Jakub Tomek

Thanks so much to everyone involved, including Xin Zhou, Hector Martinez-Navarro, Maxx Holmes, Lucas Arantes Berg, Tom Bury, Marketa Tomkova, Emily Jo, Norbert Nagy, Ambre Bertrand, Alfonso Bueno-Orovio, @physicsoftheheart.bsky.social, Don Bers, Blanca Rodriguez, and Jordi Heijman!

Finally, if you want to study how a signalling pathway, a drug, or a nonstandard channel affect physiology, model generality is key for obtaining a complete picture of the effects and benefits/risks.
Happy to answer any questions/discuss suitability for your projects!

Second, real-world arrhythmia arises from interactions of arrhythmia triggers (including afterdepolarisations) and substrate (alternans, steep S1-S2 restitution). To reconstruct different origins of arrhythmia, we need a single model capable of all of those. 8/X

First, it is about general credibility. Models are, like real cells, full of interconnections and feedback loops. This means if a model has a mechanistic problem in one component, this can propagate into other areas of use and cause incorrect predictions. 7/X

T-World will be made freely available as open-source code (Matlab, CellML, C, CUDA) and online graphical user interface to facilitate use by non-coders.

As a final note, why does generality of a model matter so much?
6/X

How did we achieve this? The name of the model reflects contribution of labs from the whole world over last decades. We integrate ideas from the most influential families of cardiac models (Rudy and Bers/Grandi) and numerous new ideas and improvements. 5/X

T-World demonstrates strong performance in predicting drug-induced arrhythmia risk and opens new opportunities for predicting and explaining drug efficacy, demonstrated by unpicking effects of mexiletine in Long QT syndrome 2. 4/X

Using T-World we revealed a likely sex-specific arrhythmia risk in females related to restitution properties, identified arrhythmia drivers in type 2 diabetes, and describe unexpectedly direct possible pro-arrhythmic role of NaV1.8 in heart failure. 3/X

T-World recapitulates all key cellular drivers of arrhythmia: early and delayed afterdepolarisations, alternans, and steep S1-S2 restitution. We can now study their interactions in tissue, or carry out multifactorial assessment of drugs (including contractility). 2/X

After seven years of development, we present the highly general human ventricular cardiomyocyte T-World www.biorxiv.org/content/10.1...
It represents excitation-contraction coupling, contractility, sympathetic signalling, sex differences, and it is suitable for multiscale studies. 1/X

Phew, this was close, just checked and this was the one before...

OK!
(using this as a last slide in talks, with "THE END" added; sadly, fewer and fewer people get the reference)

Regression difficulty, ranked:

Easy: Linear regression
Medium: Nonlinear regression
Hard: Mixed-effects regression
Nightmare: Sleep regression

Pro tip for reference managers. If you are using Zotero to change in-text references' style from Author-year to numbered, it is not working no matter what, and you're getting desperate...

... do make sure it's not a text where you previously inserted references using Mendeley. 🤦‍♂️

Was reading a book randomly and found a 14th century depiction of peer review...

Anthem Blue Cross Blue Shield Won’t Pay for the Complete Duration of Anesthesia for Patients’ Surgical Procedures In an unprecedented move, Anthem Blue Cross Blue Shield plans representing Connecticut, New York and Missouri have unilaterally declared it will no longer pay for anesthesia care if the surgery or pro...

You were saying?
www.asahq.org/about-asa/ne...

Jakub Tomek wins 3R's prize from European Commission

Former postdoc Jakub Tomek has been awarded by the European Commission for his work on a computational model of a human ventricular myocyte (ToR-Ord) as part of Prof Blanca Rodriguez’s Computational Cardiovascular Science Team. www.dpag.ox.ac.uk/news/jakub-t...
@jakubtomek.bsky.social @ec.europa.eu

(from @pudukhepa.bsky.social )

Yes, it's often called epsilon in calculus and is quite a key concept!

I'd love that. Both computationally and experimentally, it would be great. I think the need for independence and niche at all costs preventing this is a bit silly and is not good for people, nor science.

Ten traktor je navíc vynikající v tom, že ten komín s trochou fantazie vypadá jako lahev vína. Pro KDU ideál.

The feeling before the next round of grant applications...

During my Oxford PhD, I was ok living on stipend that was much lower than what UK students labelled as "basically unlivable". It's a lot about expectations, what's considered a "basic standard", and what one finds rewarding in life. 4/4

I think the importance of money is in part cultural. First, earning lots of money is more important to Americans than people from most other places. Second, US people have a higher threshold for what is "a lot of money". For me, 70k as postdoc is huge. 55 was ok (in Davis). 3/4

It really struck me at Davis, when I heard PhD students and younger speaking, how they already at that phase knew they'd go into industry, do a startup, etc. It seems that they're now well-aware of the career uncertainty, eternal struggles, and limited salaries.
2/4

My impression from talking to people was mostly what you have already. It used to be outweighed by work that is fulfilling and leads to meaningful outcomes, but that is much more clearly possible in industry than it used to. So that unmasks the other underlying issues.
1/4

Beyond science itself, I care about academia becoming a nicer and fairer environment to everyone.

Love to talk about music, tea, statistics, and many other things (in no particular order).

Development, calibration, and validation of a novel human ventricular myocyte model in health, disease, and drug block A computer model of human cardiomyocyte was produced and validated on independent datasets, overcoming shortcomings of its predecessors, also yielding broadly relevant insights and results on major io...

Hello world! For people not familiar with my Twitter account, I'm an interdisciplinary researcher in cardiology, with focus on arrhythmia mechanisms, cellular physiology, and building comprehensive virtual cell models such as ToR-ORd elifesciences.org/articles/48890