Christian Thomas

Neuropathologist @ University Hospital Münster. Passionate about nanopore sequencing, metagenomics and bioinformatics 🧬

[Rafael Irizarry @rafalab]

Biologists, stop putting UMAP plots in your papers!

UMAP is a powerful tool for exploratory data analysis, but without a clear understanding of how it works, it can easily lead to confusion and misinterpretation.

Link to @simplystats blogpost below.

[Christian Thomas @thomachr87]

Metagenomic @nanopore sequencing of CSF identifies Borrelia miyamotoi as an unexpected cause of meningitis. 🧬 Read the full article here: https://t.co/Ut31e5US7h

[Christian Thomas @thomachr87]

High-coverage viral sequencing from FFPE samples—explore our protocol: https://t.co/VTKeH1x4Si
@TwistBioscience

[Christian Thomas @thomachr87]

@keithdurkin @ulrichschueller @LschweizerLeo @nanopore We did not compare different DNA extraction methods. In our hands, the ligation sequencing kit and R10.4.1 flow cells worked well, whereas R9.4.1 flow cells ran into trouble. You could probably check DIN values of your input DNA and quality of your library.

[Christian Thomas @thomachr87]

Always thought #Nanopore sequencing from #FFPE is impossible? Explore our paper: https://t.co/8KuCZxvRYw. Methylation & CNV profiling of CNS tumors. Great collaboration with @ulrichschueller and @LschweizerLeo. @nanopore

[Christian Thomas @thomachr87]

@r_sankowski @ulrichschueller @LschweizerLeo @nanopore We used our regular DNA extraction method, Maxwell RSC FFPE Plus DNA Kit (Promega).

[Christian Thomas @thomachr87]

@r_sankowski @ulrichschueller @LschweizerLeo @nanopore Thanks, @r_sankowski. No apative sampling needed, just plain sequencing (~100 Mb sufficient in most cases). Oligodendrogliomas on Flongles required only < 20 Mb sequencing.

[Christian Thomas @thomachr87]

Nanopore Sequencing of FFPE-DNA: 250 Mb with N50 of 1.35 kb after 1.5 hrs! Median Q > 12 😍
@nanopore

[Junge Neuropathologen @JungeNPath]

Good vibes at #ICN2023

[Professor Booty PhD @ProfBootyPhD]

I think we need to talk about how devastating this cancer microbiome refutation paper from
@StevenSalzberg1
and colleagues is. It really speaks to how devoid of critical thinking and intellectual depth our glam publishing ecosystem has become. 1/n
https://t.co/wWsHTa4K8x

[Pouya Jamshidi, MD @PJamshidi_MD]

Check out our #AANP2023 poster on neurovascular complications of anti-amyloid-beta immunotherapy ⁦@neuropathology⁩ ⁦@ElishevaShanes⁩ ⁦@MccordMatt⁩ ⁦@MaggieFlanagan⁩ ⁦@RudyCastellani⁩ ⁦@NU_Pathology⁩ ⁦⁦⁩ ⁦@NUMesulamCenter⁩ ⁦

[Free Neuropathology @FreeNeuropatho]

Free Neuropathology is now indexed by PubMed and PubMed Central. The PMC website of the journal is here: https://t.co/WaMM6F9dkl

[Free Neuropathology @FreeNeuropatho]

What's new in neuromuscular disease? Check out this excellent update by Marta Margeta #UCSF #Neuropathology: https://t.co/oigmfIKqGM

[Jonas Schmidt-Chanasit @ChanasitJonas]

Our #arbovirology Team is attending to #ECV2023 with our newly developed Illumina iseq100-based viral #metagenomic pipeline for #virus 🦠 discovery. Its a simple and very sensitive #protocol that is available for low-budget/low-setting labs + mobile platform for #outbreak scenarios.

[Christian Thomas @thomachr87]

@CraigHorbinski But #ChatGPT is definitely enthusiastic about neuropathology! https://t.co/9sPM3Pzqn7

[Free Neuropathology @FreeNeuropatho]

ChatGPT, describe what a neuropathologist does but in the style of Donald Trump.

[Free Neuropathology @FreeNeuropatho]

ChatGPT, describe what a neuropathologist does but in the style of Donald Trump.

[Itai Yanai @ItaiYanai]

Here are my 12 guidelines for data exploration and analysis with the right attitude for discovery:
1. You never really finish analyzing a dataset. You just decide to stop and move on at some point, leaving some things undiscovered. 🧵

[Christian Thomas @thomachr87]

DNA-to-answer time < 8 hours

[Christian Thomas @thomachr87]

Nanopore sequencing enables rapid identification of bacteria in FFPE specimens! Check out our protocol: https://t.co/XT6GjH3uCd
@nanopore @NAN_Wiley @AnneAlbers12

[Allie K. Miller @alliekmiller]

ChatGPT is changing the game, and I want to share real things you can do with this AI system today.

Please save this thread and start testing this technology NOW so you’re ahead of the curve.