Allegra Via

Publication Activity (10 Years)

Years Active: 2003-2023
Publications (10 Years): 10

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Briefings Bioinform.

PLoS Comput. Biol.

Publications

Olga L. Giraldo, Renato Alves, Dimitrios Bampalikis, José M. Fernández, Eva Martin Del Pico, Fotis E. Psomopoulos, Nelson Quiñones, Dhwani Solanki, Allegra Via, Leyla Jael Castro
A metadata analysis for machine-actionable Software Management Plans. SWAT4HCLS (2023)
Leyla Jael Castro, Dietrich Rebholz-Schuhmann, Nelson Quiñones, Dimitrios Bampalikis, Olga L. Giraldo, Eva Martin Del Pico, Allegra Via, Dhwani Solanki, Lukas Geist, Fotis E. Psomopoulos, Renato Alves, José María Fernández González
A metadata schema for machine-actionable Software Management Plans. DaMaLOS (2023)
Kim T. Gurwitz, Prakash Singh Gaur, Louisa J. Bellis, Lee D. Larcombe, Eva Alloza, Balint Laszlo Balint, Alexander Botzki, Jure Dimec, Victoria Dominguez Del Angel, Pedro L. Fernandes, Eija Korpelainen, Roland Krause, Mateusz Kuzak, Loredana Le Pera, Brane Leskosek, Jessica M. Lindvall, Diana Marek, Paula Andrea Martínez, Tuur Muyldermans, Ståle Nygård, Patricia M. Palagi, Hedi Peterson, Fotis E. Psomopoulos, Vojtech Spiwok, Celia W. G. van Gelder, Allegra Via, Marko Vidak, Daniel Wibberg, Sarah L. Morgan, Gabriella Rustici
A framework to assess the quality and impact of bioinformatics training across ELIXIR. PLoS Comput. Biol. 16 (7) (2020)
Leyla J. García, Michelle Barker, Neil P. Chue Hong, Fotis E. Psomopoulos, Jennifer L. Harrow, Daniel S. Katz, Mateusz Kuzak, Paula Andrea Martínez, Allegra Via
Software as a first-class citizen in research. DaMaLOS (2020)
Leyla J. García, Bérénice Batut, Melissa L. Burke, Mateusz Kuzak, Fotis E. Psomopoulos, Ricardo Arcila, Teresa K. Attwood, Niall Beard, Denise Carvalho-Silva, Alexandros C. Dimopoulos, Victoria Dominguez Del Angel, Michel Dumontier, Kim T. Gurwitz, Roland Krause, Peter McQuilton, Loredana Le Pera, Sarah L. Morgan, Päivi Rauste, Allegra Via, Pascal Kahlem, Gabriella Rustici, Celia W. G. van Gelder, Patricia M. Palagi
Ten simple rules for making training materials FAIR. PLoS Comput. Biol. 16 (5) (2020)
Allegra Via, Teresa K. Attwood, Pedro L. Fernandes, Sarah L. Morgan, Maria Victoria Schneider, Patricia M. Palagi, Gabriella Rustici, Rochelle E. Tractenberg
A new pan-European Train-the-Trainer programme for bioinformatics: pilot results on feasibility, utility and sustainability of learning. Briefings Bioinform. 20 (2) (2019)
Mateusz Kuzak, Jen Harrow, Rafael C. Jimenez, Paula Andrea Martínez, Fotis E. Psomopoulos, Radka Svobodová Vareková, Allegra Via
Lesson Development for Open Source Software Best Practices Adoption. eScience (2018)
Rafael C. Jiménez, Mateusz Kuzak, Monther Alhamdoosh, Michelle Barker, Bérénice Batut, Mikael Borg, Salvador Capella-Gutiérrez, Neil P. Chue Hong, Martin Cook, Manuel Corpas, Madison Flannery, Leyla J. García, Josep Lluis Gelpí, Simon Gladman, Carole A. Goble, Montserrat González Ferreiro, Alejandra N. González-Beltrán, Philippa C. Griffin, Björn A. Grüning, Jonas Hagberg, Petr Holub, Rob W. W. Hooft, Jon C. Ison, Daniel S. Katz, Brane Leskosek, Federico López-Gómez, Luis J. Oliveira, David Mellor, Rowland Mosbergen, Nicola J. Mulder, Yasset Pérez-Riverol, Robert Pergl, Horst Pichler, Bernard J. Pope, Ferran Sanz, Maria Victoria Schneider, Victoria Stodden, Radoslaw Suchecki, Radka Svobodová Vareková, Harry-Anton Talvik, Ilian T. Todorov, Andrew E. Treloar, Sonika Tyagi, Maarten van Gompel, Daniel Vaughan, Allegra Via, Xiaochuan Wang, Nathan S. Watson-Haigh, Steve Crouch
