PUBLICATIONS


285 entries « 1 of 6 »

2024

Journal Articles

1.

Massimo Bellanda; Milena Damulewicz; Barbara Zambelli; Elisa Costanzi; Francesco Gregoris; Stefano Mammi; Silvio C. E. Tosatto; Rodolfo Costa; Giovanni Minervini; Gabriella M. Mazzotta

A PDZ scaffolding/CaM-mediated pathway in Cryptochrome signaling Journal Article

In: Protein Science, vol. 33, no. 3, 2024, ISSN: 09618368, (Cited by: 0).

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2.

Damiano Piovesan; Davide Zago; Parnal Joshi; M. Clara De Paolis Kaluza; Mahta Mehdiabadi; Rashika Ramola; Alexander Miguel Monzon; Walter Reade; Iddo Friedberg; Predrag Radivojac; Silvio C. E. Tosatto

CAFA-evaluator: a Python tool for benchmarking ontological classification methods Journal Article

In: Bioinformatics Advances, vol. 4, no. 1, 2024, ISSN: 26350041, (Cited by: 2; All Open Access, Gold Open Access).

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3.

Francesco Gregoris; Giovanni Minervini; Silvio C. E. Tosatto

In Silico Exploration of AHR-HIF Pathway Interplay: Implications for Therapeutic Targeting in ccRCC Journal Article

In: Genes, vol. 15, no. 9, 2024, ISSN: 20734425, (Cited by: 0; All Open Access, Gold Open Access).

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4.

Ilenia Inciardi; Elena Rizzotto; Francesco Gregoris; Benedetta Fongaro; Alice Sosic; Giovanni Minervini; Patrizia Polverino de Laureto

Catechol-induced covalent modifications modulate the aggregation tendency of α-synuclein: An in-solution and in-silico study Journal Article

In: BioFactors, 2024, ISSN: 09516433, (Cited by: 1).

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5.

Alessio Del Conte; Giorgia F Camagni; Damiano Clementel; Giovanni Minervini; Alexander Miguel Monzon; Carlo Ferrari; Damiano Piovesan; Silvio C. E Tosatto

RING 4.0: Faster residue interaction networks with novel interaction types across over 35,000 different chemical structures Journal Article

In: Nucleic Acids Research, vol. 52, no. W1, pp. W306 – W312, 2024, ISSN: 03051048, (Cited by: 5; All Open Access, Gold Open Access).

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6.

Paula Nazarena Arrías; Zarifa Osmanli; Estefanía Peralta; Patricio Manuel Chinestrad; Alexander Miguel Monzon; Silvio C. E. Tosatto

Diversity and structural-functional insights of alpha-solenoid proteins Journal Article

In: Protein Science, vol. 33, no. 11, 2024, ISSN: 09618368, (Cited by: 0; All Open Access, Hybrid Gold Open Access).

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7.

Shantanu Jain; Constantina Bakolitsa; Steven E. Brenner; Predrag Radivojac; John Moult; Susanna Repo; Roger A. Hoskins; Gaia Andreoletti; Daniel Barsky; Ajithavalli Chellapan; Hoyin Chu; Navya Dabbiru; Naveen K. Kollipara; Melissa Ly; Andrew J. Neumann; Lipika R. Pal; Eric Odell; Gaurav Pandey; Robin C. Peters-Petrulewicz; Rajgopal Srinivasan; Stephen F. Yee; Sri Jyothsna Yeleswarapu; Maya Zuhl; Ogun Adebali; Ayoti Patra; Michael A. Beer; Raghavendra Hosur; Jian Peng; Brady M. Bernard; Michael Berry; Shengcheng Dong; Alan P. Boyle; Aashish Adhikari; Jingqi Chen; Zhiqiang Hu; Robert Wang; Yaqiong Wang; Maximilian Miller; Yanran Wang; Yana Bromberg; Paola Turina; Emidio Capriotti; James J. Han; Kivilcim Ozturk; Hannah Carter; Giulia Babbi; Samuele Bovo; Pietro Di Lena; Pier Luigi Martelli; Castrense Savojardo; Rita Casadio; Melissa S. Cline; Greet De Baets; Sandra Bonache; Orland Díez; Sara Gutiérrez-Enríquez; Alejandro Fernández; Gemma Montalban; Lars Ootes; Selen Özkan; Natàlia Padilla; Casandra Riera; Xavier De la Cruz; Mark Diekhans; Peter J. Huwe; Qiong Wei; Qifang Xu; Roland L. Dunbrack; Valer Gotea; Laura Elnitski; Gennady Margolin; Piero Fariselli; Ivan V. Kulakovskiy; Vsevolod J. Makeev; Dmitry D. Penzar; Ilya E. Vorontsov; Alexander V. Favorov; Julia R. Forman; Marcia Hasenahuer; Maria S. Fornasari; Gustavo Parisi; Ziga Avsec; Muhammed H. Çelik; Thi Yen Duong Nguyen; Julien Gagneur; Fang-Yuan Shi; Matthew D. Edwards; Yuchun Guo; Kevin Tian; Haoyang Zeng; David K. Gifford; Jonathan Göke; Jan Zaucha; Julian Gough; Graham R. S. Ritchie; Adam Frankish; Jonathan M. Mudge; Jennifer Harrow; Erin L. Young; Yao Yu; …

CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods Journal Article

In: Genome Biology, vol. 25, no. 1, 2024, ISSN: 14747596, (Cited by: 11; All Open Access, Gold Open Access).

