Gonzalo Parra
@gonzaparra.bsky.social
Ramón y Cajal Junior Group Leader @BSC_CNS 🇦🇷🇪🇸🏳️🌈 ENFJ | Bioinformatics | 3DSIG Co-Chair | @fi_uner, @exactas_uba, @mpi_bpc, @embl, @dkfz alumnus | @iscb BoD | Opinions my own
Reposted by Gonzalo Parra
I have two open positions @ALMU @crg.eu:
1. Imaging Scientist (permanent position. Deadline 11th Nov.) recruitment.crg.eu/content/jobs...
2. Entry-Level Imaging Scientist (12 months fixed-term position. Deadline 18th Nov.) recruitment.crg.eu/content/jobs...
Reposts appreciated.
1. Imaging Scientist (permanent position. Deadline 11th Nov.) recruitment.crg.eu/content/jobs...
2. Entry-Level Imaging Scientist (12 months fixed-term position. Deadline 18th Nov.) recruitment.crg.eu/content/jobs...
Reposts appreciated.
November 3, 2025 at 2:01 PM
I have two open positions @ALMU @crg.eu:
1. Imaging Scientist (permanent position. Deadline 11th Nov.) recruitment.crg.eu/content/jobs...
2. Entry-Level Imaging Scientist (12 months fixed-term position. Deadline 18th Nov.) recruitment.crg.eu/content/jobs...
Reposts appreciated.
1. Imaging Scientist (permanent position. Deadline 11th Nov.) recruitment.crg.eu/content/jobs...
2. Entry-Level Imaging Scientist (12 months fixed-term position. Deadline 18th Nov.) recruitment.crg.eu/content/jobs...
Reposts appreciated.
Last week to apply to join our recently created lab as a PhD Student!
Join us to research about protein computational biophysics, evolution, machine learning , and human mutations!
Description and link to apply here:
www.bsc.es/join-us/job-...
Join us to research about protein computational biophysics, evolution, machine learning , and human mutations!
Description and link to apply here:
www.bsc.es/join-us/job-...
596_25_LS_ESB_R1
Reference: 596_25_LS_ESB_R1
Job title: PhD student in computational biophysics and machine learning (R1, FPI)
 
About BSC
 
The Barcelona Supercomputing Center - Centro Nacion
www.bsc.es
October 22, 2025 at 9:11 AM
Last week to apply to join our recently created lab as a PhD Student!
Join us to research about protein computational biophysics, evolution, machine learning , and human mutations!
Description and link to apply here:
www.bsc.es/join-us/job-...
Join us to research about protein computational biophysics, evolution, machine learning , and human mutations!
Description and link to apply here:
www.bsc.es/join-us/job-...
Reposted by Gonzalo Parra
Our Metabuli taxonomic classifier is now available as an app compatible with Windows, Linux, and macOS. It features an interactive visualization developed by @sunjaelee.bsky.social, along with improvements to Metabuli by @jbeom.bsky.social.
📄 academic.oup.com/bioinformati...
📄 academic.oup.com/bioinformati...
October 16, 2025 at 1:01 PM
Our Metabuli taxonomic classifier is now available as an app compatible with Windows, Linux, and macOS. It features an interactive visualization developed by @sunjaelee.bsky.social, along with improvements to Metabuli by @jbeom.bsky.social.
📄 academic.oup.com/bioinformati...
📄 academic.oup.com/bioinformati...
Reposted by Gonzalo Parra
From @gonzaparra.bsky.social et al., in @plos.org #Computational #Biology | Impact of the #COVID-19 pandemic on computational biology early career researchers: A global retrospective study | #Bioinformatics #Education #OpenScience CC/ @iscb.bsky.social 🧬 🖥️ 🧪🔓
⬇️
journals.plos.org/ploscompbiol...
⬇️
journals.plos.org/ploscompbiol...
