Axel Janssen

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

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.

Evolution of Colistin Resistance in the Klebsiella pneumoniae Complex Follows Multiple Evolutionary Trajectories with Variable Effects on Fitness and Virulence Characteristics The increasing prevalence of multidrug-resistant Klebsiella pneumoniae has led to a resurgence in the use of colistin as a last-resort drug. Colistin is a cationic antibiotic that selectively acts on ...

We have done it, and we’ve used 25% LB (pmc.ncbi.nlm.nih.gov/articles/PMC...), which we got from another paper (journals.asm.org/doi/10.1128/...).

What other methods did you run into? Did you plan on using another medium?

👏 And another one from @jwveening.bsky.social @dmf-unil.bsky.social @unil.bsky.social @mvmazzuoli.bsky.social @axeljanssen.bsky.social

Published in @natcomms.nature.com 👇

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! 👏🏻

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?

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

Beursafhankelijkheid wetenschappers beknot academische vrijheid - ScienceGuide Het huidige beoordelingsproces van subsidieaanvragen is oneerlijk, vindt de helft van de Nederlandse wetenschappers.

"...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/

Now updated!

www.biorxiv.org/content/10.1...

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...

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...

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.

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.

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-...

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!

Hier wordt gewerkt aan de afbraak van het hoger onderwijs Eppo Bruins was bijna bijzonder hoogleraar, maar toen werd hij minister die de sloopkogel door het hoger onderwijs haalt. Is Bruins een principeloze baantjesjager? vraagt columnist Dirk-Jan Scheffers ...

Deze is voor jou, @eppobruins.bsky.social
ukrant.nl/hier-wordt-g...

‘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.

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.

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...

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)

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

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...

Dual CRISPRi-Seq for genome-wide genetic interaction studies identifies key genes involved in the pneumococcal cell cycle https://www.biorxiv.org/content/10.1101/2024.08.14.607739v1 A major goal in biology is to uncover the relationship between genotype and phenotype. However, iden

Dual CRISPRi-Seq for genome-wide genetic interaction studies identifies key genes involved in the pneumococcal cell cycle https://www.biorxiv.org/content/10.1101/2024.08.14.607739v1

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

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

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

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!

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!

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!

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.

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.

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.

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!

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...

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