Works by Via, Allegra

Results: 34

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

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_1, p. D268, doi. 10.1093/nar/gkq936

By:

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

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_1, p. D261, doi. 10.1093/nar/gkq1104

By:

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

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2010, v. 38, p. D167, doi. 10.1093/nar/gkp1016

By:

Gould, Cathryn M.;
Diella, Francesca;
Via, Allegra;
Puntervoll, Pål;
Gemünd, Christine;
Chabanis-Davidson, Sophie;
Michael, Sushama;
Sayadi, Ahmed;
Bryne, Jan Christian;
Chica, Claudia;
Seiler, Markus;
Davey, Norman E.;
Haslam, Niall;
Weatheritt, Robert J.;
Budd, Aidan;
Hughes, Tim;
Paś, Jakub;
Rychlewski, Leszek;
Travé, Gilles;
Aasland, Rein

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2008, v. 36, p. D240

By:

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

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W451, doi. 10.1093/nar/gkm296

By:

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

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W416, doi. 10.1093/nar/gkm228

By:

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

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2007, v. 35, p. d229, doi. 10.1093/nar/gkl922

By:

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

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2005, v. 33, n. suppl 2, p. w133, doi. 10.1093/nar/gki499

By:

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

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2003, v. 31, n. 13, p. 3625, doi. 10.1093/nar/gkg545

By:

Puntervoll, Pål;
Linding, Rune;
Gemünd, Christine;
Chabanis-Davidson, Sophie;
Mattingsdal, Morten;
Cameron, Scott;
Martin, David M. A.;
Ausiello, Gabriele;
Brannetti, Barbara;
Costantini, Anna;
Ferrè, Fabrizio;
Maselli, Vincenza;
Via, Allegra;
Cesareni, Gianni;
Diella, Francesca;
Superti-Furga, Giulio;
Wyrwicz, Lucjan;
Ramu, Chenna;
McGuigan, Caroline;
Gudavalli, Rambabu

Publication type:

Article

The Mastery Rubric for Bioinformatics: A tool to support design and evaluation of career-spanning education and training.

Published in:

PLoS ONE, 2019, v. 14, n. 11, p. 1, doi. 10.1371/journal.pone.0225256

By:

Tractenberg, Rochelle E.;
Lindvall, Jessica M.;
Attwood, Teresa K.;
Via, Allegra

Publication type:

Article

Seq2Struct: a resource for establishing sequence-structure links.

Published in:

Bioinformatics, 2005, v. 21, n. 4, p. 551, doi. 10.1093/bioinformatics/bti049

By:

Via, Allegra;
Zanzoni, Andreas;
Helmer-Citterich, Manuela

Publication type:

Article

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

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 2, p. 405, doi. 10.1093/bib/bbx112

By:

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

Publication type:

Article

Best practices in bioinformatics training for life scientists.

Published in:

Briefings in Bioinformatics, 2013, v. 14, n. 5, p. 528, doi. 10.1093/bib/bbt043

By:

Via, Allegra;
Blicher, Thomas;
Bongcam-Rudloff, Erik;
Brazas, Michelle D.;
Brooksbank, Cath;
Budd, Aidan;
De Las Rivas, Javier;
Dreyer, Jacqueline;
Fernandes, Pedro L.;
van Gelder, Celia;
Jacob, Joachim;
Jimenez, Rafael C.;
Loveland, Jane;
Moran, Federico;
Mulder, Nicola;
Nyrönen, Tommi;
Rother, Kristian;
Schneider, Maria Victoria;
Attwood, Teresa K.