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8.

Hamidreza Ghafouri; Tamas Lazar; Alessio Del Conte; Luiggi G. Tenorio Ku; Peter Tompa; Silvio C. E. Tosatto; Alexander Miguel Monzon; Maria C. Aspromonte; Pau Bernadó; Belén Chaves-Arquero; Lucia Beatriz Chemes; Damiano Clementel; Tiago N. Cordeiro; Carlos A. Elena-Real; Michael Feig; Isabella C. Felli; Carlo Ferrari; Julie D. Forman-Kay; Tiago Gomes; Frank Gondelaud; Claudiu C. Gradinaru; Tâp Ha-Duong; Teresa Head-Gordon; Pétur O. Heidarsson; Giacomo Janson; Gunnar Jeschke; Emanuela Leonardi; Zi Hao Liu; Sonia Longhi; Xamuel L. Lund; Maria J. Macias; Pau Martin-Malpartida; Davide Mercadante; Assia Mouhand; Gabor Nagy; María Victoria Nugnes; José Manuel Pérez-Cañadillas; Giulia Pesce; Roberta Pierattelli; Damiano Piovesan; Federica Quaglia; Sylvie Ricard-Blum; Paul Robustelli; Amin Sagar; Edoardo Salladini; Lucile Sénicourt; Nathalie Sibille; João M. C. Teixeira; Thomas E. Tsangaris; Mihaly Varadi

PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins Journal Article

In: Nucleic Acids Research, vol. 52, no. D1, pp. D536 – D544, 2024, ISSN: 03051048, (Cited by: 13; All Open Access, Gold Open Access).

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9.

Elisa Granocchio; Luca Andreoli; Santina Magazù; Daniela Sarti; Emanuela Leonardi; Alessandra Murgia; Claudia Ciaccio

Expanding the clinical phenotype of SHANK2-related disorders: childhood apraxia of speech in a patient with a novel SHANK2 pathogenic variant Journal Article

In: European Child and Adolescent Psychiatry, 2024, ISSN: 10188827, (Cited by: 0).

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10.

Juan Mac Donagh; Abril Marchesini; Agostina Spiga; Maximiliano José Fallico; Paula Nazarena Arrías; Alexander Miguel Monzon; Aimilia-Christina Vagiona; Mariane Gonçalves-Kulik; Pablo Mier; Miguel A. Andrade-Navarro

Structured Tandem Repeats in Protein Interactions Journal Article

In: International Journal of Molecular Sciences, vol. 25, no. 5, 2024, ISSN: 16616596, (Cited by: 1; All Open Access, Gold Open Access, Green Open Access).

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11.

Maria Cristina Aspromonte; Maria Victoria Nugnes; Federica Quaglia; Adel Bouharoua; Silvio C. E. Tosatto; Damiano Piovesan; Vasileios Sagris; Vasilis J. Promponas; Anastasia Chasapi; Erzsébet Fichó; Galo E. Balatti; Gustavo Parisi; Martín González Buitrón; Gabor Erdos; Matyas Pajkos; Zsuzsanna Dosztányi; Laszlo Dobson; Alessio Del Conte; Damiano Clementel; Edoardo Salladini; Emanuela Leonardi; Fatemeh Kordevani; Hamidreza Ghafouri; Luiggi G. Tenorio Ku; Alexander Miguel Monzon; Carlo Ferrari; Zsófia Kálmán; Juliet F. Nilsson; Jaime Santos; Carlos Pintado-Grima; Salvador Ventura; Veronika Ács; Rita Pancsa; Mariane Goncalves Kulik; Miguel A. Andrade-Navarro; Pedro José Barbosa Pereira; Sonia Longhi; Philippe Le Mercier; Julian Bergier; Peter Tompa; Tamas Lazar

DisProt in 2024: improving function annotation of intrinsically disordered proteins Journal Article

In: Nucleic Acids Research, vol. 52, no. D1, pp. D434 – D441, 2024, ISSN: 03051048, (Cited by: 15; All Open Access, Gold Open Access).

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12.

Federica Quaglia; Anastasia Chasapi; Maria Victoria Nugnes; Maria Cristina Aspromonte; Emanuela Leonardi; Damiano Piovesan; Silvio C. E. Tosatto

Best practices for the manual curation of intrinsically disordered proteins in DisProt Journal Article

In: Database, vol. 2024, 2024, ISSN: 17580463, (Cited by: 1; All Open Access, Gold Open Access).

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2023

Journal Articles

13.

