Perera Lluna, Alexandre
Total activity: 102
Professional category
Tenure-track 2 lecturers
Doctoral courses
Doctor en Ciencias Físicas
University degree
Ingeniero Superior en Electrónica
Licendiado en Ciencias Físicas
Research group
CREB - Biomedical Engineering Research Centre
SISBIO - Biomedical Signals and Systems
Department
Department of Automatic Control
School
Barcelona School of Nautical Studies (FNB)
E-mail
alexandre.pereraupc.edu
Contact details
UPC directory Open in new window
Orcid
0000-0001-6427-851X Open in new window
Links of interest
B2SLab Open in new window

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1 to 50 of 102 results
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    Data simulation in machine olfaction with the R package chemosensors  Open access

     Ziyatdinov, Andrey; Perera Lluna, Alexandre
    PLoS one
    Date of publication: 2014-02
    Journal article

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    In machine olfaction, the design of applications based on gas sensor arrays is highly dependent on the robustness of the signal and data processing algorithms. While the practice of testing the algorithms on public benchmarks is not common in the field, we propose software for performing data simulations in the machine olfaction field by generating parameterized sensor array data. The software is implemented as an R language package chemosensors which is open-access, platform-independent and self-contained. We introduce the concept of a virtual sensor array which can be used as a data generation tool. In this work, we describe the data simulation workflow which basically consists of scenario definition, virtual array parameterization and the generation of sensor array data. We also give examples of the processing of the simulated data as proof of concept for the parameterized sensor array data: the benchmarking of classification algorithms, the evaluation of linear- and non-linear regression algorithms, and the biologically inspired processing of sensor array data. All the results presented were obtained under version 0.7.6 of the chemosensors package whose home page is chemosensors.r-forge.r-project.org.

  • Peak aggregation as an innovative strategy for improving the predictive power of LC-MS metabolomic profiles

     Fernandez Albert, Francesc; Llorach, Rafael; Andres LaCueva, Cristina; Perera Lluna, Alexandre
    Analytical chemistry
    Date of publication: 2014-02-28
    Journal article

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  • Automatic capacitor bank identification in power distribution systems

     Perera Lluna, Alexandre; Manivannan, Karthick; Xu, Peng; Gutierrez Osuna, Ricardo; Benner, Carl; Russell, B. Don
    Electric power systems research
    Date of publication: 2014-06-01
    Journal article

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    Tracking the performance and health of capacitor banks in distribution systems is a challenging task due to their high number and the widespread geographical distribution of feeder circuits. In this work we propose a signal processing technique capable of identifying and characterizing the number of capacitor banks connected to a standard North-American feeder circuit. The way the technique is applied allows a real-time remote monitoring of their operation, automatically identifying the switching activity for each capacitor bank connected. The technique is based on an unsupervised clustering of the three phase reactance step magnitudes. We demonstrate that using only passive monitoring of conventional substation bus PTs and feeder CTs, without any communication, nor visual inspection, to individual banks, it is possible to predict the number of capacitor banks on the distribution feeder and track their performance and activity over time. (C) 2014 Elsevier B.V. All rights reserved.

  • Effect of genetic regions on the correlation between single point mutation variability and morbidity

     Brunel, Helena; Gallardo Chacon, Juan José; Vallverdú Ferrer, Montserrat; Caminal Magrans, Pedro; Perera Lluna, Alexandre
    Computers in biology and medicine
    Date of publication: 2013-06-01
    Journal article

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    Cross-species sequence comparisons have suggested that cross-species sequence variability is correlated with functionality. The goal of this study was to extend this observation at different genetic regions, focusing on the morbidity of Single Nucleotide Polymorphisms (SNPs). A set of deleterious SNPs was compared to a set of neutral SNPs. Both samples were stratified according to the location of the SNPs at different genetic regions. Deleterious SNPs were observed to be less variable across species than neutral SNPs, these differences being significant for missense mutations (p=1.1×10-9p=1.1×10-9), SNPs in introns (p=6.4×10-3p=6.4×10-3), and SNPs in unknown regions (p=8×10-4p=8×10-4).

  • A biomimetic approach to machine olfaction, featuring a very large-scale chemical sensor array and embedded neuro-bio-inspired computation

     Marco Colas, Santiago; Gutierrez Galvez, Agustín; Lansner, Anders; Martinez, Dominique; Rospars, Jean Piere; Beccherelli, Romeo; Perera Lluna, Alexandre; Pearce, Timmothy Charles; Verschure, Paulus Franciscus Maria Joseph; Persaud, Krishna C.
    Microsystem technologies-Micro-and nanosystems-Information storage and processing
    Date of publication: 2013-12-21
    Journal article

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  • A software tool for large-scale synthetic experiments based on polymeric sensor arrays

     Ziyatdinov, Andrey; Fernandez Diaz, Eduard; Chaudry, A.; Marco Colas, Santiago; Persaud, Krishna C.; Perera Lluna, Alexandre
    Sensors and actuators B. Chemical
    Date of publication: 2013-02-01
    Journal article

