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GUILDify: a web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms

Emre Guney, Javier Garcia-Garcia, Baldo Oliva
2014 Computer applications in the biosciences : CABIOS  
Here, we present GUILDify, an easy-to-use web server for the phenotypic characterization of genes.  ...  GUILDify web server does not restrict the prioritization to any predefined phenotype, supports multiple species and accepts userspecified genes.  ...  We have developed GUILDify, a free and easy-to-use web server for prioritization of genes using PPI networks.  ... 
doi:10.1093/bioinformatics/btu092 pmid:24532728 fatcat:nif7bx2c7re4tolgrdjwognwp4

In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm

Laura Artigas, Mireia Coma, Pedro Matos-Filipe, Joaquim Aguirre-Plans, Judith Farrés, Raquel Valls, Narcis Fernandez-Fuentes, Juan de la Haba-Rodriguez, Alex Olvera, Jose Barbera, Rafael Morales, Baldo Oliva (+2 others)
2020 PLoS ONE  
Simultaneously, GUILDify v2.0 web server has been used as an alternative method to corroborate the effect of pirfenidone and melatonin against the infection of SARS-CoV-2.  ...  These evidences, together with the fact that from a medical point of view both drugs are considered safe and can be combined with the current standard of care treatments for COVID-19 makes this combination  ...  Pablo Coto from the Hospital Vital Alvarez-Buylla (Asturias, Spain) for his collaboration about details about the COVID-19 infection and specially the SARS molecular characterization, and Dr.  ... 
doi:10.1371/journal.pone.0240149 pmid:33006999 fatcat:cp4xh7sgk5gqbmd7rosa6iqzcu

COSNet: An R package for label prediction in unbalanced biological networks

Marco Frasca, Giorgio Valentini
2017 Neurocomputing  
In this context, classes are usually characterized by a high imbalance, i.e. positive examples for a class are much less than those negative.  ...  COSNet deals with the label imbalance problem by implementing a novel parametric model of Hopfield Network (HN), whose output levels and activation thresholds of neurons are parameters to be automatically  ...  GUILDify (http://sbi.imim.es/web/GUILDify.php) and PhenoPred (http://www.phenopred.org), web-servers to discover gene-disease associations.  ... 
doi:10.1016/j.neucom.2015.11.096 fatcat:nxnf5zim5bggnodhnlhx5m5ypi

An ensemble learning approach for modeling the systems biology of drug-induced injury

Joaquim Aguirre-Plans, Janet Piñero, Terezinha Souza, Giulia Callegaro, Steven J. Kunnen, Ferran Sanz, Narcis Fernandez-Fuentes, Laura I. Furlong, Emre Guney, Baldo Oliva
2021 Biology Direct  
Results We searched for gene signatures in CMap gene expression data by using two approaches: phenotype-gene associations data from DisGeNET, and a non-parametric test comparing gene expression of DILI-Concern  ...  Conclusions When using CMap gene expression data, searching for a specific gene signature among the landmark genes improves the quality of the classifiers, but it is still limited by the intrinsic noise  ...  Acknowledgements J.A.P. would like to thank the organization of the CAMDA 2019 challenge and specifically Maciej Kańduła for the support given with the independent hold-out test set.  ... 
doi:10.1186/s13062-020-00288-x pmid:33435983 fatcat:u2kaf6ruivghvk2jnwixlrkkhe

In-silico simulated prototype-patients using TPMS technology to study a potential adverse effect of sacubitril and valsartan

Guillem Jorba, Joaquim Aguirre-Plans, Valentin Junet, Cristina Segú-Vergés, José Luis Ruiz, Albert Pujol, Narcís Fernández-Fuentes, José Manuel Mas, Baldo Oliva, Hans-Peter Brunner-La Rocca
2020 PLoS ONE  
Data and accession to software are available at http://sbi.upf.edu/data/tpms/.  ...  TPMS operates by (1) modelling the responses in humans with an accurate description of a protein network and (2) applying a Multilayer Perceptron-like and sampling strategy to find all plausible solutions  ...  For this purpose, we used GUILDify v2.0 [23], a web server that extends the information of disease-gene associations through the protein-protein interactions network.  ... 
doi:10.1371/journal.pone.0228926 pmid:32053711 fatcat:b4f63b6cmzdi3fignwytohpqde

Prediction of Adverse Drug Reaction Linked to Protein Targets Using Network-Based Information and Machine Learning

Cristiano Galletti, Joaquim Aguirre-Plans, Baldo Oliva, Narcis Fernandez-Fuentes
2022 Frontiers in Bioinformatics  
The implementation of the predictor is based on a machine learning classifier that integrates a set of eight independent network-based features.  ...  These include a network diffusion-based score, identification of protein modules based on network clustering algorithms, functional similarity among proteins, network distance to proteins that are part  ...  Features GUILDify Score GUILDify is a web server of network diffusion-based algorithms used for a wide range of network medicine applications (Aguirre-Plans et al., 2019) .  ... 
doi:10.3389/fbinf.2022.906644 doaj:ada394d460d342ef9ed505ea758039d6 fatcat:fcq5k3r2m5h25do4x5tezqzn4m