Risultati finali
Collection of TRP datasets
Report on the state-of-the-art of TRP-related HMMs and TRP covariance analysis.Report on the function of new TRP families.
Report on the function of new TRP families
Report on examples of TRP evolution through internal duplication of coding sequence and repeat units recycled by evolution in globular structures.Report on examples of TRP evolution through internal duplication of coding sequence and repeat units recycled by evolution in globular structures
Report on mapping and analysis of exon boundaries on TRPs, comparison with their modularity, and TRP amino acid vs DNA sequence variability.Report on mapping and analysis of exon boundaries on TRPs comparison with their modularity and TRP amino acid vs DNA sequence variability
Symposia/Remote Symposia Period 2Symposia Period 2. Europe: 2 x All-Hands Meeting, 1 x Dissemination Training School, 1 x Final Dissemination meeting. Latin America: 2 x Annual Latin America Visit.
TRP function, localization and organism distribution enrichment analysis.TRP function localization and organism distribution enrichment analysis
Symposia/Remote Symposia Period 1Symposia Period 1 Europe 2 x AllHands Meeting 1 x Dissemination Training School Latin America 2 x Annual Latin America Visit
Report about TRP roles in PPI networks and interaction with RNA/DNA molecules and role of TRPs in host interactions with viruses and pathogens.Report about TRP roles in PPI networks and interaction with RNADNA molecules and role of TRPs in host interactions with viruses and pathogens
Report on TRP disorder, low-complexity, transmembrane domain overlap and examples of cooperative TRP folding.Report on TRP disorder lowcomplexity transmembrane domain overlap and examples of cooperative TRP folding
Report on TRP sequence and structural classification as well as sequence and structural clustering of the TRP universe.Cookbook for TRP annotation best-practices. Report about data format gold-standard, technical and implementation best-practices for TRP web resources.
Cookbook for TRP annotation bestpractices Report about data format goldstandard technical and implementation bestpractices for TRP web resources
Report on SLIMs in TRPs.Report on SLIMs in TRPs
Software for sequence- and structure-based pairwise TRP alignment.
Cross-link of generated TRP data into core data resources (e.g. InterPro) and related resources.Platform and metrics for TRP tools benchmarking, including consensus detection of sequence- and structure-based methods
Platform and metrics for TRP tools benchmarking, including consensus detection of sequence- and structure-based methods.
Deployment of TRP database APIs.Software for automatic TRP region and unit annotation
Software for the identification of homologous TRPs from sequence databases.
Integration of novel classification in TRP databases.
Curation of Pfam TRP-related HMMs.
Software for modeling TRP regions by homology
Pubblicazioni
Autori:
Lisanna Paladin; Mathieu Schaeffer; Pascale Gaudet; Monique Zahn-Zabal; Pierre-André Michel; Damiano Piovesan; Silvio C. E. Tosatto; Amos Marc Bairoch
Pubblicato in:
Bioinformatics, Numero 8, 2020, ISSN 1367-4803
Editore:
Oxford University Press
DOI:
10.1093/bioinformatics/btaa055
Autori:
Del Conte A.; Monzon A. M.; Clementel D.; Camagni G. F.; Minervini G.; Tosatto S. C. E.; Piovesan D.
Pubblicato in:
Bioinformatics, Numero 16, 2023, ISSN 1367-4803
Editore:
Oxford University Press
DOI:
10.1093/bioinformatics/btad260
Autori:
M. Leticia Ferrelli; Matías L. Pidre; Ruben García-Domínguez; Lucas N. Alberca; DMaría del Saz-Navarro; Carlos Santana-Molina; Damien P. Devos
Pubblicato in:
Journal of Structural Biology, Numero 8, 2023, ISSN 1047-8477
Editore:
Academic Press
DOI:
10.1016/j.jsb.2023.107987
Autori:
Martina Bevilacqua, Lisanna Paladin, Silvio C E Tosatto, Damiano Piovesan
Pubblicato in:
Bioinformatics, 2021, ISSN 1367-4803
