Jonas Fuchs

Fascinated about virus evolution. Working on SARS-CoV-2. PostDoc at the Institute of Virology @Uniklinik_Fr

[Jonas Fuchs @_JonasFuchs]

Ok, so I did a thing... I build a serverless mutliple sequence alignment viewer that generates publication ready pdfs. Give me your thoughts (its still in dev 😄).

Access it online:
https://t.co/hwIwvUHQOR

Open source code:
https://t.co/jfwwr9WmdM

#opensource #Bioinformatics

[Jonas Fuchs @_JonasFuchs]

@BortzGroup @ZaminIqbal @nanopore Jup we also did ONT in our study.

[Jonas Fuchs @_JonasFuchs]

New preprint is out! Go check it out:
varVAMP: automated pan-specific primer design for tiled full genome sequencing and qPCR of highly diverse viral pathogens

Thanks to all the super cool people involved in this project :).

https://t.co/YhbqofnQcg

[Jonas Fuchs @_JonasFuchs]

We just released a major update for varVAMP allowing the design of PCR primers on highly variable alignments. Now it finds more primers, allows to predict off-targets with a BLAST db and more. Go check it out. Credits go to Wolfgang Maier @galaxyproject

https://t.co/lzyGXaREAk

[Simona Cristea @simocristea]

MEGA-CRISPR (multiplexed effector guide arrays) is an alternative to CRISPR editing that edits RNA instead of DNA. It swaps the DNA-cutting enzyme Cas9 for an RNA-cutting alternative called Cas13d. As mRNA doesn’t last very long in a cell, any potential mistakes disappear fast.

MEGA-CRISPR can shut down the production of multiple proteins, turning off up to 10 genes at once.

To showcase the power of this system, a new paper addressed a really important clinical problem: T cell exhaustion in immunotherapy treatment for cancer patients. What this means is that, when either natural or engineered T cells (such as in CAR-T therapy) are chronically activated too many times by a tumor for example, they lose their effectiveness and ultimately stop reacting.

The paper tunes exhaustion markers using an antibiotic switch of varying dose, creating a system that can essentially react dynamically and turn genes on/off as a function of a varying input.

This system is an important advance because
(1) editing mRNA is more versatile & less consequential than editing DNA
(2) it can edit very many genes at a time (up to 10)
(3) it can tune these many genes on/off using an external input

Exciting times ahead for cell therapies in oncology!

https://t.co/Jmff2A20T3

[Mirjam Schilling @MirjamSchilling]

Our case report of a fatal WNV infection in a travelling horse is now out in @EIDjournal... Get your horses vaccinated! @APHAgovuk

[Jonas Fuchs @_JonasFuchs]

https://t.co/aBcmDegkLj

varVAMP is now awailable at https://t.co/4FTBcKatjF. varVAMP is a command line tool to design primers for highly variable alignments. For non-command line users usegalaxy now provides an intuitive online-solution. Thanks @galaxyproject and Wolfgang Maier!

[Martin Hölzer @martinhoelzer]

We find DNA/RNA contamination in seq data, seq collections, & asssemblies. Either from biological sources, spike-ins, unwanted targets.

We provide an easy-to-use @nextflowio pipeline for reference- and mapping-based decontamination, latest release:

https://t.co/Wv7LlPn9jd

[Johannes Köster (@johanneskoester.bsky.social) @johanneskoester]

I am happy to finally announce the release of #Snakemake 8.0! In about half a year, we have modernized large parts of the code base. Most importantly, Snakemake 8.0 introduces a versatile plugin system, redesigned support for external storage, and modernized documentation. (1/n)

[Jonas Fuchs @_JonasFuchs]

Just updated virHEAT (https://t.co/fntDGNWosL) to version 0.6 (conda and pip). Let's you visualize microbial evolution at the snp level as a heatmap. Now you can restrict the plot to specific genomic regions with --zoom. SARS-COV-2 example:
#SARSCoV2 #Bioinformatics

[Ming "Tommy" Tang @tangming2005]

How to choose the right machine-learning method?
https://t.co/jDypuhDD7H

[Hugh Kearns @ithinkwellHugh]

Really scary!!

[Michelle Wille @DuckSwabber]

From Influenza A to an incredible diversity of viruses - great comprehensive analysis of Orthomyxoviruses!
👉https://t.co/CsNkYjF1HO

[Jonas Fuchs @_JonasFuchs]

@Flahless1 We have done designs for quite a few viruses but not for noroviruses so far. If you want I can give it a go or walk you through it! Just drop me a mail.

[Jonas Fuchs @_JonasFuchs]

Just updated varVAMP to version 0.9.4. Designed for pan-specific primer design for full viral genome sequencing: https://t.co/rjJGWbrL1j. Now used to design a novel pan-lineage primer scheme for SARS-CoV-2. Thx to @martinhoelzer for providing the alignment. In silico, not tested!

[Jonas Fuchs @_JonasFuchs]

@cinnetcrash1 The only thing varVAMP needs is an alignment. So an alignment of a variable bacterial gene is just fine. I have tested it up to 200 kb, but then it runs a bit due to the complexity of the graph that is used to find the best scheme. So go for it! If you need help let me kow!

[Ryan Hisner @LongDesertTrain]

Really happy to see our paper on SARS-CoV-2 evolution in the Omicron era out in @Nature Microbiology today.

I'd normally write a thread outlining our paper, but I've not felt well for a while & can't focus well enough to do much of anything. Will try to write one later.

[Olivier Schwartz Lab @Virus_Immunity]

#Sotrovimab therapy elicits antiviral activities against #Omicron BQ.1.1 and XBB.1.5 in sera of immunocompromised patients.
Congrats to @Timothee_B and colleagues for studying neutralizing and non-neutralizing antibody activities
https://t.co/5S4T0gkLrI

[Jonas Fuchs @_JonasFuchs]

Happy to have finalized this small project.
https://t.co/ZkXtiYXcOl
Create interactive coverage plots from your mapped viral read and usefull tracks such as genbank files.