Impact of the COVID-19 pandemic on computational biology early career researchers: A global retrospective study
The COVID-19 pandemic led to devastating physical, psychological, and financial impacts on millions of people across the world. Amidst a rapidly evolving research landscape, the global scientific comm...
journals.plos.org
October 16, 2025 at 4:43 PM
From @gonzaparra.bsky.social et al., in @plos.org #Computational #Biology | Impact of the #COVID-19 pandemic on computational biology early career researchers: A global retrospective study | #Bioinformatics #Education #OpenScience CC/ @iscb.bsky.social 🧬 🖥️ 🧪🔓
⬇️
journals.plos.org/ploscompbiol...
⬇️
journals.plos.org/ploscompbiol...
Interesting work that we conducted from the Student Council of
@iscb.bsky.social to estimate the impact of the COVID19 pandemics on early career researchers in computational biology!
Thanks for leading this effort Farzana Rahman and to the entire team!
journals.plos.org/ploscompbiol...
@iscb.bsky.social to estimate the impact of the COVID19 pandemics on early career researchers in computational biology!
Thanks for leading this effort Farzana Rahman and to the entire team!
journals.plos.org/ploscompbiol...
October 15, 2025 at 9:05 PM
Interesting work that we conducted from the Student Council of
@iscb.bsky.social to estimate the impact of the COVID19 pandemics on early career researchers in computational biology!
Thanks for leading this effort Farzana Rahman and to the entire team!
journals.plos.org/ploscompbiol...
@iscb.bsky.social to estimate the impact of the COVID19 pandemics on early career researchers in computational biology!
Thanks for leading this effort Farzana Rahman and to the entire team!
journals.plos.org/ploscompbiol...
A collab referred me to this paper which I of course read when it came out in 2013. However, as a mid-way PhD student my capacity to deeply understand its details was pretty limited. 12 years later, I can understand much more! I really recomend this jewel!
doi.org/10.1063/1.48...
doi.org/10.1063/1.48...
October 14, 2025 at 7:28 PM
A collab referred me to this paper which I of course read when it came out in 2013. However, as a mid-way PhD student my capacity to deeply understand its details was pretty limited. 12 years later, I can understand much more! I really recomend this jewel!
doi.org/10.1063/1.48...
doi.org/10.1063/1.48...
Reposted by Gonzalo Parra
as a philosopher, I can confirm we don't know what thinking is
as a cognitive scientist, I can confirm we don't know how humans think
October 10, 2025 at 10:15 PM
as a philosopher, I can confirm we don't know what thinking is
Repeat with me: 👏🏼 Scores 👏🏼 are👏🏼 not👏🏼 metrics👏🏼!!
it's a personal battle 🤣 I've become Don Quijote against the windmills. Still, I believe that speech accuracy is fundamental un scientific speech even when we all can interpolate the right meaning.
it's a personal battle 🤣 I've become Don Quijote against the windmills. Still, I believe that speech accuracy is fundamental un scientific speech even when we all can interpolate the right meaning.
October 10, 2025 at 10:44 AM
Repeat with me: 👏🏼 Scores 👏🏼 are👏🏼 not👏🏼 metrics👏🏼!!
it's a personal battle 🤣 I've become Don Quijote against the windmills. Still, I believe that speech accuracy is fundamental un scientific speech even when we all can interpolate the right meaning.
it's a personal battle 🤣 I've become Don Quijote against the windmills. Still, I believe that speech accuracy is fundamental un scientific speech even when we all can interpolate the right meaning.
Reposted by Gonzalo Parra
Which mutations rewire function of regulatory DNA?
Excited to share SEAM: Systematic Explanation of Attribtuion-based Mechanisms. SEAM is an explainable AI method that dissects cis-regulatory mechanisms learned by seq2fun genomic deep learning models.
Led by @EESetiz
1/N 🧵👇
Excited to share SEAM: Systematic Explanation of Attribtuion-based Mechanisms. SEAM is an explainable AI method that dissects cis-regulatory mechanisms learned by seq2fun genomic deep learning models.
Led by @EESetiz
1/N 🧵👇
October 9, 2025 at 12:03 PM
Which mutations rewire function of regulatory DNA?
