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Aldert Zomer

@aldertzomer.bsky.social
905 followers 508 following 117 posts

Associate Professor at Utrecht University, Infectious Diseases & Immunology. (meta)genomes, AMR, zoonotic pathogens. Cookie and cake connoisseur. publications: scholar.google.com/citations?hl=nl&…

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Reposted by Aldert Zomer
Kate Baker @ksbakes.bsky.social · 25/09/2026
We have an open Assistant/Associate Professor position in Pathogen Biology at the Department of Genetics - come and join us! 🦠 🧫 🧬https://www.cam.ac.uk/jobs/assistantassociate-professor-in-pathogen-genetics-pc51175
cam.ac.uk
Assistant/Associate Professor in Pathogen Genetics
Applications are invited for an Assistant or Associate Professorship in Pathogen Genetics to be held in the Department of Genetics. We are searching for a talented individual with a track record of fu...
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Bas E. Dutilh @bedutilh.bsky.social · 25/09/2026
Are you into sequence graphs and looking for a PhD position in viral ecology? Join the VEO Group in beautiful Jena, Germany! 👇👇 jobs.uni-jena.de/jobposting/a...
jobs.uni-jena.de
Doctoral Researcher in Bioinformatics: Quantifying quasispecies: Tool development and applications
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Conor (Conchúr) Meehan @conmeehan.bsky.social · 23/09/2026
We are looking for someone with a strong background in metagenomics and epidemiology to join our team for ~2 years at UKHSA to work on the mSCAPE programme. Please see (and share) the link below and feel free to message me with any enquiries. www.healthjobsuk.com/job/Canary_W...
healthjobsuk.com
Job vacancy: Senior Scientist (Epidemiology), UK Health Security Agency, Canary Wharf, London | trac.jobs
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David Cleary @bacterioskeptic.bsky.social · 17/09/2026
Senior Bioinformatician role at UKHSA Porton tinyurl.com/vwfpza8a
tinyurl.com
Senior Bioinformatician at UK Health Security Agency — Porton, England, United Kingdom | LinkedIn Jobs
Apply for Senior Bioinformatician at UK Health Security Agency in Porton, England, United Kingdom. Full-time Mid-Senior level role. See responsibilities, qualifications, and similar jobs on LinkedIn.
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Will Matlock @wtmatlock.bsky.social · 09/09/2026
Does an AMR gene on a plasmid diversify differently to an AMR gene on a chromosome? We are looking for a PhD student to work on this question in Bath!
gw4biomed.ac.uk
Turning up the volume: plasmid copy number and gene duplications as drivers of antimicrobial resistance evolution - GW4 BioMed MRC DTP
Project Code IIAR27Ba Matlock Project Type Wet lab Research Theme Infection, Immunity, and Antimicrobial Resistance Project Summary Download Summary Plasmids are important drivers of antimicrobial res...
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Hanna Kokko @kokkonut.bsky.social · 04/09/2026
Are you into mathematical modelling of ecological and evolutionary systems? Look at this job ad for a senior lecturer in Lund. I've visited many times, splendid compact city, splendid department! lu.varbi.com/en/what:job/...
lu.varbi.com
Senior Lecturer in Computational Biology
Lund University welcomes applicants with different backgrounds and experiences. Gender equality, equal opportunities and diversity are fundamental principles in all parts of the University’s activit
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Yonatan Grad @yhgrad.bsky.social · 04/09/2026
Postdoc position in infectious disease epi, genomics, applied stats to join our work on sampling strategies for pathogen genomics surveillance. Based in Shirlee Wohl’s group at BWH but to work closely with my team. See ad here: massgeneralbrigham.wd1.myworkdayjobs.com/en-US/MGBExt...
massgeneralbrigham.wd1.myworkdayjobs.com
Postdoctoral Fellow
Site: The Brigham and Women's Hospital, Inc. Mass General Brigham relies on a wide range of professionals, including doctors, nurses, business people, tech experts, researchers, and systems analysts t...
