Silvio C. E. Tosatto

@article{SCOPUS_ID:105030612709,

title = {Empowering biological knowledgebases: advances in human-in-the-loop AI-driven literature curation},

author = {Valerie Wood and Matt Jeffryes and Andrew F. Green and Matthias Blum and Sandra Orchard and Simona Panni and Federica Quaglia and Raul Rodriguez-Esteban and James Seager and Silvio C. E. Tosatto and Ulrike Wittig and Melissa Harrison},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-105030612709&origin=inward},

doi = {10.1093/bioadv/vbag028},

year  = {2026},

date = {2026-01-01},

journal = {Bioinformatics Advances},

volume = {6},

number = {1},

publisher = {Oxford University Press},

abstract = {© The Author(s) 2026. Published by Oxford University Press.Biological knowledgebases facilitate discovery across the life sciences by structuring experimental findings into human-readable and computable formats. These essential resources are maintained by a small number of professional biocurators worldwide and face combined chronic underfunding and the exponential growth of the literature. In this perspective, we review how artificial intelligence, particularly large language models and agentic systems, can augment literature-curation workflows. Applications include literature recommendation, entity recognition, data extraction, summarization, ontology development, and quality control with emphasis on published use cases at Global Core BioData Resources and ELIXIR Core Data Resources. We identify key challenges, including the scarcity of training data, difficulty in extracting complex relationships, and concerns about error propagation. To address these challenges, we propose a human-in-the-loop framework where generative artificial intelligence approaches accelerate routine tasks while curators provide critical evaluation and domain expertise. We also propose practical recommendations for the community, including the creation of shared benchmark datasets, harmonized evaluation frameworks, and best-practice guidelines for transparent human-in-the-loop AI deployment in biocuration. These synergistic partnerships will be critical to ensure biological rigour, accelerating knowledge integration while maintaining the quality essential for trusted biological resources.},

note = {Cited by: 0; Open Access},

keywords = {},

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}

@article{SCOPUS_ID:105033513263,

title = {The missing link in FAIR data policy: biodata resources in life sciences},

author = {Lucy Poveda and Gavin Farrell and Silvio C. E. Tosatto and Monique Zahn-Zabal and Patrick Ruch and Julien Gobeill and Robert M. Waterhouse and Christophe Dessimoz},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-105033513263&origin=inward},

doi = {10.1038/s41597-026-06690-w},

year  = {2026},

date = {2026-01-01},

journal = {Scientific Data},

volume = {13},

number = {1},

publisher = {Nature Research},

abstract = {© The Author(s) 2026.In the life sciences, FAIR principles have reshaped research policy, but their implementation still relies largely on individual researchers – many of whom lack the expertise or support needed to make data truly reusable. Realising FAIR’s promise requires sustained investment in the infrastructures that organise, standardise, and curate data: deposition databases and knowledgebases. These biodata resources are especially critical for AI, which depends on large, high-quality, and consistent data. Landmark advances like AlphaFold and the COVID-19 response illustrate how sustained curation and standardisation in expert resources such as UniProt and the Protein Data Bank have enabled rapid innovation. Yet biodata resources remain precariously funded, jeopardising long-term sustainability and the expert workforce they require. To support ambitious, data-driven science, funders must align policy and budgets by establishing dedicated mechanisms that allocate a small (e.g., 1%), but strategic and stable share, of research funding to core data infrastructures. This would maximise the value of public investment, strengthen open science and international collaboration, and unlock the full potential of FAIR.},

note = {Cited by: 0; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:105027746750,

title = {The Gene Ontology knowledgebase in 2026},

author = {Suzi A Aleksander and James P Balhoff and Seth Carbon and J. Michael Cherry and Dustin Ebert and Marc Feuermann and Pascale Gaudet and Nomi L Harris and David P Hill and Patrick Kalita and Raymond Lee and Huaiyu Mi and Sierra Moxon and Christopher J Mungall and Anushya Muruganujan and Tremayne Mushayahama and Paul W Sternberg and Paul D Thomas and Kimberly Van Auken and Edith D Wong and Valerie Wood and Jolene Ramsey and Deborah A Siegele and Rex L Chisholm and Robert Dodson and Petra Fey and Maria Cristina Aspromonte and Maria Victoria Nugnes and Ximena Aixa Castro Naser and Silvio C. E Tosatto and Michelle Giglio and Suvarna Nadendla and Giulia Antonazzo and Helen Attrill and Nicholas H Brown and Gil Dos Santos and Steven Marygold and Katja Röper and Victor Strelets and Christopher J Tabone and Jim Thurmond and Pinglei Zhou and Rossana Zaru and Ruth C Lovering and Colin Logie and Daqing Chen and Alexandra Naba and Karen Christie and Lori Corbani and Li Ni and Dmitry Sitnikov and Cynthia Smith and James Seager and Laurel Cooper and Justin Elser and Pankaj Jaiswal and Parul Gupta and Sushma Naithani and Pascal Carme and Kim Rutherford and Jeffrey L De Pons and Melinda R Dwinell and G. Thomas Hayman and Mary L Kaldunski and Anne E Kwitek and Stanley J. F Laulederkind and Marek A Tutaj and Mahima Vedi and Shur-Jen Wang and Peter D'Eustachio and Lucila Aimo and Kristian Axelsen and Alan Bridge and Nevila Hyka-Nouspikel and Anne Morgat and Gene Goldbold and Stacia R Engel and Stuart R Miyasato and Robert S Nash and Gavin Sherlock and Shuai Weng and Erika Bakker and Tanya Z Berardini and Leonore Reiser and Andrea Auchincloss and Ghislaine Argoud-Puy and Marie-Claude Blatter and Emmanuel Boutet and Lionel Breuza and Cristina Casals-Casas and Elisabeth Coudert and Anne Estreicher and Maria Livia Famiglietti and Arnaud Gos and Nadine Gruaz-Gumowski and Chantal Hulo and Florence Jungo and Philippe Le Mercier and Damien Lieberherr and Patrick Masson and ...},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-105027746750&origin=inward},

