iiinova — where your digital self keeps evolving

Reposted by Axel Janssen

Best of Wikipedia @bestofwikipedia.bsky.social · 25/07/2026

The Picture of the Day of Saturday 25 July 2026 on @wikipedia.org is: Lavaux. Credits: Lorenz Poffet.

Lavaux is a region in the canton of Vaud in Switzerland, in the district of Lavaux-Oron. The region consists of 830 hectares (2,100 acres) of terraced vineyards that stretch for about 30 kilometres (19 mi) along the south-facing northern shores of Lake Geneva. The region is designated a UNESCO World Heritage Site with the formal name Lavaux, Vineyard Terraces. The vine terraces in the area date to the 11th century, under the rule of Benedictine and Cistercian monasteries. The main variety of wine grape grown here is Chasselas. This photograph shows an aerial view of the terraced vineyards of Lavaux near the village of Rivaz, overlooking Lake Geneva. Type: photograph. Credits: Lorenz Poffet.

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Jan-Willem Veening @veeninglab.com · 07/08/2025

Of course, we ( @axeljanssen.bsky.social) setup a genome browser with a track with sgRNA target sites for easy target validation and gene hunting

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Axel Janssen @axeljanssen.bsky.social · 07/08/2025

Don't miss out on our work on Haemophilus influenzae fitness profiling using CRISPRi-Seq! Visit our HaemoBrowse genome browser as well: haemobrowse.veeninglab.com.

haemobrowse.veeninglab.com

HaemoBrowse

Genome browser for Haemophilus influenzae

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Reposted by Axel Janssen

MV Mazzuoli @mvmazzuoli.bsky.social · 23/04/2025

OUT NOW! 👇🏼We built a make-or-break Prime editing tool—have a read to discover how it’s changing the way we do genomic engineering. www.nature.com/articles/s41... @JWVeening @AxelJans & all others authors! 👏🏻

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Axel Janssen @axeljanssen.bsky.social · 13/03/2025

I'm by no means an expert, but I've used it a fair number of times for some analyses. I'd happy to help where I can. Can you let me know what problems you are experiencing?

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Reposted by Axel Janssen

micamer.bsky.social @micamer.bsky.social · 11/03/2025

We would love feedback on a new NCBI-BLAST service we are launching today: sky-blast.com Under the hood it's the same BLAST executable and databases provided by NCBI, with a replica of the NIH's interface - providing an alternative to the US gov service that's less congested, faster & more reliable

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Reposted by Axel Janssen

Dirk-Jan Scheffers 🟥 @dirkscheffers.bsky.social · 16/12/2024

"...opvallend is dat slechts 31 procent van de respondenten die ervaring heeft met het beoordelen van subsidieaanvragen dit proces eerlijk vindt. “Zelfs succesvolle aanvragers en commissieveteranen vinden het beoordelingsproces voor subsidieaanvragen niet eerlijk”, concluderen de auteurs." 1/

scienceguide.nl

Beursafhankelijkheid wetenschappers beknot academische vrijheid - ScienceGuide

Het huidige beoordelingsproces van subsidieaanvragen is oneerlijk, vindt de helft van de Nederlandse wetenschappers.

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Reposted by Axel Janssen

Jan-Willem Veening @veeninglab.com · 31/10/2024

Checkout this preprint from Bevika Sewgoolam! She used CRISPRi-seq to determine antibiotic-stress signatures, specifically of pneumococci treated with fluoroquinolone antibiotics. It's a really powerful approach revealing a surprising antibiotic combination therapy. www.biorxiv.org/content/10.1...

biorxiv.org

Genome-wide antibiotic-CRISPRi profiling identifies LiaR activation as a strategy to resensitize fluoroquinolone-resistant Streptococcus pneumoniae

Streptococcus pneumoniae is a human pathogen that has become increasingly resistant to the synthetic fluoroquinolone antibiotics that target bacterial topoisomerases. To identify pathways that are ess...

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Axel Janssen @axeljanssen.bsky.social · 25/10/2024

Again, thanks to all co-authors for their work on this as well, and other Veening lab members for their continued feedback and bug reports.

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Axel Janssen @axeljanssen.bsky.social · 25/10/2024

We have now also added the ability to view pair-wise genome alignments to PneumoBrowse2. Find this option in the "Linear Synteny" or "Dotplot" alignments views (bottom), or in separate data tracks (per genome). Thanks for the excellent reviewer comments on this.

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Axel Janssen @axeljanssen.bsky.social · 25/10/2024

Do you use D39V, TIGR4, EF3030, BHN418, or another pneumococcal strain in your research? Easily browse their genome on PneumoBrowse 2 pneumobrowse2.veeninglab.com! Now out in shiny PDF in Nucleic Acids Research! Do you have any feedback? Please let us know! academic.oup.com/nar/advance-...

pneumobrowse2.veeninglab.com

PneumoBrowse

Genome browser for Streptococcus pneumoniae

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Reposted by Axel Janssen

Sophie G Martin @sophiemartinlab.bsky.social · 23/10/2024

The Martin lab has an open postdoc position at the interface of #cytoskeleton and #condensate biology, in a fantastic research community! If interested, do not hesitate to contact us: mocel.unige.ch/research-gro... Please RT!

