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Riccardo Percudani

@percud.bsky.social
87 followers 138 following 606 posts

Father of Eva and Adele, husband of Ariane. Teacher and researcher at the University of Parma (Italy): biochemistry & bioinformatics, metabolic pathways, coevolution.

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Riccardo Percudani @percud.bsky.social · 15/09/2026
From an unannotated gene to a new enzyme: screening 5,764 P. aeruginosa mutants linked PA14_24190 to a mysterious tRNA modification and experiments established it as tRNA(Ile)-aminovaleramididine synthetase —a novel PLP-dependent activity. www.nature.com/articles/s41...
nature.com
Pyridoxal-phosphate-dependent biosynthesis of aminovaleramide by AvaS in tRNA - Nature Chemical Biology
Sun, Wu et al. identify AvaS as a pyridoxal-phosphate-dependent RNA-modifying enzyme, producing the tRNA modification ava2C from k2C in bacteria and plants and linking RNA chemistry to translational r...
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Riccardo Percudani @percud.bsky.social · 05/09/2026
Wrapping up a great #ECCB2026 in Geneva with our poster, presented by Giovanni Merici. Thanks to the organizers for a successful meeting and to everyone who stopped by to discuss our work
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Riccardo Percudani @percud.bsky.social · 01/09/2026
Very interesting Ng’s talk on *predicts cognate pairing of heavy and light immunoglobulin chains at #Eccb2026*
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Riccardo Percudani @percud.bsky.social · 31/08/2026
“We not only have to share data, but also share the benefits of sharing data.” Powerful opening keynote by Jeremy Farrar at #ECCB2026 in Geneva — with no slides.
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Reposted by Riccardo Percudani
Marco Malatesta @marcomala46.bsky.social · 17/07/2026
🚀 Excited to share our latest work on bioRxiv! We identify L2HGDH as an integral component of the COQ metabolon, physically interacting with the complex and fueling coenzyme Q biosynthesis by reducing quinone intermediates. #bioRxiv #CoQ #Mitochondria #StructuralBiology #Metabolism #CryoEM
biorxiv.org
L-2-hydroxyglutarate recycling is linked to coenzyme Q biosynthesis
The mitochondrial COQ metabolon catalyzes the late stages of the biosynthesis of coenzyme Q, an essential and ubiquitous cofactor. Here, by integrating coevolution, coexpression, colocalization and do...
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Reposted by Riccardo Percudani
bioRxiv Biochemistry @biorxiv-biochem.bsky.social · 10/06/2026
Human ASPDH is a 2-aminomuconate reductase that produces L-2-aminohex-3-enedioic acid in tryptophan catabolism www.biorxiv.org/content/10.64898/20…
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Riccardo Percudani @percud.bsky.social · 21/05/2026
ProteomeLM: A proteome-scale language model enables accurate and rapid prediction of protein–protein interactions and gene essentiality across taxa | PNAS www.pnas.org/doi/10.1073/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Riccardo Percudani @percud.bsky.social · 10/02/2026
Irena Maus (ELIXIR-DE) with Integrating ELIXIR Germany Within the European Infrastructure closes a stimulating Elixir All-Hands meeting in Bari @elixir-it.bsky.social
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Riccardo Percudani @percud.bsky.social · 03/12/2025
Deeply saddened by the passing of Amos Bairoch, a true pioneer of bioinformatics and biological databases. His contributions shaped our field. www.sib.swiss/news/amos-ba...
sib.swiss
Amos Bairoch, Swiss pioneer of bioinformatics, passes away
We are deeply saddened to announce the passing of our co-founder and Group Leader Amos Bairoch. Emeritus professor at the University of Geneva, he shaped the development of bioinformatics over more th...
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Reposted by Riccardo Percudani
Life Metabolism @lifemetabolism.bsky.social · 25/11/2025
Urate metabolism, in the gut url: academic.oup.com/lifemeta/art...
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Riccardo Percudani @percud.bsky.social · 22/11/2025
A new component of the CatSper ion channel identified! Great collaboration with Jean-Ju Chung (Yale School of Medicine) and Jianping Wu (Westlake University). www.nature.com/articles/s41...
