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Thomas Clavel

@tclavel.bsky.social
224 followers 175 following 24 posts

Passoniate microbiome researcher; www.clavel.ukaachen.de

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Reposted by Thomas Clavel
Joel Selkrig @jselkrig.bsky.social · 29/09/2026
How do gut bacteria cope with both proteolytic stress and phage attack? 🧵👇 Our latest preprint is live! Ulcerative colitis (UC) creates a distinct gut environment: protease activity rises, the virome shifts, and phages expand. #Microbiome #Bacteriophages #IBD www.biorxiv.org/content/10.6...
biorxiv.org
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Nature Reviews Immunology @natrevimmunol.nature.com · 22/09/2026
A Review by @katrinkierdorf.bsky.social, Markus Sperandio, Mathias Hornef & @philipp359.bsky.social discusses how perinatal immunity is tailored to mediate the transition to postnatal life through a high degree of temporal plasticity.
nature.com
Plasticity of the infant immune system during the perinatal period - Nature Reviews Immunology
Immune plasticity during the perinatal period enables mammalian offspring to successfully navigate the transition from prenatal, intrauterine life to postnatal, extrauterine life. This Review highligh...
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Nature Microbiology @natmicrobiol.nature.com · 28/08/2026
The September issue is now online! Read about: 🔧Microbial engineering 📚FAIR microbial collections 🔄Crossfeeding in soil 🍄Candida infections/virulence 🛡️Antiviral defenses in bacteria 🦠Giant virus catalogue 🦟Plasmodium surviellance 💉Measles and much more! #MicroSky www.nature.com/nmicrobiol/v...
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Thomas Clavel @tclavel.bsky.social · 26/08/2026
Drawing on the team’s knowledge acquired over the years, we share our thoughts here on how to enhance microbiome research with FAIR collections of microbial strains: 🔥 www.nature.com/articles/s41... @nfdi4microbiota.bsky.social, @spp2474.bsky.social, @dsmz.bsky.social, @natmicrobiol.nature.com.
nature.com
A roadmap to create FAIR collections of microbial strains - Nature Microbiology
Here the authors propose guidance on the process of establishing a state-of-the-art collection of microorganisms, including project planning, strain deposition and the naming of new taxa.
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Mucosal Immunology @mucosalimmunol.bsky.social · 24/08/2026
Register today for Having #IMPACTT6: Advancing Microbiome Research Symposium @impactt-microbiome.bsky.social: www.impactt-microbiome.ca/having-impac...
impactt-microbiome.ca
Having IMPACTT 2026 Symposium - IMPACTT microbiome
Join us in 2026 in Canmore, AB, Canada for a 2.5 day in-person symposium dedicated to microbiome research.
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NFDI4Microbiota @nfdi4microbiota.bsky.social · 17/08/2026
📢 Flex Funds Call for 2027 is now open! Contribute to advancing #FAIRData, #OpenScience, infrastructure, workflows, or training in #microbiology! 💶 Funding: €10,000–€40,000/project 📅 Funding period: Apr–Dec 2027 📆 Application deadline: Oct 11 👉️ More details: nfdi4microbiota.de/newsroom/fle...
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cemess_vienna @cemess.bsky.social · 23/04/2026
Joana Séneca, Petra Pjevac and David Berry from the Joint Microbiome Facility (JMF) and DOME | CeMESS contributed to a new study, led by scientists at Uniklinik RWTH Aachen, benchmarking a key method used to characterize the microbial contents of our digestive tracts. www.nature.com/articles/s41...
nature.com
Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis - Nature Microbiology
A comparison of sequencing of complex mock communities performed at multiple depths and analysed using different methods establishes minimum standards that can ensure the accuracy of metagenomic analy...
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Tom Hitch @tcahitch.bsky.social · 16/07/2026
PhD advert for the new lab in Hong Kong! We are hiring a PhD student to merge large-scale metagenomics with 3D structural analysis and immunology. If you have experience in any of these areas and are motivated to learn the others, get in contact; lnkd.in/ggr3T4sQ
CUHK campus in Hong Kong
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Nature Communications @natcomms.nature.com · 16/07/2026
#Probiotics Administration of a live gut bacterium (*) to Crohn's disease patients appears to be safe and modulates immune gene expression in the ileum, supporting its potential use as a biotherapeutic (* Faecalibacterium prausnitzii)
dlvr.it
Faecalibacterium prausnitzii EXL01 for the Maintenance of Steroid-induced Clinical Response or Remission in Patients with Crohn’s Disease: a first in human trial - Nature Communications
In this clinical trial the authors show that EXL01, a live bacterial therapy based on F. prausnitzii, can be safely administered to Crohn’s disease patients, showing immune gene modulation in the ileum and supporting its potential as a biotherapeutic.
