Alexandre Perera-Lluna
Polytechnic University of Catalonia
GeneDeep learningAlgorithmMachine learningPhysicsInternal medicineRamachandran plotKEGGArtificial intelligenceCardiologyPattern recognitionChemistryProtein function predictionMetabolomicsContext (language use)Biological networkR packageNetwork analysisMathematicsTorsion (mechanics)Computer scienceComputational biologyMedicineCluster analysisIdentification (information)Biology
44Publications
12H-index
414Citations
Publications 36
Newest
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#1Sergio Picart-Armada (UPC: Polytechnic University of Catalonia)H-Index: 5
#2Wesley K. ThompsonH-Index: 68
Last. Alexandre Perera-Lluna (UPC: Polytechnic University of Catalonia)H-Index: 12
view all 4 authors...
MOTIVATION Network diffusion and label propagation are fundamental tools in computational biology, with applications like gene-disease association, protein function prediction and module discovery. More recently, several publications have introduced a permutation analysis after the propagation process, due to concerns that network topology can bias diffusion scores. This opens the question of the statistical properties and the presence of bias of such diffusion processes in each of its applicati...
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#1Josep Marín-Llaó (Fraunhofer Society)H-Index: 5
#2Sarah Mubeen (Fraunhofer Society)H-Index: 5
Last. Daniel Domingo-Fernández (Fraunhofer Society)H-Index: 9
view all 6 authors...
SUMMARY High-throughput screening yields vast amounts of biological data which can be highly challenging to interpret. In response, knowledge-driven approaches emerged as possible solutions to analyze large datasets by leveraging prior knowledge of biomolecular interactions represented in the form of biological networks. Nonetheless, given their size and complexity, their manual investigation quickly becomes impractical. Thus, computational approaches, such as diffusion algorithms, are often emp...
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#1Angela Lopez-del Rio (UPC: Polytechnic University of Catalonia)H-Index: 1
#2Sergio Picart-Armada (UPC: Polytechnic University of Catalonia)H-Index: 5
Last. Alexandre Perera-Lluna (UPC: Polytechnic University of Catalonia)H-Index: 12
view all 3 authors...
In silico analysis of biological activity data has become an essential technique in pharmaceutical development. Specifically, the so-called proteochemometric models aim to share information between targets in machine learning ligand-target activity prediction models. However, bioactivity data sets used in proteochemometric modeling are usually imbalanced, which could potentially affect the performance of the models. In this work, we explored the effect of different balancing strategies in deep l...
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Last. Alexandre Perera-Lluna (UPC: Polytechnic University of Catalonia)H-Index: 12
view all 13 authors...
Background: Rare disease communities are spread around the globe and segmented by their condition. Little research has been performed on the majority of rare diseases. Most patients who are affected by a rare disease have no research on their condition because of a lack of knowledge due to absence of common groups in the research community. Objective: We aimed to develop a safe and secure community of rare disease patients, without geographic or language barriers, to promote research. Methods: C...
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#1Angela Lopez-del Rio (UPC: Polytechnic University of Catalonia)H-Index: 1
#2Maria Jesus Martin (EMBL-EBI: European Bioinformatics Institute)H-Index: 41
Last. Rabie Saidi (EMBL-EBI: European Bioinformatics Institute)H-Index: 8
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The use of raw amino acid sequences as input for deep learning models for protein functional prediction has gained popularity in recent years. This scheme obliges to manage proteins with different lengths, while deep learning models require same-shape input. To accomplish this, zeros are usually added to each sequence up to a established common length in a process called zero-padding. However, the effect of different padding strategies on model performance and data structure is yet unknown. We p...
Source
#1Sergio Picart-Armada (UPC: Polytechnic University of Catalonia)H-Index: 5
#2Wesley K. Thompson (UCSD: University of California, San Diego)H-Index: 68
Last. Alexandre Perera-Lluna (UPC: Polytechnic University of Catalonia)H-Index: 12
view all 4 authors...
Motivation: Network diffusion and label propagation are fundamental tools in computational biology, with applications like gene-disease association, protein function prediction and module discovery. More recently, several publications have introduced a permutation analysis after the propagation process, due to concerns that network topology can bias diffusion scores. This opens the question of the statistical properties and the presence of bias of such diffusion processes in each of its applicat...
Source
#2Maria Jesus MartinH-Index: 41
Last. Rabie SaidiH-Index: 11
view all 4 authors...
Source
#1Sergio Picart-Armada (UPC: Polytechnic University of Catalonia)H-Index: 5
#2Steven J. BarrettH-Index: 1
Last. Benoit H. DessaillyH-Index: 18
view all 6 authors...
In-silico identification of potential target genes for disease is an essential aspect of drug target discovery. Recent studies suggest that successful targets can be found through by leveraging genetic, genomic and protein interaction information. Here, we systematically tested the ability of 12 varied algorithms, based on network propagation, to identify genes that have been targeted by any drug, on gene-disease data from 22 common non-cancerous diseases in OpenTargets. We considered two biolog...
20 CitationsSource
#1Samir Kanaan-Izquierdo (UPC: Polytechnic University of Catalonia)H-Index: 3
#2Andrey Ziyatdinov (Harvard University)H-Index: 10
Last. Alexandre Perera-Lluna (UPC: Polytechnic University of Catalonia)H-Index: 12
view all 4 authors...
Multiview datasets are the norm in bioinformatics, often under the label multi-omics. Multiview data is gathered from several experiments, measurements or feature sets available for the same subjects. Recent studies in pattern recognition have shown the advantage of using multiview methods of clustering and dimensionality reduction; however, none of these methods are readily available to the extent of our knowledge. Multiview extensions of four well-known pattern recognition methods are proposed...
4 CitationsSource