Eukaryotic tree showing coevolution of CatSper subunits
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Reposted by Riccardo Percudani
phy_papers @phypapers.bsky.social · 30/10/2025
Profylo: A Python Package for Phylogenetic Profile Comparison and Analysis pubmed.ncbi.nlm.nih.gov/41160131
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Riccardo Percudani @percud.bsky.social · 08/10/2025
Great new machine learning study from @unipr researchers Read it here 👉 doi.org/10.1007/s109...
doi.org
Analyzing RL components for Wagner’s framework via Brouwer’s conjecture - Machine Learning
In this work, we continue the study and systematization started in our previous work (Angileri et al. in: Lecture notes in computer science 15243 LNAI, 2025, pp 325–338. https://doi.org/10.1007/978-3-031-78977-9_21 ) of Wagner’s Reinforcement Learning framework to investigate graph conjectures. After identifying three main directions that impact the framework’s performance (the environment dynamics, the RL algorithm and the neural network used as a function approximator), we conduct an ablation study to evaluate the effectiveness of each component, analyzing several variations of them. The experiments compare three environment dynamics, implemented as Gym spaces (Linear, Local and Global), two algorithms [PPO and the Cross-Entropy method (Wagner in Constructions in combinatorics via neural networks, 2021, https://arxiv.org/abs/2104.14516 )], different neural network structures (Multi-Layer Perceptron and Graph Neural Networks) and reward systems. This study was intended not only to test the framework’s capabilities, but also to identify a configuration of environment, algorithm, and neural network that can be effective when exploring graph spaces, even with a complex target. For this reason, all the experiments were executed on Brouwer’s Conjecture. We also present the data collected with the various trained models, as these interesting configurations can be used in the inference process on the problem. Our analysis shows that a proper calibration of the individual components of the framework can significantly improve its performance, suggesting effective settings for addressing complex problems and contributing to the study of Brouwer’s Conjecture. All the codes and data are open source and available at https://github.com/CuriosAI/graph_conjectures .
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Riccardo Percudani @percud.bsky.social · 04/09/2025
Michael Galperin is a wizard.
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Riccardo Percudani @percud.bsky.social · 03/09/2025
Using bioinformatics for identifying and plugging metabolic pathway holes | PNAS www.pnas.org/doi/10.1073/...
pnas.org
Using bioinformatics for identifying and plugging metabolic pathway holes | PNAS
Using bioinformatics for identifying and plugging metabolic pathway holes
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Riccardo Percudani @percud.bsky.social · 11/08/2025
The activity and expression of adenylosuccinate lyase were reduced during modern human evolution, affecting brain and behavior | PNAS www.pnas.org/doi/10.1073/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Riccardo Percudani @percud.bsky.social · 01/08/2025
We used coevolutionary analysis of KEGG networks to identify the gene linked to L-xylulose formation in human metabolism and Garrod's pentosuria. #Bioinformatics #Genomics #Biochemistry Now in PNAS: t.co/iPIhrbUmxz (Preprint: www.researchsquare.com/article/rs-6...)
Coevolution in human metabolism
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Riccardo Percudani @percud.bsky.social · 24/07/2025
Structural variation in human genome based on pangenome analysis. Tobias Marschall at #ISMBECCB2025
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Riccardo Percudani @percud.bsky.social · 23/07/2025
Charlotte Dean on the future of AI-driven drug discovery #ISMBECCB2025 key note
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Riccardo Percudani @percud.bsky.social · 22/07/2025
Erva Ulusoy presenting ProtHGT: protein function prediction using biological knowledge graphs and LLM at #ISMBECCB2025
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Riccardo Percudani @percud.bsky.social · 22/07/2025
Clara De Paolis Kaluza on the past, present, and future of CAFA at #ISMBECCB2025
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Riccardo Percudani @percud.bsky.social · 22/07/2025
Matthias Blum: integrating AI in InterPro. #ismbeccb2025 function COSI
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Riccardo Percudani @percud.bsky.social · 22/07/2025
Erik Sonnhammer nicely presenting the FunCoup database and the complexity of functional networks at the #Ismbeccb2025
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Riccardo Percudani @percud.bsky.social · 22/07/2025
Nicola Bordin: novel domain arrangements but no novel folds in the metagenome billion-scale protein universe. Nicely reported at the #ismbeccb2025
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Riccardo Percudani @percud.bsky.social · 22/07/2025
Paul D. Thomas illustrating the GO annotation as derived from evolutionary modeling at #ismbeccb2025
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Riccardo Percudani @percud.bsky.social · 22/07/2025
The birth and death of protein domains in metazoa presented by Maureen Stolzer at the #ismbeccb2025 functon-evolution section
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Riccardo Percudani @percud.bsky.social · 22/07/2025
Marc Robinson-Rechavi, the funcional divergence of orthologs and paralogs, and the Bgee database at the function-EvolCompBiol section of #ismbeccb2025
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Riccardo Percudani @percud.bsky.social · 22/07/2025
Overton prize James Zou illuminating the future of computational biology in his #ismbeccb2025 keynote on AI agents.
