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Excellence Hub on Phase Transitions in Aging and Age-Related Disorders

Deliverables

Detailed Dissemination, Communication and Outreach Plan (DCOP)

Detailed Dissemination Communication and Outreach Plan DCOP

ESS1 and ESS2 plan
Report on computational analysis of protein phase separations
Report on publications on PhasAGE topics in high impact journals by the coordinating institution

Introduction in the Continuous reporting tool on the Funding and tenders portal of peerreviewed publications on intrinsically disordered proteinsphase separation of the coordinating entity during the three years preceding the start date of the project

PhasAGE Management Handbook

Publications

The evolution and polymorphism of mono-amino acid repeats in androgen receptor and their regulatory role in health and disease

Author(s): Attila Meszaros, Junaid Ahmed, Giorgio Russo, Peter Tompa, Tamas Lazar
Published in: Frontiers in Medicine, 2022, ISSN 2296-858X
Publisher: Frontiers
DOI: 10.3389/fmed.2022.1019803

DispHScan: A Multi-Sequence Web Tool for Predicting Protein Disorder as a Function of pH

Author(s): Carlos Pintado-Grima, Valentín Iglesias, Jaime Santos, Vladimir N Uversky, Salvador Ventura
Published in: Biomolecules, 2021, ISSN 2218-273X
Publisher: MDPI
DOI: 10.3390/biom11111596

Degron masking outlines degronons, co-degrading functional modules in the proteome

Author(s): Mainak Guharoy, Tamas Lazar, Mauricio Macossay-Castillo, Peter Tompa
Published in: Communications Biology, 2022, ISSN 2399-3642
Publisher: Nature
DOI: 10.1038/s42003-022-03391-z

Advances in Nucleotide Repeat Expansion Diseases: Transcription Gets in Phase

Author(s): Ana S. Figueiredo, Joana R. Loureiro, Sandra Macedo-Ribeiro, Isabel Silveira
Published in: Cells, 2023, ISSN 2073-4409
Publisher: MDPI
DOI: 10.3390/cells12060826

Cryo-EM structure of hnRNPDL-2 fibrils, a functional amyloid associated with limb-girdle muscular dystrophy D3

Author(s): Javier Garcia-Pardo, Andrea Bartolomé-Nafría, Antonio Chaves-Sanjuan, Marcos Gil-Garcia, Cristina Visentin, Martino Bolognesi, Stefano Ricagno, Salvador Ventura
Published in: Nature Communications, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-35854-0

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

Author(s): Alexander Miguel Monzon, Damiano Piovesan, Monika Fuxreiter
Published in: Biomolecules, 2022, ISSN 2218-273X
Publisher: MDPI
DOI: 10.3390/biom12010092

Databases for intrinsically disordered proteins

Author(s): Damiano Piovesan; Alexander Miguel Monzon; Federica Quaglia; Silvio C. E. Tosatto
Published in: Acta Crystallographica Section D, Issue 1, 2022, ISSN 0907-4449
Publisher: Blackwell Publishing Inc.
DOI: 10.1107/s2059798321012109

Computational methods to predict protein aggregation

Author(s): Susanna Navarro, Salvador Ventura
Published in: Current Opinion in Structural Biology, 2022, ISSN 1879-033X
Publisher: Elsevier
DOI: 10.1016/j.sbi.2022.102343

Biological colloids: Unique properties of membraneless organelles in the cell

Author(s): Anna Bratek-Skicki, Margot Van Nerom, Dominique Maes, Peter Tompa
Published in: Advances in Colloid and Interface Science, 2022, ISSN 1873-3727
Publisher: ELSEVIER
DOI: 10.1016/j.cis.2022.102777

CARs-DB: A Database of Cryptic Amyloidogenic Regions in Intrinsically Disordered Proteins

Author(s): Carlos Pintado-Grima; Oriol Bárcenas; Zoe Manglano-Artuñedo; Rita Vilaça; Sandra Macedo-Ribeiro; Irantzu Pallarès; Jaime Santos; Salvador Ventura
Published in: Frontiers in Molecular Biosciences, Issue 1, 2022, ISSN 2296-889X
Publisher: Frontiers
DOI: 10.3389/fmolb.2022.882160

SARS‐CoV‐2 variants preferentially emerge at intrinsically disordered protein sites helping immune evasion

Author(s): Federica Quaglia; Edoardo Salladini; Marco Carraro; Giovanni Minervini; Silvio C.E. Tosatto; Philippe Le Mercier
Published in: The FEBS Journal, Issue 1, 2022, ISSN 1742-464X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/febs.16379

In-Silico Analysis of pH-Dependent Liquid-Liquid Phase Separation in Intrinsically Disordered Proteins

Author(s): Carlos Pintado-Grima, Oriol Bárcenas, Salvador Ventura
Published in: Biomolecules, 2022, ISSN 2218-273X
Publisher: MDPI
DOI: 10.3390/biom12070974

A Review of Fifteen Years Developing Computational Tools to Study Protein Aggregation

Author(s): Carlos Pintado-Grima; Oriol Bárcenas; Andrea Bartolomé-Nafría; Marc Fornt-Suñé; Valentín Iglesias; Javier Garcia-Pardo; Salvador Ventura
Published in: Biophysica, Issue 1, 2023, ISSN 2673-4125
Publisher: MDPI
DOI: 10.3390/biophysica3010001