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Brent Toderian @brenttoderian.bsky.social · 28/08/2026
Does replacing parking with bike-lanes hurt restaurant business? Of course not, as this new peer-reviewed STUDY of 15 years of Montreal data showed. ACTUALLY, downtown experienced significant restaurant growth after bike lanes were installed. @momentummag.bsky.social momentummag.com/do-bike-lane...
Separated bike-lane with people riding in Montreal.
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Quadram Institute @quadraminstitute.bsky.social · 29/07/2026
🆕 Vacancy! We're looking for a well-rounded Postdoctoral Research Scientist to join a collaborative team working on the study of microbiome-host interactions using New Approach Methodologies with living microbiomes. 💷 £39,000 to £46,500 🗓️ Apply by 17 August 2026 ➡️https://buff.ly/ulMNG5O
Research Scientist vacancy graphic with microbes in the background that reads "Research Scientist. Study microbiome-host interactions using New Approach Methodologies with living microbiomes. Salary: £39,000 to £46,500. Contract until March 2028. Apply by 17 August 2026."
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Martin Hunt @martibartfast.bsky.social · 26/06/2026
Like Artemis/ACT but wish it was easier to install and more modern? Try Seqhiker. 🧬 Native desktop app (no Java) for Windows/mac/linux 🖱️ Drag-n-drop FASTA/GenBank/GFF3/BAM/VCF files 🔍 Genome browsing and ACT-style comparison ✨ Themes (customisable) and a Vim mode Docs: seqhiker.readthedocs.io
seqhiker.readthedocs.io
The Seqhiker's Guide
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Kimberly Kline 🏔 @kimingeneva.bsky.social · 09/07/2026
🚨Join us at the University of Geneva! We're seeking an outstanding junior researcher to apply for an ERC or SNSF Starting Grant with our institutional support in host–pathogen interactions, bacteriology, virology, parasitology, or mycology. www.unige.ch/medecine/mim... Please share!
unige.ch
Open call : MIMOL Junior Group Leader’s application for a Starting Grant - Microbiology and molecular medicine - UNIGE
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Aldert Zomer @aldertzomer.bsky.social · 10/07/2026
Just saw that Olymvax reported the efficacy of their phase 3 clinical trial results of their S. aureus vaccine. 73% efficacy. Impressive. static.sse.com.cn/disclosure/l... (in Chinese but translation is straight forward using AI)
static.sse.com.cn
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Andrea Vettiger @avettiger.bsky.social · 03/07/2026
Excited to see our story published in @natmicrobiol.nature.com today! It’s been a long journey. We answered a major outstanding question: why does E. coli encode two aPBPs, yet only one plays a critical role in ensuring reliable PG fortification during cell division?
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Mar Hicks @histoftech.bsky.social · 21/06/2026
“A slow, heavy desert lizard called the Gila monster can go months between meals. In the early 1990s, a physician-scientist named John Eng grew curious about how it keeps its blood sugar steady across those long fasts… Years later, a synthetic version of that molecule became the first GLP-1 drugs”
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Antimicrobial resistance #AMR @antimicrobial.bsky.social · 21/06/2026
Welcome for complicated UTIs w/ resistant bugs but oral carbapenem lower the last barrier protecting this important antibiotic class Convenience for patients must not become convenience for prescribers, otherwise we may pay with increased carbapenem resistance #AMR www.cidrap.umn.edu/antimicrobia...
cidrap.umn.edu
FDA approves new oral antibiotic for complicated urinary tract infections
Utebzi is the first oral carbapenem antibiotic approved in the US.
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Zach Weinersmith @zachweinersmith.bsky.social · 21/06/2026
Happy Father's Dad! www.smbc-comics.com/comic/number...
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Prof Jenny Rohn @jennyrohn.bsky.social · 21/06/2026
Pros and cons to this new #UTI treatment option #UTISky
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Marie Phillips @mariephillips.bsky.social · 16/06/2026
No, it's because only 3.1 percent of the Dutch population live in poverty as opposed to 20 percent of the British population. The Guardian really needs to stop publishing irresponsible lifestyle crap as news. (The Avondvierdaagse is a nice tradition though.) www.theguardian.com/lifeandstyle...
theguardian.com
Dutch children are unusually happy and healthy. Is it because of the Avondvierdaagse?