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Riccardo Percudani @percud.bsky.social · 21/07/2025
Adam Gudys presenting at the EvolCompgen section of #ISMBECCB2025 FAMSA2: protein multiple alignment at the protein universe scale
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Riccardo Percudani @percud.bsky.social · 21/07/2025
Amos Bairoch resuming 45 y of #biocuration in his #ISMBECCB2025 keynote
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Riccardo Percudani @percud.bsky.social · 20/07/2025
Janet Thornton introducing John Jumper for the opening keynote at #ismbeccb2025
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Riccardo Percudani @percud.bsky.social · 07/07/2025
I'm attending #ISMBECCB2025 in Liverpool, United Kingdom from July 20-24. Who else is going? Register here and don't miss it! invt.io/1bxbsd8t5hg
invt.io
I'm participating the ISMB/ECCB 2025 conference, join me!
Register now
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Riccardo Percudani @percud.bsky.social · 17/05/2025
Predicting Protein Function in the AI and Big Data Era | Biochemistry pubs.acs.org/doi/10.1021/...
pubs.acs.org
Predicting Protein Function in the AI and Big Data Era
It is an exciting time for researchers working to link proteins to their functions. Most techniques for extracting functional information from genomic sequences were developed several years ago, with ...
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Reposted by Riccardo Percudani
Stephen Turner @stephenturner.us · 25/04/2025
EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals www.nature.com/articles/s41... 🧬🖥️🧪 #Rstats bioconductor.org/packages/Syn...
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Riccardo Percudani @percud.bsky.social · 06/01/2025
Louis Nicolas Vauquelin (1763–1829), a French chemist, is best known for discovering chromium and beryllium. However, his contributions to biochemistry are often overlooked—he was the first to isolate several iconic metabolites. 1/4
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Riccardo Percudani @percud.bsky.social · 06/01/2025
👇 all tweets below were automatically imported from my X archive with github.com/marcomaroni-... so please disregard the dates 👇
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Riccardo Percudani @percud.bsky.social · 14/11/2024
Pierre-Régis Burgel presenting the keynote speech at the 22nd convention of investigators in Cystic Fibrosis.
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Riccardo Percudani @percud.bsky.social · 08/11/2024
Mitochondria never cease to amaze x.com/Nature/status/185452999292901…
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Riccardo Percudani @percud.bsky.social · 30/10/2024
Our #bioinformatics course assistants love using ChatGPT visuals in the computer lab exercises. I found this #BLAST visual quite punching!
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Riccardo Percudani @percud.bsky.social · 27/08/2024
High-resolution cryoEM structure of UapA, the original member of the NAT transporter. While UapA transports uric acid, other members of this family transport ascorbate. Linus Pauling proposed an evolutionary connection between uric acid and ascorbate (vitamin C) t.co/lWwaenhMwO
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Riccardo Percudani @percud.bsky.social · 16/07/2024
2024 ISCB Innovator Award recipient, Dr. Sui-In Lee, concludes the #ISMB2024 congress with a powerful message: the researchers' goal is not to publish in prestigious journals, but to push the boundaries of human knowledge.
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Riccardo Percudani @percud.bsky.social · 16/07/2024
Thomas Lengauer explains the behind the doors of publishing in Bioinformatics Advances @BioinfoAdv, the open access journal of the International Society for Computational Biology. #ISMB2024
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Riccardo Percudani @percud.bsky.social · 16/07/2024
Alex Bateman discusses fair and unfair uses of generative AI and LLMs in scientific publishing at #ISMB2024. Unmissable if one want to use GTP for assistance.
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Riccardo Percudani @percud.bsky.social · 15/07/2024
Yannis Nevers nicely reporting at #ISMB2024 about OMArk, a software for genome quality assessment -a fundamental issue for downstream analysis.
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Riccardo Percudani @percud.bsky.social · 15/07/2024
Burkhard Rost introducing with energy and clarity VespaG: fast and accurate protein variant fitness prediction using Language Models. (the G stands for GEMME). VarI-COSI #ISMB2024
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Riccardo Percudani @percud.bsky.social · 15/07/2024
ISCB Overton Award recipient Martin Steinegger @thesteinegger discusses his cutting-edge algorithms and reveals his unconventional career journey, however full of famous mentors.
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Riccardo Percudani @percud.bsky.social · 14/07/2024
Mahta Mehdiabadi nicely presenting the work of @BioComputingUP on disordered protein prediction at #ISMB2024
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Riccardo Percudani @percud.bsky.social · 14/07/2024
Fascinating Gonzalo Parra talk about protein local frustration and the evolution of function and structure at #ISMB2024
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Riccardo Percudani @percud.bsky.social · 14/07/2024
Rafael Najmanovich opens the 2nd day at #ISMB2024 Function Cosi talking about Fast, high-performance biophysics-based computational methods in function prediction.
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Riccardo Percudani @percud.bsky.social · 13/07/2024
Very inspiring talk by Valérie de Crécy-Lagard at the Function Cosi. Predicting protein function is gaining new knowledge, not transferring the known functions. AI is still unable to solve the first problem. #ISMB2024
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