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    Predictability of gene ontology slim-terms from primary structure information in Embryophyta plant proteins  Open access

     Jaramillo-Garzón, Jorge Alberto; Gallardo Chacon, Juan José; Castellanos Domínguez, Germán; Perera Lluna, Alexandre
    BMC bioinformatics
    Date of publication: 2013-02-26
    Journal article

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  • Biologically inspired large scale chemical sensor arrays and embedded data processing

     Marco Colas, Santiago; Gutierrez-Galvez, Agustin; Lansner, Anders; Martinez, Dominique; Rospars, Jean Piere; Beccherelli, Romeo; Perera Lluna, Alexandre; Pearce, Timmothy Charles; Vershure, Paul; Persaud, Krishna C.
    SPIE Optical Systems Design
    Presentation of work at congresses

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    Biological olfaction outperforms chemical instrumentation in specificity, response time, detection limit, coding capacity, time stability, robustness, size, power consumption, and portability. This biological function provides outstanding performance due, to a large extent, to the unique architecture of the olfactory pathway, which combines a high degree of redundancy, an efficient combinatorial coding along with unmatched chemical information processing mechanisms. The last decade has witnessed important advances in the understanding of the computational primitives underlying the functioning of the olfactory system. EU Funded Project NEUROCHEM (Bio-ICT-FET- 216916) has developed novel computing paradigms and biologically motivated artefacts for chemical sensing taking inspiration from the biological olfactory pathway. To demonstrate this approach, a biomimetic demonstrator has been built featuring a large scale sensor array (65K elements) in conducting polymer technology mimicking the olfactory receptor neuron layer, and abstracted biomimetic algorithms have been implemented in an embedded system that interfaces the chemical sensors. The embedded system integrates computational models of the main anatomic building blocks in the olfactory pathway: The olfactory bulb, and olfactory cortex in vertebrates (alternatively, antennal lobe and mushroom bodies in the insect). For implementation in the embedded processor an abstraction phase has been carried out in which their processing capabilities are captured by algorithmic solutions. Finally, the algorithmic models are tested with an odour robot with navigation capabilities in mixed chemical plumes.

  • Genetic association analysis of complex diseases through information theoretic metrics and linear pleiotropy  Open access

     Brunel Montaner, Helena
    Defense's date: 2013-11-14
    Universitat Politècnica de Catalunya
    Theses

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    Esta tesis combina métodos lineales y no lineales con el fin de identificar variantes genéticas responsables de rasgos complejos.En primer lugar, se han propuesto dos estrategias de asociación de one-locus. La primera consiste en definir y caracterizar unaprueba de asociación no lineal basada en la medida de información mutua, y teniendo en cuenta la estructura genética de lapoblación. Para ello, se han utilizado los datos del GAW17 y, dado que corresponden a datos simulados cuya solución esconocida, este estudio ha servido para caracterizar el rendimiento de la prueba de asociación no lineal en comparación con losmétodos lineales estándar. La metodología propuesta ha recuperado los resultados obtenidos usando métodos lineales yademás ha identificado un SNP relacionado con la enfermedad. En términos de rendimiento, ambos métodos han mostradocifras similares de precisión en clasificación (AUC).La segunda alternativa consiste en un estudio exploratorio sobre la relación entre la variabilidad de secuencias entre especies ila asociación con la enfermedad, para diferentes regiones genómicas. Se han comparado dos conjuntos de SNPs, uno formadopor SNPs previamente asociados con enfermedades y el otro formado por SNPs neutros. Ambos han sido estratificados segúnla región genómica de los SNPs, característica que pudo influenciar su conservación entre especies. Se ha observado que parala mayoría de regiones genómicas, los SNPs asociados a enfermedades tienden a estar significativamente menos variablesentre especies que los SNPs neutros.En segundo lugar, se ha propuesto una metodología no lineal novedosa para asociación genética multiloci, con el objetivo dedetectar la asociación entre combinaciones de varios SNPs y fenotipos complejos. EL método propuesto, denominado MISS, seha basado en la significación estadística de la información mutua. Esta aproximación se ha comparado con el MLR (MultipleLinear Regression), un método estándar para asociación genética multiloci. Ambos se han aplicado como criterio de relevanciaen un algoritmo flotante de selección de características multi- solución (MSSFFS), propuesto en el contexto de asociaciónmultiloci. También se han comparado con MECPM, un algoritmo para la búsqueda predictiva de interacciones multilocales conun criterio de máxima entropía. Los tres métodos se han aplicado a los SNPs del gen F7 y los niveles de FVII en sangre con losdatos del proyecto GAIT. El método propuesto (MISS) ha mejorado los resultados obtenidos con los otros métodos, detectandonuevas interacciones entre SNPs. Los resultados están en concordancia con resultados funcionales encontrados en la literaturadonde los SNPs candidatos fueron descritos como elementos funcionales relacionados con el fenotipo.En tercer lugar, se ha propuesto un entorno metodológico lineal para el análisis simultáneo de múltiples fenotipos. Lametodología consiste en construir nuevas variables fenotípicas, denominadas metafenotipos, que capturen la actividad conjuntade un grupo de fenotipos que actúen en cascada en una determinada ruta metabólica. Estas nuevas variables se han usado enlos posteriores análisis de asociación con el fin de identificar elementos genéticos relacionados con el proceso biológicosubyacente, en su conjunto. Como implementación práctica, la metodología se ha aplicado a los datos del proyecto GAIT, paraidentificar marcadores genéticos relacionados con el proceso de la coagulación en su totalidad. Tres modelos matemáticos sehan usado para la definición de los metafenotipos, un modelo PCA y dos modelos ICA. Usando esta aproximación novedosa, sehan identificado asociaciones previamente reportadas y se han propuesto nuevos candidatos con un posible efecto global sobrela cascada de la coagulación como conjunto.

