Oleksandr Petrenko

New insights into alcohol-related liver disease: in the recent preprint, we mapped niche-specific cell interactions at ultra-high resolution (2μm spots), described hepatic niche markers, and cell subtypes defined by them. Stay tuned!
#ALD #SpatialBiology #Fibrosis 🧪

www.biorxiv.org/content/10.1...

Apparently so!
The first two cases were documented there, a fascinating discovery.

Can we please take a moment and congratulate my colleague
@georg-semmler.bsky.social with publication of his study on Tangier disease, an extremely rare disease caused by ABCA1 defect with no existing treatment?
Great journey with lipidomids & metabolomics of TD 🧪

academic.oup.com/jcem/advance...

Recently, I had several conversations with my American friends regarding Trump's statements on #Ukraine and the "urgent need" for elections in Ukraine. Given that this topic is of high speculation currently, I am sharing a personal viewpoint from a recent reply:

After years of confronting the russian propaganda narrative on "NATO-funded bioweapon research in Ukraine," I feel somewhat disappointed that it's not true. If it was, that would be a hell of a PhD project idea without even needing to leave my own country.

It's fantastic to see more scientists 🧑‍🔬👨‍🔬, including here at the MUW campus in Vienna, joining bsky. Research feeds here are real gems.

However, we should consider the risks of further internet fragmentation & botnets (witnessed both on recent topics and ru-🇺🇦 war). No good/working solutions so far.

Wow, thanks a lot for your recommendations! Followed 😊

By the way, any #hepatology / #biomarkers / target discovery / #multiomics / #SystemsBiology scientists around on Bluesky?

Trying to find colleagues to follow :)
🧪

Graphical abstract of the study focusing on the exploration of metabolomic profiles in PSVD

/5 This project has been a rewarding ~four-year journey since the initial discussions with my colleagues Georg Semmler and Bernhard Scheiner. Thanks to the patients, clinical team, collaborators, and CeMM Molecular Discovery Platform for making this possible!

Img: graphical abstract.

Two curves showing performance of the named metabolites in the prediction of PSVD

/4 Together with colleagues from the University of Barcelona Clinical Hospital, we showed the role of taurocholic acid or taurocholic/L-aspartic acid ratio in distinguishing PSVD from healthy and cirrhosis profiles accordingly (AUROC = 0.9 / 0.72) in validation.

Img: Fig. 5E

Figure from the publication representing two machine learning model parameters and performance distinguishing PSVD from healthy and cirrhotic' metabolic profiles.

3/ We used machine learning models that distinguished PSVD from healthy individuals using a six-metabolite panel (sensitivity 0.95, specificity 1), and from cirrhosis with four metabolites (0.8 & 0.9). Adipic acid was in both.

Img: Fig. 4 (license: CC BY-NC-ND 4.0 & further)

2/ We discovered adipic acid perturbations in PSVD. It's neither a primary human nor gut microbiome metabolite and is processed via β-oxidation. In PSVD, however, its metabolism appears disrupted. Could this suggest (epi)genetic regulation issues in key enzymes?

Screenshot of a research paper with the title "Metabolomic profiles differentiate between porto-sinusoidal vascular disorder, liver cirrhosis, and healthy individuals"

1/ 🧪🧵Porto-sinusoidal vascular disorder (#PSVD) is a rare condition. Despite its known hallmarks, much remains unclear, including its pathobiology and the potential for non-invasive testing.

Our new paper explores PSVD from a metabolomics angle:
jhep-reports.eu/article/S258...

Hi Monika,

Here's my ORCID for joining the feed:

orcid.org/0000-0002-85...

The resilience of Ukrainian scientists We have asked Ukrainian scientists how they have been able to persist in pursuing their research since the beginning of the full-scale invasion of Ukraine by the Russian Federation in February of 2022...

In the newest issue, Cell Systems published a Voices piece detailing the impact of the Russian invasion on Ukrainian scientists. Among the co-authors, many members of our community contributed with their stories.

www.cell.com/cell-systems...

We are incredibly proud to share that more than 200 Ukrainian students enrolled in our practical course on RNA-sequencing data analysis.
Those who participated in the coursework, completed tests, and submitted course projects received certificates - but more importantly, skills for independent work.

Nah, not in my usecase. The connection similar to the usual SSH to the login node only. Then, the Jupyter script has to be executed via scheduler on an interactive node to get the link, and the VS code automatically forwards ports for you. Then, connect to remote kernel inside .ipynb, and it's done.

By the way, an option could be:
* Using VS Code as development IDE;
* connecting via its SSH to cluster;
* running Jupyter with R kernel via cluster scheduler with necrssary resources;
* creating .ipynb notebook, connecting to the kernel;
* and it works :)
This is the way I'm working on my projects

R all the way!
(except when there's a better toolkit for specific task in Python - e.g., it is the case for graph analysis)

So, what's your favorite for everyday tasks in #ComputationalBiology? #Python or #R?