Allegra Via

According to our database, Allegra Via authored at least 38 papers between 2003 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

A metadata analysis for machine-actionable Software Management Plans.

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

Proceedings of the 14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2023), 2023

A metadata schema for machine-actionable Software Management Plans.

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

Proceedings of the 3rd Workshop on Metadata and Research (objects) Management for Linked Open Science, 2023

2020

A framework to assess the quality and impact of bioinformatics training across ELIXIR.

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

PLoS Comput. Biol., 2020

Ten simple rules for making training materials FAIR.

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

PLoS Comput. Biol., 2020

Software as a first-class citizen in research.

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

Proceedings of the DaMaLOS, 2020

2019

A new pan-European Train-the-Trainer programme for bioinformatics: pilot results on feasibility, utility and sustainability of learning.

Allegra Via, Teresa K. Attwood, Pedro L. Fernandes, Sarah L. Morgan, Maria Victoria Schneider, Patricia M. Palagi, Gabriella Rustici, Rochelle E. Tractenberg

Briefings Bioinform., 2019

2018

Lesson Development for Open Source Software Best Practices Adoption.

Mateusz Kuzak, Jen Harrow, Rafael C. Jiménez, Paula Andrea Martínez, Fotis E. Psomopoulos, Radka Svobodová Vareková, Allegra Via

Proceedings of the 14th IEEE International Conference on e-Science, 2018

2017

Four simple recommendations to encourage best practices in research software.

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 L. 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

F1000Research, 2017

The FAIRification of Data and the Potential of FAIR Resources Demonstrated, in Practice, at the Rome Bring Your Own Data Workshop.

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

Proceedings of the 10th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4LS 2017), 2017

2016

Tools and data services registry: a community effort to document bioinformatics resources.

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. Jiménez, 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

Nucleic Acids Res., 2016

2015

The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers.

Manuel Corpas, Rafael C. Jiménez, 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

Bioinform., 2015

2013

TiPs: a database of therapeutic targets in pathogens and associated tools.

Rosalba Lepore, Anna Tramontano, Allegra Via

Bioinform., 2013

iAnn: an event sharing platform for the life sciences.

Rafael C. Jiménez, 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

Bioinform., 2013

Best practices in bioinformatics training for life scientists.

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. Jiménez, Jane E. Loveland, Federico Morán, Nicola J. Mulder, Tommi H. Nyrönen, Kristian Rother, Maria Victoria Schneider, Teresa K. Attwood

Briefings Bioinform., 2013

2012

ELM - the database of eukaryotic linear motifs.

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

Nucleic Acids Res., 2012

Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers.

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. Jiménez, Jane E. Loveland, Jennifer McDowall, Philip Jones, Brendan W. Vaughan, Rodrigo Lopez, Teresa K. Attwood, Catherine Brooksbank

Briefings Bioinform., 2012

2011

Ten Simple Rules for Developing a Short Bioinformatics Training Course.

Allegra Via, Javier De Las Rivas, Teresa K. Attwood, David Landsman, Michelle D. Brazas, Jack A. M. Leunissen, Anna Tramontano, Maria Victoria Schneider

PLoS Comput. Biol., 2011

Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites.

Andreas Zanzoni, Daniel Carbajo, Francesca Diella, Pier Federico Gherardini, Anna Tramontano, Manuela Helmer-Citterich, Allegra Via

Nucleic Acids Res., 2011

Phospho.ELM: a database of phosphorylation sites - update 2011.

Holger Dinkel, Claudia Chica, Allegra Via, Cathryn M. Gould, Lars Juhl Jensen, Toby J. Gibson, Francesca Diella

Nucleic Acids Res., 2011

Identification of the Schistosoma mansoni Molecular Target for the Antimalarial Drug Artemether.

Rosalba Lepore, Silvia Simeoni, Domenico Raimondo, Antonia Caroli, Anna Tramontano, Allegra Via

J. Chem. Inf. Model., 2011

2010

ELM: the status of the 2010 eukaryotic linear motif resource.

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

Nucleic Acids Res., 2010

Bioinformatics training: a review of challenges, actions and support requirements.

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

Briefings Bioinform., 2010

2009

A structure filter for the Eukaryotic Linear Motif Resource.

Allegra Via, Cathryn M. Gould, Christine Gemünd, Toby J. Gibson, Manuela Helmer-Citterich

BMC Bioinform., 2009

2008

Phospho.ELM: a database of phosphorylation sites - update 2008.

Francesca Diella, Cathryn M. Gould, Claudia Chica, Allegra Via, Toby J. Gibson

Nucleic Acids Res., 2008

FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures.

Gabriele Ausiello, Pier Federico Gherardini, Paolo Marcatili, Anna Tramontano, Allegra Via, Manuela Helmer-Citterich

BMC Bioinform., 2008

2007

Phospho3D: a database of three-dimensional structures of protein phosphorylation sites.

Andreas Zanzoni, Gabriele Ausiello, Allegra Via, Pier Federico Gherardini, Manuela Helmer-Citterich

Nucleic Acids Res., 2007

3dLOGO: a web server for the identification, analysis and use of conserved protein substructures.

Allegra Via, Daniele Peluso, Pier Federico Gherardini, Emanuele de Rinaldis, Teresa Colombo, Gabriele Ausiello, Manuela Helmer-Citterich

Nucleic Acids Res., 2007

SH3-Hunter: discovery of SH3 domain interaction sites in proteins.

Enrico Ferraro, Daniele Peluso, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich

Nucleic Acids Res., 2007

False occurrences of functional motifs in protein sequences highlight evolutionary constraints.

Allegra Via, Pier Federico Gherardini, Enrico Ferraro, Gabriele Ausiello, Gianpaolo Scalia Tomba, Manuela Helmer-Citterich

BMC Bioinform., 2007

Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites.

Gabriele Ausiello, Daniele Peluso, Allegra Via, Manuela Helmer-Citterich

BMC Bioinform., 2007

2006

A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity.

Enrico Ferraro, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich

Bioinform., 2006

2005

pdbFun: mass selection and fast comparison of annotated PDB residues.

Gabriele Ausiello, Andreas Zanzoni, Daniele Peluso, Allegra Via, Manuela Helmer-Citterich

Nucleic Acids Res., 2005

A neural strategy for the inference of SH3 domain-peptide interaction specificity.

Enrico Ferraro, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich

BMC Bioinform., 2005

Query3d: a new method for high-throughput analysis of functional residues in protein structures.

Gabriele Ausiello, Allegra Via, Manuela Helmer-Citterich

BMC Bioinform., 2005

Seq2Struct: a resource for establishing sequence-structure links.

Allegra Via, Andreas Zanzoni, Manuela Helmer-Citterich

Bioinform., 2005

2004

A structural study for the optimisation of functional motifs encoded in protein sequences.

Allegra Via, Manuela Helmer-Citterich

BMC Bioinform., 2004

Phospho.ELM: A database of experimentally verified phosphorylation sites in eukaryotic proteins.

Francesca Diella, Scott Cameron, Christine Gemünd, Rune Linding, Allegra Via, Bernhard Küster, Thomas Sicheritz-Pontén, Nikolaj Blom, Toby J. Gibson

BMC Bioinform., 2004

2003

ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins.

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

Nucleic Acids Res., 2003