    The main goal of this thesis was to help in the identification of genetic variants that are responsible for complex traits, combining both linear and nonlinear approaches. First, two one-locus approaches were proposed. The first one defined and characterized a novel nonlinear test of genetic association, based on the mutual information measure. This test takes into account the genetic structure of the population. It was applied to the GAW17 dataset and compared to the standard linear test of association. Since the solution of the GAW17 simulation model was known, this study served to characterize the performance of the proposed nonlinear methods in comparison to the linear one. The proposed nonlinear test was able to recover the results obtained with linear methods but also detected an additional SNP in a gene related with the phenotype. In addition, the performance of both tests in terms of their accuracy in classification (AUC) was similar. In contrast, the second approach was an exploratory study on the relationship between SNP variability among species and SNP association with disease, at different genetic regions. Two sets of SNPs were compared, one containing deleterious SNPs and the other defined by neutral SNPs. Both sets were stratified depending on the region where the polymorphisms were located, a feature that may have influenced their conservation across species. It was observed that, for most functional regions, SNPs associated to diseases tend to be significantly less variable across species than neutral SNPs. Second, a novel nonlinear methodology for multiloci genetic association was proposed with the goal of detecting association between combinations of SNPs and a phenotype. The proposed method was based on the mutual information of statistical significance, called MISS. This approach was compared with MLR, the standard linear method used for genetic association based on multiple linear regressions. Both were applied as a relevance criterion of a new multi-solution floating feature selection algorithm (MSSFFS), proposed in the context of multi-loci genetic association for complex diseases. Both were also compared with MECPM, an algorithm for searching predictive multi-loci interactions with a criterion of maximum entropy. The three methods were tested on the SNPs of the F7 gene, and the FVII levels in blood, with the data from the GAIT project. The proposed nonlinear method (MISS) improved the results of traditional genetic association methods, detecting new SNP-SNP interactions. Most of the obtained sets of SNPs were in concordance with the functional results found in the literature where the obtained SNPs have been described as functional elements correlated with the phenotype. Third, a linear methodological framework for the simultaneous study of several phenotypes was proposed. The methodology consisted in building new phenotypic variables, named metaphenotypes, that capture the joint activity of sets of phenotypes involved in a metabolic pathway. These new variables were used in further association tests with the aim of identifying genetic elements related with the underlying biological process as a whole. As a practical implementation, the methodology was applied to the GAIT project dataset with the aim of identifying genetic markers that could be related to the coagulation process as a whole and thus to thrombosis. Three mathematical models were used for the definition of metaphenotypes, corresponding to one PCA and two ICA models. Using this novel approach, already known associations were retrieved but also new candidates were proposed as regulatory genes with a global effect on the coagulation pathway as a whole.

  • Choi-Williams distribution to describe coding and non-coding regions in primary transcript pre-mRNA

     Melia, U.; Vallverdú Ferrer, Montserrat; Clarià Sancho, Francesc; Gallardo Chacon, Joan Josep; Perera Lluna, Alexandre; Caminal Magrans, Pedro
    Journal of Medical and Biological Engineering
    Date of publication: 2012-05-28
    Journal article

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  • A subspace method for the detection of transcription factor binding sites

     Pairó Castiñeira, Erola; Maynou Fernández, Joan; Marco Colas, Santiago; Perera Lluna, Alexandre
    Bioinformatics
    Date of publication: 2012-05
    Journal article

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  • Network-based enrichment analysis of gene expression through protein-protein interaction data

     Massanet Vila, Raimon Jaume; Fernandez Albert, Francesc; Perera Lluna, Alexandre; Caminal Magrans, Pedro
    IEEE Engineering in Medicine and Biology Society
    Presentation's date: 2012-09-01
    Presentation of work at congresses

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    High-throughput analysis of gene expression data is subject to technological and statistical issues that confuse the underlying expression-condition associations. In this contribution a network-based candidate gene prioritization strategy was applied to the enrichment of a publicly available gene expression dataset, focused on the study of the mechanosensitivity of genes exposed to altered pulmonary matrix stiffness. Results suggested that some genes which had not been taken into account in the original study could have an important role in the processes causing, or affected by, pulmonary fibrosis.