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Reposted by Axel Janssen

Frans van Heest @fransvanheest.bsky.social · 12/09/2024

Bij het aanvragen van een Vidi-subsidie verlangt NWO dat universiteiten toezeggen de aanvrager een vaste positie te zullen geven. Dat hindert onderzoekers met een tijdelijk contract, want veel universiteiten willen zo’n toezegging alleen doen bij medewerkers in vaste dienst, stelt Mehrdad Alipour.

scienceguide.nl

‘Geen vast contract, geen kans: verborgen ongelijkheid in NWO-beleid voor Vidi-subsidies’ - ScienceGuide

Universiteiten willen alleen vast personeel een inbeddingsverklaring geven bij Vidi-aanvragen, schrijft Mehrdad Alipour.

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Reposted by Axel Janssen

Sara Mitri @saramitri.bsky.social · 12/09/2024

Our bacterial community breeding experiment is now published! doi.org/10.1038/s414... Huge congratulations to Flora, Björn and all co-authors on making a very ambitious project a reality! In short: you can select communities to improve pollutant degradation (with caveats)

doi.org

Artificial selection improves pollutant degradation by bacterial communities - Nature Communications

Artificial selection is a promising way to improve microbial community functions. Here, Arias-Sánchez et al. evaluate a method inspired by genetic algorithms to select small bacterial communities of k...

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Reposted by Axel Janssen

Jan-Willem Veening @veeninglab.com · 17/08/2024

Genome-wide dual CRISPRi-seq! Knocking down every gene with every other gene in the pneumococcus, identifying > 4000 genetic interactions (GIs), most of which have never been reported. www.biorxiv.org/content/10.1...

biorxiv.org

Dual CRISPRi-Seq for genome-wide genetic interaction studies identifies key genes involved in the pneumococcal cell cycle

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

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Reposted by Axel Janssen

Renske van Raaphorst 🟥 @vrrenske.bsky.social · 09/08/2024

It was already a very useful resource, now it is an absolutely fabulous resource!

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Reposted by Axel Janssen

Willem van Schaik @wvschaik.bsky.social · 09/08/2024

We are looking for a Network Manager for TARGet (Transdisciplinary Antimicrobial Resistance Genomics network). Apply by scanning the QR code or via www.birmingham.ac.uk/jobs

A job posting for a research project manager at the University of Birmingham.

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Axel Janssen @axeljanssen.bsky.social · 09/08/2024

Thanks to co-authors Paddy Gibson, Afonso Bravo, Vincent de Bakker, Jelle Slager, and @jwveening.bsky.social for all their hard work, other members of the Veening lab for input and feedback, and Doran Pauka for his support. Feedback is always welcome   We hope you enjoy!

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Axel Janssen @axeljanssen.bsky.social · 09/08/2024

For each gene, we also provide direct links to other databases, such as PneumoWiki, the NCBI, UniProt, PaperBLAST, AlphaFold, and Foldseek, to allow further discovery of biological functions by end-users!

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Axel Janssen @axeljanssen.bsky.social · 09/08/2024

These genomes were all sequenced using long-read sequencing techniques (either PacBio or Nanopore sequencing), and we provide the genome methylaton, and genome annotations. Their genomes sequences are available on the NCBI as well!

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Axel Janssen @axeljanssen.bsky.social · 09/08/2024

By upgrading to JBrowse 2, we could add other genomes. We added the genomes of 18 other phylogenetically diverse S. pneumoniae strains (orange), including commonly used strains in laboratories such as TIGR4, BHN418, and EF3030, but also Pneumococcal Molecular Epidemiology Network reference strains.

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Axel Janssen @axeljanssen.bsky.social · 09/08/2024

The annotation of D39V has also been updated to reflect the state of the art in pneumococcal genome biology. We have added new locus tags, changes to gene names, new protein functions, transcription factor binding sites, and much more.

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Axel Janssen @axeljanssen.bsky.social · 09/08/2024

For example, we have added new genome-wide data tracks to show raw data from Ribo-Seq, ChIP-Seq, and Hi-C experiments. We have also included gene-essentiality data across a wide range of environmental conditions from CRISPRi-seq experiments.

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Axel Janssen @axeljanssen.bsky.social · 09/08/2024

PneumoBrowse 2 has had several major upgrades. We have completely rebuilt it in JBrowse 2, further curated the already detailed manual curration of the S. pneumoniae D39V genome, and added 18 other phylogenetically S. pneumoniae genomes, including TIGR4, and much, much more!

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Axel Janssen @axeljanssen.bsky.social · 09/08/2024

Did you like PneumoBrowse, our pneumococcal genome browser? We just released the newest version: PneumoBrowse 2! Try it out on pneumobrowse2.veeninglab.com, and read the preprint! www.biorxiv.org/content/10.1...

pneumobrowse2.veeninglab.com

PneumoBrowse

Genome browser for Streptococcus pneumoniae

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Reposted by Axel Janssen

Mathijs Bouman @mathijsbouman.nl · 12/07/2024

fd.nl/opinie/15232...