Four simple recommendations to encourage best practices in research software. F1000Research 6 (2017)
Claudio Carta, Marco Roos, Annika Jacobsen, Rajaram Kaliyaperumal, Mark Thompson, Mark D. Wilkinson, Ronald Cornet, Andra Waagmeester, David van Enckevort, Mascha Jansen, Luana Licata, Allegra Via, Domenica Taruscio
The FAIRification of Data and the Potential of FAIR Resources Demonstrated, in Practice, at the Rome Bring Your Own Data Workshop. SWAT4LS (2017)
Jon C. Ison, Kristoffer Rapacki, Hervé Ménager, Matús Kalas, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan M. Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn A. Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael C. Jimenez, Nick S. Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Micetic, Rune Møllegaard Friborg, Sébastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter M. Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vareková, Silvio C. E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen E. Parkinson, Peter Løngreen, Søren Brunak
Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. 44 (Database-Issue) (2016)
Manuel Corpas, Rafael C. Jimenez, Erik Bongcam-Rudloff, Aidan Budd, Michelle D. Brazas, Pedro L. Fernandes, Bruno A. Gaëta, Celia W. G. van Gelder, Eija Korpelainen, Fran Lewitter, Annette McGrath, Daniel MacLean, Patricia M. Palagi, Kristian Rother, Jan Taylor, Allegra Via, Mick Watson, Maria Victoria Schneider, Teresa K. Attwood
The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers. Bioinform. 31 (1) (2015)
Rafael C. Jimenez, Juan P. Albar, Jong Bhak, Marie-Claude Blatter, Thomas Blicher, Michelle D. Brazas, Catherine Brooksbank, Aidan Budd, Javier De Las Rivas, Jacqueline Dreyer, Marc A. van Driel, Michael J. Dunn, Pedro L. Fernandes, Celia W. G. van Gelder, Henning Hermjakob, Vassilios Ioannidis, David Phillip Judge, Pascal Kahlem, Eija Korpelainen, Hans-Joachim Kraus, Jane E. Loveland, Christine Mayer, Jennifer McDowall, Federico Morán, Nicola J. Mulder, Tommi H. Nyrönen, Kristian Rother, Gustavo A. Salazar, Reinhard Schneider, Allegra Via, Jose M. Villaveces, Ping Yu, Maria Victoria Schneider, Teresa K. Attwood, Manuel Corpas
iAnn: an event sharing platform for the life sciences. Bioinform. 29 (15) (2013)
Allegra Via, Thomas Blicher, Erik Bongcam-Rudloff, Michelle D. Brazas, Catherine Brooksbank, Aidan Budd, Javier De Las Rivas, Jacqueline Dreyer, Pedro L. Fernandes, Celia W. G. van Gelder, Joachim Jacob, Rafael C. Jimenez, Jane E. Loveland, Federico Morán, Nicola J. Mulder, Tommi H. Nyrönen, Kristian Rother, Maria Victoria Schneider, Teresa K. Attwood
Best practices in bioinformatics training for life scientists. Briefings Bioinform. 14 (5) (2013)
Rosalba Lepore, Anna Tramontano, Allegra Via
TiPs: a database of therapeutic targets in pathogens and associated tools. Bioinform. 29 (14) (2013)
