Michael Jahn

We have a new paper out on BioRxiv, featuring the largest and most comprehensive #CRISPRi repression library in #cyanobacteria (Synechocystis). We found many interesting #fitness #tradeoffs 🦠☀️⬇️. Great team effort with Rui Miao, @paulsimv, @KiyanS1. biorxiv.org/content/10.110…

I don't know anything about #glioblastoma, but this incredible piece of work by @RouvenHoefflin and co-authors ➡️ doi.org/10.1016/j.cell… was just published in Cell. It features nested #treemaps that were generated with my #R #package #WeightedTreepaps. Available on CRAN📈📊

@flamholz I totally agree. This was the motivation for making the package.

@mich_jahn R is a big improvement over running JavaScript via D3, which is what I’ve been doing!

Neat visualization: these circular hierarchical #treemaps were made with my #R package #WeightedTreemaps which you can now find on #CRAN. They show internal migration in China. Image credits go to Gu & Xu, 2022 doi.org/10.1177/239980…

@flamholz Hi Avi, haven't considered it yet but as an R package should be easy to wrap into any existing workflow. In the end you might as well call it from python, only input argument is a (pandas) data frame and some additional parameters.

@mich_jahn Any chance you want to make a python version?

New toolbox for engineering of #streptococcus pyogenes from our lab! Big effort from Nina @biologistninja 👏

Lastly a shout out to the three fantastic groups that were involved in this project: Paul Hudson's lab in Stockholm @paulsimv, Max Plack Unit for the Science of Pathogens @mpusp_pathogens, and Oliver Lenz lab in Berlin @Lenz_Group 🙏

- surprisingly, deletion of hydrogenase-related genes boosted growth, and we show that the relief from associated protein cost is responsible for this phenomenon - figure shows how growth rate roughly correlates with estimated relief from protein burden by KO

🚨 New preprint out! If you're interested in #ralstonia #cupriavidus #co2fixation #lithoautotrophy or #formate, this might be something for you. We probed the hydrogen consuming bacterium C. necator H16 with a genome scale barcoded transposon library. 1/n biorxiv.org/cgi/content/sh…

The Plant Cell in a Nutshell: A CRISPRi library screen reveals growth-robustness tradeoffs in Synechocystis plantae.org/a-crispri-libr… @mich_jahn @ASPB #PlantSci

At the core, the pipeline is using the excellent packages from the #crisprVerse suite for #R #bioconductor, developed by the team around @JayPykw . Many thanks for this great foundational work 👏

A new #snakemake pipeline is available from us for the genome-scale design of #CRISPR and #CRISPRi #library guides 🐍🛢️🔧📚 ! With this you can design thousands of guides in short time with just one line of code. github.com/MPUSP/snakemak…

Aaaannnnd our paper is now published in @ThePlantCell @OUPAcademic. Preliminary version here: doi.org/10.1093/plcell…. I also like to thank the reviewers for very fair and encouraging comments 💚👏, and the journal for the smooth publication process.

And for the #MachineLearning #CRISPR #guideRNA interested, we also used thousands of our guide RNAs to find important patterns for the design of efficient guide RNAs in #cyanobacteria.

We have a new paper out on BioRxiv, featuring the largest and most comprehensive #CRISPRi repression library in #cyanobacteria (Synechocystis). We found many interesting #fitness #tradeoffs 🦠☀️⬇️. Great team effort with Rui Miao, @paulsimv, @KiyanS1. biorxiv.org/content/10.110…

Was a pleasure to contribute to this paper from the Schulte Lab! 📉📊

CRISPR interference screens reveal growth–robustness tradeoffs in Synechocystis sp. PCC 6803 across growth conditions (Rui Miao, Michael Jahn, Kiyan Shabestary, Gilles Peltier, Elton P Hudson) buff.ly/474DQDr @mich_jahn @ASPB #PlantSci

Hurry up! You have 4 days to submit your abstract. And don't forget to apply for @FEMSmicro bursary! 👉 efbiotechnology.org/microbialstress #microbiology #microbialstress #microbial #microorganisms #callforabstracts #earlybird #bursary #FEMSbursary

@binlai89 @vdlorenzo_CNB @UFZ_de Yes, absolutely! We also have resources (pipelines) for designing libraries and processing functional genomics data. Let me know when you get this project started, I'd be happy to collaborate, on whichever level. I'm now at MPUSP Berlin.

@mich_jahn @vdlorenzo_CNB @UFZ_de Super! Let's keep in touch.

4-year PhD position offered in @binlai89 Lab @UFZ_de Leipzig for developing CRISPRi approaches to screen & identify the membrane transporter(s) of Synechocystis, and then conduct protein engineering to improve the transportation kinetics. More details here👇