Laboratory of Computational Systems Biotechnology led by @Vassily_13 Databases: https://xitter.cf/t.co/kdLhSi2CbQ (NEW: ReKinDLE) Opensource: https://xitter.cf/t.co/RJeBF8fVn4
Lausanne, Switzerland
Joined August 2017
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🚀 New preprint from @epfl_en’s Laboratory of Computational Systems Biotechnology (LCSB)!
We present “Multi-omics–driven kinetic modeling reveals metabolic vulnerabilities and differential drug-response dynamics in ovarian cancer.”
🔗 biorxiv.org/content/10.1101/…
By integrating multi-omics data with enzyme kinetics, we generated a population of near–genome-scale kinetic models that capture BRCA1-mutant vs wild-type ovarian cancer physiology.
These models reveal network-wide control principles & drug-response dynamics.
This work by Toumpe, Masid, Hatzimanikatis & Miskovic (@epfl_en LCSB) provides a resource for exploring metabolic regulation, vulnerabilities, and precision oncology.
All models are openly available.
#systemsbiology #cancermetabolism #multiomics #precisiononcology #openscience
the real LCSB retweeted
Our review made the cover in ACS Synthetic Biology! 🎉🧬
We explore how large-scale kinetic models are shaping the future of metabolic engineering — check it out here 👉 pubs.acs.org/toc/asbcd6/14/8
Big thanks to the team and @ACSPublications! #MyACSCover #SyntheticBiology
Excited to share our new preprint, where we present NIS, a framework that distills GEMs into interpretable modules, enabling direct cross-species comparisons of fueling pathways, biosynthesis, and environmental exchanges.
Congratulations to the authors!
👏 A big thank you to my co-authors Meric Ataman & Vassily Hatzimanikatis for this great collaboration!
🔍 Read more: doi.org/10.1101/2025.08.08.6…
Our latest work on Salmonella metabolism in the murine gut is now at @PLOSCompBiol ! Congratulations to the authors @EVayena, @FuchsiLea, @HomaMP4, Konrad Lagoda, Bidong Nguyen, Wolf D. Hardt, and @vassily_13!
journals.plos.org/ploscompbi…
the real LCSB retweeted
This work showcases one of the few successful integrations of kinetic modeling and experiments to optimize cell factories. It highlights the power of NOMAD (nature.com/articles/s41467-0…) in accelerating and improving strain design!
the real LCSB retweeted
Excited to share our preprint on boosting p-coumaric acid production in S. cerevisiae! 🎉 In collaboration with Irina Borodina's group (@Irina__Borodina), we used our NOMAD framework for strain design strategies. Read more: biorxiv.org/content/10.1101/…
A new baby from our creative workshop:
Want to efficiently create large-scale dynamic models of metabolism that fit experimental data and reliably predict metabolic responses to various perturbations? Our new method does just that! Check it out here: nature.com/articles/s41929-0….
We are thrilled to announce that our generative ML method for kinetic modeling (biorxiv.org/content/10.1101/…) has been accepted to @NatureCatalysis. Congratulations to Subham (@astro_dank), Bharath (@bharathnarayana), Michael (@moret1788), Vassily (@Vassily_13), and Misko (@Misko_L34)
Happy to share a preprint of our new work in which we combined graph-search algorithms and constraint-based optimization to find the best retrobiosynthesis pathways for producing valuable compounds in a host biorxiv.org/content/10.1101/…
Our latest work is now out at Metabolic Engineering! Congratulations to the authors @oftadehomid and @Vassily_13!
Our new paper describes how computational models can capture the #plasmid metabolic burden and help optimize #recombinant expression of proteins
sciencedirect.com/science/ar…
Our recent publication in @NatureComms, “Rational strain design with minimal phenotype perturbation” by Narayanan et al., has been showcased in the recent Editors’ Highlights for Biotechnology and Methods focus (nature.com/collections/idhhg…).
Congratulations to Bharath (@bharathnarayana), Daniel (@realDRWeilandt), Maria, Misko (@Misko_L34), and @Vassily_13 for this nice work (nature.com/articles/s41467-0…)
Check out our preprint on now on bioaRxiv!!!
Congratulations to all the authors! @oftadehomid @aslisahin2205 @EVayena @vassily_13
A preprint of our recent work is now available! In this paper we present a framework to infer nutrient competition and cross-feeding in microbial communities. Many thanks for the support we received from @NCCRMicrobiomes.
biorxiv.org/content/10.1101/…
the real LCSB retweeted
Our latest work on metabolic engineering using kinetic models and process systems engineering methods is out nature.com/articles/s41467-0…! Congrats to Bharath (@bharathnarayana), Daniel (@realDRWeilandt
), Maria, Misko (@Misko_L34), and @Vassily_13
.
Our latest work on metabolic engineering using kinetic models and process systems engineering methods is out nature.com/articles/s41467-0…! Congrats to Bharath (@bharathnarayana), Daniel (@realDRWeilandt
), Maria, Misko (@Misko_L34), and @Vassily_13
.
Excited to announce that our latest work in now online ! This time the team significantly expanded on their previous tool, BridgIT, an enzyme annotation for orphan and novel reactions, to bring you the new and improved BridgIT+ ! Read the thread below to find out more :)
Curious and want to dive deeper? Check out our preprint on Bioarxiv: biorxiv.org/content/10.1101/…
Congratulations to all the authors for this fantastic achievement! Homa (@HomaMP4), Anastasia (@AnastasiaSves), Misko (@Misko_L34) and Vassily (@vassily_13) !!