Excited to share SEAM: Systematic Explanation of Attribtuion-based Mechanisms. SEAM is an explainable AI method that dissects cis-regulatory mechanisms learned by seq2fun genomic deep learning models.
Led by @EESetiz
1/N 🧵👇
Excited to share SEAM: Systematic Explanation of Attribtuion-based Mechanisms. SEAM is an explainable AI method that dissects cis-regulatory mechanisms learned by seq2fun genomic deep learning models.
Led by @EESetiz
1/N 🧵👇
Reposted by Gonzalo Parra
Nobel Laureate Professor Sir John Gurdon dies aged 92 cam.ac.uk/research/news/…
Very sad news. A remarkable scientist! He will be always with us.🌻www.cam.ac.uk/research/new...92
Very sad news. A remarkable scientist! He will be always with us.🌻www.cam.ac.uk/research/new...92
Nobel Laureate Professor Sir John Gurdon dies aged 92
It is with great sadness that the University shares the news of the death of Professor Sir John Gurdon, founder of the Gurdon Institute.
www.cam.ac.uk
October 8, 2025 at 9:51 AM
Reposted by Gonzalo Parra
🚀 As first official act, we are hiring! 🎓
We’re looking for a PhD student to work at the interface of computational biophysics, machine learning & human mutations. 📌 FPI fellowship, 4 years fully funded!
More information here:
www.bsc.es/join-us/job-...
We’re looking for a PhD student to work at the interface of computational biophysics, machine learning & human mutations. 📌 FPI fellowship, 4 years fully funded!
More information here:
www.bsc.es/join-us/job-...
After months of buildup, it’s finally real! 🎉 The Evolutionary Systems Biophysics Group (ESBG) is officially alive at @bsc-cns.bsky.social . Proud to start this new adventure as a Ramon y Cajal Junior Group Leader🧬
Thanks to all who have been part of this process!
tinyurl.com/4r9vf4zx
Thanks to all who have been part of this process!
tinyurl.com/4r9vf4zx
October 2, 2025 at 8:12 AM
🚀 As first official act, we are hiring! 🎓
We’re looking for a PhD student to work at the interface of computational biophysics, machine learning & human mutations. 📌 FPI fellowship, 4 years fully funded!
More information here:
www.bsc.es/join-us/job-...
We’re looking for a PhD student to work at the interface of computational biophysics, machine learning & human mutations. 📌 FPI fellowship, 4 years fully funded!
More information here:
www.bsc.es/join-us/job-...
Reposted by Gonzalo Parra
After months of buildup, it’s finally real! 🎉 The Evolutionary Systems Biophysics Group (ESBG) is officially alive at @bsc-cns.bsky.social . Proud to start this new adventure as a Ramon y Cajal Junior Group Leader🧬
Thanks to all who have been part of this process!
tinyurl.com/4r9vf4zx
Thanks to all who have been part of this process!
tinyurl.com/4r9vf4zx
October 2, 2025 at 8:06 AM
After months of buildup, it’s finally real! 🎉 The Evolutionary Systems Biophysics Group (ESBG) is officially alive at @bsc-cns.bsky.social . Proud to start this new adventure as a Ramon y Cajal Junior Group Leader🧬
Thanks to all who have been part of this process!
tinyurl.com/4r9vf4zx
Thanks to all who have been part of this process!
tinyurl.com/4r9vf4zx
🚀 As first official act, we are hiring! 🎓
We’re looking for a PhD student to work at the interface of computational biophysics, machine learning & human mutations. 📌 FPI fellowship, 4 years fully funded!
More information here:
www.bsc.es/join-us/job-...
We’re looking for a PhD student to work at the interface of computational biophysics, machine learning & human mutations. 📌 FPI fellowship, 4 years fully funded!
More information here:
www.bsc.es/join-us/job-...
