Jonas Fuchs

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: jonas-fuchs.github.io/MSAexplorer/sh… Open source code: github.com/jonas-fuchs/MS… #opensource #Bioinformatics

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

@_JonasFuchs @ZaminIqbal 🦠🧬 Very cool — can’t wait to try it! Works with @nanopore?

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 :). biorxiv.org/content/10.110…

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 github.com/jonas-fuchs/va…

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! nature.com/articles/d4158…

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

usegalaxy.eu/?tool_id=tools… varVAMP is now awailable at usegalaxy.eu. 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!

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: github.com/rki-mf1/clean/…

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)

Just updated virHEAT (github.com/jonas-fuchs/vi…) 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

How to choose the right machine-learning method? buff.ly/2PfOLGk

Really scary!!

From Influenza A to an incredible diversity of viruses - great comprehensive analysis of Orthomyxoviruses! 👉journals.asm.org/doi/10.1128/jv…

@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.

Just updated varVAMP to version 0.9.4. Designed for pan-specific primer design for full viral genome sequencing: github.com/jonas-fuchs/va…. 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!

@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!

@_JonasFuchs This is looking cool. I wonder if this tool is only for viral pathogens? Can we use this for bacteria for specific genes as well?

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.

#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 sciencedirect.com/science/articl…

Happy to have finalized this small project. github.com/jonas-fuchs/BA… Create interactive coverage plots from your mapped viral read and usefull tracks such as genbank files.