Once a year, Dutch kids, parents and teachers take part in a walking festival, heading out for four nights in a single week to explore their neighbourhoods, exercise and make friends. It’s a tradition...
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Sasha Gusev @sashagusevposts.bsky.social · 07/06/2026
I wrote about AI in academia. "PhD-level thinking", LLM bias, grunt work, alignment, AGI, data center water use, AI politics -- something for everyone.
open.substack.com
Thoughts on AI in academia
PhD-level thinking, LLM bias, alignment, AGI, data centers, and AI politics
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Zamin Iqbal @zaminiqbal.bsky.social · 25/05/2026
This is awful to hear, describing how Sean Eddy (HMMER, infernal, pfam, rfam) has been defunded. The letter said his work "had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated," www.npr.org/2026/05/21/n...
npr.org
Researchers say the Trump administration is finding new ways to punish science
Even with federal grants largely restored, scientists say the Trump administration is still preventing those funds from reaching them. The consequences, they say, are already becoming clear.
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Molecular Biology and Evolution @molbioevol.bsky.social · 25/05/2026
Wong et al. present IQ-TREE version 3, with new features including mixture models, gene and site concordance factors, integration with phylogenomic divergence time estimation, and a fully featured sequence simulator. 🔗 doi.org/10.1093/molbev/msag117 #evobio #molbio #compbio
MBE | IQ-TREE 3: phylogenomic inference software using complex evolutionary models
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Rob Patro @robp.bsky.social · 27/03/2026
The people who believe that generative AI development & adoption everywhere is the ultimate goal & the first order predictor of success are insufferable. So are the people who think that AI can't ever produce anything useful and that everything they do produce is "slop". I miss reasoned arguments.
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Daniel Tamarit @danieltamarit.bsky.social · 22/05/2026
I'm looking for an enthusiastic student to join my team as a PhD candidate on archaeal genome evolution 🦠💻 Work in beautiful Utrecht, at @binfutrecht.bsky.social, an international group full of caring, amazing scientists, and with frequent cake breaks! www.uu.nl/en/organisat... Please share! 🙏
uu.nl
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Patrick Jansen 🐾 @patrickjansen.bsky.social · 23/05/2026
"De ongebreidelde concentratie van macht en geld in de handen van een kleine groep is niet alleen oneerlijk, maar ondermijnt zichzelf door de feitelijke en emotionele ontkoppeling die daaruit volgt." Uitstekende #column van Robbert Dijkgraaf. Tom en Daisy, houd ze tegen. www.nrc.nl/nieuws/2026/...
nrc.nl
Column | Onverschillige mensen
Robbert Dijkgraaf: De groeiende achteloosheid in de geopolitiek en het bedrijfsleven heeft alles te maken met de toenemende ongelijkheid, schrijft Robbert Dijkgraaf.
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Tami Lieberman @contaminatedsci.bsky.social · 27/04/2026
Get your applications in today or tomorrow if you're interested!
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Quadram Institute @quadraminstitute.bsky.social · 26/04/2026
Do you have a PhD (or equivalent) in biology, bioinformatics, computer science or a related discipline? Check out our current vacancy ⤵️ 💷 £37,500 to £43,350 🗓️ Apply by 17 May 2026 ➡️ buff.ly/tUT3tBw
A social media card with a photo of fermented food and the text "Research Scientist (Data Science) to investigate how novel fermented plant-based foods influence the human gut microbiome, Salary: £37.500 to £43,350, Contract length: 2 years, Apply by 17 May 2026"
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Aldert Zomer @aldertzomer.bsky.social · 17/04/2026
Just out in npj Antimicrobials & Resistance @natureportfolio.nature.com www.nature.com/articles/s44... We looked at what actually happens to AMR on pig farms when you reduce antimicrobial use through real-world, coaching-based interventions.
nature.com
Changes in antimicrobial resistance profiles of Escherichia coli and the metagenome on Dutch pig farms after antimicrobial usage interventions - npj Antimicrobials and Resistance
npj Antimicrobials and Resistance - Changes in antimicrobial resistance profiles of Escherichia coli and the metagenome on Dutch pig farms after antimicrobial usage interventions
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Global Flyway Network @globalflyway.bsky.social · 15/04/2026
The molluscivorous red knots may eat seagrass rhizomes. To examine this ability, bird were fed plant-based rabbit pellets before being reversed back to protein-rich pellets. They rapidly adjusted to eating rabbit food! eur01.safelinks.protection.outlook.com?url=https%3A...
