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daanspeth.bsky.social
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
globdb.org
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daanspeth.bsky.social
Daan Speth @daanspeth.bsky.social · Jun 10
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
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Reposted by Daan Speth
filiphusnik.bsky.social
Filip Husnik @filiphusnik.bsky.social · 3d
Pretty excited to share our new preprint!
Non-photosynthetic Plastid Replacement by a Primary Plastid in the Making
www.biorxiv.org/content/10.1...
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Reposted by Daan Speth
tunglejic.bsky.social
Tung Le @tunglejic.bsky.social · 2d
new preprint from our group & Antoine Hocher: www.biorxiv.org/content/10.1...
A fantastic collaboration with Antoine, with Jovana Kaljevic' initiated the collaboration and drives the project.
Versatile NTP recognition and domain fusions expand the functional repertoire of the ParB-CTPase fold beyond chromosome segregation
Nucleotide triphosphate (NTP)-dependent molecular switches regulate essential cellular processes by cycling between active and inactive states through nucleotide binding and hydrolysis. These mechanis...
www.biorxiv.org
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Reposted by Daan Speth
ewanbirney.bsky.social
Ewan Birney @ewanbirney.bsky.social · 4d
A reminder that the PhD program for EMBL is open for winter recruitment round. If you want to understand life at a molecular level and have a quantitative science (you don't have to have done biology - we love our mathematicians/physcists/chemists!) apply www.embl.org/about/info/e...
Application – EMBL International PhD Programme
www.embl.org
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Reposted by Daan Speth
paulbrainey.bsky.social
Paul Rainey @paulbrainey.bsky.social · 7d
Two new positions are available at the MPI for Evolutionary Biology to support development of our genomics facility. Both stand to become permanent. Both offer a ton of opportunity to engage in a wide range of creative science.

Pls repost 🙏

www.evolbio.mpg.de/3838377/job_...
Two full-time positions | Bioinformatician (m/f/d) + Applications Specialist (m/f/d) - Molecular Biology
The Genome Facility at the Max Planck Institute for Evolutionary Biology in Plön is seeking to fill two positions (full time) to support and expand our core facility services.
www.evolbio.mpg.de
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Reposted by Daan Speth
ameliarandich.bsky.social
Amelia Randich @ameliarandich.bsky.social · 11d
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)! 🦠
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Reposted by Daan Speth
astrobiomike.org
Mike Lee @astrobiomike.org · 11d
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
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Reposted by Daan Speth
couchmicroscopy.bsky.social
Julia Van Etten @couchmicroscopy.bsky.social · 10d
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
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Reposted by Daan Speth
teppo-h.bsky.social
Teppo Hiltunen @teppo-h.bsky.social · 13d
Professor (full) or Associate Professor (tenure track) in Microbial Genetics of Health (U. Turku Finland). Competitive starting package included! Please share.

