Excellent work
10.03.2026 09:57
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Excellent work
Person: say, i am alive. Computer: I am alive. Person: oh my god.
New preprint out! We present a global optimization metaheuristic that performs exceptionally well on tough model calibration problems in systems biology.
Host-aware Identification of Intrinsic Gene Expression Biopart Parameters from Combinatorial Libraries
doi.org/10.64898/202...
Our workflow combines identifiability analysis, robust global optimization, stability checks, and predictive power assessment into a coherent pipeline. Through case studies of increasing complexity, we demonstrate how this approach leads to more reliable models.
But anyone who has worked with them knows the challenges: nonlinearity, identifiability issues, unstable simulations, underfitting, overfittingโฆ
In this work, we present an integrated workflow designed to tackle these challenges.
Microbial communities play a central role in human and planetary health, yet the quantitative principles governing their behavior are still far from understood.
Dynamic models based on ODEs hold enormous potential for uncovering these principles
First paper of PhD student Ana Paredes-Vรกzquez www.linkedin.com/in/ana-pared... , co-supervised by Eva Balsa-Canto www.linkedin.com/in/eva-balsa... and myself.
Interested in microbial ecology?
Our latest paper, โIdentification of dynamic models of microbial communities: A workflow addressing identifiability and modeling pitfalls,โ is now out in PLOS Computational Biology journals.plos.org/ploscompbiol... .
comic strip with call and response text. who are we? CEOs what do we want? AI! AI to do what? We don't know! When do we want it? Right now!
every company in 2025
The guy who got famous betting against the housing market in 2007 just before that bubble burst - played by Christian Bale jn โThe Big Shortโ - just wagered $1 billion on the collapse of the AI boom.
www.wsj.com/livecoverage...
Weโre excited about the potential of gIOC to deepen our understanding of the living world and welcome your thoughts and feedback.
๐ ๐ฅ๐ฒ๐ฎ๐ฑ ๐๐ต๐ฒ ๐ณ๐๐น๐น ๐ฝ๐๐ฏ๐น๐ถ๐ฐ๐ฎ๐๐ถ๐ผ๐ป ๐ต๐ฒ๐ฟ๐ฒ: authors.elsevier.com/sd/article/S...
Our paper introduces ๐๐ฒ๐ป๐ฒ๐ฟ๐ฎ๐น๐ถ๐๐ฒ๐ฑ ๐๐ป๐๐ฒ๐ฟ๐๐ฒ ๐ข๐ฝ๐๐ถ๐บ๐ฎ๐น ๐๐ผ๐ป๐๐ฟ๐ผ๐น (๐ด๐๐ข๐), a data-driven framework to reverse-engineer these fundamental principles directly from observations.
Nature is filled with optimal designs, from efficient metabolic pathways to the hexagonal structure of honeycombs. But how can we uncover the hidden rules (the objectives and constraints)?
๐ New paper out: "Generalized Inverse Optimal Control and Its Application in Biology"
Joint work with Sebastian Sager โ www.mathopt.de/people/sager/
Just published in ๐๐ก๐ก๐จ๐๐ ๐ฅ๐๐ฉ๐๐๐ช๐ฆ ๐๐ก ๐๐ข๐ก๐ง๐ฅ๐ข๐
๐ Link: authors.elsevier.com/sd/article/S...
Optimality principles directly from observations!
Free access to this article at authors.elsevier.com/a/1lVrl8jbph...
โ๏ธ We cover recent advances and open challenges in:
- Model structure selection
- Identifiability
- Parameter estimation
- Uncertainty quantification
- Model reliability
If you are interested in how mathematical models help unravel biological complexity, we hope you will find it useful!
๐ New Paper Published!
๐ Title: "Mechanistic dynamic modelling of biological systems: the road ahead"
๐ Journal: Current Opinion in Systems Biology
๐ doi.org/10.1016/j.co...
This is review/opinion paper co-authored with Alejandro F. Villaverde afvillaverde.webs.uvigo.gal
We tackle key challenges in ODE-based models: identifiability, instability, underfitting, & overfitting.
Our integrated approach offers a roadmap to more reliable & predictive microbiome models.
๐ฌ Check it at: doi.org/10.1101/2025... #Microbiome #Ecology #Modeling #MicrobialCommunities
๐จ New preprint out! ๐จ
Our latest work discusses the complexities of mathematically modelling microbial communities.
Joint work with Ana Paredes and @balsacanto.bsky.social
๐ฌ doi.org/10.1101/2025... #Microbiome #Ecology #Modeling
๐จ New paper out!
Novel algorithms for uncertainty quantification in systems biology using conformal inference.
Joint work with Alberto Portela and Marcos Matabuena www.marcosmatabuena.com
๐ Read more: doi.org/10.1371/jour... #SystemsBiology #UQ
๐ @bcbhubcsic.bsky.social l is pleased to share the recorded seminars from April 2! ๐ฅ Watch the presentation of the tool pyDock by juanfdezrecio.bsky.social (ICVV) & MEIGO by @julio-r-banga.bsky.social @mbgcsic.bsky.social ๐บ Available now ๐ pyDock youtu.be/yvH8-1kg94Y ๐MEIGO youtu.be/T68sGGf2N9c
Fully-funded PhD opportunity in mathematical biology and applied mathematics with Pascal Buenzli and me at Queensland University of Technology in Brisbane, Australia. Details at smb.org/Member-Forum... @smbmathbiology.bsky.social
Lungfish xkcd.com/3064
I shared a controversial take the other day at an event and I decided to write it down in a longer format: Iโm afraid AI won't give us a "compressed 21st century"
Here: thomwolf.io/blog/scienti...
It's an extension of this interview discussion from the AI summit: youtu.be/AxBd3G0lFLs?...
Today marks the beginning of OpenRxiv, which replaces bioRxiv and medRxiv, the world's largest preprint platform for life and medical science
openrxiv.org/introducing-...
@openrxiv.bsky.social
How gut microbiome research needs to move forward. Going multi-omics, getting to causality, rigorous clinical studies
www.cell.com/cell/fulltex...
@cellpress.bsky.social
RNA xkcd.com/3056
You first.