  • Multiview approach to spectral clustering

     Kanaan Izquierdo, Samir; Ziyatdinov, Andrey; Massanet Vila, Raimon Jaume; Perera Lluna, Alexandre
    IEEE Engineering in Medicine and Biology Society
    Presentation's date: 2012-08-29
    Presentation of work at congresses

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  • Método mejorado de agrupamiento espectral por ordenador y usos del mismo

     Kanaan Izquierdo, Samir; Ziyatdinov, Andrey; Massanet Vila, Raimon Jaume; Perera Lluna, Alexandre
    Date of request: 2012-08-01
    Invention patent

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  • A method and a computer program for metabolomic data analysis

     Fernandez Albert, Francesc; Llorach Asunción, Rafael; Andres Lacueva, Cristina; Perera Lluna, Alexandre
    Date of request: 2012-06-12
    Invention patent

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  • Biologically inspired computation for chemical sensing

     Fonollosa, Jordi; Gutierrez-Galvez, Agustin; Lansner, Anders; Martinez, Dominique; Rospars, Jean Piere; Beccherelli, Romeo; Perera Lluna, Alexandre; Pearce, Timmothy Charles; Vershure, Paul; Persaud, Krishna C.; Marco Colas, Santiago
    Procedia Computer Science
    Date of publication: 2011-09-05
    Journal article

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  • Herramientas de procesado de señal y bioinformática para la evaluación multinivel de desórdenes cardiovasculares y la monitorización

     Vallverdú Ferrer, Montserrat; Ziyatdinov, Andrey; Brunel Montaner, Helena; Massanet Vila, Raimon Jaume; Perera Lluna, Alexandre
    Participation in a competitive project

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  • A new computational assisted bioinformatics workflow for the comprehensive analysis of LC-MS based nutrimetabolomic studies.

     Fernandez Albert, Francesc; Perera Lluna, Alexandre; Andrés-Lacueva, C.; Llorach Asunción, Rafael
    International Workshop on Metabolomics & Proteomics
    Presentation's date: 2011-09-12
    Presentation of work at congresses

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  • A new computational assisted bioinformatics workflow to identify polyphenols biotransformation markers on LC-MS based nutrimetabolomics studies

     Fernandez Albert, Francesc; Perera Lluna, Alexandre; Andrés-Lacueva, C.; Llorach Asunción, Rafael
    International Conference on Polyphenols and Health
    Presentation's date: 2011-10-18
    Presentation of work at congresses

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  • Un nuevo algoritmo para el análisis de estudios de nutrimetabolómica basados en LC-MS

     Fernandez Albert, Francesc; Llorach Asunción, Rafael; Andrés-Lacueva, C.; Perera Lluna, Alexandre
    Congreso Anual de la Sociedad Española de Ingeniería Biomédica
    Presentation's date: 2011
    Presentation of work at congresses

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    MEET: Motif Elements Estimation Toolkit  Open access

     Pairó Castiñeira, Erola; Maynou Fernández, Joan; Vallverdú Ferrer, Montserrat; Caminal Magrans, Pedro; Marco Colas, Santiago; Perera Lluna, Alexandre
    IEEE Engineering in Medicine and Biology Society
    Presentation's date: 2011-09-02
    Presentation of work at congresses

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    MEET is an R package that integrates a set of algorithms for the detection of transcription factor binding sites(TFBS). The MEET R package includes five motif searching algorithms: MEME/MAST(Multiple Expectation-Maximization for Motif Elicitation), Q-residuals, MDscan (Motif Discovery scan), ITEME (Information Theory Elements for Motif Estimation)and MATCH. In addition MEET allows the user to work with different alignment algorithms: MUSCLE (Multiple Sequence Comparison by Log-Expectation), ClustalW and MEME. The package can work in two modes, training and detection. The training mode allows the user to choose the best parameters of a detector. Once the parameters are chosen, the detection mode allows to analyze a genome looking for binding sites. Both modes can combine the different alignment and detection methods, offering multiple possibilities. Combining the alignments and the detection algorithms makes possible the comparison between detection models at the same level, without having to care about the differences produced during the alignment process. The MEET R package can be downloaded from http://sisbio.recerca.upc.edu/R/MEET_1.0. tar.gz

    Postprint (author’s final draft)

  • Priorización mejorada de genes candidatos usando información de interacción entre proteínas

     Massanet Vila, Raimon Jaume; Brunel Montaner, Helena; Martínez-Pérez, Angel; Soria Fernández, José Manuel; Perera Lluna, Alexandre
    Congreso Anual de la Sociedad Española de Bioingeniería
    Presentation's date: 2011
    Presentation of work at congresses

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  • A large scale virtual gas sensor array

     Ziyatdinov, Andrey; Fernandez Diaz, Eduard; Chaudry, A.; Marco Colas, Santiago; Persaud, Krishna C; Perera Lluna, Alexandre
    International Symposium on Olfaction and Electronic Nose
    Presentation's date: 2011
    Presentation of work at congresses

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    Odour mapping under strong backgrounds with a metal oxide sensor array  Open access

     Ziyatdinov, Andrey; Blanco Calvo, Jose Maria; Bermudez Badia, Sergi; Lechon, Miguel; Marco Colas, Santiago; Verschure, Paul; Perera Lluna, Alexandre
    International Symposium on Olfaction and Electronic Nose
    Presentation's date: 2011
    Presentation of work at congresses

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    This text describes the data from an initial set of navigation experiments in the scope of the Bio-ICT European project NEUROCHEM (...) This poster shows that a preprocessing based on Independent Component Analysis is able to discriminate two odour sources. Further work will include automatic determination of the number of components present in the tunnel and the application of the Neurochem platform in surge-and-cast behavioral models.