Alessio Del Conte; Mahta Mehdiabadi; Adel Bouhraoua; Alexander Miguel Monzon; Silvio C. E. Tosatto; Damiano Piovesan

Critical assessment of protein intrinsic disorder prediction (CAID) – Results of round 2 Journal Article

In: Proteins: Structure, Function and Bioinformatics, vol. 91, no. 12, pp. 1925 – 1934, 2023, ISSN: 08873585, (Cited by: 20; All Open Access, Hybrid Gold Open Access).

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14.

Damiano Piovesan; Alessio Del Conte; Damiano Clementel; Alexander Miguel Monzon; Martina Bevilacqua; Maria Cristina Aspromonte; Javier A Iserte; Fernando E Orti; Cristina Marino-Buslje; Silvio C. E Tosatto

MobiDB: 10 years of intrinsically disordered proteins Journal Article

In: Nucleic Acids Research, vol. 51, no. 1 D, pp. D438 – D444, 2023, ISSN: 03051048, (Cited by: 61; All Open Access, Gold Open Access, Green Open Access).

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15.

Eric W. Deutsch; Juan Antonio Vizcaíno; Andrew R. Jones; Pierre-Alain Binz; Henry Lam; Joshua Klein; Wout Bittremieux; Yasset Perez-Riverol; David L. Tabb; Mathias Walzer; Sylvie Ricard-Blum; Henning Hermjakob; Steffen Neumann; Tytus D. Mak; Shin Kawano; Luis Mendoza; Tim Van Den Bossche; Ralf Gabriels; Nuno Bandeira; Jeremy Carver; Benjamin Pullman; Zhi Sun; Nils Hoffmann; Jim Shofstahl; Yunping Zhu; Luana Licata; Federica Quaglia; Silvio C. E. Tosatto; Sandra E. Orchard

Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work Journal Article

In: Journal of Proteome Research, vol. 22, no. 2, pp. 287 – 301, 2023, ISSN: 15353893, (Cited by: 24; All Open Access, Hybrid Gold Open Access).

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16.

Diana Piol; Laura Tosatto; Emanuela Zuccaro; Eric N. Anderson; Antonella Falconieri; Maria J. Polanco; Caterina Marchioretti; Federica Lia; Joseph White; Elisa Bregolin; Giovanni Minervini; Sara Parodi; Xavier Salvatella; Giorgio Arrigoni; Andrea Ballabio; Albert R. La Spada; Silvio C. E. Tosatto; Fabio Sambataro; Diego L. Medina; Udai B. Pandey; Manuela Basso; Maria Pennuto

Antagonistic effect of cyclin-dependent kinases and a calcium-dependent phosphatase on polyglutamine-expanded androgen receptor toxic gain of function Journal Article

In: Science Advances, vol. 9, no. 1, 2023, ISSN: 23752548, (Cited by: 6; All Open Access, Gold Open Access).

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17.

Nahuel Escobedo; Alexander Miguel Monzon; María Silvina Fornasari; Nicolas Palopoli; Gustavo Parisi

Combining Protein Conformational Diversity and Phylogenetic Information Using CoDNaS and CoDNaS-Q Journal Article

In: Current Protocols, vol. 3, no. 5, 2023, ISSN: 26911299, (Cited by: 0; All Open Access, Green Open Access).

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18.

Giorgia F. Camagni; Giovanni Minervini; Silvio C. E. Tosatto

Structural Characterization of Hypoxia Inducible Factor α—Prolyl Hydroxylase Domain 2 Interaction through MD Simulations Journal Article

In: International Journal of Molecular Sciences, vol. 24, no. 5, 2023, ISSN: 16616596, (Cited by: 2; All Open Access, Gold Open Access).

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19.

Paula Nazarena Arrías; Alexander Miguel Monzon; Damiano Clementel; Soroush Mozaffari; Damiano Piovesan; Andrey V. Kajava; Silvio C. E. Tosatto

The repetitive structure of DNA clamps: An overlooked protein tandem repeat Journal Article

In: Journal of Structural Biology, vol. 215, no. 3, 2023, ISSN: 10478477, (Cited by: 2; All Open Access, Hybrid Gold Open Access).

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20.

Maria Santa Rocca; Giovanni Minervini; Cinzia Vinanzi; Alberto Bottacin; Federica Lia; Carlo Foresta; Maria Pennuto; Alberto Ferlin

Mutational Screening of Androgen Receptor Gene in 8224 Men of Infertile Couples Journal Article

In: Journal of Clinical Endocrinology and Metabolism, vol. 108, no. 5, pp. 1181 – 1191, 2023, ISSN: 0021972X, (Cited by: 2; All Open Access, Bronze Open Access).

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21.

