Arnau Montagud
@arnaumontagud.bsky.social
380 followers 910 following 36 posts
Tenured Researcher on Computational Systems Biology Institute for Integrative Systems Biology (@i2sysbio.bsky.social), @csic.es visitor at @bsc-cns.bsky.social, @alfonsovalencia.bsky.social team also at @[email protected]
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Reposted by Arnau Montagud
beatrizurda.bsky.social
🚨 New in PNAS!
🧬 64% of disease co-occurrences can be explained by transcriptomic similarities.

Comorbidities aren’t random—they have a molecular basis.

Here’s how we found it 👇 (1/n)

🔗 doi.org/10.1073/pnas.2421060122

@alfonsovalencia.bsky.social
Reposted by Arnau Montagud
beatrizurda.bsky.social
8/ Science already takes time, I hope to help make it worth it.

Finally, terrified, we sent it to PNAS @pnas.org.
After one round of review, reports came back: supportive. Positive.
Accepted 🎉 🎉
Reposted by Arnau Montagud
beatrizurda.bsky.social
1/ Everything that could go wrong in paper publishing… did.
A story of patience, absurdity, and persistence 🌀 <1min

From Alfonso Valencia’s lab and a very stubborn PhD student (me).
arnaumontagud.bsky.social
Great opportunity to learn about computational systems biology modelling at the Wellcome Genome Campus in December.

If you are interested in signing up, do so as soon as possible as the deadline is August 25!
eventswcs.bsky.social
Learn computational approaches to leverage biological networks for solving #biomedical disease challenges, at #ComputationalBiology25 course.

🗓️ Course dates: 7-12 December 2025
💸 Bursary support available

Apply by 25 August 📩
📎 Find out more about sessions and instructors: bit.ly/4knNAi6
Wellcome Connecting Science 
Computational Systems Biology for Digital Medicine 

Course dates: 7-12 December 2025 
Location: Wellcome Genome Campus, UK

Apply by 25 August
Reposted by Arnau Montagud
alfonsovalencia.bsky.social
>> My conclusion: we do not have to demonstrate anything they have to change and adapt to the evolution of science / biology<<

And computational biology is an essential component of biology.

(It is ridiculous to have to say this in 2025)
arnaumontagud.bsky.social
We are being crushed between people that tell us to do experiments and the ones that tell us to use AI for the models...
arnaumontagud.bsky.social
and good luck with that! :/
arnaumontagud.bsky.social
I was told by them "La hipótesis es sólida y el enfoque original. Sin embargo, no se explica con claridad cómo se validarán experimentalmente las simulaciones, lo que debilita en parte la consistencia del planteamiento." There was no validation intended...
One more thing to fix in Spanish science!
Reposted by Arnau Montagud
i2sysbio.es
Original article: www.nature.com/articles/s41...
🧬🖥️ 👩‍🔬 🧪
The article explains how long-read transcriptomics enables the study of isoform expression, discovery of novel RNAs, gene annotation in understudied species, and differential expression between paternal and maternal chromosomes, etc.
Transcriptomics in the era of long-read sequencing - Nature Reviews Genetics
Advances in long-read sequencing are driving the implementation of these technologies for transcriptome profiling. The authors provide a comprehensive guide to long-read RNA sequencing, including expe...
www.nature.com
Reposted by Arnau Montagud
vincent-noel.fr
Two PhD positions to work on important and cool topics. And to make it even better, with some very nice and good people.
arnaumontagud.bsky.social
📢 Exciting news! We will soon open two PhD positions at @i2sysbio.bsky.social @csic.es, in research projects in collaboration with the @bsc-cns.bsky.social. Both are related to tools to simulate biological tissues. Here’s the description of the open positions. #PhDpositions #PhDOpportunities
👇
arnaumontagud.bsky.social
... it's dissolving humanity and culture and science...
Without pause and time to think and reflect, and dedication to reach deeper into a problem, we only have the appearance of science.
The incentives are all in the wrong side.
kendrawcandraw.bsky.social
This tech accelerationism is training people to just do the appearance of work: a headline, art that looks almost normal from a distance, to complete things as fast as possible and move onto the next... it's dissolving humanity and culture at large
Reposted by Arnau Montagud
i2sysbio.es
🚨 Two PhD positions available in the lab of @arnaumontagud.bsky.social in I2SysBio 🇪🇸. Both are related to simulations of biological tissues
arnaumontagud.bsky.social
📢 Exciting news! We will soon open two PhD positions at @i2sysbio.bsky.social @csic.es, in research projects in collaboration with the @bsc-cns.bsky.social. Both are related to tools to simulate biological tissues. Here’s the description of the open positions. #PhDpositions #PhDOpportunities
👇
arnaumontagud.bsky.social
🎯 This is a fantastic opportunity to work on cutting-edge research in a recently opened lab!
💶 The two positions are fully funded by a CIDE GenT project from GVA.
🔗 If interested, check the PDFs & stay tuned—positions open late spring/early summer for just 2 weeks! ⏳ Don’t miss out! 🧨
arnaumontagud.bsky.social
🔍 Requirements:
🎓 BSc and MSc in Computer Science or related.
💻 Strong C++, scientific computing, & HPC skills.
🚀 Experience with OpenMP, MPI, performance analysis is a big plus!

More info: drive.google.com/file/d/13toU...
Montagud_CS_PhD_position.pdf
drive.google.com
arnaumontagud.bsky.social
📊 Implementing best practices in software development (versioning, docs, testing).
🌐 Ensuring scalability & efficiency with unit tests & CI/CD.
👇
arnaumontagud.bsky.social
💻 Position 2: Engineering & HPC-Oriented (Multiscale Modelling)

The tasks include:
⚡ Applying parallel & distributed computing expertise to agent-based simulations.
🛠️ Leveraging CAD tools & GUIs for simulation setup.
🔧 Developing physically-sound agent-based functions for tissue simulation.
👇
arnaumontagud.bsky.social
🔍 Requirements:
🎓 BSc and MSc in Biology, Biochemistry, Biotechnology, or related.
🧪 Knowledge of microbial metabolism, cell biology, & programming.
💡 Experience with metabolic/signalling models or single-cell analysis is a plus!

More info: drive.google.com/file/d/1Bfc2...
Montagud_Bio_PhD_position.pdf
drive.google.com
arnaumontagud.bsky.social
📝 Test available tools for microbial community simulation.
🧬 Integrate multiscale models of metabolism & signalling pathways.
🧫 Contribute to developing a tissue metabolism modelling tool.
👇
arnaumontagud.bsky.social
🌱 Position 1: Biology-Oriented (Microbial Communities & Metabolism Modelling)

The selected candidate will:
🦠 Build metabolic models of microbial communities.
🤝 Simulate symbiotic relationships between different cell types.
🔄 Study the effect of perturbations on microbial interactions.
👇
arnaumontagud.bsky.social
📢 Exciting news! We will soon open two PhD positions at @i2sysbio.bsky.social @csic.es, in research projects in collaboration with the @bsc-cns.bsky.social. Both are related to tools to simulate biological tissues. Here’s the description of the open positions. #PhDpositions #PhDOpportunities
👇
Reposted by Arnau Montagud
cantinilab.bsky.social
Excited to see scPRINT published in @natcomms.nature.com ! scPRINT is a large cell model for the inference of gene networks pre-trained on 50Mcells with innovative pretraining tasks inspired from biology. Work led by @jkobject.com