    Postprint (author’s final draft)

  • Algoritmo de búsqueda de secuencias cis-regulatorias basado en el análisis del incremento de la información mediante la divergencia de Rényi

     Maynou Fernández, Joan; Vallverdú Ferrer, Montserrat; Caminal Magrans, Pedro; Perera Lluna, Alexandre
    Congreso Anual de la Sociedad Española de Bioingeniería
    Presentation's date: 2011-11-17
    Presentation of work at congresses

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  • Analysis of incomplete gene expression dataset through protein-protein interaction information

     Massanet Vila, Raimon Jaume; Padró Capmany, Teresa; Cardús, Anna; Badimón, Lina; Caminal Magrans, Pedro; Perera Lluna, Alexandre
    IEEE Engineering in Medicine and Biology Society
    Presentation's date: 2011
    Presentation of work at congresses

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    This paper shows a graph based method to analyze proteomic expression data. The method allows the prediction of the expression of genes not measured by the gene expression technology based on the local connectivity properties of the measured differentially expressed gene set. The prediction of the expression jointly with the stability of this prediction as a function of the variation of the initial expressed set is computed. The method is able to correctly predict one third of the proteins with independence of variations on the selection of the initial set. The algorithm is validated through a Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometer (MALDI-TOF) protein expression experiment aiming the study of the protein expression patterns and post-translational modifications in human endothelial vascular cells exposed to atherosclerotic levels of Low Density Lipoproteins (LDL).

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    Caracterización y análisis de las interacciones de regulación entre los factores de transcripción y los genes  Open access

     Maynou Fernández, Joan; Pairó Castiñeira, Erola; Massanet Vila, Raimon Jaume; Vallverdú Ferrer, Montserrat; Caminal Magrans, Pedro; Perera Lluna, Alexandre
    Congreso Anual de la Sociedad Española de Bioingeniería
    Presentation's date: 2011-11-17
    Presentation of work at congresses

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    El estudio y la comprensión de las redes de interacción entre proteínas es fundamental para entender el funcionamiento de los diferentes procesos biológicos a nivel celular. El conjunto de interacciones entre proteínas, definido como interactoma, es muy complejo debido al número y a los diferentes tipos de interacciones existentes. En este contexto, estudiar las interacciones de regulación entre proteína y ácido desoxirribonucleico (Factor de Transcripción -ADN) es importante para comprender el nivel de expresión de los genes afectados. El principal objetivo de este trabajo es la caracterización desde el punto de vista estadístico de los factores de transcripción que regulan un gen y de los genes regulados por un factor de transcripción. Los datos han sido obtenidos de la base de datos String 1 y de la aplicación de minería de datos de SabioSciences 2. El trabajo se centra en las interacciones de regulación TF-gen para el organismo Homo sapiens.

    Postprint (author’s final draft)

  • Evaluation of fish spoilage by means of a single metal oxide sensor under temperature modulation

     Perera Lluna, Alexandre; Pardo, Antonio; Barretino, Diego; Hierlemann, Andreas; Marco Colas, Santiago
    Sensors and actuators B. Chemical
    Date of publication: 2010-04-29
    Journal article

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  • Drift compensation of gas sensor array data by Orthogonal Signal Correction

     Padilla, Marta; Perera Lluna, Alexandre; Montoliu, Ivan; Chaudry, A.; Persaud, Krishna C.; Marco Colas, Santiago
    Chemometrics and intelligent laboratory systems
    Date of publication: 2010-01-15
    Journal article

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  • MISS: a non-linear methodology based on mutual information for genetic association studies in both population and sib-pairs analysis

     Brunel Montaner, Helena; Gallardo Chacón, Joan Josep; Buil Calvo, José Antonio; Vallverdú Ferrer, Montserrat; Soria, José Manuel; Caminal Magrans, Pedro; Perera Lluna, Alexandre
    Bioinformatics
    Date of publication: 2010-08-01
    Journal article

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  • Computational Detection of Transcription Factor Binding Sites Through Differential Rényi Entropy

     Maynou Fernández, Joan; Gallardo Chacón, Joan Josep; Vallverdú Ferrer, Montserrat; Caminal Magrans, Pedro; Perera Lluna, Alexandre
    IEEE transactions on information theory
    Date of publication: 2010-02-15
    Journal article

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  • Drift compensation of gas sensor array data by common principal component analysis