Charlotte Gehin; Museer A. Lone; Winston Lee; Laura Capolupo; Sylvia Ho; Adekemi M. Adeyemi; Erica H. Gerkes; Alexander P. A. Stegmann; Estrella López-Martín; Eva Bermejo-Sánchez; Beatriz Martínez-Delgado; Christiane Zweier; Cornelia Kraus; Bernt Popp; Vincent Strehlow; Daniel Gräfe; Ina Knerr; Eppie R. Jones; Stefano Zamuner; Luciano A. Abriata; Vidya Kunnathully; Brandon E. Moeller; Anthony Vocat; Samuel Rommelaere; Jean-Philippe Bocquete; Evelyne Ruchti; Greta Limoni; Marine Van Campenhoudt; Samuel Bourgeat; Petra Henklein; Christian Gilissen; Bregje W. Bon; Rolph Pfundt; Marjolein H. Willemsen; Jolanda H. Schieving; Emanuela Leonardi; Fiorenza Soli; Alessandra Murgia; Hui Guo; Qiumeng Zhang; Kun Xia; Christina R. Fagerberg; Christoph P. Beier; Martin J. Larsen; Irene Valenzuela; Paula Fernández-Álvarez; Shiyi Xiong; Robert Śmigiel; Vanesa López-González; Lluís Armengol; Manuela Morleo; Angelo Selicorni; Annalaura Torella; Moira Blyth; Nicola S. Cooper; Valerie Wilson; Renske Oegema; Yvan Herenger; Aurore Garde; Ange-Line Bruel; Frederic Tran Mau-Them; Alexis B. R. Maddocks; Jennifer M. Bain; Musadiq A. Bhat; Gregory Costain; Peter Kannu; Ashish Marwaha; Neena L. Champaigne; Michael J. Friez; Ellen B. Richardson; Vykuntaraju K. Gowda; Varunvenkat M. Srinivasan; Yask Gupta; Tze Y. Lim; Simone Sanna-Cherchi; Bruno Lemaitre; Toshiyuki Yamaji; Kentaro Hanada; John E. Burke; Ana Marjia Jakšić; Brian D. McCabe; Paolo De Los Rios; Thorsten Hornemann; Giovanni D’Angelo; Vincenzo A. Gennarino

CERT1 mutations perturb human development by disrupting sphingolipid homeostasis Journal Article

In: Journal of Clinical Investigation, vol. 133, no. 10, 2023, ISSN: 00219738, (Cited by: 11; All Open Access, Gold Open Access).

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22.

Alessio Del Conte; Adel Bouhraoua; Mahta Mehdiabadi; Damiano Clementel; Alexander Miguel Monzon; Silvio C. E. Tosatto; Damiano Piovesan; Alex S. Holehouse; Daniel Griffith; Ryan J. Emenecker; Ashwini Patil; Ronesh Sharma; Tatsuhiko Tsunoda; Alok Sharma; Yi Jun Tang; Bin Liu; Claudio Mirabello; Björn Wallner; Burkhard Rost; Dagmar Ilzhöfer; Maria Littmann; Michael Heinzinger; Lea I. M. Krautheimer; Michael Bernhofer; Liam J. McGuffin; Isabelle Callebaut; Tristan Bitard Feildel; Jian Liu; Jianlin Cheng; Zhiye Guo; Jinbo Xu; Sheng Wang; Nawar Malhis; Jörg Gsponer; Chol-Song Kim; Kun-Sop Han; Myong-Chol Ma; Lukasz Kurgan; Sina Ghadermarzi; Akila Katuwawala; Bi Zhao; Zhenling Peng; Zhonghua Wu; Gang Hu; Kui Wang; Md Tamjidul Hoque; Md Wasi Ul Kabir; Michele Vendruscolo; Pietro Sormanni; Min Li; Fuhao Zhang; Pengzhen Jia; Yida Wang; Michail Yu Lobanov; Oxana V. Galzitskaya; Wim Vranken; Adrián Díaz; Thomas Litfin; Yaoqi Zhou; Jack Hanson; Kuldip Paliwal; Zsuzsanna Dosztányi; Gábor Erdős

CAID prediction portal: A comprehensive service for predicting intrinsic disorder and binding regions in proteins Journal Article

In: Nucleic Acids Research, vol. 51, no. W1, pp. W62 – W69, 2023, ISSN: 03051048, (Cited by: 16; All Open Access, Gold Open Access).

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23.

Bálint Mészáros; András Hatos; Nicolas Palopoli; Federica Quaglia; Edoardo Salladini; Kim Van Roey; Haribabu Arthanari; Zsuzsanna Dosztányi; Isabella C. Felli; Patrick D. Fischer; Jeffrey C. Hoch; Cy M. Jeffries; Sonia Longhi; Emiliano Maiani; Sandra Orchard; Rita Pancsa; Elena Papaleo; Roberta Pierattelli; Damiano Piovesan; Iva Pritisanac; Luiggi Tenorio; Thibault Viennet; Peter Tompa; Wim Vranken; Silvio C. E. Tosatto; Norman E. Davey

Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions Journal Article

In: Nature Methods, vol. 20, no. 9, pp. 1291 – 1303, 2023, ISSN: 15487091, (Cited by: 7; All Open Access, Bronze Open Access, Green Open Access).

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24.

Andras Hatos; João M. C Teixeira; Susana Barrera-Vilarmau; Attila Horvath; Silvio C. E Tosatto; Michele Vendruscolo; Monika Fuxreiter

FuzPred: A web server for the sequence-based prediction of the context-dependent binding modes of proteins Journal Article

In: Nucleic Acids Research, vol. 51, no. W1, pp. W198 – W206, 2023, ISSN: 03051048, (Cited by: 8; All Open Access, Gold Open Access).

