Alexandre Perera Lluna

alex1Welcome to my site. My name is Alexandre Perera Lluna, sometimes Alex Perera. I hold a degree in Physics, a second degree in electrical engineering, and a PhD in physics by the University of Barcelona. I am currently leading  the B2SLab. This lab belongs to the Research Center for Biomedical Engineering (CREB) of the Universitat Politècnica de Catalunya (Polytechnic University of Catalonia, UPC), in the sunny city of Barcelona. It is a great city for research, culture and leisure. I am really in love with this city, where I was born.

At B2SLab, we are trying to mix Bioinformatics and Bioengineering, mainly towards cardiovascular research. Our main focus, however, is applied signal processing, machine learning and statistical pattern recognition.  We have some experience in solving problems in data integration and data fusion, metabolomics, high throughput enrichment, Bioengineering and others.

Since October 2019 I have been appointed as head of the Research Center for Biomedical Engineering at UPC (CREB-UPC Centre de Recerca en Enginyeria Biomèdica).

e-mail

Teaching

I teach at UPC, at the Master in Biomedical Engineering,where I teach two subjects Introduction to Bioinformatics and Data Mining for Biomedical Databases.  I also teach at the Master ‘s degree in Automatic Control and Robotics, where I teach some real time systems and scientific python.

I have also been writing some material for several classes, please check my:

I am (slowly) writing some shiny apps for teaching:

Publications

You can also check my journal papers, also listed with the publications for all the group or google scholar.

