A. Via

发表

SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family.

M. Helmer-Citterich, B. Brannetti, G. Cesareni, 2000, Journal of molecular biology.

Protein Structural Motifs : Identification , Annotation and Use in Function Prediction Allegra Via

A. Tramontano, A. Via, 2011 .

Three-dimensional view of the surface motif associated with the P-loop structure: cis and trans cases of convergent evolution.

A Valencia, A. Valencia, M. Helmer-Citterich, 2000, Journal of molecular biology.

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

Cathryn M. Gould, T. Gibson, L. Jensen, 2010, Nucleic acids research.

Protein surface similarities: a survey of methods to describe and compare protein surfaces

F. Ferrè, M. Helmer-Citterich, B. Brannetti, 2000, Cellular and Molecular Life Sciences CMLS.

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

A. Tramontano, D. Raimondo, Francesco Baldini, 2011, BMC Evolutionary Biology.

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

A. Via, S. Krishna, R. Lepore, 2012, Malaria Journal.

gkm 228 3 dLOGO : a web server for the identification , analysis and use of conserved protein substructures

M. Helmer-Citterich, G. Ausiello, T. Colombo, 2007 .

On the Mechanism of Chloroquine Resistance in Plasmodium falciparum

A. Tramontano, M. Chinappi, P. Marcatili, 2010, PloS one.

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

A. Tramontano, A. Via, A. Sayadi, 2011, PloS one.

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

M. Helmer-Citterich, G. Ausiello, A. Via, 2005, BMC Bioinformatics.

Managing Your Biological Data with Python

Kristian Rother, Allegra Via, Anna Tramontano, 2014 .

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

Pedro L. Fernandes, Louisa J. Bellis, Gabriella Rustici, 2018, PLoS Comput. Biol..

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

Pedro L. Fernandes, Louisa J. Bellis, Prakash Singh Gaur, 2018, PLoS Comput. Biol..

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

Leszek Rychlewski, Peer Bork, Allegra Via, 2003, Nucleic Acids Res..

ELM: the status of the 2010 eukaryotic linear motif resource

Jakub Pas, Leszek Rychlewski, Aidan Budd, 2009, Nucleic Acids Res..

AI applications in functional genomics

T. Colombo, A. Via, V. Morea, 2021, Computational and structural biotechnology journal.

Digestive peptidase evolution in holometabolous insects led to a divergent group of enzymes in Lepidoptera.

A. Tramontano, A. Via, M. Silva-Filho, 2015, Insect biochemistry and molecular biology.

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

Allegra Via, Lars Juhl Jensen, Toby J. Gibson, 2007, Nucleic Acids Res..

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

Nikolaj Blom, Allegra Via, Toby J. Gibson, 2004, BMC Bioinformatics.

ELM—the database of eukaryotic linear motifs

Richard J. Edwards, Aidan Budd, Allegra Via, 2011, Nucleic Acids Res..

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

Anna Tramontano, Allegra Via, Domenico Raimondo, 2011, J. Chem. Inf. Model..

A structure filter for the Eukaryotic Linear Motif Resource

Allegra Via, Manuela Helmer-Citterich, Toby J. Gibson, 2009, BMC Bioinformatics.

From sequence to structural analysis in protein phosphorylation motifs.

Allegra Via, Manuela Helmer-Citterich, Francesca Diella, 2011, Frontiers in bioscience.

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

Anna Tramontano, Allegra Via, Manuela Helmer-Citterich, 2010, Nucleic Acids Res..

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

Pedro L. Fernandes, Allegra Via, Maria Victoria Schneider, 2017, Briefings Bioinform..

A prismatic view of protein phosphorylation in health and disease

Andreas Zanzoni, A. Via, 2015, Front. Genet..

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

Enrico Ferraro, Allegra Via, Gabriele Ausiello, 2006, Bioinform..

Data integration in biological research: an overview

R. Jimenez, M. Schneider, A. Via, 2015, Journal of Biological Research-Thessaloniki.

Data integration in biological research: an

Rafael C. Jimenez, Allegra Via, Maria Victoria Schneider, 2015 .

Ten simple rules for making training materials FAIR

Mateusz Kuzak, Celia W. G. van Gelder, Michel Dumontier, 2020, PLoS Comput. Biol..

The ELIXIR-EXCELERATE Train-the-Trainer pilot programme: empower researchers to deliver high-quality training

Pedro L. Fernandes, Allegra Via, Gabriella Rustici, 2017, F1000Research.

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

Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich, 2006, Nucleic Acids Res..

Report on the training needs identified across the ELIXIR community

C. Ponting, T. Attwood, E. Korpelainen, 2016 .

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

Allegra Via, Teresa K. Attwood, Rochelle E. Tractenberg, 2019, bioRxiv.