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25.

Niels Vos; Jack Reilly; Mariet W Elting; Philippe M Campeau; David Coman; Zornitza Stark; Tiong Yang Tan; David J Amor; Simran Kaur; Miya Stjohn; Angela T Morgan; Benjamin A Kamien; Chirag Patel; Matthew L Tedder; Giuseppe Merla; Paolo Prontera; Marco Castori; Kai Muru; Felicity Collins; John Christodoulou; Janine Smith; Bruria Ben Zeev; Alessandra Murgia; Emanuela Leonardi; Natacha Esber; Antonio Martinez-Monseny; Didac Casas-Alba; Matthew Wallis; Marcel Mannens; Michael A Levy; Raissa Relator; Marielle Alders; Bekim Sadikovic

DNA methylation episignatures are sensitive and specific biomarkers for detection of patients with KAT6A/KAT6B variants Journal Article

In: Epigenomics, vol. 15, no. 6, pp. 351 – 367, 2023, ISSN: 17501911, (Cited by: 3).

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26.

Suzi A. Aleksander; James Balhoff; Seth Carbon; J. Michael Cherry; Harold J. Drabkin; Dustin Ebert; Marc Feuermann; Pascale Gaudet; Nomi L. Harris; David P. Hill; Raymond Lee; Huaiyu Mi; Sierra Moxon; Christopher J. Mungall; Anushya Muruganugan; Tremayne Mushayahama; Paul W. Sternberg; Paul D. Thomas; Kimberly Van Auken; Jolene Ramsey; Deborah A. Siegele; Rex L. Chisholm; Petra Fey; Maria Cristina Aspromonte; Maria Victoria Nugnes; Federica Quaglia; Silvio Tosatto; Michelle Giglio; Suvarna Nadendla; Giulia Antonazzo; Helen Attrill; Gil Dos Santos; Steven Marygold; Victor Strelets; Christopher J. Tabone; Jim Thurmond; Pinglei Zhou; Saadullah H. Ahmed; Praoparn Asanitthong; Diana Luna Buitrago; Meltem N. Erdol; Matthew C. Gage; Mohamed Ali Kadhum; Kan Yan Chloe Li; Miao Long; Aleksandra Michalak; Angeline Pesala; Armalya Pritazahra; Shirin C. C. Saverimuttu; Renzhi Su; Kate E. Thurlow; Ruth C Lovering; Colin Logie; Snezhana Oliferenko; Judith Blake; Karen Christie; Lori Corbani; Mary E. Dolan; Li Ni; Dmitry Sitnikov; Cynthia Smith; Alayne Cuzick; James Seager; Laurel Cooper; Justin Elser; Pankaj Jaiswal; Parul Gupta; Sushma Naithani; Manuel Lera-Ramirez; Kim Rutherford; Valerie Wood; Jeffrey L. De Pons; Melinda R. Dwinell; G. Thomas Hayman; Mary L. Kaldunski; Anne E. Kwitek; Stanley J. F. Laulederkind; Marek A. Tutaj; Mahima Vedi; Shur-Jen Wang; Peter D’Eustachio; Lucila Aimo; Kristian Axelsen; Alan Bridge; Nevila Hyka-Nouspikel; Anne Morgat; Stacia R. Engel; Kalpana Karra; Stuart R. Miyasato; Robert S. Nash; Marek S. Skrzypek; Shuai Weng; Edith D. Wong; Erika Bakker; Tanya Z. Berardini; Leonore Reiser; Andrea Auchincloss; Ghislaine Argoud-Puy; Marie-Claude Blatter; Emmanuel Boutet; …

The Gene Ontology knowledgebase in 2023 Journal Article

In: Genetics, vol. 224, no. 1, 2023, ISSN: 00166731, (Cited by: 570; All Open Access, Hybrid Gold Open Access).

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27.

Alexander Miguel Monzon; Paula Nazarena Arrías; Arne Elofsson; Pablo Mier; Miguel A. Andrade-Navarro; Martina Bevilacqua; Damiano Clementel; Alex Bateman; Layla Hirsh; Maria Silvina Fornasari; Gustavo Parisi; Damiano Piovesan; Andrey V. Kajava; Silvio C. E. Tosatto

A STRP-ed definition of Structured Tandem Repeats in Proteins Journal Article

In: Journal of Structural Biology, vol. 215, no. 4, 2023, ISSN: 10478477, (Cited by: 3; All Open Access, Hybrid Gold Open Access).

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28.

Alessio Del Conte; Alexander Miguel Monzon; Damiano Clementel; Giorgia F. Camagni; Giovanni Minervini; Silvio C. E. Tosatto; Damiano Piovesan

RING-PyMOL: residue interaction networks of structural ensembles and molecular dynamics Journal Article

In: Bioinformatics, vol. 39, no. 5, 2023, ISSN: 13674803, (Cited by: 8; All Open Access, Gold Open Access, Green Open Access).

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29.