Holger Dinkel, Sushama Michael, Robert J. Weatheritt, Norman E. Davey, Kim Van Roey, Brigitte Altenberg, Grischa Toedt, Bora Uyar, Markus Seiler, Aidan Budd, Lisa Jödicke, Marcel A. Dammert, Christian Schroeter, Maria Hammer, Tobias Schmidt, Peter Jehl, Caroline McGuigan, Magdalena Dymecka, Claudia Chica, Katja Luck, Allegra Via, Andrew Chatr-aryamontri, Niall J. Haslam, Gleb Grebnev, Richard J. Edwards, Michel O. Steinmetz, Heike Meiselbach, Francesca Diella, Toby J. Gibson
ELM - the database of eukaryotic linear motifs. Nucleic Acids Res. 40 (Database-Issue) (2012)
Maria Victoria Schneider, Peter Walter, Marie-Claude Blatter, James Watson, Michelle D. Brazas, Kristian Rother, Aidan Budd, Allegra Via, Celia W. G. van Gelder, Joachim Jacob, Pedro L. Fernandes, Tommi H. Nyrönen, Javier De Las Rivas, Thomas Blicher, Rafael C. Jimenez, Jane E. Loveland, Jennifer McDowall, Philip Jones, Brendan W. Vaughan, Rodrigo Lopez, Teresa K. Attwood, Catherine Brooksbank
Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers. Briefings Bioinform. 13 (3) (2012)
Allegra Via, Javier De Las Rivas, Teresa K. Attwood, David Landsman, Michelle D. Brazas, Jack A. M. Leunissen, Anna Tramontano, Maria Victoria Schneider
Ten Simple Rules for Developing a Short Bioinformatics Training Course. PLoS Comput. Biol. 7 (10) (2011)
Rosalba Lepore, Silvia Simeoni, Domenico Raimondo, Antonia Caroli, Anna Tramontano, Allegra Via
Identification of the Schistosoma mansoni Molecular Target for the Antimalarial Drug Artemether. J. Chem. Inf. Model. 51 (11) (2011)
Holger Dinkel, Claudia Chica, Allegra Via, Cathryn M. Gould, Lars Juhl Jensen, Toby J. Gibson, Francesca Diella
Phospho.ELM: a database of phosphorylation sites - update 2011. Nucleic Acids Res. 39 (Database-Issue) (2011)
Andreas Zanzoni, Daniel Carbajo, Francesca Diella, Pier Federico Gherardini, Anna Tramontano, Manuela Helmer-Citterich, Allegra Via
Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites. Nucleic Acids Res. 39 (Database-Issue) (2011)
Cathryn M. Gould, Francesca Diella, Allegra Via, Pål Puntervoll, Christine Gemünd, Sophie Chabanis-Davidson, Sushama Michael, Ahmed Sayadi, Jan Christian Bryne, Claudia Chica, Markus Seiler, Norman E. Davey, Niall J. Haslam, Robert J. Weatheritt, Aidan Budd, Tim Hughes, Jakub Pas, Leszek Rychlewski, Gilles Travé, Rein Aasland, Manuela Helmer-Citterich, Rune Linding, Toby J. Gibson
ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Res. 38 (Database-Issue) (2010)
Maria Victoria Schneider, James Watson, Teresa K. Attwood, Kristian Rother, Aidan Budd, Jennifer McDowall, Allegra Via, Pedro L. Fernandes, Tommi H. Nyrönen, Thomas Blicher, Philip Jones, Marie-Claude Blatter, Javier De Las Rivas, David Phillip Judge, Wouter van der Gool, Catherine Brooksbank
Bioinformatics training: a review of challenges, actions and support requirements. Briefings Bioinform. 11 (6) (2010)
Allegra Via, Cathryn M. Gould, Christine Gemünd, Toby J. Gibson, Manuela Helmer-Citterich
A structure filter for the Eukaryotic Linear Motif Resource. BMC Bioinform. 10 (2009)
Francesca Diella, Cathryn M. Gould, Claudia Chica, Allegra Via, Toby J. Gibson
Phospho.ELM: a database of phosphorylation sites - update 2008. Nucleic Acids Res. 36 (Database-Issue) (2008)
