Arnau Montagud
@arnaumontagud.bsky.social
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 @arnaumontagud@fediscience.org
Institute for Integrative Systems Biology (@i2sysbio.bsky.social), @csic.es
visitor at @bsc-cns.bsky.social, @alfonsovalencia.bsky.social team
also at @arnaumontagud@fediscience.org
Reposted by Arnau Montagud
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 🧪
#ImmunoSky #DigitalTwin 🧪
October 9, 2025 at 2:05 AM
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 🧪
#ImmunoSky #DigitalTwin 🧪
Reposted by Arnau Montagud
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...
@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...
Building Immune Digital Twins: An International and Transdisciplinary Community Effort
Digital twins, initially developed for industrial applications, are set to make significant
advancements in medicine and healthcare. They have demonstrated promising potential
for drug development and...
www.immunoinformaticsjournal.com
October 9, 2025 at 2:05 AM
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...
@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...
Reposted by Arnau Montagud
🚨 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
🧬 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
September 2, 2025 at 11:42 AM
🚨 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
🧬 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
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 🎉 🎉
Finally, terrified, we sent it to PNAS @pnas.org.
After one round of review, reports came back: supportive. Positive.
Accepted 🎉 🎉
September 2, 2025 at 6:37 PM
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 🎉 🎉
Finally, terrified, we sent it to PNAS @pnas.org.
After one round of review, reports came back: supportive. Positive.
Accepted 🎉 🎉
Reposted by Arnau Montagud
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).
A story of patience, absurdity, and persistence 🌀 <1min
From Alfonso Valencia’s lab and a very stubborn PhD student (me).
September 2, 2025 at 6:37 PM
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).
A story of patience, absurdity, and persistence 🌀 <1min
From Alfonso Valencia’s lab and a very stubborn PhD student (me).
Reposted by Arnau Montagud
📢🔬 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
🗓 2 de septiembre
www.i2sysbio.es/communicatio...
✍ Asistencia gratuita bajo previa inscripción.
@moldrug.bsky.social @protoqsar.bsky.social
Registration is now open for the 2nd Public-Private Collaboration Workshop on Computational Biology at I2SysBio
<p><strong>The I2SysBio (CSIC-UV) will hold its second Public-Private Collaboration Workshop, a meeting that will bring together researchers, companies and organisations from the sector to discuss eme...
www.i2sysbio.es
July 29, 2025 at 8:00 AM
📢🔬 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
🗓 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!
If you are interested in signing up, do so as soon as possible as the deadline is August 25!
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
🗓️ Course dates: 7-12 December 2025
💸 Bursary support available
Apply by 25 August 📩
📎 Find out more about sessions and instructors: bit.ly/4knNAi6
August 1, 2025 at 9:50 AM
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!
If you are interested in signing up, do so as soon as possible as the deadline is August 25!
Reposted by Arnau Montagud
>> 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)
And computational biology is an essential component of biology.
(It is ridiculous to have to say this in 2025)
July 31, 2025 at 4:16 PM
>> 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)
And computational biology is an essential component of biology.
(It is ridiculous to have to say this in 2025)
Reposted by Arnau Montagud
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…
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…
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 the National University of Singapore, as well as the University of Washington and Columbia University in the U.S. Most of the papers involve the field of computer science.
www.schneier.com
July 7, 2025 at 11:21 AM
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…
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…
Reposted by Arnau Montagud
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.
🧬🖥️ 👩🔬 🧪
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
May 9, 2025 at 8:46 AM
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.
🧬🖥️ 👩🔬 🧪
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.
Reposted by Arnau Montagud
🦑🧪 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... ⬇️
A more effective extraction method has been identified for obtaining high-quality DNA in less than ideal conditions
<p><strong>The ‘<a href="https://i2sysbio.es/groups/19/">Microbial Single-Cell Genomics</a>' research group at the Institute for Integrative Systems Biology I2SysBio (University of Valencia-...
www.i2sysbio.es
May 13, 2025 at 7:30 AM
🦑🧪 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... ⬇️
Reposted by Arnau Montagud
Two PhD positions to work on important and cool topics. And to make it even better, with some very nice and good people.
📢 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
👇
👇
May 12, 2025 at 5:52 PM
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.
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.
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
May 8, 2025 at 7:34 AM
... 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.
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.
Reposted by Arnau Montagud
🚨 Two PhD positions available in the lab of @arnaumontagud.bsky.social in I2SysBio 🇪🇸. Both are related to simulations of biological tissues
📢 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
👇
👇
May 6, 2025 at 4:10 PM
🚨 Two PhD positions available in the lab of @arnaumontagud.bsky.social in I2SysBio 🇪🇸. Both are related to simulations of biological tissues
📢 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
👇
👇
May 6, 2025 at 8:46 AM
📢 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
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
I am super happy to annonce that after 9 months under review the first paper of my PhD: scPRINT is finally available on Nature Comms! 🎉🧬
www.nature.com/artic...
www.nature.com/artic...
scPRINT: pre-training on 50 million cells allows robust gene network predictions
Nature Communications - Authors present a state-of-the-art cell foundation model trained on 50 million cells. They show that the model generates a meaningful gene network and has zero-shot...
www.nature.com
April 16, 2025 at 1:16 PM
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
Reposted by Arnau Montagud
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... 🧪🦠💻🧬
April 4, 2025 at 7:34 AM
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... 🧪🦠💻🧬
Reposted by Arnau Montagud
⭐️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
⬇️
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
⬇️
https://cfrioux.github.io⬇️
April 8, 2025 at 6:28 AM
⭐️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
⬇️
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
⬇️
Reposted by Arnau Montagud
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.
March 25, 2025 at 9:47 AM
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.