Editore:
Oxford University Press
DOI:
10.1093/bioinformatics/btab764
Autori:
Matteo Delucchi, Elke Schaper, Oxana Sachenkova, Arne Elofsson and Maria Anisimova
Pubblicato in:
Genes, 2020, ISSN 2073-4425
Editore:
Multidisciplinary Digital Publishing Institute (MDPI)
DOI:
10.3390/genes11040407
Autori:
Gustavo Parisi; Nicolas Palopoli; Silvio C. E. Tosatto; María Silvina Fornasari; Peter Tompa
Pubblicato in:
Current Research in Structural Biology, Numero 8, 2021, ISSN 2665-928X
Editore:
Elsevier
DOI:
10.1016/j.crstbi.2021.06.002
Autori:
Ian Walsh, Dmytro Fishman, Dario Garcia-Gasulla, Tiina Titma, Gianluca Pollastri, ELIXIR Machine Learning Focus Group, Jennifer Harrow, Fotis E. Psomopoulos & Silvio C. E. Tosatto
Pubblicato in:
Nature Methods, 2021, ISSN 1548-7091
Editore:
Nature Publishing Group
DOI:
10.1038/s41592-021-01205-4
Autori:
Alexander Miguel Monzon; Marco Necci; Federica Quaglia; Ian Walsh; Giuseppe Zanotti; Damiano Piovesan; Silvio C. E. Tosatto
Pubblicato in:
International Journal of Molecular Sciences, Numero 8, 2020, ISSN 1422-0067
Editore:
Multidisciplinary Digital Publishing Institute (MDPI)
DOI:
10.1101/2020.02.17.952028
Autori:
Damiano Clementel, Alessio Del Conte, Alexander Miguel Monzon, Giorgia F Camagni, Giovanni Minervini, Damiano Piovesan, Silvio C E Tosatto
Pubblicato in:
Nucleic Acids Research, 2022, ISSN 0305-1048
Editore:
Oxford University Press
DOI:
10.1093/nar/gkac365
Autori:
Manuel, Bezerra-Brandao; Ronaldo Romario, Tunque Cahui; Layla, Hirsh
Pubblicato in:
Journal of Structural Biology, Numero 6, 2023, ISSN 1047-8477
Editore:
Academic Press
DOI:
10.1016/j.jsb.2023.108033
Autori:
Piovesan, Damiano; Zago, Davide; Joshi, Parnal; Kaluza, M. Clara De Paolis; Monzon, Alexander Miguel; Reade, Walter; Friedberg, Iddo; Radivojac, Predrag; Tosatto, Silvio C. E.
Pubblicato in:
Bioinformatics Advances, Numero 16, 2024, ISSN 2635-0041
Editore:
Oxford University Press
DOI:
10.1093/bioadv/vbae043
Autori:
Erdozain Bagolin, Sofía Agostina; Barrionuevo, Emilia Mercedes; Ripoll, Lucas; Mier, Pablo; Andrade Navarro, Miguel A.
Pubblicato in:
Journal of Structural Biology, Numero 11, 2023, ISSN 1047-8477
Editore:
Academic Press
DOI:
10.1016/j.jsb.2023.107962
Autori:
Vladimir Perovic; Jeremy Y Leclercq; Neven Sumonja; Francois Richard; Francois Richard; Nevena Veljkovic; Andrey V. Kajava
Pubblicato in:
Bioinformatics, Numero 8, 2020, ISSN 1367-4803
Editore:
Oxford University Press
DOI:
10.1093/bioinformatics/btaa121
Autori:
Lisanna Paladin; Martina Bevilacqua; Sara Errigo; Damiano Piovesan; Ivan Mičetić; Marco Necci; Alexander Miguel Monzon; María Laura Fabre; José Luis López; Juliet F. Nilsson; Javier Rios; Pablo Lorenzano Menna; Maia Diana Eliana Cabrera; Martin Gonzalez Buitron; Mariane Gonçalves Kulik; Sebastian Fernandez-Alberti; María Silvina Fornasari; Gustavo Parisi; Antonio Lagares; Layla Hirsh; Migue
Pubblicato in:
Nucleic Acids Research, Numero 4, 2021, ISSN 0305-1048
Editore:
Oxford University Press
DOI:
10.1093/nar/gkaa1097
Autori:
Del Conte A.; Mehdiabadi M.; Bouhraoua A.; Monzon A. M.; Tosatto S. C. E.; Piovesan D.
Pubblicato in:
Proteins: Structure, Function and Bioinformatics, Numero 15, 2023, ISSN 0887-3585
Editore:
Wiley-Liss Inc
DOI:
10.1002/prot.26582
Autori:
Claudio Bassot, Arne Elofsson
Pubblicato in:
PLOS Computational Biology, 2021, ISSN 1553-734X
Editore:
Public Library of Science
DOI:
10.1371/journal.pcbi.1008798
Autori:
Agustín Ormazábal; Matías Sebastián Carletti; Tadeo Enrique Saldaño; Martín Gonzalez-Buitron; Julia Marchetti; Nicolas Palopoli; Alex Bateman
Pubblicato in:
PLoS ONE, Numero 11, 2023, ISSN 1932-6203
Editore:
Public Library of Science
DOI:
10.1371/journal.pone.0290890
Autori:
Lisanna Paladin, Marco Necci, Damiano Piovesan, Pablo Mier, Miguel A.Andrade-Navarro, Silvio C.E.Tosatto
Pubblicato in:
Journal of Structural Biology, 2022, ISSN 1047-8477
Editore:
Academic Press
DOI:
10.1016/j.jsb.2020.107608
Autori:
Max A. Verbiest; Oxana Lundström; Feifei Xia; Michael Baudis; Tugce Bilgin Sonay; Maria Anisimova
Pubblicato in:
Scientific Reports, Numero 18, 2024, ISSN 2045-2322
Editore:
Nature Publishing Group
DOI:
10.1101/2023.11.29.569189
Autori:
Max A. Verbiest, Matteo Delucchi, Tugce Bilgin Sonay and Maria Anisimova
Pubblicato in:
Frontiers in Bioinformatics, 2021, ISSN 2673-7647
Editore:
Frontiers Media
DOI:
10.3389/fbinf.2021.685844
Autori:
András Hatos, Federica Quaglia, Damiano Piovesan, Silvio C E Tosatto
Pubblicato in:
Database, 2021, ISSN 1758-0463
Editore:
Oxford University Press
DOI:
10.1093/database/baab019
Autori:
Pablo Mier, Miguel A. Andrade-Navarro
Pubblicato in:
BMC Ecology and Evolution, 2020, ISSN 2730-7182
Editore:
Springer Nature
DOI:
10.1186/s12862-020-01626-3
Autori:
Mohamed Kamel, Kristina Kastano, Pablo Mier, Miguel A. Andrade
Pubblicato in:
Journal of Molecular Biology, 2021, ISSN 0022-2836
Editore:
Academic Press
DOI:
10.1016/j.jmb.2021.166895
Autori:
Hamidreza Ghafouri; Tamas Lazar; Alessio Del Conte; Luiggi G Tenorio Ku; 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
Pubblicato in:
Nucleic Acids Research, Numero 16, 2024, ISSN 0305-1048
Editore:
Oxford University Press
DOI:
10.1093/nar/gkad947
Autori:
Matteo Delucchi; Paulina Näf; Spencer Bliven; Maria Anisimova
Pubblicato in:
Frontiers in Bioinformatics, Numero 5, 2021, ISSN 2673-7647
Editore:
Frontiers Media
DOI:
10.21256/zhaw-22764
Autori:
Jaina Mistry; Sara Chuguransky; Lowri Williams; Matloob Qureshi; Gustavo A. Salazar; Erik L. L. Sonnhammer; Silvio C. E. Tosatto; Lisanna Paladin; Shriya Raj; Lorna Richardson; Robert D. Finn; Alex Bateman
Pubblicato in:
Nucleic Acids Research, Numero 5, 2020, ISSN 0305-1048
Editore:
Oxford University Press
DOI:
10.1093/nar/gkaa913
Autori:
Monzon, Alexander Miguel; Arrías, Paula Nazarena; Elofsson, Arne; Mier, Pablo; Andrade-Navarro, Miguel A; Bevilacqua, Martina; Clementel, Damiano; Bateman, Alex; Hirsh, Layla; Fornasari, Maria Silvina; Parisi, Gustavo; Piovesan, Damiano; Kajava, Andrey V; Tosatto, Silvio C E
Pubblicato in:
Journal of Structural Biology, Numero 5, 2023, ISSN 1047-8477
Editore:
Academic Press
DOI:
10.1016/j.jsb.2023.108023
Autori:
Federica Quaglia, Rama Balakrishnan, Susan M Bello, Nicole Vasilevsky
Pubblicato in:
Database, 2022, ISSN 1758-0463
Editore:
Oxford University Press
DOI:
10.1093/database/baac027
Autori:
Maria Cristina Aspromonte; Maria Victoria Nugnes; Federica Quaglia; Adel Bouharoua; 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;
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Nucleic Acids Research, Numero 18, 2024, ISSN 0305-1048
Editore:
Oxford University Press
DOI:
10.1093/nar/gkad928
Autori:
Patryk Jarnot; Joanna Ziemska-Legiecka; László Dobson; Matthew Merski; Pablo Mier; Miguel A. Andrade-Navarro; John M. Hancock; Zsuzsanna Dosztányi; Lisanna Paladin; Marco Necci; Damiano Piovesan; Silvio C. E. Tosatto; Vasilis J. Promponas; Marcin Grynberg; Aleksandra Gruca
Pubblicato in:
Nucleic Acids Research, Numero 7, 2020, ISSN 0305-1048
Editore:
Oxford University Press
DOI:
10.1093/nar/gkaa339
Autori:
Max Verbiest; Mikhail Maksimov; Ye Jin; Maria Anisimova; Melissa Gymrek; Tugce Bilgin Sonay
Pubblicato in:
Journal of Evolutionary Biology, Numero 18, 2023, ISSN 1010-061X
Editore:
Blackwell Publishing Inc.
DOI:
10.1111/jeb.14106
Autori:
Federica Quaglia
Pubblicato in:
Abstract booklet of the 14th Annual Biocuration Conference (virtual), including invited speakers talks and poster session presentations, 2021
Editore:
Zenodo
DOI:
10.5281/zenodo.5570276
Autori:
Nahuel Escobedo, Ronaldo Romario Tunque Cahui, Gastón Caruso, Emilio García Ríos, Layla Hirsh, Alexander Miguel Monzon, Gustavo Parisi, VNicolas Palopoli
Pubblicato in:
bioRxiv, 2022, ISSN 2692-8205
Editore:
bioRxiv
DOI:
10.1101/2022.02.15.480082
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