  1. Sergi Picart-Armada, Wesley K. Thompson, Alfonso Buil, Alexandre Perera-LLuna, The effect of statistical normalisation on network propagation scores (2020), Bioinformatics, In Press [Link]
  2. A Lopez-del Rio, M Martin, A Perera-Lluna, R Saidi, Effect of sequence padding on the performance of deep learning models in archaeal protein functional prediction (2020), Scientific Reports 10 (1), 1-14
  3. Elizabeth Carolina Jiménez, Claudia Avella-Garcia, James Kustow, Sally Cubbin, Montse Corrales, Vanessa Richarte, Flavia Lorena Esposito, Imanol Morata, Alexandre Perera, Paloma Varela, Jose Cañete, Stephen V Faraone, Hans Supèr, Josep Antoni Ramos-Quiroga, Eye vergence responses during an attention task in adults with ADHD and clinical controls, Journal of attention disorders (2020), 1087054719897806
  4. Sergio Picart-Armada, Steven J Barrett, David R Willé, Alexandre Perera-Lluna, Alex Gutteridge, Benoit H Dessailly, Benchmarking network propagation methods for disease gene identification (2019), PLoS computational biology 15 (9), e1007276
  5. S Kanaan-Izquierdo, A Ziyatdinov, MA Burgueño, A Perera-Lluna, Multiview: a software package for multiview pattern recognition methods (2019), Bioinformatics 35 (16), 2877-2879
  6. Josep Lupón, Giovana Gavidia-Bovadilla, Elena Ferrer, Marta de Antonio, Alexandre Perera-Lluna, Jorge López-Ayerbe, Mar Domingo, Julio Núñez, Elisabet Zamora, Pedro Moliner, Evelyn Santiago-Vacas, Javier Santesmases, Antoni Bayés-Genis (2019) Heart Failure With Preserved Ejection Fraction Infrequently Evolves Toward a Reduced Phenotype in Long-Term Survivors, Circulation: Heart Failure 12 (3), e005652
  7. Angela Lopez-del Rio, Alfons Nonell-Canals, David Vidal, Alexandre Perera-Lluna (2019) Evaluation of Cross-Validation Strategies in Sequence-Based Binding Prediction Using Deep Learning, Journal of chemical information and modeling 59 (4), 1645-1657
  8. Alba Castells-Sánchez, Francesca Roig Coll, Noemi Lamonja Vicente, Marina Altés-Magret, Pere Torán-Montserrat, Marc Via, Alberto Garcia-Molina, Jose Maria Tormos, Antonio Heras, M Teresa Alzamora, Rosa Forés, Guillem Pera, Rosalia Dacosta-Aguayo, Juan José Soriano-Raya, Cynthia Maria Caceres, Pilar Montero-Alía, Juan José Monter-Alía, M Mercedes Jiménez González, Maria Hernandez-Perez, Alexandre Perera-Lluna, George Andre Grove, Josep Munuera, Sira Domènech, Kirk I Erickson, Maria Mataro (2019) Effects and Mechanisms of Cognitive, Aerobic Exercise, and Combined Training on Cognition, Health, and Brain Outcomes in Physically Inactive Older Adults: The Projecte Moviment Protocol, Frontiers in aging neuroscience 11, 216
  9. Haizea Ziarrusta, Leire Mijangos, Sergio Picart-Armada, Mireia Irazola, Alexandre Perera-Lluna, Aresatz Usobiaga, Ailette Prieto, Nestor Etxebarria, Maitane Olivares, Olatz Zuloaga “Non-targeted metabolomics reveals alterations in liver and plasma of gilt-head bream exposed to oxybenzone” Chemosphere 211, 624-631. Link
  10. Josep Lupón, Giovana Gavidia-Bovadilla, Elena Ferrer, Marta de Antonio, Alexandre Perera-Lluna, Jorge López-Ayerbe, Mar Domingo, Julio Núñez, Elisabet Zamora, Pedro Moliner, Patricia Díaz-Ruata, Javier Santesmases, Antoni Bayés-Genís, “Dynamic trajectories of left ventricular ejection fraction in heart failure“, Journal of the American College of Cardiology 72 (6), 591-601. Link 
  11. Hernández-Lara AB, Perera-Lluna A and Serradell-López E (2019), “Applying learning analytics to students’ interaction in business simulation games. The usefulness of learning analytics to know what students really learn”, Computers in Human Behavior. Pergamon. Computers in Human Behavior 92, 600-612 Link
  12. Sergio Picart-Armada, Francesc Fernández-Albert, Maria Vinaixa, Oscar Yanes, Alexandre Perera-Lluna (2018) FELLA: an R package to enrich metabolomics data, BMC bioinformatics 19 (1), 538
  13. Kanaan-Izquierdo S, Ziyatdinov A and Perera-Lluna A (2018), “Multiview and multifeature spectral clustering using common eigenvectors”, Pattern Recognition Letters. Vol. 102, pp. 30-36. North-Holland. Link
  14. Caminal P, Sola F, Gomis P, Guasch E, Perera A, Soriano N and Mont L (2018), “Validity of the Polar V800 monitor for measuring heart rate variability in mountain running route conditions”, European Journal of Applied Physiology. , pp. 1-9. Springer Berlin Heidelberg. Link