Decoding the role of coiled-coil motifs in human prion-like proteins

Author(s): Molood Behbahanipour, Javier García-Pardo, Salvador Ventura
Published in: Prion, 2021, ISSN 1933-690X
Publisher: Taylor & Francis
DOI: 10.1080/19336896.2021.1961569

F/YGG-motif is an intrinsically disordered nucleic-acid binding motif

Author(s): Joris Van Lindt, Tamas Lazar, Donya Pakravan , Manon Demulder, Attila Meszaros , Ludo Van Den Bosch, Dominique Maes, Peter Tompa
Published in: RNA Biology, 2022, ISSN 1555-8584
Publisher: Taylor and Francis
DOI: 10.1080/15476286.2022.2066336

The Repeating, Modular Architecture of the HtrA Proteases

Author(s): Matthew Merski, Sandra Macedo-Ribeiro, Rafal M. Wieczorek, Maria W. Górna
Published in: Biomolecules, 2022, ISSN 2218-273X
Publisher: MDPI
DOI: 10.3390/biom12060793

Intrinsic protein disorder uncouples affinity from binding specificity

Author(s): Tamas Lazar, Agnes Tantos, Peter Tompa, Eva Schad
Published in: Protein Science, 2022, ISSN 1469-896X
Publisher: Wiley
DOI: 10.1002/pro.4455

Exploring cryptic amyloidogenic regions in prion-like proteins from plants

Author(s): Carlos Pintado-Grima, Jaime Santos, Valentín Iglesias, Zoe Manglano-Artuñedo, Irantzu Pallarès, Salvador Ventura
Published in: Frontiers in Plant Science, 2023, ISSN 1664-462X
Publisher: Frontiers Media S. A.
DOI: 10.3389/fpls.2022.1060410

ECO: the Evidence and Conclusion Ontology, an update for 2022

Author(s): 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
Published in: Nucleic Acids Research, 2022, Page(s) D1515–D1521, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab1025

FuzDB: a new phase in understanding fuzzy interactions

Author(s): Andras Hatos, Alexander Miguel Monzon, Silvio C E Tosatto, Damiano Piovesan, Monika Fuxreiter
Published in: Nucleic Acids Research, 2022, Page(s) D509–D517, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab1060

A3D database: structure-based predictions of protein aggregation for the human proteome

Author(s): Aleksandra E Badaczewska-Dawid, Javier Garcia-Pardo, Aleksander Kuriata, Jordi Pujols, Salvador Ventura, Sebastian Kmiecik
Published in: Bioinformatics, 2022, Page(s) 3121–3123, ISSN 1367-4811
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btac215

DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation.

Author(s): Federica Quaglia; Federica Quaglia; Bálint Mészáros; Edoardo Salladini; András Hatos; Rita Pancsa; Lucía B. Chemes; Mátyás Pajkos; Tamas Lazar; Tamas Lazar; Samuel Peña-Díaz; Jaime Santos; Veronika Ács; Nazanin Farahi; Nazanin Farahi; Erzsébet Fichó; Maria Cristina Aspromonte; Claudio Bassot; Anastasia Chasapi; Norman E. Davey; Radoslav Davidovic; László Dobson; Arne Elofsson; Gábor
Published in: Nucleic Acids Research, Issue 1, 2021, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab1082

Development of Small Molecules Targeting α-Synuclein Aggregation: A Promising Strategy to Treat Parkinson’s Disease

Author(s): Samuel Peña-Díaz,Javier García-Pardo, Salvador Ventura
Published in: Pharmaceutics, 2023, ISSN 1999-4923
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/pharmaceutics15030839

A fish herpesvirus highlights functional diversities among Zα domains related to phase separation induction and A-to-Z conversion

Author(s): Mamadou Amadou Diallo; Sébastien Pirotte; Yunlong Hu; Léa Morvan; Krzysztof Rakus; Nicolás M Suárez; Lee PoTsang; Hisao Saneyoshi; Yan Xu; Andrew J Davison; Peter Tompa; Joel L Sussman; Alain Vanderplasschen
Published in: Nucleic Acids Research, Issue 1, 2023, Page(s) 806–830, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkac761

SGnn: A Web Server for the Prediction of Prion-Like Domains Recruitment to Stress Granules Upon Heat Stress

Author(s): Valentín Iglesias, Jaime Santos, Juan Santos-Suárez, Carlos Pintado-Grima, Salvador Ventura
Published in: Frontiers in Molecular Biosciences, 2021, ISSN 2296-889X
Publisher: Frontiers
DOI: 10.3389/fmolb.2021.718301

A Novel Tandem-Tag Purification Strategy for Challenging Disordered Proteins

Author(s): Attila Mészáros, Kevin Muwonge, Steven Janvier, Junaid Ahmed, Peter Tompa
Published in: Biomolecules, 2022, ISSN 2218-273X
Publisher: MDPI
DOI: 10.3390/biom12111566

A Robust Assay to Monitor Ataxin-3 Amyloid Fibril Assembly

Author(s): Francisco Figueiredo; Mónica Lopes-Marques; Bruno Almeida; Nena Matscheko; Pedro M. Martins; Alexandra Silva; Sandra Macedo-Ribeiro
Published in: Cells, Issue Volume 11; Issue 12; Pages: 1969, 2022, ISSN 2073-4409
Publisher: MDPI
DOI: 10.3390/cells11121969

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