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Sara Mitri @saramitri.bsky.social · 11/07/2024

We're looking for an enthusiastic experimentalist PhD student to join our interdisciplinary group interested in the ecology & evolution of microbial communities unil.ch/mitrilab. Apply tinyurl.com/mu5swnk8 before Aug 31! Bonus: Lausanne is a beautiful place to live!

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Axel Janssen @axeljanssen.bsky.social · 01/07/2024

🚨New work alarm🚨 Very happy to see this work out, together with Monica, @mvmazzuoli.bsky.social, Anne-Stephanie, Xue, and @jwveening.bsky.social. We developed make-or-break Prime Editing, through which we can make a wide variety of mutations. Read more on BioRxiv!

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Yolanda Schaerli @yschaerli.bsky.social · 02/04/2024

Very happy to share our latest preprint DMF UNIL: Jung and Gábor controlled the ring patterns in E. coli colonies generated by a synthetic oscillator with optogenetics. We observed synchronisation, resonance, entrainment, undertone, period doubling and even chaos! Feedback welcome.

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Willem van Schaik @wvschaik.bsky.social · 20/03/2024

Job claxon: 18-month PDRA position in my group on the correlation between gut microbiome composition and psychological status in a unique military cohort: www.jobs.ac.uk/job/DGQ655/r... Email me for details!

jobs.ac.uk

Research Fellow at University of Birmingham

An opportunity for an academic position as a Research Fellow is available, as advertised on jobs.ac.uk. Apply now and explore other academic job openings.

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Reposted by Axel Janssen

Jessica Blair @jessicamablair.bsky.social · 15/02/2024

Funded PhD opportunity with me and Dr Tim Overton. This scholarship is open to Black British students & will investigate the links between efflux, energy metabolism & drug resistance. Please get in touch with us if you would like more information! www.birmingham.ac.uk/study/postgr...

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Reposted by Axel Janssen

Kimberly Kline 🏔 @kimingeneva.bsky.social · 06/02/2024

PhD student opening! We are collaborating with the team of David Johnson @EawagResearch to understand E. faecalis polymicrobial community assembly, interactions, and consequences for AMR and infection. Details of the position and how to apply can be found here: tinyurl.com/ywa52a6a.

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Reposted by Axel Janssen

Stephan Gruber @gruberlab.bsky.social · 02/02/2024

Our new work on the Wadjet (JET) anti-plasmid defence system is out: authors.elsevier.com/a/1iXM53vVUP... Showing structures of SMC complexes on extruded DNA (first time?) and blockage (!) of DNA extrusion by obstacles on DNA and more...

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Philipp Engel @pengellab.bsky.social · 16/01/2024

Two PhD positions available in our lab @FBM_UNIL. We are looking for microbiologists interested in microbiota-host interactions, symbiosis, metabolomics, and social bees! Lausanne is amazing: Vibrant scientific environment & high quality of life 🇨🇭🚞🏂🌄🧪🐝🦠 shorturl.at/ptyOT shorturl.at/dipvA

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Willem van Schaik @wvschaik.bsky.social · 16/01/2024

Enterococci doing weird stuff claxon! Very excited that our manuscript 'Integration of vanHAX downstream of a ribosomal RNA operon restores vancomycin resistance in a susceptible Enterococcus faecium strain' has been published in npj Antimicrobials and Resistance www.nature.com/articles/s44...

nature.com

Integration of vanHAX downstream of a ribosomal RNA operon restores vancomycin resistance in a susce...

npj Antimicrobials and Resistance - Integration of vanHAX downstream of a ribosomal RNA operon restores vancomycin resistance in a susceptible Enterococcus faecium strain

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Axel Janssen @axeljanssen.bsky.social · 15/01/2024

alle klinkers kunnen tussen de letters worden geplaatst voor een geldig NLs woord

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Axel Janssen @axeljanssen.bsky.social · 12/01/2024

staten met een militaire basis van een ander land (om exact te zijn, die in je hint)

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Eduardo Rocha @epcrocha.bsky.social · 15/12/2023

New postdoc position in our lab for a project led by Marie Touchon (bioinformatics) and with O Tenaillon (experiments) on the evolution and dynamics of microbial genomes to understand their diversification by gene flow. Check research.pasteur.fr/en/job/postd...

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Willem van Schaik @wvschaik.bsky.social · 11/01/2024

Ross McInnes, a post-doc in my group, will sadly be leaving in Spring 2024 as we reach the end of a grant. He is now looking for a job. Ross is excellent and has a skill set that includes molecular biology, functional and comparative genomics, and microbiome research: rosssmcinnes.github.io

rosssmcinnes.github.io

Ross S McInnes

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Axel Janssen @axeljanssen.bsky.social · 08/01/2024

This was a little Christmas break project to learn about python and Github Actions. Any ideas, recommendations, and suggestions are welcome!

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