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Reposted by Gonzalo Parra

Carmelo Ferrai @carmeloferrai.bsky.social · 20h

@gurdoninstitute.bsky.social

Carmelo Ferrai @carmeloferrai.bsky.social · 1d

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

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

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Reposted by Gonzalo Parra

Gonzalo Parra @gonzaparra.bsky.social · 6d

🚀 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-...

Gonzalo Parra @gonzaparra.bsky.social · 6d

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

2 9 16

Gonzalo Parra @gonzaparra.bsky.social · 5d

Thanks! 🙌

Reposted by Gonzalo Parra

Gonzalo Parra @gonzaparra.bsky.social · 6d

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

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Gonzalo Parra @gonzaparra.bsky.social · 6d

Gracias! 😱

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Gonzalo Parra @gonzaparra.bsky.social · 6d

🚀 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-...

Gonzalo Parra @gonzaparra.bsky.social · 6d

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

2 9 16

Gonzalo Parra @gonzaparra.bsky.social · 6d

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

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Reposted by Gonzalo Parra

Larry Hunter @proflhunter.bsky.social · 13d

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

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Reposted by Gonzalo Parra

Zamin Iqbal @zaminiqbal.bsky.social · 13d

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

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Gonzalo Parra @gonzaparra.bsky.social · 16d

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

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Reposted by Gonzalo Parra

Saez-Rodriguez Group @saezlab.bsky.social · 21d

🥁 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.

🧶⬇️

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Reposted by Gonzalo Parra

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 21d

New review on computational design of intrinsically disordered proteins 🖥️🍝 by @giuliotesei.bsky.social @fpesce.bsky.social & 👴

doi.org/10.48550/arX...

Figure 3 from the paper with the caption: "Role of machine learning in de novo design of IDRs. (A) Machine-learning models can be trained on diverse data sources, from molecular dynamics simulations to annotations of cellular localization and protein structures from the Protein Data Bank. (B) Often implemented as neural networks using sequence-encoded features as input, these models can initially be trained on a limited region of sequence space as surrogate models. Through active learning, additional simulations are performed during the design campaign to generate new data, and the surrogate model is retrained on the expanded dataset to progressively improve its accuracy. (C) Machine-learning models have been developed to predict biophysical observables, biological annotations, and protein structures. When combined, machine-learning models can be used to identify a set of sequences that strike a trade-off between multiple design objectives, defining a Pareto front."

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Reposted by Gonzalo Parra

Stephanie Wankowicz @stephanieaw.bsky.social · 27d

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

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Reposted by Gonzalo Parra

judewells.bsky.social @judewells.bsky.social · 20d

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.

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Reposted by Gonzalo Parra

Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 21d

www.science.org/doi/10.1126/...

Mapping early human blood cell differentiation using single-cell proteomics and transcriptomics

Single-cell transcriptomics (scRNA-seq) has facilitated the characterization of cell state heterogeneity and recapitulation of differentiation trajectories. However, the exclusive use of mRNA measurem...

www.science.org

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Gonzalo Parra @gonzaparra.bsky.social · 21d

That is great!!! It is for sure super useful! Thanks a lot!

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Reposted by Gonzalo Parra

Andrian Gajigan @adi-gajigan.bsky.social · 21d

Naiavirus: an enveloped giant virus with a pleomorphic, flexible tail
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

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Gonzalo Parra @gonzaparra.bsky.social · 21d

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!