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Melanie Blokesch @mblokesch.bsky.social · 10/04/2026
Excited to share our new paper out today in @science.org 🎉 We show that HGT via natural competence drives diversification of chromosomal integrons in V. cholerae 🤩 Below a 🧵 on key findings incl. background on natural competence in V. cholerae 1/ #microsky #phagesky www.science.org/doi/10.1126/...
science.org
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Liz Batty @lizbatty.bsky.social · 28/03/2026
Ryan Gosling who taught you to balance a centrifuge
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Daniel Hurdiss @danielhurdiss.bsky.social · 27/03/2026
The newly established NeCEN Utrecht is looking for a #cryoEM scientist! www.uu.nl/en/organisat... Work with a new Krios 5 + pFIB and support cutting-edge life science research. 📍 Utrecht | 🗓 Apply by 30 April Please share with your network!
uu.nl
Cryo-electron microscopy scientist
Join our team to contribute to the operation and innovation of state-of-the-art cryo-electron microscopes and empower groundbreaking research.
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Aldert Zomer @aldertzomer.bsky.social · 24/02/2026
Our faculty has a particularly interesting PhD position open on antimicrobial resistance, effects of antibiotics treatment on the microbiome and resistome, restoration of the equine microbiome using FMT. www.uu.nl/en/organisat... Please contact Mathijs Theelen, email address in the link below.
uu.nl
PhD candidate in Equine Intestinal Microbiome and Resistome
Join this PhD project to study how the equine gut microbiome and resistome can improve gastrointestinal health and combat antimicrobial resistance.
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Jim Shaw @jimshaw.bsky.social · 28/01/2026
Announcing a new tool for "denoising" long-read amplicon sequences: savont. Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay. 1/4 github.com/bluenote-157...
github.com
GitHub - bluenote-1577/savont: Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads
Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads - bluenote-1577/savont
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Quadram Institute @quadraminstitute.bsky.social · 23/12/2025
We’re looking for a Summer Intern to generate microscopy videos of bacteria bursting in response to administering antibiotics as part of a public education video on the uses of antibiotics and risks of misuse 🔬 🗓️ Apply by 5 January ➡️ buff.ly/YlUQUho
Vacancy graphic showing a microbial microscopy image on a computer. The text reads "Bursting Bugs Summer Internship. To generate microscopy videos of bacteria bursting in response to administering antibiotics. Salary: £3,270 total. Contract length: 5 weeks. Apply by 5 January 2026."
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Torsten Seemann @torstenseemann.bsky.social · 13/12/2025
💾 Shovill 1.4.1 has been released! The best way to de novo assemble microbial genomes from Illumina FASTQ. Major fixes to the SKESA module, plasmid mode for the Spades module, and more error checking. #bioinformatiocs #genomics #microbiology github.com/tseemann/sho...
github.com
Releases · tseemann/shovill
⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads - tseemann/shovill
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Ragnar {Groot Koerkamp} @curiouscoding.nl · 10/12/2025
If you ever need to fuzzy search some DNA, sassy is your tool. Please spread the word; I think many people just outside my own circle could benefit from this :) cc @rickbitloo.bsky.social github.com/RagnarGrootK...
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Aldert Zomer @aldertzomer.bsky.social · 08/12/2025
MetaPointFinder: A new approach for detecting mutation-driven antimicrobial resistance directly from metagenomic reads. Fills a major gap in current resistome profiling by capturing chromosomal AMR mutations that metagenome tools miss. github.com/aldertzomer/...