     Ziyatdinov, Andrey; Marco Colas, Santiago; Chaudry, A.; Persaud, Krishna C.; Caminal Magrans, Pedro; Perera Lluna, Alexandre
    Sensors and actuators B. Chemical
    Date of publication: 2010-04-29
    Journal article

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  • RENOVACION DE LA RED TEMATICA EN INGENIERIA BIOMEDICA (REDINBIO)

     Mañanas Villanueva, Miguel Angel; Giraldo Giraldo, Beatriz F.; Gomis Román, Pedro; Jane Campos, Raimon; Vallverdú Ferrer, Montserrat; Perera Lluna, Alexandre; Caminal Magrans, Pedro
    Participation in a competitive project

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    Medidas basadas en teoría de grafos y la predicción de la morbosidad de genes  Open access

     Massanet Vila, Raimon Jaume; Caminal Magrans, Pedro; Perera Lluna, Alexandre
    Congreso Anual de la Sociedad Española de Bioingeniería
    Presentation's date: 2010-11
    Presentation of work at congresses

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    Estudios previos sugieren que las redes de interacción entre proteínas presentan propiedades de la teoría de grafos que pueden tener cierta relación con la morbosidad de los genes. En particular, se ha sugerido que cuando un polimor smo afecta a un gen, es más probable que se produzca una enfermedad si el grado de ese gen en una red de interacción entre proteínas es elevado. Sin embargo, estos resultados no tienen en cuenta el posible sesgo intro- ducido en los datos por la variación en la cantidad de información que se tiene sobre los diferentes genes. En este trabajo se intenta modelar la morbosidad de genes como una combinación lineal de los grados de los nodos en redes de interacción entre proteínas y la cantidad de información sobre genes disponible en la literatura. Un conjunto de 7461 genes y 3665 enfermedades reportadas en la base de datos Online Mendelian Inheritance in Man (OMIM) fue utilizado conjuntamente con una red de interacciones entre proteínas de 9630 nodos y 38756 interacciones de la Human Proteome Resource Database (HPRD). La cantidad de información disponible para cada gen se ha medido minando la base de datos PubMed. Los resultados sugieren que la correlación entre el grado de un nodo en la red de interacciones entre proteínas y la morbosidad del gen que el nodo representa es consecuencia, al menos en una parte considerable, de la variación en la cantidad de información disponible para los diferentes genes. Aunque los resultados sugieren una correlación positiva entre el grado de un nodo y su morbosidad, los autores creen que esta correlación debe ser considerada con precaución puesto que podría estar afectada por factores que no se consideraron en este estudio.

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    Herramientas bioinformáticas para el análisis de resultados de experimentos de expresión génica  Open access

     Massanet Vila, Raimon Jaume; Gallardo Chacón, Joan Josep; Padró Capmany, Teresa; Badimón, Lina; Caminal Magrans, Pedro; Perera Lluna, Alexandre
    Congreso Anual de la Sociedad Española de Ingeniería Biomédica
    Presentation of work at congresses

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    En este estudio se propone una metodología que combina datos de expresión diferencial con información de expresión entre proteínas. El objetivo es enriquecer los resultados de un experimento de expresión con nuevos genes que no fueron tenidos en cuenta en el diseño del experimento pero que podrían tener cierta relevancia en los procesos que muestran expresión diferencial. El método se basa en el estudio de las vías proteómicas que conectan genes con expresión diferencial significativa.

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    Graph theory-based measures as predictors of gene morbidity  Open access

     Massanet Vila, Raimon Jaume; Caminal Magrans, Pedro; Perera Lluna, Alexandre
    IEEE Engineering in Medicine and Biology Society
    Presentation's date: 2010-09
    Presentation of work at congresses

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    Previous studies have suggested that some graph properties of protein interaction networks might be related with gene morbidity. In particular, it has been suggested that when a polymorphism affects a gene, it is more likely to produce a disease if the node degree in the interaction network is higher than for other genes. However, these results do not take into account the possible bias introduced by the variance in the amount of information available for different genes. This work models the relationship between the morbidity associated with a gene and the degrees of the nodes in the protein interaction network controlling the amount of information available in the literature. A set of 7461 genes and 3665 disease identifiers reported in the Online Mendelian Inheritance in Man (OMIM) was mined jointly with 9630 nodes and 38756 interactions of the Human Proteome Resource Database (HPRD). The information available from a gene was measured through PubMed mining. Results suggest that the correlation between the degree of a node in the protein interaction network and its morbidity is largely contributed by the information available from the gene. Even though the results suggest a positive correlation between the degree of a node and its morbidity while controlling the information factor, we believe this correlation has to be taken with caution for it can be affected by other factors not taken into account in this study.