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Emma Slack @mucosalimmunology.bsky.social · 01/07/2026
We are recruiting a lab manager for my group in Oxford. This is a lovely team doing great things, and you could be an important part of it! See here: www.path.ox.ac.uk/vacancy/lab-... Please spread the word!
path.ox.ac.uk
Lab Manager - Molecular Immunology - Dunn School
Laboratory Manager/Senior Scientist position in the Molecular Mucosal Immunology group at Oxford
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Cell Host & Microbe @cp-cellhostmicrobe.bsky.social · 25/06/2026
Universal microbiome signature for CRC Large gut microbiome meta-analysis of colorectal cancer uncovers CRC microbiome signatures universal across ages & sequencing methods & modifiable by dietary interventions, ie fiber. www.cell.com/cell-host-mi...
cell.com
Meta-analysis reveals microbiome signatures for colorectal cancer that are universal across age groups and sequencing methods
Pekel, Karcher, et al. present the largest gut microbiome meta-analysis of colorectal cancer to date, integrating 6,779 amplicon and shotgun sequencing profiles. They establish a robust microbiome sig...
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Thomas Clavel @tclavel.bsky.social · 25/06/2026
Excellent work by our one and only #CharliePauvert. We use it in all our high-throughput anaerobic cultivation projects. More to come... 💫
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Thomas Clavel @tclavel.bsky.social · 03/06/2026
Gut epithelium responses to bile acids 👉 rdcu.be/fmcUe
rdcu.be
Modulation of intestinal bile acids influences colonic mucosal responses
Scientific Reports - Modulation of intestinal bile acids influences colonic mucosal responses
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NFDI4Microbiota @nfdi4microbiota.bsky.social · 28/05/2026
📝 Only a few days left to submit your abstract! Take the opportunity to present your research, workflows, tools, and #FAIR data management approaches at the Boosting Biodata Bootcamp 2026! 👉 Abstract submission: events.hifis.net/event/3702/a... 📅 Submission deadline: 1 June #biology #rdm #nfdi
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Anna S. Weiss @annasophieweiss.bsky.social · 26/05/2026
So happy to see this out 🎉 it all started with a discussion group of ECR brought together by the NCCR Microbiomes and cumulated in this primer on microbial community ecology. This was such a fun group project, where I learned a lot about how cool both microbial and human communities are 🤩
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Prof. Ruth Ley FRS @microbiome.bsky.social · 03/05/2026
Come and work with us in a beautiful corner of Germany: 5 years of funding for your microbiology research and lots of great colleagues 🦠🧫
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Nature Microbiology @natmicrobiol.nature.com · 24/04/2026
Out Now! Benchmarking shotgun metagenomics #MicroSky
go.nature.com
Benchmarking shotgun metagenomics
Nature Microbiology, Published online: 24 April 2026; doi:10.1038/s41564-026-02344-0Shotgun metagenomic sequencing is a comprehensive untargeted next-generation sequencing method that enables culture-independent analysis of complex microbial communities. Comparing the results of several metagenome-based analyses at various sequencing depths for known input illustrates which methods and amounts of data are most suitable for determining microbial composition, accuracy of metagenome-assembled genomes and functional coverage.
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Elisabetta Cacace @elisca.bsky.social · 24/04/2026
Check out our work on E. coli capsules! Including a 3x extended catalog of capsule loci from >37K genomes, a scalable tool to type them in silico (kTYPr) and new associations with ecology and disease! A joint effort from @microbiomeresearch.bsky.social @mucosalimmunology.bsky.social at @ethz.ch.
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Thomas Clavel @tclavel.bsky.social · 21/04/2026
Strain diversity influences microbiome functions, and can be assessed with metagenome-assembled genomes (MAGs). But many MAGs are inaccurate! Benchmarking of shotgun sequencing by ⭐ @treichelnicole.bsky.social ⭐ with @nfdi4microbiota.bsky.social , in @natmicrobiol.nature.com 👉 rdcu.be/feAWc
rdcu.be
Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis
Nature Microbiology - A comparison of sequencing of complex mock communities performed at multiple depths and analysed using different methods establishes minimum standards that can ensure the...