Publication type:

Article

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

Published in:

Briefings in Bioinformatics, 2012, v. 13, n. 3, p. 383, doi. 10.1093/bib/bbr064

By:

Schneider, Maria V.;
Walter, Peter;
Blatter, Marie-Claude;
Watson, James;
Brazas, Michelle D.;
Rother, Kristian;
Budd, Aidan;
Via, Allegra;
van Gelder, Celia W. G.;
Jacob, Joachim;
Fernandes, Pedro;
Nyrönen, Tommi H.;
De Las Rivas, Javier;
Blicher, Thomas;
Jimenez, Rafael C.;
Loveland, Jane;
McDowall, Jennifer;
Jones, Phil;
Vaughan, Brendan W.;
Lopez, Rodrigo

Publication type:

Article

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

Published in:

Briefings in Bioinformatics, 2010, v. 11, n. 6, p. 544, doi. 10.1093/bib/bbq021

By:

Schneider, Maria Victoria;
Watson, James;
Attwood, Teresa;
Rother, Kristian;
Budd, Aidan;
McDowall, Jennifer;
Via, Allegra;
Fernandes, Pedro;
Nyronen, Tommy;
Blicher, Thomas;
Jones, Phil;
Blatter, Marie-Claude;
De Las Rivas, Javier;
Judge, David Phillip;
van der Gool, Wouter;
Brooksbank, Cath

Publication type:

Article

Molecular evolution of a gene cluster of serine proteases expressed in the Anopheles gambiae female reproductive tract.

Published in:

BMC Evolutionary Biology, 2011, v. 11, n. 1, p. 72, doi. 10.1186/1471-2148-11-72

By:

Mancini, Emiliano;
Tammaro, Federica;
Baldini, Francesco;
Via, Allegra;
Raimondo, Domenico;
George, Phillip;
Audisio, Paolo;
Sharakhov, Igor V.;
Tramontano, Anna;
Catteruccia, Flaminia;
Torre, Alessandra della

Publication type:

Article

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

Published in:

Bioinformatics, 2015, v. 31, n. 1, p. 140, doi. 10.1093/bioinformatics/btu601

By:

Corpas, Manuel;
Jimenez, Rafael C.;
Bongcam-Rudloff, Erik;
Budd, Aidan;
Brazas, Michelle D.;
Fernandes, Pedro L.;
Gaeta, Bruno;
van Gelder, Celia;
Korpelainen, Eija;
Lewitter, Fran;
McGrath, Annette;
MacLean, Daniel;
Palagi, Patricia M.;
Rother, Kristian;
Taylor, Jan;
Via, Allegra;
Watson, Mick;
Schneider, Maria Victoria;
Attwood, Teresa K.

Publication type:

Article

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

Published in:

Bioinformatics, 2013, v. 29, n. 14, p. 1821, doi. 10.1093/bioinformatics/btt289

By:

Lepore, Rosalba;
Tramontano, Anna;
Via, Allegra

Publication type:

Article

ELIXIR Europe on the Road to Sustainable Research Software.

Published in:

2019

By:

Kuzak, Mateusz;
Harrow, Jen;
Martinez, Paula Andrea;
Psomopoulos, Fotis E.;
Via, Allegra

Publication type:

Abstract

Characterization of the differences in the cyclopiazonic acid binding mode to mammalian and P. Falciparum Ca<sup>2+</sup> pumps: A computational study.

Published in:

Proteins, 2015, v. 83, n. 3, p. 564, doi. 10.1002/prot.24734

By:

Di Marino, Daniele;
D'Annessa, Ilda;
Coletta, Andrea;
Via, Allegra;
Tramontano, Anna

Publication type:

Article

Artemether resistance in vitro is linked to mutations in PfATP6 that also interact with mutations in PfMDR1 in travellers returning with Plasmodium falciparum infections.

