.biorxiv.org/content/10.1101/2025.09.16.676506v1
t.co
Reposted by Daan Speth
microbesplanet.bsky.social
The 28th European Nitrogen Cycle meeting (ENC28) brought together over 70 participants from 13 countries at @cemess.bsky.social @univie.ac.at! Inspiring CoE Microplanet closing lecture by Jan Willem Erisman. Thanks to all the speakers and participants for making it such a stimulating event.
Reposted by Daan Speth
epcrocha.bsky.social
Willing to join us @pasteur.fr for a PhD for a project on how interactions between mobile genetic elements shape bacterial adaptation? Subject to be tailored to candidates with keen interest in evolution, genomics, computational biology, microbiology. Check www.pasteur.fr/en/education...