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Steven Salzberg @stevensalzberg.bsky.social · 30/03/2026
In my latest column, I explain some of my reasons for being deeply skeptical about AI models that claim to understand DNA, genes, and genomes: stevensalzberg.substack.com/p/ai-is-star...
stevensalzberg.substack.com
AI is starting to look like pseudoscience
Not all of it, but some scientists are too eager to believe their own hype
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NFDI4Microbiota @nfdi4microbiota.bsky.social · 23/03/2026
📢 Are you at #VAAM2026? 👉 Stop by the NFDI4Microbiota booth to learn how we can support you with training, data analysis, and making your microbiome research easier to share, reuse, and scale. And don’t miss today’s panel discussion at 1:30 in Lecture Hall B! We’d love to meet you 👋!
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NFDI4Microbiota @nfdi4microbiota.bsky.social · 04/03/2026
Are you at #DGE26? 👋 So are we! Stop by the NFDI4Microbiota booth to explore how we can help make your microbiome research FAIR and easier to share, reuse, and amplify. Let’s connect, exchange ideas, and talk data. We’d love to meet you! #microbiome #NFDI #FAIR #rdm
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Joel Selkrig @jselkrig.bsky.social · 18/02/2026
Registration for the 18th Annual Seeon Conference on Microbiota, Probiotics and Host is now open! 🎉 We’re looking forward to welcoming you in Seeon! When: June 24-26 Where: Seeon Monastery, Germany (near Munich) Program: www.dghm.org/seeon/ Registration: app1.edoobox.com/SPP1656/Seeo...
dghm.org
Seeon - Deutsche Gesellschaft für Hygiene und Mikrobiologie
Microbiota, Probiotics and Host    Seeon- Save the date 2026 Registration Abstract Template 2026   We are looking forward to meeting you there! Don’t forget your swimwear, sunscreen and running gear ...
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NFDI4Microbiota @nfdi4microbiota.bsky.social · 13/02/2026
☕ Join our next NFDI4Microbiota Tandem Coffee Talk! 📅 Mon, 23 Feb 2026 | 14:00–15:00 CET 🎙️ Prof. Dr. Bas E. Dutilh & Dr. Noriko Cassman 💬 “Learning phage-host interactions from curated big data” & “VirJenDB: a FAIR (meta)data and analysis platform for viruses” 👉 More info here: tinyurl.com/5y7h6wfh
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RWTH Aachen University @rwth.bsky.social · 05/02/2026
Prof. Carolin Schneider von der Uniklinik RWTH Aachen forscht mit KI-Fachleuten zur Krebsprävention. Ziel ist die personalisierte Strategie: "Wir glauben, dass wir gute Modelle entwickeln können, die die Einzel-Faktoren berücksichtigen, die jemand mitbringt." ➡️ www1.wdr.de/mediathek/au...
www1.wdr.de
Krebsforscherin: "Prävention ins Zentrum stellen"
Ärztin Carolin Schneider forscht mit KI-Experten an der RWTH Aachen zur Krebsprävention. Ziel ist die personalisierte Strategie: "Wir glauben, dass wir gute Modelle entwickeln können, die die Einzel-F...
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Lisa Maier Lab | Tübingen @lisamaierlab.bsky.social · 22/12/2025
We’re hiring 2 Postdocs (f/m/d) in Drug–Microbiome–Host Interactions 🦠💊 Focus: how non-antibiotic drugs shape the gut microbiome, drug efficacy & side effects. #PostdocJobs #Microbiome #AcademicJobs Full job ad: lisamaierlab.com/wp-content/u...
lisamaierlab.com
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Thomas Clavel @tclavel.bsky.social · 19/12/2025
Now published 🔥 Feeding your gut microbes with complex carbohydrates can help preventing colorectal cancer by reducing the production of secondary bile acids. Perhaps NiMe diet @jenswalter15.bsky.social? THX team & Sören Ocvirk ⭐ Thx www.sfb.tum.de/1371/microbi.... Article 👉 doi.org/10.1136/gutj...
doi.org
Secondary bile acid production by gut bacteria promotes Western diet-associated colorectal cancer
Background Western diet and associated production of secondary bile acids (BAs) have been linked to the development of sporadic colorectal cancer (CRC). Despite observational studies showing that seco...
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NFDI4Microbiota @nfdi4microbiota.bsky.social · 16/12/2025
Save the Date! 📅 The NFDI4Microbiota Annual Conference 2026 will take place 15–17 September 2026 and will be a joint event with other biodata-related NFDI consortia. Stay tuned for more details! #onenfdi #NFDI4Microbiota #rdm #microbiota
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 16/12/2025
📍Our paper is out!📍 Here, we show the development of a GC-MS/MS method for the quantification of 120 compounds produced by gut bacteria, including short-chain fatty acids, indols, nucleotides, organic acids, and amino acid derivatives. Check it out! link.springer.com/article/10.1...
link.springer.com
Development of a GC-MS/MS method to quantify 120 gut microbiota-derived metabolites - Analytical and Bioanalytical Chemistry
The gut microbiota produces metabolites that are important for host physiology and have critical roles in the development of diseases, such as metabolic disorders, cardiovascular diseases, and cancer....