Published in:

Malaria Journal, 2012, v. 11, n. 1, p. 131, doi. 10.1186/1475-2875-11-131

By:

Pillai, Dylan R.;
Lau, Rachel;
Khairnar, Krishna;
Lepore, Rosalba;
Via, Allegra;
Staines, Henry M.;
Krishna, Sanjeev

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-S2-S2

By:

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

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2007, v. 8, p. S24, doi. 10.1186/1471-2105-8-S1-S24

By:

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

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2005, v. 6, p. S5, doi. 10.1186/1471-2105-6-S4-S5

By:

Ausiello, Gabriele;
Via, Allegra;
Helmer-Citterich, Manuela

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2005, v. 6, p. S13, doi. 10.1186/1471-2105-6-S4-S13

By:

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

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2004, v. 5, p. 79, doi. 10.1186/1471-2105-5-79

By:

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

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2004, v. 5, p. 50, doi. 10.1186/1471-2105-5-50

By:

Via, Allegra;
Helmer-Citterich, Manuela

Publication type:

Article

Ten Simple Rules for Developing a Short Bioinformatics Training Course.

Published in:

2011

By:

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

Publication type:

Editorial

The Crystal Structure of <i>Giardia duodenalis</i> 14-3-3 in the Apo Form: When Protein Post-Translational Modifications Make the Difference.

Published in:

PLoS ONE, 2014, v. 9, n. 3, p. 1, doi. 10.1371/journal.pone.0092902

By:

Fiorillo, Annarita;
di Marino, Daniele;
Bertuccini, Lucia;
Via, Allegra;
Pozio, Edoardo;
Camerini, Serena;
Ilari, Andrea;
Lalle, Marco

Publication type:

Article

Exploiting Publicly Available Biological and Biochemical Information for the Discovery of Novel Short Linear Motifs.

Published in:

PLoS ONE, 2011, v. 6, n. 7, p. 1, doi. 10.1371/journal.pone.0022270

By:

Sayadi, Ahmed;
Briganti, Leonardo;
Tramontano, Anna;
Via, Allegra

Publication type:

Article

On the Mechanism of Chloroquine Resistance in Plasmodium falciparum.

Published in:

PLoS ONE, 2010, v. 5, n. 11, p. 1, doi. 10.1371/journal.pone.0014064

By:

Chinappi, Mauro;
Via, Allegra;
Marcatili, Paolo;
Tramontano, Anna

Publication type:

Article

Ten simple rules for making training materials FAIR.

Published in:

2020

By:

Garcia, Leyla;
Batut, Bérénice;
Burke, Melissa L.;
Kuzak, Mateusz;
Psomopoulos, Fotis;
Arcila, Ricardo;
Attwood, Teresa K.;
Beard, Niall;
Carvalho-Silva, Denise;
Dimopoulos, Alexandros C.;
del Angel, Victoria Dominguez;
Dumontier, Michel;
Gurwitz, Kim T.;
Krause, Roland;
McQuilton, Peter;
Le Pera, Loredana;
Morgan, Sarah L.;
Rauste, Päivi;
Via, Allegra;
Kahlem, Pascal

Publication type:

Editorial

A FAIRification roadmap for ELIXIR Software Management Plans.

Published in:

Research Ideas & Outcome Journal, 2022, p. 1, doi. 10.3897/rio.8.e94608

By:

Giraldo, Olga;
Alves, Renato;
Bampalikis, Dimitrios;
Fernandez, Jose M.;
del Pico, Eva Martin;
Psomopoulos, Fotis E.;
Via, Allegra;
Castro, Leyla Jael

Publication type:

Article

Molecular In-Depth on the Epidemiological Expansion of SARS-CoV-2 XBB.1.5.

Published in:

Microorganisms, 2023, v. 11, n. 4, p. 912, doi. 10.3390/microorganisms11040912

By:

Scarpa, Fabio;
Azzena, Ilenia;
Locci, Chiara;
Casu, Marco;
Fiori, Pier Luigi;
Ciccozzi, Alessandra;
Angeletti, Silvia;
Imperia, Elena;
Giovanetti, Marta;
Maruotti, Antonello;
Borsetti, Alessandra;
Cauda, Roberto;
Cassone, Antonio;
Via, Allegra;
Pascarella, Stefano;
Sanna, Daria;
Ciccozzi, Massimo

Publication type:

Article