Emanuela Leonardi; Maria Cristina Aspromonte; Denise Drongitis; Elisa Bettella; Lucia Verrillo; Roberta Polli; Meriel McEntagart; Laura Licchetta; Robertino Dilena; Stefano D’Arrigo; Claudia Ciaccio; Silvia Esposito; Vincenzo Leuzzi; Annalaura Torella; Demetrio Baldo; Fortunato Lonardo; Giulia Bonato; Serena Pellegrin; Franco Stanzial; Renata Posmyk; Ewa Kaczorowska; Miryam Carecchio; Monika Gos; Sylwia Rzońca-Niewczas; Maria Giuseppina Miano; Alessandra Murgia

Expanding the genetics and phenotypic spectrum of Lysine-specific demethylase 5C (KDM5C): a report of 13 novel variants Journal Article

In: European Journal of Human Genetics, vol. 31, no. 2, pp. 202 – 215, 2023, ISSN: 10184813, (Cited by: 5; All Open Access, Green Open Access).

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30.

Elizabeth Martínez-Pérez; Mátyás Pajkos; Silvio C. E. Tosatto; Toby J. Gibson; Zsuzsanna Dosztanyi; Cristina Marino-Buslje

Pipeline for transferring annotations between proteins beyond globular domains Journal Article

In: Protein Science, vol. 32, no. 7, 2023, ISSN: 09618368, (Cited by: 2; All Open Access, Hybrid Gold Open Access).

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31.

Typhaine Paysan-Lafosse; Matthias Blum; Sara Chuguransky; Tiago Grego; Beatriz Lázaro Pinto; Gustavo A. Salazar; Maxwell L. Bileschi; Peer Bork; Alan Bridge; Lucy Colwell; Julian Gough; Daniel H. Haft; Ivica Letunić; Aron Marchler-Bauer; Huaiyu Mi; Darren A. Natale; Christine A. Orengo; Arun P. Pandurangan; Catherine Rivoire; Christian J. A. Sigrist; Ian Sillitoe; Narmada Thanki; Paul D. Thomas; Silvio C. E. Tosatto; Cathy H. Wu; Alex Bateman

InterPro in 2022 Journal Article

In: Nucleic Acids Research, vol. 51, no. D1, pp. D418 – D427, 2023, ISSN: 03051048, (Cited by: 934; All Open Access, Gold Open Access).

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Books

32.

Fotis Psomopoulos; Carole Coble; Leyla Jael Castro; Jennifer Harrow; Silvio C. E. Tosatto

A roadmap for defining machine learning standards in life sciences Book

World Scientific Publishing Co. Pte. Ltd., 2023, ISBN: 978-981126567-9; 978-981126566-2, (Cited by: 0).

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2022

Journal Articles

33.

Franco Pradelli; Giovanni Minervini; Silvio C. E. Tosatto

Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models Journal Article

In: Bioinformatics, vol. 38, no. 18, pp. 4440 – 4441, 2022, ISSN: 13674803, (Cited by: 1).

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34.

Damiano Piovesan; Alexander Miguel Monzon; Silvio C. E. Tosatto

Intrinsic protein disorder and conditional folding in AlphaFoldDB Journal Article

In: Protein Science, vol. 31, no. 11, 2022, ISSN: 09618368, (Cited by: 44; All Open Access, Hybrid Gold Open Access).

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35.

Federica Quaglia; András Hatos; Edoardo Salladini; Damiano Piovesan; Silvio C. E. Tosatto

Exploring Manually Curated Annotations of Intrinsically Disordered Proteins with DisProt Journal Article

In: Current Protocols, vol. 2, no. 7, 2022, ISSN: 26911299, (Cited by: 4; All Open Access, Hybrid Gold Open Access).

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36.

Margot A. Cousin; Emma L. Veale; Nikita R. Dsouza; Swarnendu Tripathi; Robyn G. Holden; Maria Arelin; Geoffrey Beek; Mir Reza Bekheirnia; Jasmin Beygo; Vikas Bhambhani; Martin Bialer; Stefania Bigoni; Cyrus Boelman; Jenny Carmichael; Thomas Courtin; Benjamin Cogne; Ivana Dabaj; Diane Doummar; Laura Fazilleau; Alessandra Ferlini; Ralitza H. Gavrilova; John M. Graham; Tobias B. Haack; Jane Juusola; Sarina G. Kant; Saima Kayani; Boris Keren; Petra Ketteler; Chiara Klöckner; Tamara T. Koopmann; Teresa M. Kruisselbrink; Alma Kuechler; Laëtitia Lambert; Xénia Latypova; Robert Roger Lebel; Magalie S. Leduc; Emanuela Leonardi; Andrea M. Lewis; Wendy Liew; Keren Machol; Samir Mardini; Kirsty McWalter; Cyril Mignot; Julie McLaughlin; Alessandra Murgia; Vinodh Narayanan; Caroline Nava; Sonja Neuser; Mathilde Nizon; Davide Ognibene; Joohyun Park; Konrad Platzer; Céline Poirsier; Maximilian Radtke; Keri Ramsey; Cassandra K. Runke; Maria J. Guillen Sacoto; Fernando Scaglia; Marwan Shinawi; Stephanie Spranger; Ee Shien Tan; John Taylor; Anne-Sophie Trentesaux; Filippo Vairo; Rebecca Willaert; Neda Zadeh; Raul Urrutia; Dusica Babovic-Vuksanovic; Michael T. Zimmermann; Alistair Mathie; Eric W. Klee

Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome Journal Article

In: Genome Medicine, vol. 14, no. 1, 2022, ISSN: 1756994X, (Cited by: 9; All Open Access, Gold Open Access, Green Open Access).