After months of buildup, it’s finally real! 🎉 The Evolutionary Systems Biophysics Group (ESBG) is officially alive at @bsc-cns.bsky.social . Proud to start this new adventure as a Ramon y Cajal Junior Group Leader🧬
Thanks to all who have been part of this process!
tinyurl.com/4r9vf4zx
Thanks to all who have been part of this process!
tinyurl.com/4r9vf4zx
October 2, 2025 at 8:12 AM
🚀 As first official act, we are hiring! 🎓
We’re looking for a PhD student to work at the interface of computational biophysics, machine learning & human mutations. 📌 FPI fellowship, 4 years fully funded!
More information here:
www.bsc.es/join-us/job-...
We’re looking for a PhD student to work at the interface of computational biophysics, machine learning & human mutations. 📌 FPI fellowship, 4 years fully funded!
More information here:
www.bsc.es/join-us/job-...
After months of buildup, it’s finally real! 🎉 The Evolutionary Systems Biophysics Group (ESBG) is officially alive at @bsc-cns.bsky.social . Proud to start this new adventure as a Ramon y Cajal Junior Group Leader🧬
Thanks to all who have been part of this process!
tinyurl.com/4r9vf4zx
Thanks to all who have been part of this process!
tinyurl.com/4r9vf4zx
October 2, 2025 at 8:06 AM
After months of buildup, it’s finally real! 🎉 The Evolutionary Systems Biophysics Group (ESBG) is officially alive at @bsc-cns.bsky.social . Proud to start this new adventure as a Ramon y Cajal Junior Group Leader🧬
Thanks to all who have been part of this process!
tinyurl.com/4r9vf4zx
Thanks to all who have been part of this process!
tinyurl.com/4r9vf4zx
Reposted by Gonzalo Parra
Whole brain dynamics in the ~10s regime shows synchronized propagation of topographically organized rotating waves, driving behavior, calcium fluxes, band-limited power, metabolism, blood flow, etc. All can be predicted from time-lagged embedding of pupil size alone! www.nature.com/articles/s41...
Arousal as a universal embedding for spatiotemporal brain dynamics - Nature
Reframing of arousal as a latent dynamical system can reconstruct multidimensional measurements of large-scale spatiotemporal brain dynamics on the timescale of seconds in mice.
www.nature.com
September 25, 2025 at 8:16 PM
Whole brain dynamics in the ~10s regime shows synchronized propagation of topographically organized rotating waves, driving behavior, calcium fluxes, band-limited power, metabolism, blood flow, etc. All can be predicted from time-lagged embedding of pupil size alone! www.nature.com/articles/s41...
Reposted by Gonzalo Parra
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
September 25, 2025 at 9:29 PM
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
LinkedIn just notified about my 4th year annyversary working at the @bsc-cns.bsky.social, time flies!!! It's been a great chapter so far in my scientific journey!! A lot of projects on the list! #ILoveScience
September 22, 2025 at 9:25 AM
LinkedIn just notified about my 4th year annyversary working at the @bsc-cns.bsky.social, time flies!!! It's been a great chapter so far in my scientific journey!! A lot of projects on the list! #ILoveScience
Reposted by Gonzalo Parra
🥁 Check out our new preprint on OmniPath, the prior knowledge resource for #SystemsBiology, and its brand-new OmniPath Explorer web app! 🥳
📖 Preprint: www.biorxiv.org/content/10.1...
🔍 Explorer: explore.omnipathdb.org
OmniPath integrates 160+ resources for multi-omics analysis & modeling.
🧶⬇️
📖 Preprint: www.biorxiv.org/content/10.1...
🔍 Explorer: explore.omnipathdb.org
OmniPath integrates 160+ resources for multi-omics analysis & modeling.
🧶⬇️
September 17, 2025 at 1:10 PM
🥁 Check out our new preprint on OmniPath, the prior knowledge resource for #SystemsBiology, and its brand-new OmniPath Explorer web app! 🥳
📖 Preprint: www.biorxiv.org/content/10.1...
🔍 Explorer: explore.omnipathdb.org
OmniPath integrates 160+ resources for multi-omics analysis & modeling.