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Jörg Vogel @jorg-vogel-lab.bsky.social · 12/12/2025
Franziska Faber and I are recruiting shared postdocs, PhD students to work on Fusobacterium & new BGCs. www.helmholtz-hiri.de/fileadmin/HI...
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Lisa Maier Lab | Tübingen @lisamaierlab.bsky.social · 09/12/2025
New paper from the lab! Led by Patrick Müller: we show that non-antibiotic compounds — but not macrolide antibiotics — can induce an efflux pump that protects Bacteroidaceae from macrolides. A neat twist on drug–microbe interactions... www.tandfonline.com/doi/full/10....
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DSMZ Digital Diversity @dsmzd3.bsky.social · 22/11/2025
📣 Open position: We are looking for a new #ScientificLead for the #SILVA database 🧬🖥️ You will be responsible for guiding the development of this important resource and for curating the SILVA taxonomy🌳and more! 👉 www.dsmz.de/dsmz/career/... Read and share ‼️ #sciencejobs 🦠🧪 #career #taxonomy
📣 Open position: We are looking for a new #ScientificLead for the #SILVA database 🧬🖥️
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Tom Hitch @tcahitch.bsky.social · 14/11/2025
Want to delineate genera? We have been optimising POCP, and propose POCPu, which stops the 'double counting' of proteins in POCP by only allowing unique matches. We also speed up, and benchmarked, the analysis using DIAMOND; peerj.com/articles/202... (now implemented in Protologger)
peerj.com
Fast and robust estimate of bacterial genus novelty using the percentage of conserved proteins with unique matches (POCPu)
Accurate taxonomic assignment of bacterial genomes is essential for identifying novel taxa and for stable classification to enable robust comparison between studies. Bacterial genus delineation relies...
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Thomas Clavel @tclavel.bsky.social · 14/11/2025
Great work from our FAIR science master Charlie (www.linkedin.com/in/charliepa...) to delineate bacterial genera: peerj.com/articles/202.... We hope this will help many. The POCPu calculation is now implemented in protologger.bi.denbi.de by @tcahitch.bsky.social. Thanks for the hard work you 2 ⭐⭐
peerj.com
Fast and robust estimate of bacterial genus novelty using the percentage of conserved proteins with unique matches (POCPu)
Accurate taxonomic assignment of bacterial genomes is essential for identifying novel taxa and for stable classification to enable robust comparison between studies. Bacterial genus delineation relies...
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NFDI4Microbiota @nfdi4microbiota.bsky.social · 05/11/2025
Need a hand with your #Nextflow or #nfcore pipeline? Join our weekly drop-in session — every Friday 10–11 CET with Daniel Straub (Uni Tübingen). Ask questions, get tips, and connect with the community! 📍 Zoom: tinyurl.com/mwz84xvb #Bioinformatics #OpenScience #NFDI4Microbiota
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Thomas Clavel @tclavel.bsky.social · 30/10/2025
A place to be 👇 Highly recommended ⭐⭐⭐⭐⭐
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Emma Slack @mucosalimmunology.bsky.social · 30/10/2025
We have an opening for a postdoctoral researcher in my group at the Botnar Institute for Immune Engineering in Basel, Switzerland. The project is aimed at developing novel mucosal adjuvants for application in oral vaccines. Deadline to apply 16.11.25! Please re-post 🔬🧬 join.com/companies/im...
join.com
Botnar Institute of Immune Engineering - BIIE (Zürich): Postdoctoral Researcher (100%): Mechanisms of action of mucosal adjuvants
Botnar Institute of Immune Engineering - BIIE has a job opening for Postdoctoral Researcher (100%): Mechanisms of action of mucosal adjuvants in Zürich (published: 30.10.2025). Apply now or check the ...
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NFDI4Microbiota @nfdi4microbiota.bsky.social · 24/10/2025
☕ Grab your coffee and join our next NFDI4Microbiota Coffee Talk! 📅 Mon, 27 Oct 2025 | 14:30–15:30 CET 🎙️ Daniel Straub (QBiC Tübingen) 💬 “Meta-omics Analysis at a Bioinformatics Core Facility – As FAIR as Possible”. More info here: nfdi4microbiota.de/c...
