benceszalai.bsky.social
Computational systems biology - research team lead at Turbine. Previously post-doc at RWTH Aachen and Semmelweis.
11 posts
110 followers
193 following
Getting Started
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Thanks to all the coauthors, Eszter Varga, Daniel Dimitrov, @juliosaezrod.bsky.social , László Hunyady and especially to first author Szilvia Barsi who led this project from start to finish! 6/6
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Using an IO dataset of nivolumab-treated renal cancer patients, we found that:
- PD1 or PDL1 expression didn't predict survival
- PD1 activity (from RIDDEN) did associate with survival.
This shows that receptor activity could be a more effective biomarker than expression. 5/n
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RIDDEN’s receptor-specific signatures align with regulons of transcription factors downstream of receptors. 4/n
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We benchmarked RIDDEN on various receptor perturbation datasets, including the recent in vivo Immune Dictionary data nature.com/articles/s41..., and found good predictive performance. 3/n
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We combined prior knowledge from OmniPath omnipathdb.org with LINCS L1000 perturbation transcriptomics clue.io to build models that infer receptor activity. Instead of focusing on receptor expression, we predict activity using the expression of receptor-regulated genes. 2/n
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Unfortunately not - planed to go but did manage to do it. but that is a great conference! :)
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Quantitative biology to molecular mechanisms? :)
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fully agree - the most dangerous thing in computational biology is to blindly thrust data / tools / workflows, even the "good" ones