Gabriele Ausiello, Pier Federico Gherardini, Paolo Marcatili, Anna Tramontano, Allegra Via, Manuela Helmer-Citterich
FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures. BMC Bioinform. 9 (S-2) (2008)
Allegra Via, Daniele Peluso, Pier Federico Gherardini, Emanuele de Rinaldis, Teresa Colombo, Gabriele Ausiello, Manuela Helmer-Citterich
3dLOGO: a web server for the identification, analysis and use of conserved protein substructures. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Andreas Zanzoni, Gabriele Ausiello, Allegra Via, Pier Federico Gherardini, Manuela Helmer-Citterich
Phospho3D: a database of three-dimensional structures of protein phosphorylation sites. Nucleic Acids Res. 35 (Database-Issue) (2007)
Gabriele Ausiello, Daniele Peluso, Allegra Via, Manuela Helmer-Citterich
Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites. BMC Bioinform. 8 (S-1) (2007)
Enrico Ferraro, Daniele Peluso, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich
SH3-Hunter: discovery of SH3 domain interaction sites in proteins. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Allegra Via, Pier Federico Gherardini, Enrico Ferraro, Gabriele Ausiello, Gianpaolo Scalia Tomba, Manuela Helmer-Citterich
False occurrences of functional motifs in protein sequences highlight evolutionary constraints. BMC Bioinform. 8 (2007)
Enrico Ferraro, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich
A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity. Bioinform. 22 (19) (2006)
Gabriele Ausiello, Andreas Zanzoni, Daniele Peluso, Allegra Via, Manuela Helmer-Citterich
pdbFun: mass selection and fast comparison of annotated PDB residues. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Enrico Ferraro, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich
A neural strategy for the inference of SH3 domain-peptide interaction specificity. BMC Bioinform. 6 (S-4) (2005)
Allegra Via, Andreas Zanzoni, Manuela Helmer-Citterich
Seq2Struct: a resource for establishing sequence-structure links. Bioinform. 21 (4) (2005)
Gabriele Ausiello, Allegra Via, Manuela Helmer-Citterich
Query3d: a new method for high-throughput analysis of functional residues in protein structures. BMC Bioinform. 6 (S-4) (2005)
Allegra Via, Manuela Helmer-Citterich
A structural study for the optimisation of functional motifs encoded in protein sequences. BMC Bioinform. 5 (2004)
Francesca Diella, Scott Cameron, Christine Gemünd, Rune Linding, Allegra Via, Bernhard Küster, Thomas Sicheritz-Pontén, Nikolaj Blom, Toby J. Gibson
Phospho.ELM: A database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinform. 5 (2004)
Pål Puntervoll, Rune Linding, Christine Gemünd, Sophie Chabanis-Davidson, Morten Mattingsdal, Scott Cameron, David M. A. Martin, Gabriele Ausiello, Barbara Brannetti, Anna Costantini, Fabrizio Ferrè, Vincenza Maselli, Allegra Via, Gianni Cesareni, Francesca Diella, Giulio Superti-Furga, Lucjan Stanislaw Wyrwicz, Chenna Ramu, Caroline McGuigan, Rambabu Gudavalli, Ivica Letunic, Peer Bork, Leszek Rychlewski, Bernhard Küster, Manuela Helmer-Citterich, William N. Hunter, Rein Aasland, Toby J. Gibson
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res. 31 (13) (2003)