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

S. Pascarella, A. Maruotti, A. Via, 2023, Microorganisms.

Data integration in biological research: an overview

Rafael C. Jimenez, Allegra Via, Maria Victoria Schneider, 2015, Journal of Biological Research-Thessaloniki.

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

Silvio C. E. Tosatto, Anthony Bretaudeau, Burkhard Rost, 2015, Nucleic Acids Res..

Genetic and structural genome-based survey reveals the low potential for epidemiological expansion of the SARS-CoV-2 XBB.1.5 sublineage

S. Pascarella, A. Maruotti, A. Via, 2023, Journal of Infection.

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

Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich, 2008, BMC Bioinformatics.

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

Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich, 2007, BMC Bioinformatics.

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

Allegra Via, Manuela Helmer-Citterich, M. Helmer-Citterich, 2004, BMC Bioinformatics.

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

Allegra Via, Enrico Ferraro, Gabriele Ausiello, 2005, BMC Bioinformatics.

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

A. Via, S. Camerini, A. Ilari, 2014, PloS one.

Resources and tools for rare disease variant interpretation

E. Capriotti, R. Casadio, S. Pascarella, 2023, Frontiers in Molecular Biosciences.

Four simple recommendations to encourage best practices in research software

Daniel S. Katz, Yasset Perez-Riverol, Mateusz Kuzak, 2017, F1000Research.

Characterization of the differences in the cyclopiazonic acid binding mode to mammalian and P. Falciparum Ca2+ pumps: A computational study

A. Tramontano, A. Via, A. Coletta, 2015, Proteins.

Guidelines for curriculum and course development in higher education and training

T. Attwood, A. Via, J. Lindvall, 2020 .

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

Allegra Via, Jessica M Lindvall, Teresa K Attwood, 2019, PloS one.

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

Allegra Via, Enrico Ferraro, Gabriele Ausiello, 2007, Nucleic Acids Res..

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

Celia W. G. van Gelder, Rafael C. Jimenez, Marie-Claude Blatter, 2011, Briefings Bioinform..

Ten Simple Rules for Developing a Short Bioinformatics Training Course

Anna Tramontano, Michelle D. Brazas, Javier De Las Rivas, 2011, PLoS Comput. Biol..

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

Marie-Claude Blatter, Thomas Blicher, Catherine Brooksbank, 2010, Briefings Bioinform..

How pathogens use linear motifs to perturb host cell networks.

Allegra Via, Bora Uyar, Christine Brun, 2015, Trends in biochemical sciences.

Course design: Considerations for trainers – a Professional Guide

Allegra Via, Teresa K. Attwood, Patricia M. Palagi, 2020 .

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

Silvio C. E. Tosatto, Radka Svobodová Vareková, Victor de la Torre, 2015, Nucleic Acids Res..

Investigation of a potential mechanism for the inhibition of SmTGR by Auranofin and its implications for Plasmodium falciparum inhibition.

A. Tramontano, A. Via, R. Lepore, 2012, Biochemical and biophysical research communications.

Four simple recommendations to encourage best practices in research software

Alejandra N. González-Beltrán, V. Stodden, D. Mellor, 2018 .

Lesson Development for Open Source Software Best Practices Adoption

Mateusz Kuzak, Rafael C. Jimenez, Allegra Via, 2018, 2018 IEEE 14th International Conference on e-Science (e-Science).

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

Cathryn M. Gould, T. Gibson, F. Diella, 2007, Nucleic acids research.

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

Anna Tramontano, Allegra Via, Rosalba Lepore, 2013, Bioinform..

The Eukaryotic Linear Motif Resource (ELM): Regulatory Sites in Proteins

T. Gibson, F. Diella, Katja Luck, 2009 .

A FAIRification roadmap for ELIXIR Software Management Plans

Olga X. Giraldo, A. Via, Dimitrios Bampalikis, 2022, Research Ideas and Outcomes.

False occurrences of functional motifs in protein sequences highlight evolutionary constraints

Enrico Ferraro, Allegra Via, Gabriele Ausiello, 2007, BMC Bioinformatics.

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

Cathryn M. Gould, T. Gibson, L. Jensen, 2010, Nucleic Acids Res..

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

T. Gibson, T. Sicheritz-Pontén, B. Kuster, 2004 .

The ELIXIR-EXCELERATE Train-the-Trainer pilot programme: empower researchers to deliver high-quality training [version 1; peer review: 2 approved]

Pedro L. Fernandes, T. Attwood, A. Via, 2021 .

Best practices in bioinformatics training for life scientists

Federico Morán, Celia W. G. van Gelder, Rafael C. Jimenez, 2013, Briefings Bioinform..

Development of Computational Tools for the Inference of Protein Interaction Specificity Rules and Functional Annotation Using Structural Information

M. Helmer-Citterich, G. Ausiello, B. Brannetti, 2003, Comparative and functional genomics.

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

M. Helmer-Citterich, G. Ausiello, T. Colombo, 2007, Nucleic Acids Res..