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37.

Mihaly Varadi; Stephen Anyango; David Armstrong; John Berrisford; Preeti Choudhary; Mandar Deshpande; Nurul Nadzirin; Sreenath S. Nair; Lukas Pravda; Ahsan Tanweer; Bissan Al-Lazikani; Claudia Andreini; Geoffrey J. Barton; David Bednar; Karel Berka; Tom Blundell; Kelly P. Brock; Jose Maria Carazo; Jiri Damborsky; Alessia David; Sucharita Dey; Roland Dunbrack; Juan Fernandez Recio; Franca Fraternali; Toby Gibson; Manuela Helmer-Citterich; David Hoksza; Thomas Hopf; David Jakubec; Natarajan Kannan; Radoslav Krivak; Manjeet Kumar; Emmanuel D. Levy; Nir London; Jose Ramon Macias; Madhusudhan M. Srivatsan; Debora S. Marks; Lennart Martens; Stuart A. McGowan; Jake E. McGreig; Vivek Modi; R. Gonzalo Parra; Gerardo Pepe; Damiano Piovesan; Jaime Prilusky; Valeria Putignano; Leandro G. Radusky; Pathmanaban Ramasamy; Atilio O. Rausch; Nathalie Reuter; Luis A. Rodriguez; Nathan J. Rollins; Antonio Rosato; Paweł Rubach; Luis Serrano; Gulzar Singh; Petr Skoda; Carlos Oscar S. Sorzano; Jan Stourac; Joanna I. Sulkowska; Radka Svobodova; Natalia Tichshenko; Silvio C. E. Tosatto; Wim Vranken; Mark N. Wass; Dandan Xue; Daniel Zaidman; Janet Thornton; Michael Sternberg; Christine Orengo; Sameer Velankar

PDBe-KB: collaboratively defining the biological context of structural data Journal Article

In: Nucleic Acids Research, vol. 50, no. D1, pp. D534 – D542, 2022, ISSN: 03051048, (Cited by: 49; All Open Access, Gold Open Access).

Abstract | Links:

38.

Alexander Miguel Monzon; Damiano Piovesan; Monika Fuxreiter

Molecular Determinants of Selectivity in Disordered Complexes May Shed Light on Specificity in Protein Condensates Journal Article

In: Biomolecules, vol. 12, no. 1, 2022, ISSN: 2218273X, (Cited by: 4; All Open Access, Gold Open Access, Green Open Access).

Abstract | Links:

39.

Antonella Falconieri; Giovanni Minervini; Federica Quaglia; Geppo Sartori; Silvio C. E. Tosatto

Characterization of the pVHL Interactome in Human Testis Using High-Throughput Library Screening Journal Article

In: Cancers, vol. 14, no. 4, 2022, ISSN: 20726694, (Cited by: 1; All Open Access, Gold Open Access).

Abstract | Links:

40.

Andras Hatos; Alexander Miguel Monzon; Silvio C. E. Tosatto; Damiano Piovesan; Monika Fuxreiter

FuzDB: A new phase in understanding fuzzy interactions Journal Article

In: Nucleic Acids Research, vol. 50, no. D1, pp. D509 – D517, 2022, ISSN: 03051048, (Cited by: 31; All Open Access, Gold Open Access, Green Open Access).

Abstract | Links:

41.

Emanuela Leonardi; Castrense Savojardo; Giovanni Minervini

Molecular Effects of Mutations in Human Genetic Diseases Journal Article

In: International Journal of Molecular Sciences, vol. 23, no. 12, 2022, ISSN: 16616596, (Cited by: 0; All Open Access, Gold Open Access).

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42.

Federica Quaglia; Bálint Meszáros; Edoardo Salladini; András Hatos; Rita Pancsa; Lucía B. Chemes; Mátyás Pajkos; Tamas Lazar; Samuel Peña-Díaz; Jaime Santos; Veronika Ács; Nazanin Farahi; Erzsebet Fichó; Maria Cristina Aspromonte; Claudio Bassot; Anastasia Chasapi; Norman E. Davey; Radoslav Davidović; Laszlo Dobson; Arne Elofsson; Gábor Erdos; Pascale Gaudet; Michelle Giglio; Juliana Glavina; Javier Iserte; Valentín Iglesias; Zsófia Kálmán; Matteo Lambrughi; Emanuela Leonardi; Sonia Longhi; Sandra Macedo-Ribeiro; Emiliano Maiani; Julia Marchetti; Cristina Marino-Buslje; Attila Meszáros; Alexander Miguel Monzon; Giovanni Minervini; Suvarna Nadendla; Juliet F. Nilsson; Marian Novotný; Christos A. Ouzounis; Nicolás Palopoli; Elena Papaleo; Pedro Jose Barbosa Pereira; Gabriele Pozzati; Vasilis J. Promponas; Jordi Pujols; Alma Carolina Sanchez Rocha; Martin Salas; Luciana Rodriguez Sawicki; Eva Schad; Aditi Shenoy; Tamás Szaniszló; Konstantinos D. Tsirigos; Nevena Veljkovic; Gustavo Parisi; Salvador Ventura; Zsuzsanna Dosztányi; Peter Tompa; Silvio C. E. Tosatto; Damiano Piovesan