🧶⬇️
📖 Preprint: www.biorxiv.org/content/10.1...
🔍 Explorer: explore.omnipathdb.org
OmniPath integrates 160+ resources for multi-omics analysis & modeling.
🧶⬇️
Reposted by Gonzalo Parra
New review on computational design of intrinsically disordered proteins 🖥️🍝 by @giuliotesei.bsky.social @fpesce.bsky.social & 👴
doi.org/10.48550/arX...
doi.org/10.48550/arX...
September 17, 2025 at 4:17 PM
New review on computational design of intrinsically disordered proteins 🖥️🍝 by @giuliotesei.bsky.social @fpesce.bsky.social & 👴
doi.org/10.48550/arX...
doi.org/10.48550/arX...
Reposted by Gonzalo Parra
Structural bioinformatics is incredibly powerful on its own or when paired with theory or experiment. One of the PDB's superpowers isn’t from one structure, but comparing many to uncover folds, binding sites, and subtle conformational shifts. chemrxiv.org/engage/chemr...
10 Rules for a Structural Bioinformatic Analysis
The Protein Data Bank (PDB) is one of the richest open‑source repositories in biology, housing over 277,000 macromolecular structural models alongside much of the experimental data that underpins thes...
chemrxiv.org
September 11, 2025 at 2:28 PM
Structural bioinformatics is incredibly powerful on its own or when paired with theory or experiment. One of the PDB's superpowers isn’t from one structure, but comparing many to uncover folds, binding sites, and subtle conformational shifts. chemrxiv.org/engage/chemr...
Reposted by Gonzalo Parra
It was lovely to speak at the CATH 30 symposium, celebrating 30 years of the @cathgene3d.bsky.social protein structure classification database. I was presenting recent work on our new generative protein-family language model: preprint coming soon.
September 18, 2025 at 10:33 AM
It was lovely to speak at the CATH 30 symposium, celebrating 30 years of the @cathgene3d.bsky.social protein structure classification database. I was presenting recent work on our new generative protein-family language model: preprint coming soon.
Reposted by Gonzalo Parra
Reposted by Gonzalo Parra
Naiavirus: an enveloped giant virus with a pleomorphic, flexible tail
nature.com/articles/s41467-025-63463-6
nature.com/articles/s41467-025-63463-6
Naiavirus: an enveloped giant virus with a pleomorphic, flexible tail - Nature Communications
Rodrigues and Queiroz et al. report the discovery of Naiavirus, the largest enveloped virus, isolated from a Brazil biome. With an oval capsid and flexible tail, its giant genome holds many novel gene...
nature.com
September 17, 2025 at 3:36 PM
Naiavirus: an enveloped giant virus with a pleomorphic, flexible tail
nature.com/articles/s41467-025-63463-6
nature.com/articles/s41467-025-63463-6
Dear Colleagues. We are in need of a molecular dynamics trajectory of a "folding upon binding event" where a protein with an IDR folds into its partner. Do you know of any published and available trajectory that we could use?? Thanksss a lot!
September 17, 2025 at 5:40 PM
Dear Colleagues. We are in need of a molecular dynamics trajectory of a "folding upon binding event" where a protein with an IDR folds into its partner. Do you know of any published and available trajectory that we could use?? Thanksss a lot!
Reposted by Gonzalo Parra
Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data.
@ruoshiz.bsky.social @milot.bsky.social
www.nature.com/articles/s41...
@ruoshiz.bsky.social @milot.bsky.social
www.nature.com/articles/s41...
De novo discovery of conserved gene clusters in microbial genomes with Spacedust - Nature Methods
This work presents Spacedust, a tool for de novo identification of conserved gene clusters from metagenomic data.
www.nature.com
September 16, 2025 at 1:25 PM
Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data.
@ruoshiz.bsky.social @milot.bsky.social
www.nature.com/articles/s41...
@ruoshiz.bsky.social @milot.bsky.social
www.nature.com/articles/s41...