Oleksandr Petrenko
@opetrenko.bsky.social
🇺🇦 scientist-physician | Target Discovery | Chronic Liver Disease | Fibrosis | #SystemsBiology | #CompBio.
Researching as cell & computer wizard @ MedUni Vienna & CeMM.
orcid.org/0000-0002-8586-4910
One from @genomicsUA.bsky.social
Researching as cell & computer wizard @ MedUni Vienna & CeMM.
orcid.org/0000-0002-8586-4910
One from @genomicsUA.bsky.social
Apparently so!
The first two cases were documented there, a fascinating discovery.
The first two cases were documented there, a fascinating discovery.
March 5, 2025 at 6:39 PM
Apparently so!
The first two cases were documented there, a fascinating discovery.
The first two cases were documented there, a fascinating discovery.
Wow, thanks a lot for your recommendations! Followed 😊
September 6, 2024 at 4:36 AM
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 :)
🧪
Trying to find colleagues to follow :)
🧪
September 5, 2024 at 6:00 PM
By the way, any #hepatology / #biomarkers / target discovery / #multiomics / #SystemsBiology scientists around on Bluesky?
Trying to find colleagues to follow :)
🧪
Trying to find colleagues to follow :)
🧪
/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.
Img: graphical abstract.
September 5, 2024 at 12:19 PM
/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.
Img: graphical abstract.
/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
Img: Fig. 5E
September 5, 2024 at 12:18 PM
/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
Img: Fig. 5E
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)
Img: Fig. 4 (license: CC BY-NC-ND 4.0 & further)
September 5, 2024 at 12:17 PM
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)
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?
September 5, 2024 at 12:15 PM
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?
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.
October 23, 2023 at 8:36 AM
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
* 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
October 23, 2023 at 6:19 AM
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
* 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)
(except when there's a better toolkit for specific task in Python - e.g., it is the case for graph analysis)
October 22, 2023 at 8:44 AM
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)
(except when there's a better toolkit for specific task in Python - e.g., it is the case for graph analysis)