DisProt in 2022: Improved quality and accessibility of protein intrinsic disorder annotation Journal Article

In: Nucleic Acids Research, vol. 50, no. D1, pp. D480 – D487, 2022, ISSN: 03051048, (Cited by: 110; All Open Access, Gold Open Access).

Abstract | Links:

43.

Martina Bevilacqua; Lisanna Paladin; Silvio C. E. Tosatto; Damiano Piovesan

ProSeqViewer: an interactive, responsive and efficient TypeScript library for visualization of sequences and alignments in web applications Journal Article

In: Bioinformatics, vol. 38, no. 4, pp. 1129 – 1130, 2022, ISSN: 13674803, (Cited by: 5).

Abstract | Links:

44.

Damiano Piovesan; Miguel Arbesú; Monika Fuxreiter; Miquel Pons

Editorial: Fuzzy Interactions: Many Facets of Protein Binding Journal Article

In: Frontiers in Molecular Biosciences, vol. 9, 2022, ISSN: 2296889X, (Cited by: 3; All Open Access, Gold Open Access, Green Open Access).

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45.

Damiano Clementel; Alessio Del Conte; Alexander Miguel Monzon; Giorgia F Camagni; Giovanni Minervini; Damiano Piovesan; Silvio C. E Tosatto

RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles Journal Article

In: Nucleic Acids Research, vol. 50, no. W1, pp. W651 – W656, 2022, ISSN: 03051048, (Cited by: 86; All Open Access, Gold Open Access, Green Open Access).

Abstract | Links:

46.

Federica Quaglia; Edoardo Salladini; Marco Carraro; Giovanni Minervini; Silvio C. E. Tosatto; Philippe Le Mercier

SARS-CoV-2 variants preferentially emerge at intrinsically disordered protein sites helping immune evasion Journal Article

In: FEBS Journal, vol. 289, no. 14, pp. 4240 – 4250, 2022, ISSN: 1742464X, (Cited by: 22; All Open Access, Hybrid Gold Open Access).

Abstract | Links:

47.

Andras Hatos; Silvio C. E Tosatto; Michele Vendruscolo; Monika Fuxreiter

FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid-liquid phase separation and aggregation of proteins Journal Article

In: Nucleic Acids Research, vol. 50, no. W1, pp. W337 – W344, 2022, ISSN: 03051048, (Cited by: 55; All Open Access, Gold Open Access).

Abstract | Links:

48.

David E. Godler; Ling Ling; Dinusha Gamage; Emma K. Baker; Minh Bui; Michael J. Field; Carolyn Rogers; Merlin G. Butler; Alessandra Murgia; Emanuela Leonardi; Roberta Polli; Charles E. Schwartz; Cindy D. Skinner; Angelica M. Alliende; Lorena Santa Maria; James Pitt; Ronda Greaves; David Francis; Ralph Oertel; Min Wang; Cas Simons; David J. Amor

Feasibility of Screening for Chromosome 15 Imprinting Disorders in 16579 Newborns by Using a Novel Genomic Workflow Journal Article

In: JAMA Network Open, vol. 5, no. 1, 2022, ISSN: 25743805, (Cited by: 17; All Open Access, Gold Open Access, Green Open Access).

Abstract | Links:

49.

Suvarna Nadendla; Rebecca Jackson; James Munro; Federica Quaglia; Bálint Mészáros; Dustin Olley; Elizabeth T. Hobbs; Stephen M. Goralski; Marcus Chibucos; Christopher John Mungall; Silvio C. E. Tosatto; Ivan Erill; Michelle G. Giglio

ECO: The Evidence and Conclusion Ontology, an update for 2022 Journal Article

In: Nucleic Acids Research, vol. 50, no. D1, pp. D1515 – D1521, 2022, ISSN: 03051048, (Cited by: 23; All Open Access, Gold Open Access).

Abstract | Links:

50.

Nahuel Escobedo; Ronaldo Romario Tunque Cahui; Gastón Caruso; Emilio García Ríos; Layla Hirsh; Alexander Miguel Monzon; Gustavo Parisi; Nicolas Palopoli

CoDNaS-Q: a database of conformational diversity of the native state of proteins with quaternary structure Journal Article

In: Bioinformatics, vol. 38, no. 21, pp. 4959 – 4961, 2022, ISSN: 13674803, (Cited by: 1; All Open Access, Bronze Open Access).

Abstract | Links:

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