Figure two from the paper linked below: The BIDT WG and connected Systems Biology communities.
An international team of immunologists, clinicians, experimentalists, computational biologists, and engineers is building an Immune Digital Twin to transform human healthcare for immune-mediated diseases.
#ImmunoSky #DigitalTwin 🧪
By Niarakis et al., including:
@athinacp.bsky.social
@eirini-tsirvouli.bsky.social
@hasanbalci.bsky.social
@ozanozisik.bsky.social
@arnaumontagud.bsky.social
@subbannayya.bsky.social
@mkutmon.bsky.social
Learn about their 5-year plan: www.immunoinformaticsjournal.com/article/S266...
🚨 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
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 🎉 🎉
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).
📢🔬 Abierto el plazo de inscripción para la II Jornada de Colaboración Público-Privada sobre Biología Computacional del #I2SysBio (@csic.es - @uv.es).
🗓 2 de septiembre
www.i2sysbio.es/communicatio...
✍ Asistencia gratuita bajo previa inscripción.
@moldrug.bsky.social @protoqsar.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!
>> 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)
We are being crushed between people that tell us to do experiments and the ones that tell us to use AI for the models...
and good luck with that! :/
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!
Hiding Prompt Injections in Academic Papers
Academic papers were found to contain hidden instructions to LLMs: It discovered such prompts in 17 articles, whose lead authors are affiliated with 14 institutions including Japan's Waseda University, South Korea's KAIST, China's Peking University and…
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.
🦑🧪 I2SysBio researchers participate in Catalan Initiative for the Earth Biogenome Project @catbiogenoma.bsky.social of the Institut d'Estudis Catalans @iec.cat. Recently, Maria Dzunkova's @dzunkovam.bsky.social team published a paper in Ecology and Evolution 🌐 www.i2sysbio.es/communicatio... ⬇️
Two PhD positions to work on important and cool topics. And to make it even better, with some very nice and good people.
... 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.
🚨 Two PhD positions available in the lab of @arnaumontagud.bsky.social in I2SysBio 🇪🇸. Both are related to simulations of biological tissues
🎯 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! 🧨
🔍 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...
📊 Implementing best practices in software development (versioning, docs, testing).
🌐 Ensuring scalability & efficiency with unit tests & CI/CD.
👇
💻 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.
👇
🔍 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...
📝 Test available tools for microbial community simulation.
🧬 Integrate multiscale models of metabolism & signalling pathways.
🧫 Contribute to developing a tissue metabolism modelling tool.
👇
🌱 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.
👇
📢 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
👇
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
Alfred Fillol @alfredfisa.bsky.social, Arnau Montagud @arnaumontagud.bsky.social and Guillem Salazar @guillemsalazar.bsky.social are the three scientists who joined the Faculty of our institute I2SysBio last year. Follow them on Bluesky! More info on our website www.i2sysbio.es/communicatio... 🧪🦠💻🧬
⭐️We are hiring! ⭐️
We have 2 open postdoctoral positions in systems biology in Bordeaux, France.
- 1️⃣ 2 years (+ 2) in metabolic modelling for cultivating uncultured bacteria.
- 2️⃣ 18 months (+ 14 mo) in metabolic modelling of the rumen microbiome for methane reduction
More info: cfrioux.github.io
⬇️
HubBCB-01 @CSIC.es. Impacto del microbioma respiratorio humano en la introducción de un nuevo patógeno. IP Mireia Coscolla (I2SYSBIO, Valencia) Cinco meses, cinco mensualidades de 600€, 20 horas/semana. Nota media de grado al menos 7. Si grado terminado, matriculado master bioinformática o similar.