Reposted by Arnau Montagud
Beca JAE-Intro ICU 2025 para realización TFM en bioinformática (HubBCB-14), bajo la dirección de @christinatoft.bsky.social en el @i2sysbio.bsky.social
5 meses, 20h/semana, 600euros/mes
Solicitudes hasta 16 Abril '25
más información en:
sede.csic.gob.es/tramites/pro...
DM si interesado/a
5 meses, 20h/semana, 600euros/mes
Solicitudes hasta 16 Abril '25
más información en:
sede.csic.gob.es/tramites/pro...
DM si interesado/a
March 25, 2025 at 1:42 PM
Beca JAE-Intro ICU 2025 para realización TFM en bioinformática (HubBCB-14), bajo la dirección de @christinatoft.bsky.social en el @i2sysbio.bsky.social
5 meses, 20h/semana, 600euros/mes
Solicitudes hasta 16 Abril '25
más información en:
sede.csic.gob.es/tramites/pro...
DM si interesado/a
5 meses, 20h/semana, 600euros/mes
Solicitudes hasta 16 Abril '25
más información en:
sede.csic.gob.es/tramites/pro...
DM si interesado/a
Convocatoria JAE Intro @csic.es abierta!
El @i2sysbio.bsky.social oferta 5 plazas para personas que tengan un grado en Ciencias durante 5 meses a media jornada. Ideales para estudiantes de máster en busca de un proyecto de iniciación a la investigación.
Más info: sede.csic.gob.es/tramites/pro...
El @i2sysbio.bsky.social oferta 5 plazas para personas que tengan un grado en Ciencias durante 5 meses a media jornada. Ideales para estudiantes de máster en busca de un proyecto de iniciación a la investigación.
Más info: sede.csic.gob.es/tramites/pro...
Convocatoria JAE Intro ICU 2025 | Sede CSIC
Becas de introducción a la investigación para estudiantes universitarios.
sede.csic.gob.es
March 18, 2025 at 3:46 PM
Convocatoria JAE Intro @csic.es abierta!
El @i2sysbio.bsky.social oferta 5 plazas para personas que tengan un grado en Ciencias durante 5 meses a media jornada. Ideales para estudiantes de máster en busca de un proyecto de iniciación a la investigación.
Más info: sede.csic.gob.es/tramites/pro...
El @i2sysbio.bsky.social oferta 5 plazas para personas que tengan un grado en Ciencias durante 5 meses a media jornada. Ideales para estudiantes de máster en busca de un proyecto de iniciación a la investigación.
Más info: sede.csic.gob.es/tramites/pro...
Reposted by Arnau Montagud
Tercer día de la #2AsambleaBCBHub. Tenemos el honor de contar con Elena Cartea de @csic-vaact.bsky.social abriendo la jornada contandonos las iniciativas de @csic.es en Conexiones y PTIs.
March 14, 2025 at 8:10 AM
Tercer día de la #2AsambleaBCBHub. Tenemos el honor de contar con Elena Cartea de @csic-vaact.bsky.social abriendo la jornada contandonos las iniciativas de @csic.es en Conexiones y PTIs.
Reposted by Arnau Montagud
🚨El I2SysBio participa en los eventos internacionales celebrando la 'Biophysics Week' con el ya tradicional BIOPHYZZA 🍕🍻
*El evento es gratuito pero hay que inscribirse!*
research.uv.es/biophyzza/
@i2sysbio.bsky.social
@ucciuv.bsky.social
@biophysicalsoc.bsky.social
Ayudanos a difundir ↩️🙏
*El evento es gratuito pero hay que inscribirse!*
research.uv.es/biophyzza/
@i2sysbio.bsky.social
@ucciuv.bsky.social
@biophysicalsoc.bsky.social
Ayudanos a difundir ↩️🙏
March 8, 2025 at 8:35 AM
🚨El I2SysBio participa en los eventos internacionales celebrando la 'Biophysics Week' con el ya tradicional BIOPHYZZA 🍕🍻
*El evento es gratuito pero hay que inscribirse!*
research.uv.es/biophyzza/
@i2sysbio.bsky.social
@ucciuv.bsky.social
@biophysicalsoc.bsky.social
Ayudanos a difundir ↩️🙏
*El evento es gratuito pero hay que inscribirse!*
research.uv.es/biophyzza/
@i2sysbio.bsky.social
@ucciuv.bsky.social
@biophysicalsoc.bsky.social
Ayudanos a difundir ↩️🙏
Reposted by Arnau Montagud
🌐Europe takes a major step towards digital autonomy in supercomputing and #AI with the launch of the DARE project
💻Based on #RISCV , this EuroHPC project coordinated by BSC will deliver high-performance & energy-efficient supercomputing for research & industry.
🔗 www.bsc.es/ZyZ
💻Based on #RISCV , this EuroHPC project coordinated by BSC will deliver high-performance & energy-efficient supercomputing for research & industry.
🔗 www.bsc.es/ZyZ
March 7, 2025 at 10:11 AM
🌐Europe takes a major step towards digital autonomy in supercomputing and #AI with the launch of the DARE project
💻Based on #RISCV , this EuroHPC project coordinated by BSC will deliver high-performance & energy-efficient supercomputing for research & industry.
🔗 www.bsc.es/ZyZ
💻Based on #RISCV , this EuroHPC project coordinated by BSC will deliver high-performance & energy-efficient supercomputing for research & industry.
🔗 www.bsc.es/ZyZ
Reposted by Arnau Montagud
Really excited that Anna Niarakis will give the next CRCT #bioinformatics seminar on Friday 14th March at 11 in salle Cazaux!
March 10, 2025 at 10:10 AM
Really excited that Anna Niarakis will give the next CRCT #bioinformatics seminar on Friday 14th March at 11 in salle Cazaux!