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Protein Structure Evolution (ProSE) Seminar @proteinstructure.bsky.social · 01/09/2026

Join us next Tuesday, 5PM CET for our first ProSE after the summer! Betül Kaçar @kacarlab.bsky.social will talk about the origin and early evolution of ancient proteins! 📜🧬 tinyurl.com/prose-seminar2

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Lars Eicholt @lacholt.bsky.social · 26/08/2026

Two years ago @lassemiddendorf.bsky.social and I noticed that structure and disorder predictor are discordant for de novo emerged and randomized proteins. We now identified which sequences drive these discordant predictions and what properties they have. 1/6 www.biorxiv.org/content/10.6...

biorxiv.org

A discrete protein subset drives structure prediction discordance in orphan proteins

Structure and disorder predictors are increasingly used as decision-grade tools in protein engineering and in the analysis of newly emerged proteins, yet how the current state-of-the-art behaves on se...

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Genome Biology and Evolution @genomebiolevol.bsky.social · 24/08/2026

@timothyfuqua.bsky.social & @vakirlis.bsky.social formalize “emergence bias” as the molecular predisposition that, upon mutation, biases a genetic sequence toward or against manifesting new or latent functions or phenotypes 🔗 academic.oup.com/gbe/article/... #societyjournal #genome #evolution

academic.oup.com

Emergence Biases in Molecular Evolution

Abstract. Biases in molecular evolution can significantly influence evolutionary trajectories. They have been described in a variety of contexts, such as d

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Protein Structure Evolution (ProSE) Seminar @proteinstructure.bsky.social · 04/06/2026

Join us the last time before the summer break! Cesar A. Ramirez-Sarmiento will talk about "Unveiling the fold-switching behavior of RfaH: echoes of the past, signals of the present". As always, Tue 5PM CET, follow the link to sign-up: tinyurl.com/prose-seminar2

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Protein Structure Evolution (ProSE) Seminar @proteinstructure.bsky.social · 05/05/2026

Join ProSe next week Tuesday, when Noelia Ferruz @noeliaferruz.bsky.social is talking about "Controllable Protein Design with Protein Language Models and Reinforcment Learning", TUE, May 12, 5PM CET! Sign-up here: tinyurl.com/prose-seminar2

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Timothy Fuqua @timothyfuqua.bsky.social · 08/04/2026

Come listen to my talk about how enhancers evolve and how promoters emerge from randomly synthesized DNA sequences!

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Protein Structure Evolution (ProSE) Seminar @proteinstructure.bsky.social · 08/04/2026

Our next speaker will be Timothy Fuqua @timothyfuqua.bsky.social with "The Evolution and Emergence of Regulatory DNA", 14th April, 5PM CET. Sign-up here: tinyurl.com/prose-seminar2

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Protein Structure Evolution (ProSE) Seminar @proteinstructure.bsky.social · 03/03/2026

Our next Talk will be "Protein Origami and the Hidden Rules of Functional Innovations"! March 11th, 5PM CET. Sign-up here: tinyurl.com/prose-seminar2

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Protein Structure Evolution (ProSE) Seminar @proteinstructure.bsky.social · 09/02/2026

ProSe goes into the 2nd with a talk by Vyacheslav Tretyachenko on the pervasive alternative translation in the human proteome. Join us tomorrow via Zoom, 4PM GMT, 5PM CET.

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Protein Structure Evolution (ProSE) Seminar @proteinstructure.bsky.social · 03/02/2026

Next up in our ProSE seminar series: Vyacheslav Tretyachenko on alternative translation in the human proteome Register to join: tinyurl.com/prose-seminar2 Past seminars: tinyurl.com/ProSE-videos

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Lars Eicholt @lacholt.bsky.social · 28/01/2026

Check out our new review in Nature Reviews Genetics on de novo emerged genes and proteins. How they emerge, are lost and persist - and how de novo emerged proteins relate to randomized proteins! @bornberglab.bsky.social www.nature.com/articles/s41...

nature.com

Emergence and evolution of protein-coding de novo genes - Nature Reviews Genetics

De novo gene evolution entails the birth of new genes from previously non-coding DNA. In this Review, Bornberg-Bauer and Eicholt overview how protein-coding de novo genes are identified, the mechanist...

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Bornberglab @bornberglab.bsky.social · 28/01/2026

New review out in Nat Rev Genet: Emergence & evolution of protein-coding de novo genes by Erich and Lars Eicholt @lacholt.bsky.social. How non-coding DNA becomes translated, persists or is lost in populations, and can yield structured/functional proteins—plus methods & open questions! rdcu.be/e09SM

rdcu.be

Emergence and evolution of protein-coding de novo genes

Nature Reviews Genetics - De novo gene evolution entails the birth of new genes from previously non-coding DNA. In this Review, Bornberg-Bauer and Eicholt overview how protein-coding de novo genes...

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Reposted by Protein Structure Evolution (ProSE) Seminar

Elias Dohmen @drdomain.bsky.social · 12/11/2025

🚀We’re excited to share our new paper in Bioinformatics! We introduce a user-friendly toolkit that implements our novel DeNoFo file-format for standardised annotation of de novo gene detection workflows — enabling reproducible methodology descriptions and easier dataset comparison across studies.

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Protein Structure Evolution (ProSE) Seminar @proteinstructure.bsky.social · 10/11/2025

Join us tomorrow! Joana Pereira is talking about AI-powered classification and discovery across the protein universe. @joanampereira.bsky.social 5PM CET, link in the post and in our bio.

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Reposted by Protein Structure Evolution (ProSE) Seminar

Lars Eicholt @lacholt.bsky.social · 03/11/2025

The DeNoFo format & toolkit for annotating, assessing and comparing the tools and tresholds used in studies of de novo evolved genes is out now in Bioinformatics! Great effort led by @drdomain.bsky.social and Anna Grandchamp! academic.oup.com/bioinformati...

academic.oup.com

DeNoFo: a file format and toolkit for standardized, comparable de novo gene annotation

AbstractMotivation. De novo genes emerge from previously non-coding regions of the genome, challenging the traditional view that new genes primarily arise

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Protein Structure Evolution (ProSE) Seminar @proteinstructure.bsky.social · 28/10/2025

The next ProSE Seminar will be given by Joana Pereira @joanampereira.bsky.social (VIB, KU Leuven) 🗓️ November 11th, 5pm CET Registration is now open: tinyurl.com/prose-seminar2 Please share!

Protein Structure Evolution Seminar
November 11, 5pm CET
Title: AI-Powered Classification and Discovery Across the Protein Universe
Speaker: Joana Pereira
Organized by: Claudia Alvarez Carreno, Zachary Ardern, Lars Eicholt, Carolina Sanchez-Rocha, Sergio Romero-Romero and MD. Hassan Uz-Zaman

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Protein Structure Evolution (ProSE) Seminar @proteinstructure.bsky.social · 25/10/2025

Protein Structure Evolution (ProSe) Seminar is now on BlueSky! Every 2nd Tuesday, 4PM GMT. Sign-Up: tinyurl.com/prose-seminar2 Organized by Claudia Alvarez Carreño, Zachary Ardern, Lars Eicholt, Carolina Sanchez-Rocha, Sergio Romero Romero and Md. Hassan Uz-Zaman.

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Claudia Alvarez Carreño @claudiaalcar.bsky.social · 06/10/2025

The next Protein Structure Evolution Seminar will be given by Stephen Fried (JHU): Title: “Who Cares About Protein Refolding Anyway?: Why Some Microbes Do and Others Don’t” Date: October 14th, 5 pm CET Registration link: tinyurl.com/prose-seminar2

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