Fascinated about virus evolution. Working on SARS-CoV-2. PostDoc at the Institute of Virology @Uniklinik_Fr
Freiburg Germany
Joined November 2021
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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/MSAexp…
Open source code:
github.com/jonas-fuchs/MSAex…
#opensource #Bioinformatics
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/10.1101/…
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/varVA…
Jonas Fuchs retweeted
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/d41586-0…
Jonas Fuchs retweeted
Our case report of a fatal WNV infection in a travelling horse is now out in @EIDjournal... Get your horses vaccinated! @APHAgovuk
A fatal case of #WestNile virus occurred in a mare returning to the UK from Spain. The mare had no record of having received WNV vaccine.
Learn more in this February 2024 EID journal article:
bit.ly/3Su8qQw (Authors: Mirjam Schilling, et al.) @MirjamSchilling
usegalaxy.eu/?tool_id=toolsh…
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!
Jonas Fuchs retweeted
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/rel…
Jonas Fuchs retweeted
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/virhe…) 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
Jonas Fuchs retweeted
From Influenza A to an incredible diversity of viruses - great comprehensive analysis of Orthomyxoviruses!
👉journals.asm.org/doi/10.1128…
Jonas Fuchs retweeted
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.
How #SARSCoV2 is continuing to evolve in the Omicron era, by many of the guiding lights who have so diligently tracked this virus throughout the pandemic
nature.com/articles/s41564-0… @NatureMicrobiol by @CorneliusRoemer @PeacockFlu @DannySheward @LongDesertTrain @siamosolocani
Jonas Fuchs retweeted
#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/ar…
Just updated varVAMP to version 0.9.4. Designed for pan-specific primer design for full viral genome sequencing: github.com/jonas-fuchs/varVA…. 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!
Happy to have finalized this small project.
github.com/jonas-fuchs/BAMda…
Create interactive coverage plots from your mapped viral read and usefull tracks such as genbank files.
Updated the repo now quite a bit! Now its a bit more pretty, calculates some useful stats and can annotate vcfs. Annotated data can also be saved and more.
Install on linux and mac with: pip install bamdash
Jonas Fuchs retweeted
Want to calculate the "Percentage Of Conserved Proteins" for bacteria?
My little @nextflowio implementation of the original approach from Qin et al. 2014 now uses Diamond instead of Blast for the protein alignments (thx @GregoireMichoud for the PR!)
github.com/hoelzer/pocp
