@EVayena profile picture
Evangelia Vayena @EVayena
Joined January 2020
  • Tweets 99
  • Following 287
  • Followers 136
3 Photos and videos
🚨 New preprint! 🚨 How can we compare the metabolic capabilities of different organisms without getting lost in the complexity of genome-scale models?
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We present NIS, a framework that distills GEMs into interpretable modules, enabling direct cross-species comparisons of fueling pathways, biosynthesis, and environmental exchanges.
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👏 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…
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Evangelia Vayena retweeted
the real LCSB@realLCSB
12 Mar 2025
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…

Metabolic network reconstruction as a resource for analyzing Salmonella Typhimurium SL1344 growth...

Author summary Nontyphoidal Salmonella strains are among the most ubiquitous enteropathogens that contribute significantly to global morbidity and mortality, posing a substantial burden on public...

journals.plos.org
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Evangelia Vayena retweeted
Daniel R. Weilandt, Ph. D.@realDRWeilandt
1 Feb 2025
Very happy to see my first postdoc publication out from the Rabinowitz lab. Shoutout to my amazing colleague and co-first author @Won_Dong_Lee who already did a great job highlighting our key findings. Check out our paper to learn more about lactate homeostasis.
Won Dong Lee@Won_Dong_Lee
30 Jan 2025
Lactate elevations are a hallmark of human disease, but the mechanisms regulating lactate levels remain poorly understood. Today in @Cell_Metabolism, we uncover key mechanisms of lactate homeostasis. sciencedirect.com/science/ar…
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Evangelia Vayena retweeted
Ljubisa Miskovic@Misko_L34
18 Dec 2024
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/…

Kinetic-model-guided engineering of multiple S. cerevisiae strains improves p-coumaric acid...

The use of kinetic models of metabolism in design-build-learn-test cycles is limited despite their potential to guide and accelerate the optimization of cell factories. This is primarily due to...

biorxiv.org
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Evangelia Vayena retweeted
Lucas A. Meirelles@la_meirelles
28 Oct 2024
🚨🔬Excited to share our new paper now out in @NatureMicrobiol! Using Tn-seq live imaging in engineered airway organoids, we explored the fitness tradeoffs P. aeruginosa faces while growing and surviving antibiotic treatment on the mucosal surface. 🔗 rdcu.be/dX4RR

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Start your week with a 😊 What do you see? 🤔 What we see are microbes smiling at us! 😊💚 Follow us on Instagram instagram.com/nccrmicrobiome… for more! instagram.com/p/C-Xq0lLtOAx/

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Pareidolia is our human tendency to see meaning where there is none. In this image, you're actually looking at an agarose patch just 1 cm in diameter, covered in millions of bacterial cells (the bright white area)! 🦠💡
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These Pseudomonas putida F1 cells have been engineered to fluoresce under blue light. After a few hours of growth, they become so numerous and bright that they are visible to the naked eye. 👀We thank Tania Miguel Trabajo, UNIL, for the picture!
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Evangelia Vayena retweeted
the real LCSB@realLCSB
4 Jul 2024
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)
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Discover the artistry of the microbial world! 🧫🔬 instagram.com/p/C8EcQ7cu8rM/

NCCR Microbiomes Art Club (@nccrmicrobiomesart) • Instagram reel

instagram.com
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Let's discover the beauty of tiny life together! Follow us on Instagram for more! instagram.com/nccrmicrobiome… We thank @aslisahin2205 for the video!

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Featuring stunning artworks inspired by microbiome research from the NCCR Microbiomes consortium🇨🇭 and external experts 🌍, we delve into the vibrant wonders of the microbial universe, from human health to ecosystem functioning.
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Evangelia Vayena retweeted
the real LCSB@realLCSB
25 Jan 2024
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 .
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Evangelia Vayena retweeted
Omid Oftadeh@oftadehomid
1 Feb 2024
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/…

A constraint-based framework to reconstruct interaction networks in microbial communities

Microbial communities live in diverse habitats and significantly impact our health and the environment. However, the principles that govern their formation and evolution remain poorly understood. A...

biorxiv.org
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Evangelia Vayena retweeted
NCCR Microbiomes@NCCRMicrobiomes
1 Feb 2024
The next level of metabolic modeling for microbiomes! Congrats to @oftadehomid, @EVayena, @aslisahin2205 and the Hatzimanikatis lab @realLCSB 👍
Omid Oftadeh@oftadehomid
1 Feb 2024
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/…
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Talk alert 🚨 Thursday, 25 January 2024 9:15 - Kiran Patil (University of Cambridge): What drugs and chemicals do to our bugs? 10:30 - Ines Thiele (National University of Ireland): Advancing computational medicine with whole-body metabolic 11:45 -Light lunch and networking.
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More info: memento.epfl.ch/event/what-d… memento.epfl.ch/event/advanc…

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Where: EPFL, room CH G1 495 . See attached pdf map. (Hybrid option: epfl.zoom.us/j/69495424813)
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