Bioinformatics Scientist at Labor Berlin / Clinical Bioinfo / ❤️#rstats / @pmenzel@mstdn.science / @pmenzel.bsky.social / https://xitter.cf/t.co/DcCA1YYCha

Berlin, Germany
Joined July 2008
Amazing and comprehensive guide to adding, updating and debugging bioinformatics software tools on Bioconda by @jfy133 (expanding on his earlier blogpost) - if you do bioinformatics software dev, it is truly all you need to get started with Bioconda
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📢 We're excited to introduce Pathoplexus, a specialized sequence database for human viral pathogens! 🌍 🧬 Launching with 4 viruses, Pathoplexus.org combines modern open-source software with transparent governance to improve global pathogen sequence sharing. 1/14
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Our 2 bridge RNA papers are finally published in @Nature! Check out the incredible CryoEM structures, they're truly beautiful. A years-long rollercoaster ride, it's hard for me to imagine a more exciting project than this. Thank you to @ntperry13, @pdhsu, and our amazing team!
What if we could universally recombine, insert, delete, or invert any two pieces of DNA? In back-to-back @Nature papers, we report the discovery of bridge RNAs and 3 atomic structures of the first natural RNA-guided recombinase - a new mechanism for programmable genome design
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Reminder! Effective June 2024, older API and CLI versions of NCBI Datasets will no longer be supported. Install the latest version and learn how to access the new API (v2alpha): ow.ly/Eh2P50RSFMJ
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New research article #SARSCoV2 rapid antigen test sensitivity and viral load in newly symptomatic hospital employees in Berlin, Germany, December, 2020 to February, 2022: an observational study thelancet.com/journals/lanmi… #COVID19 #OpenAccess #OA
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First step in a community project to provide a uniformly assembled, annotated and searchable set of bacterial genomes, our preprint on our initial release of 1.9 million genome assemblies+taxonomic estimates. (figure compares with previous 661k dataset) biorxiv.org/content/10.1101/…
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There are no more borders in the European Union. However, you will always know where the Netherlands begins.
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Variability and Bias in Microbiome Metagenomic Sequencing: an Interlaboratory Study Comparing Experimental Protocols biorxiv.org/cgi/content/shor… #bioRxiv
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Release 1.17 of HTSlib, SAMtools and BCFtools is now available from GitHub. See htslib.org/download/ for links to tarballs and release notes.
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I've updated my #SARSCoV2 #22F/#XBB figure to show how it has evolved into XBB.1 & XBB.1.5 XBB.1 has an additional spike S1 mutation at G252V XBB.1.5 has a second amino-acid change at 486, taking 486S -> 486P 1/2 #XBB1 #XBB15 xitter.cf/firefoxx66/status/1587…
You might be seeing a lot about XBB these days, & we're in the process of adding it to @nextstrain, Nextclade, & CoVariants.org (as 22F). You might also be hearing it's a 'recombinant' - but what does that mean? Let's take a look. 1/9
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Can't keep up with all the interesting #ChatGPT prompts? Nothing to worry about! I curated a 🧵for you with key messages & relevant tweets on where our new academic companion #ChatGPT excels or fails in writing #Bioinformatics code, academic grants & tutorials👇
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dplyr 1.1.0 is coming soon!! 🎉🎉 We are so excited to introduce you to the new features we've been working on, including: - Temporary inline grouping with `.by` - Non-equi joins - Faster `arrange()` And SO much more! #rstats tidyverse.org/blog/2022/11/d…
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Dilbert Comic for July 17: fal.cn/3qis9
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European starlings are exceptional mimics, including human speech. Their ability at mimicry is so great that strangers have looked in vain for the human they think they have just heard speak. Jabber is 4 years old [source: buff.ly/33Z9V3G]
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We're in the middle of a giant machine learning surge, with ML-based "classifiers" being used to make all kinds of decisions at speeds that humans could never match: ML decides everything from whether you get a bank loan to what your phone's camera judges to be a human face. 1/
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Yes, we finally finished! About a year ago, we released T2T-CHM13v1.1 with no Y. Today, we have the T2T-CHM13v2.0, with all chromosomes, with Y! A paper will follow, stay tuned! Early adapters, here are a few updates for using CHM13 as an alternative reference: (1/n)
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Today is the big day! The #T2T consortium is claiming victory and announcing that we have finally uncovered every last bit of the human genome! The papers are out today 🥳🧬 science.org/toc/science/376/…
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It's that time again! MultiQC v1.12 just released 🥳 - 3 new modules (CheckQC, pbmarkdup, WhatsHap) - A bunch of new core features (tool citations, better printing, more customisation) - Many, many bugfixes... 🐛 Come get it whilst it's hot 🔥 github.com/ewels/MultiQC/rel…
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