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Torsten Seemann @torstenseemann.bsky.social · 05/12/2025
💾 ABRicate 1.2.0 has been released! This 'oversight' lasted 6 years, but with help from @finlaym.bsky.social we got CI working and updated all the databases. #bioconda #conda #bioinformatics #microbiology #genomics github.com/tseemann/abr...
github.com
Releases · tseemann/abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes - tseemann/abricate
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Langridge Lab @langridgelab.bsky.social · 30/11/2025
It's the last few days to apply for this #PhDposition starting in Oct 2026 with us @quadraminstitute.bsky.social. Do you like bacteria, genomics & puzzles?🦠🧬🧩 Do you wanna work in a cutting edge of science, with some awesome people? 😜 Please apply or share by 2 Dec 🗓️ Find out more ⬇
uea.ac.uk
PhD Out of order: investigating genetic and environmental drivers of genome rearrangement (LANGRIDGE_Q26DTP) 2026/27 | UEA
PhD Out of order: investigating genetic and environmental drivers of genome rearrangement (LANGRIDGE_Q26DTP) 2026/27 | UEA
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Courtney Milan @courtneymilan.com · 19/11/2025
I am increasingly of the opinion that people who change menus and look and feel of computer software just so that you know it's a new version should be personally forced to play tech support to my mother for five months.
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Robert Reich @rbreich.bsky.social · 15/11/2025
Amazon announced 14,000 layoffs. Its CEO made over $40M last year. UPS announced 48,000 layoffs. Its CEO made over $24M last year. Intel announced 20,000 layoffs. Its new CEO's pay package is valued at nearly $69M. This is what I mean when I say the system is rigged.
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Randall Munroe @xkcd.com · 14/11/2025
Car Size xkcd.com/3167/
4-panel vertical comic. (1) 100 Years Ago [two people standing next to bicycle with small car nearby] PERSON 1: It’s too dangerous riding a bike with these cars around. I should get a car, too. (2) 50 Years Ago [two people between smaller car and bigger car] PERSON 2 with short hair: Small cars are less safe in collisions with larger vehicles, so I should get a bigger one. (3) Today [two people between big car and even bigger car] PERSON 1: Everyone has huge SUVs now. If I don’t get the biggest one, I’m putting my family at risk. (4) Soon [two people next to large armored car with spiked clubs attached] PERSON 2: If I don’t install more whirling spike clubs, I’ll be destroyed by all the other drivers who...
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Quadram Institute @quadraminstitute.bsky.social · 03/11/2025
🎓 #PhDPosition ! 🧬 Out of order: investigating genetic and environmental drivers of genome rearrangement with Dr Gemma Langridge @langridgelab.bsky.social 📅Apply by 2 December ➡️https://buff.ly/k31MNuV
A digital illustration of DNA with the text "Funded PhD, Out of order: investigating genetic and environmental drivers of genome rearrangement, with Dr Gemma Langridge, Apply by 2 December 2025"
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Ben Langmead @benlangmead.bsky.social · 30/10/2025
October 2025 batch of Kraken 2 indexes, including core_nt and many others, available: benlangmead.github.io/aws-indexes/k2 Coming soon to K2: a feature for querying many K2 indexes as though they're a single index. Highly useful if the index you want to query is too big to build and/or fit in RAM.
benlangmead.github.io
Index zone by BenLangmead
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Gemma Langridge @gemma-langridge.bsky.social · 28/10/2025
🚨 Another funded PhD alert🚨 We are recruiting again! For a PhD student to start with us in the @langridgelab.bsky.social October 2026 - please share 👀 If you are interested in foodborne pathogens, public health and phage, look no further 🦠🏥🧬 ➡️ tinyurl.com/3zvavp2t ⬅️ Apply by 6 Jan 2026 🗓️
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Ragnar {Groot Koerkamp} @curiouscoding.nl · 23/10/2025
Really exciting that the preprint on Barbell, a new demultiplexer, is finally out! It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.
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Rick Beeloo @rickbitloo.bsky.social · 23/10/2025
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...
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Teppo Hiltunen @teppo-h.bsky.social · 30/09/2025
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...
duunitori.fi
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!
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Hall Lab @halllab.bsky.social · 30/09/2025
Come join us 2-4th March 2026 for a cracking #microbiome conference in Hinxton UK! Speaker line up is AMAZING and lots of opportunities for ECRs for selected talks, flash talks and posters. Bursaries are also available! See details below 👇
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