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 11/10/2025
A toolkit for transposon libraries and functional genomics in intestinal Bacteroidales www.biorxiv.org/content/10.1101/202…
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 24/09/2025
📍Paper alert 📍 Our new preprint is available on: chemrxiv.org/engage/chemr... Here, we show the development of a GC-MS/MS method for the quantification of 120 compounds produced by gut bacteria, including SCFA, indols, organic acids, and amino acid derivatives.
chemrxiv.org
Development of a GC-MS/MS method to quantify 120 gut microbiota-derived metabolites
The gut microbiota produces metabolites that are important for host physiology and have critical roles in the development of diseases, such as metabolic disorders, cardiovascular diseases, and cancer....
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Tom Hitch @tcahitch.bsky.social · 24/09/2025
The main work from my time in Aachen is now out 🎉 if you have wanted to make a SynCom that captures the functional-landscape of microbiota, MiMiC2 makes that possible based on metagenomic data! 1/7 doi.org/10.1093/isme...
doi.org
Function-Based Selection of Synthetic Communities Enables Mechanistic Microbiome Studies
Abstract. Understanding the complex interactions between microbes and their environment requires robust model systems such as synthetic communities (SynCom
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Thomas Clavel @tclavel.bsky.social · 18/09/2025
Interested in the design of defined microbial communities for fundamental research and applications? Hope this work & tool will help you 👇 As always @tcahitch.bsky.social has been a driving factor ⭐⭐⭐! github.com/ClavelLab/Mi...; academic.oup.com/ismej/advanc...
academic.oup.com
Validate User
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Emma Slack @mucosalimmunology.bsky.social · 10/09/2025
Come and be my colleague at the Dunn School! It‘s a brilliant place to work and exciting to be building up our immunology team. Do apply. Do pass on the news 💉🧬🦠🔬🧫
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NFDI4Microbiota @nfdi4microbiota.bsky.social · 11/09/2025
We’re heading to Jena for two exciting events! 📍 DGHM 2025 – 24 Sept Workshop: Data madness: Navigating Host Microbiomes Featuring VirJenDB – virus sequence discovery & analysis Details 👉 programme.conventus....
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Steven Salzberg @stevensalzberg.bsky.social · 03/09/2025
We're still not finding any good evidence for a microbiome in any cancer type: see our new paper in @ScienceTM led by PhD student Yuchen (Peter) Ge www.science.org/doi/10.1126/... and the accompanying news piece, www.science.org/content/arti...
science.org
Comprehensive analysis of microbial content in whole-genome sequencing samples from The Cancer Genome Atlas project
An analysis of TCGA whole-genome sequencing samples yields a comprehensive resource for investigating the role of microbes in cancer.
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Carolin Wendling @ccwendling.bsky.social · 04/09/2025
Interested in exploring prophages in your (meta)genomes, but don't know how and where to start? We've put together a beginners guide to exploring viral diversity in prokaryotes @marievasse.bsky.social @sebwielgoss.bsky.social @oxunipress.bsky.social
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NFDI4Microbiota @nfdi4microbiota.bsky.social · 19/08/2025
Planning, sequencing… and now analysis. 📊 ☕ Coffee Talk: Getting Your Microbiome Research on the Road – Managing Your Data using Qiita 🗓️ Aug 25, 2025 | 14:30 CEST 👉 More info: tinyurl.com/2m9jpf2p 👉 Workshop (Oct 22–24, Gießen): tinyurl.com/4w8mczh7
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Geraldine Zimmer-Bensch @zimmer-bensch.bsky.social · 18/08/2025
🌍 Open Call! RWTH Aachen University invites postdocs from outside the EU to apply for the “Port to Europe” Fellowship (24 months funding, all disciplines). Start your research journey at one of Europe’s top universities! 🚀 Deadline: Oct 5, 2025. 👉https://rwth-aachen.de/go/id/botjje/lidx/1
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 01/08/2025
Do you have experience in metabolomics/lipidomics/exposomics? Check out the EMBL ARISE2 Fellowship Programme! 🔗 www.embl.org/training/ari... 📩 Contact: Juan Antonio Vizcaíno — Team Leader, EMBL-EBI 🔗 www.ebi.ac.uk/people/perso... 📌 Applications close soon! 📆 30/09/2025 More info below👇
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Typas Lab @typaslab.bsky.social · 30/07/2025
Ready to lead pioneering research that bridges systems-level investigations of biological systems to molecular mechanism? The EMBL Molecular Systems Biology Unit in Heidelberg is hiring a Group Leader!
embl.wd103.myworkdayjobs.com
Group Leader – Molecular Systems Biology Unit
Are you ready to lead groundbreaking research in Molecular Systems Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group, addressing original biological ...
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