doi = {10.1093/nar/gkaf1292},

year  = {2026},

date = {2026-01-01},

journal = {Nucleic Acids Research},

volume = {54},

number = {D1},

pages = {D1779-D1792},

publisher = {Oxford University Press},

abstract = {© 2025 The Author(s). Published by Oxford University Press.The Gene Ontology (GO) knowledgebase (https://geneontology.org) is a comprehensive resource describing the functions of genes. The GO knowledgebase is regularly updated and improved. We describe here the major updates that have been made in the past 3 years. The ontology and annotations have been expanded and revised, particularly in several areas of biology: cellular metabolism, multi-organism interactions (e.g. host-pathogen), extracellular matrix proteins, chromatin remodeling (e.g. the "histone code"), and noncoding RNA functions. We have released version 2 of a comprehensive set of integrated, reviewed annotations for human genes, which we call the "functionome."We have also dramatically increased the number of GO-CAM models, with over 1500 models of metabolic and signaling pathways, primarily in human, mouse, budding and fission yeast, and fruit fly. Finally, we discuss our current recommendations and future prospects of AI in the use and development of GO.},

note = {Cited by: 9; Open Access},

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pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:105035676703,

title = {Effects of Mutations on Tandem-Repeat Proteins Conformation Mechanisms. Application to the Phosphatase PP2A},

author = {Matias Chiappinelli and Tadeo E. Saldaño and Silvio C E Tosatto and Sergei Grudinin and Gustavo Parisi and Sebastian Fernandez-Alberti},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-105035676703&origin=inward},

doi = {10.1021/acs.jcim.6c00133},

year  = {2026},

date = {2026-01-01},

journal = {Journal of chemical information and modeling},

volume = {66},

number = {7},

pages = {3976-3986},

abstract = {Tandem repeat proteins (TRPs) are composed of arrays of repeating structural units that assemble into extended, superhelical, or horseshoe-shaped architectures stabilized primarily by short-range interactions. The unique sequence-structure-dynamics-function relationships of TRPs have been the subject of extensive investigation, aiming to elucidate the molecular principles that distinguish them from globular proteins. Here we explore the effects of mutations on conformational mechanics of PR65, the HEAT-repeat scaffold of phosphatase PP2A that acts as an elastic connector between catalytic and regulatory subunits. We found that the effect of mutations on dynamics, that is associated with the collective conformational changes experienced by PR65 in its binding to the catalytic subunit, correlates with its evolutionary conservation. Besides, our study reveals a common pattern among repeat units in how mutations influence these dynamics, but it also highlights functional differences among the individual units. That is, mutations on individual units preserve a common influence on the collective dynamics of the TRP but their individual participation in function introduces additional differences in their corresponding effects of mutations. Finally, none of these aspects are observed for the subsequent conformational changes experienced during the binding of the dimer PR65-catalytic subunit complex with the regulatory subunit. We believe this work highlights both the similarities and differences between repeat units in how mutations affect their dynamics─insights that may advance our understanding of TRP mechanisms in pathogenicity─enable scaffold modifications for engineered ligand binding with diverse applications, and broadly expand our knowledge of TRP function.},

note = {Cited by: 0},

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}

@article{SCOPUS_ID:105033760847,

title = {Tandem repeats matter for the functional versatility of giant proteins},

author = {Zarifa Osmanli and Alexander Miguel Monzon and Silvio C. E. Tosatto},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-105033760847&origin=inward},

doi = {10.1016/j.tibs.2026.02.010},

year  = {2026},

date = {2026-01-01},

journal = {Trends in Biochemical Sciences},

publisher = {Elsevier Ltd},

abstract = {© 2026 Elsevier LtdGiant proteins play essential cellular roles but remain structurally challenging. Recent advances in structure determination and modeling reveal that tandem repeats are widespread in large proteins, providing modularity, adaptability, and multifunctionality. Examples including apolipoprotein B100, teneurins, and ryanodine receptors illustrate how repetition drives structural flexibility, regulatory precision, and evolutionary innovation.},

note = {Cited by: 0},

keywords = {},

pubstate = {published},

tppubtype = {article}

}