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    An information theory-based tool for characterizing the interaction environment of a protein  Open access

     Massanet Vila, Raimon Jaume; Gallardo Chacón, Joan Josep; Caminal Magrans, Pedro; Perera Lluna, Alexandre
    IEEE Engineering in Medicine and Biology Society
    Presentation's date: 2010-09
    Presentation of work at congresses

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    In recent years large amounts of information have been accumulated in proteomic, genetic and metabolic databases. Much effort has been dedicated to developing methods that successfully exploit, organize and structure this information. However, there is no application, that we know of, that semantically characterizes the interaction environment in which a protein exists. A high-throughput software package has been developed to retrieve information from publicly available databases, such as the Gene Ontology Annotation (GOA) database and the Human Proteome Resource Database (HPRD) and structure their information. This information is presented to the user as groups of semantically described dense interaction subnetworks that interact with a target protein.

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    Una herramienta basada en teoría de grafos y teoría de la información para la caracterización del entorno de interacción de un conjunto de proteínas  Open access

     Massanet Vila, Raimon Jaume; Gallardo Chacón, Joan Josep; Caminal Magrans, Pedro; Perera Lluna, Alexandre
    Congreso Anual de la Sociedad Española de Ingeniería Biomédica
    Presentation's date: 2010-09
    Presentation of work at congresses

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    En los últimos años se han acumulado grandes cantidades de información genética, proteinómica y metabólica en bases de datos públicas y privadas. Se ha dedicado un gran esfuerzo al desarrollo de herramientas capaces de explotar, estructurar y organizar esta información para poder sacar partido de ella. Sin embargo, a día de hoy no existe ninguna aplicación que caracterice el entorno en el que una proteína o conjunto de proteínas actúa. En este trabajo se ha desarrollado un paquete de software que consulta, de forma masiva, bases de datos publicas, como Gene Ontology Annotation (GOA) y Human Proteome Resource Database (HPRD) y presenta la información en ellas contenida de forma que pueda ser fácil y rápidamente interpretada por personas pertenecientes al entorno clínico y no familiarizadas con el uso de bases de datos. Para ello presenta al usuario un conjunto de grupos de proteínas que forman parte del entorno de interacción local del conjunto inicial de proteínas y que forman subredes de alta conectividad. Además describe con etiquetas semánticas los aspectos particulares de cada grupo.

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    Exons and introns characterization in nucleic acid sequences by time-frequency analysis  Open access

     Melia, Umberto Sergio Pio; Clarià Sancho, Francesc; Gallardo Chacón, Joan Josep; Caminal Magrans, Pedro; Perera Lluna, Alexandre; Vallverdú Ferrer, Montserrat
    IEEE Engineering in Medicine and Biology Society
    Presentation's date: 2010-08-31
    Presentation of work at congresses

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    A current problem in deoxyribonucleic acid (DNA) sequence analysis is to determine the exact locations of the genes and also in eukaryotes, the protein-coding regions in the mRNA primary transcript (pre-mRNA).The conversion into discrete numerical values of the symbols associated to the nucleotides of these sequences allows for a signal to address the problems related to localization and annotation of genes. In this work, thermodynamic data of free energy changes (#G°) on the formation of a duplex structure of DNA or RNA are used to convert the symbols into numerical values associated with the nucleotide sequence pre-mRNA. This study presents an analysis, based on techniques of time-frequency representation of a large number of gene sequences, in order to find variables related to pre-mRNA that could best characterize and discriminate coding regions from non-coding regions. It has been found that instantaneous frequency variables and instantaneous spectral energy variables in different frequency bands, allowed exons and introns to be correctly classified with more than 85%.

  • MEET: Motif Elements Estimation Toolki

     Pairó Castiñeira, Erola; Maynou Fernández, Joan; Vallverdú Ferrer, Montserrat; Gallardo Chacón, Joan Josep; Caminal Magrans, Pedro; Marco Colas, Santiago; Perera Lluna, Alexandre
    Congreso Anual de la Sociedad Española de Ingeniería Biomédica
    Presentation's date: 2010-11-18
    Presentation of work at congresses

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    Dimensionality reduction oriented toward the feature visualization for ischemia detection  Open access

     Delgado-Tejos, Edilson; Perera Lluna, Alexandre; Vallverdú Ferrer, Montserrat; Caminal Magrans, Pedro; Castellanos Dominguez, German
    IEEE transactions on information technology in biomedicine
    Date of publication: 2009-03-16
    Journal article

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    An effective data representation methodology on high-dimension feature spaces is presented, which allows a better interpretation of subjacent physiological phenomena (namely, cardiac behavior related to cardiovascular diseases), and is based on search criteria over a feature set resulting in an increase in the detection capability of ischemic pathologies, but also connecting these features with the physiologic representation of the ECG. The proposed dimension reduction scheme consists of three levels: projection, interpretation, and visualization. First, a hybrid algorithm is described that projects the multidimensional data to a lower dimension space, gathering the features that contribute similarly in the meaning of the covariance reconstruction in order to find information of clinical relevance over the initial training space. Next, an algorithm of variable selection is provided that further reduces the dimension, taking into account only the variables that offer greater class separability, and finally, the selected feature set is projected to a 2-D space in order to verify the performance of the suggested dimension reduction algorithm in terms of the discrimination capability for ischemia detection. The ECG recordings used in this study are fromthe European ST–T database and from the Universidad Nacional de Colombia database. In both cases, over 99% feature reduction was obtained, and classification precision was over 99% using a five-nearest-neighbor classifier (5-NN).