duunitori.fi/tyopaikat/ty...
Professor or Associate professor (Tenure Track/Full) in Microbial Genetics of Health - Turun yliopisto - Työpaikat - Duunitori
Avoin työpaikka: Professor or Associate professor (Tenure Track/Full) in Microbial Genetics of Health - Turun yliopisto, Turku. Duunitorilla lisäksi yli 30 000 muuta avointa työpaikkaa. Lue lisää nyt!
duunitori.fi
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Reposted by Daan Speth
cellarchlab.com
Ben Engel @cellarchlab.com · 13d
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! 👩‍🔬🤓
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Reposted by Daan Speth
alexjprobst.bsky.social
Alex Probst @alexjprobst.bsky.social · 16d
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!
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Reposted by Daan Speth
environmicrobio.bsky.social
Roland Hatzenpichler @environmicrobio.bsky.social · 16d
Our article on equitable reuse of public sequencing data is out! Led by @alexjprobst.bsky.social, @lhug.bsky.social, Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and myself -, co-authored by Anke Heyder, and developed in consultation with 167 scientists. tinyurl.com/n6yeanmk
A roadmap for equitable reuse of public microbiome data - Nature Microbiology
In this Consensus Statement, a consortium of microbiome scientists discuss current sequencing data sharing policies and propose the use of a Data Reuse Information (DRI) tag to promote equitable and collaborative data sharing.
tinyurl.com
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Reposted by Daan Speth
wkhuber.bsky.social
Wolfgang Huber @wkhuber.bsky.social · 14d
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...
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Reposted by Daan Speth
campy-bara.bsky.social
Sarah Svensson @campy-bara.bsky.social · 17d
Dual transposon sequencing profiles the genetic interaction landscape in bacteria | Science www.science.org/doi/10.1126/...
Dual transposon sequencing profiles the genetic interaction landscape in bacteria
Gene redundancy complicates systematic characterization of gene function as single-gene deletions may not produce discernible phenotypes. We report dual transposon sequencing (dual Tn-seq), a platform...
www.science.org
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Reposted by Daan Speth
jbdsf.bsky.social
Joe Bondy-Denomy @jbdsf.bsky.social · 17d
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
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Reposted by Daan Speth
jomcinerney.bsky.social
James McInerney @jomcinerney.bsky.social · 18d
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
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Reposted by Daan Speth
richardsever.bsky.social
Richard Sever @richardsever.bsky.social · 18d
HHMI adopts Plan U journals.plos.org/plosbiology/...
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Reposted by Daan Speth
jlsteenwyk.bsky.social
🧬Jacob L Steenwyk @jlsteenwyk.bsky.social · 18d
#PhyKIT now supports Python 3.12 and 3.13.

#Optimizations are also included in the latest release -- more details to come :)
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Reposted by Daan Speth
vscooper.micropopbio.org
Vaughn Cooper @vscooper.micropopbio.org · 19d
🚨 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
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Reposted by Daan Speth
ashish-malik.bsky.social
Ashish Malik @ashish-malik.bsky.social · 26d
📢 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.
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Reposted by Daan Speth
rrwick.bsky.social
Ryan Wick @rrwick.bsky.social · 20d
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
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Reposted by Daan Speth
harmitmalik.bsky.social
Harmit Singh Malik @harmitmalik.bsky.social · 23d
Any academic folks on H1B visas (even with stamps in passports) please get legal advice from your University attorneys before leaving the US.
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Reposted by Daan Speth
bejalab.bsky.social
BejaLab @bejalab.bsky.social · 25d
A genomic view of Earth’s biomes www.nature.com/articles/s41...
A genomic view of Earth’s biomes - Nature Reviews Genetics
Genome-wide approaches have uncovered the vast microbial and viral diversity across ecosystems. This Review explores advances in metagenomics, single-cell sequencing and functional profiling to elucid...
www.nature.com
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Reposted by Daan Speth
sazanovlab.bsky.social
Sazanov Lab @sazanovlab.bsky.social · 24d
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
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Reposted by Daan Speth
jeffinerca.bsky.social
Dr. Jennifer Pett-Ridge @jeffinerca.bsky.social · 24d
isme-microbes.org/isme-scholar...
Call for Applications – ISME Scholar Mobility Fund – ISME
ISME supports MSc/PhD graduate students and postdocs to develop academically via the Scholar Mobility Fund. Please submit your application by 1 October to study at a host institution abroad.
isme-microbes.org
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Reposted by Daan Speth
pwk2024.bsky.social
Peter Kenny @pwk2024.bsky.social · 25d
Opportunity for Senior Lecturer (Associate Professor) in Biochemistry/Microbiology at RMIT University (Melbourne Australia) ref: JR41993 | closing: 12-Oct-2025 #biochem #chemsky 🧪
rmit.wd3.myworkdayjobs.com/en-US/RMIT_C...
Senior Lecturer/Associate Professor, Biochemistry and/or Microbiology
Overview: Full-time, Continuing position Salary Academic Level C ($141,247 -$ 162,872 p.a.) or Level D ($170,080 -$ 187,373 p.a.) + 17% Superannuation Based at the Bundoora campus but may be required ...
rmit.wd3.myworkdayjobs.com
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