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    A new gene-based association test for genome-wide association studies  Open access

     Buil, Alfonso; Martínez-Pérez, Angel; Perera Lluna, Alexandre; Rib, Leonor; Caminal, Pere; Soria, José Manuel
    BMC proceedings (Online)
    Date of publication: 2009-12-15
    Journal article

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    Genome-wide association studies are widely used today to discover genetic factors that modify the risk of complex diseases. Usually, these methods work in a SNP-by-SNP fashion. We present a gene-based test that can be applied in the context of genome-wide association studies. We compare both strategies, SNP-based and gene-based, in a sample of cases and controls for rheumatoid arthritis. We obtained different results using each strategy. The SNP-based test found the PTPN22 gene while the gene-based test found the PHF19-TRAF1-C5 region. That suggests that no single strategy performs better than another in all cases and that a certain underlying genetic architecture can be delineated more easily with one strategy rather than with another.

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    Search of phenotype-related candidate genes using Gene Ontology-based semantic similarity and protein interaction information: application to Brugada syndrome  Open access

     Massanet Vila, Raimon Jaume; Gallardo Chacón, Joan Josep; Caminal Magrans, Pedro; Perera Lluna, Alexandre
    IEEE Engineering in Medicine and Biology Society
    Presentation's date: 2009-09-06
    Presentation of work at congresses

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    This work presents a methodology for finding phenotype candidate genes starting from a set of known related genes. This is accomplished by automatically mining and organizing the available scientific literature using Gene Ontology-based semantic similarity. As a case study, Brugada syndrome related genes have been used as input in order to obtain a list of other possible candidate genes related with this disease. Brugada anomaly produces a typical alteration in the Electrocardiogram and carriers of the disease show an increased probability of sudden death. Results show a set of semantically coherent proteins that are shown to be related with synaptic transmission and muscle contraction physiological processes.

  • Detección de los puntos de unión de los factores de transcripción mediante el análisis de la variabilidad de la información mutua cruzada

     Maynou Fernández, Joan; Vallverdú Ferrer, Montserrat; Clarià Sancho, Francesc; Gallardo Chacón, Joan Josep; Caminal Magrans, Pedro; Perera Lluna, Alexandre
    Congreso Anual de la Sociedad Española de Bioingeniería
    Presentation's date: 2009-11-18
    Presentation of work at congresses

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  • Búsqueda de genes candidatos mediante redes de interacciones entre proteínas y medidas de similitud semántica basadas en Gene Ontology: Aplicación al síndrome de Brugada

     Massanet Vila, Raimon Jaume; Gallardo Chacón, Joan Josep; Caminal Magrans, Pedro; Perera Lluna, Alexandre
    Congreso Anual de la Sociedad Española de Ingeniería Biomédica
    Presentation's date: 2009
    Presentation of work at congresses

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    Transcription factor binding site detection through position cross-mutual information variability analysis  Open access

     Maynou Fernández, Joan; Vallverdú Ferrer, Montserrat; Clarià Sancho, Francesc; Gallardo Chacón, Joan Josep; Caminal Magrans, Pedro; Perera Lluna, Alexandre
    IEEE Engineering in Medicine and Biology Society
    Presentation's date: 2009-09-02
    Presentation of work at congresses

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    Regulatory sequence detection is a fundamental challenge in computational biology. One key process in protein synthesis starts with the binding of the transcription factor to its binding site. Different sites can show binding to the same factor. This variability found in binding sequences increases the difficulty of their detection using computational algorithms. In this manuscript, a method for the detection of binding sites is proposed, based on the correlation between binding sequence positions through information theoretical measures. Efficiency values of the method are reported in the form of Receiver Operating Characteristic curves on the detection of different transcription factors of the Saccharomyces cerevisiae organism. We compare our results with other known motif detection Motif Discovery scan (MDscan).

  • Conservación de polimorfismos relacionados con enfermedades humanas

     Brunel, Helena; Gallardo Chacón, Joan Josep; Vallverdú Ferrer, Montserrat; Caminal Magrans, Pedro; Perera Lluna, Alexandre
    Congreso Anual de la Sociedad Española de Bioingeniería
    Presentation's date: 2009-11-18
    Presentation of work at congresses

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  • Representación tiempo-frecuencia para caracterizar secuencias de acido nucléico

     Gallardo Chacón, Joan Josep; Melia, Umberto Sergio Pio; Clarià Sancho, Francesc; Caminal Magrans, Pedro; Perera Lluna, Alexandre; Vallverdú Ferrer, Montserrat
    Congreso Anual de la Sociedad Española de Bioingeniería
    Presentation's date: 2009-11-18
    Presentation of work at congresses

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  • BIOLOGICALLY INSPIRED COMPUTATION FOR CHEMICAL SENSING

     Caminal Magrans, Pedro; Perera Lluna, Alexandre
    Participation in a competitive project

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