  15. Jaramillo-Garzón JA, Castellanos-Dominguez CG and Perera-Lluna A (2016), “Applicability of semi-supervised learning assumptions for gene ontology terms prediction”, Revista Facultad de Ingenier\ia Universidad de Antioquia. (79), pp. 19-32. Universidad de Antioquia. Link
  16. Gavidia-Bovadilla G, Kanaan-Izquierdo S, Mataró-Serrat M, Perera-Lluna A, Initiative ADN and others (2017), “Early prediction of alzheimer’s disease using null longitudinal model-based classifiers”, PloS one. Vol. 12(1), pp. e0168011. Public Library of Science. Link
  17. Maqueda M, Roca E, Brotons D, Soria JM and Perera A (2017), “Affected pathways and transcriptional regulators in gene expression response to an ultra-marathon trail: Global and independent activity approaches”, PloS one. Vol. 12(10), pp. e0180322. Public Library of Science. Link
  18. Picart-Armada S, Fernández-Albert F, Vinaixa M, Rodríguez MA, Aivio S, Stracker TH, Yanes O and Perera-Lluna A (2017), “Null diffusion-based enrichment for metabolomics data”, PloS one. Vol. 12(12), pp. e0189012. Public Library of Science. Link
  19. Picart-Armada S, Thompson WK, Buil A and Perera-Lluna A (2017), “diffuStats: an R package to compute diffusion-based scores on biological networks”, Bioinformatics 34(3):533-534 (2018). Link
  20. Vallverdú M, Ruiz-Muñoz A, Roca E, Caminal P, Rodríguez FA, Irurtia A and Perera A (2017), “Assessment of Heart Rate Variability during an Endurance Mountain Trail Race by Multi-Scale Entropy Analysis”, Entropy. Vol. 19(12), pp. 658. Multidisciplinary Digital Publishing Institute. Link
  21. Domingo-Almenara X, Brezmes J, Venturini G, Vivó-Truyols G, Perera A and Vinaixa M (2017), “Baitmet, a computational approach for GC–MS library-driven metabolite profiling”, Metabolomics. Vol. 13(8), pp. 93. Springer US. Link
  22. Ziyatdinov A, Brunel H, Martinez-Perez A, Buil A, Perera A and Soria JM (2016), “solarius: an R interface to SOLAR for variance component analysis in pedigrees”, Bioinformatics. Vol. 32(12), pp. 1901-1902. Oxford University Press. Link
  23. Domingo-Almenara X, Brezmes J, Vinaixa M, Samino S, Ramirez N, Ramon-Krauel M, Lerin C, D\iaz M, Ibáñez L, Correig X and others (2016), “eRah: A computational tool integrating spectral deconvolution and alignment with quantification and identification of metabolites in GC/MS-based metabolomics”, Analytical chemistry. Vol. 88(19), pp. 9821-9829. American Chemical Society. Link
  24. Domingo-Almenara X, Perera A and Brezmes J (2016), “Avoiding hard chromatographic segmentation: A moving window approach for the automated resolution of gas chromatography–mass spectrometry-based metabolomics signals by multivariate methods”, Journal of Chromatography A. Vol. 1474, pp. 145-151. Link
  25. Brunel H, Massanet R, Martinez-Perez A, Ziyatdinov A, Martin-Fernandez L, Souto JC, Perera A and Soria JM (2016), “The central role of KNG1 gene as a genetic determinant of coagulation pathway-related traits: Exploring metaphenotypes”, PloS one. Vol. 11(12), pp. e0167187. Public Library of Science. Link
  26. Rosa  Vázquez-Fresno; Rafael  Llorach; Alexandre Perera; Rupasri Mandal; Miguel Feliz; Francisco J Tinahones; David S Wishart (2016). Clinical Phenotype Clustering in Cardiovascular risk patients for the identification of Responsive Metabotypes after Red Wine Polyphenol intake, Journal of Nutritional Biochemistry, 28, 114-120. Link
  27. J Maynou, E Pairó, S Marco, A Perera (2015) Sequence information gain based motif analysis, BMC bioinformatics 16 (1), 1. Link.
  28. Miguel Vizoso Marta Puig F.Javier Carmona María Maqueda Adriana Velásquez Antonio Gómez Anna Labernadie Roberto Lugo Marta Gabasa Luis G. Rigat-Brugarolas Xavier Trepat Josep Ramírez Sebastian Moran Enrique Vidal Noemí Reguart Alexandre Perera Manel Esteller Jordi Alcaraz (2015). Aberrant DNA methylation in Non Small Cell Lung Cancer associated fibroblasts. Carcinogenesis, 36(12)1453–63. Link
  29. Ziyatdinov, A., & Perera, A. (2015). Synthetic benchmarks for machine olfaction: Classification, segmentation and sensor damage. Data in Brief, 3, 126-130. Link
  30. Ziyatdinov, A., Fonollosa, J., Fernández, L., Gutiérrez-Gálvez, A., Marco, S., & Perera, A. (2015). Data set from gas sensor array under flow modulation. Data in Brief, 3, 131-136. Link
  31. Domingo-Almenara, X., Perera, A., Ramírez, N., Cañellas, N., Correig, X., & Brezmes, J. (2015). Compound identification in gas chromatography/mass spectrometry-based metabolomics by blind source separation. Journal of Chromatography A, 1409, 226-233. Link
  32. Andrey Ziyatdinov, Jordi Fonollosa, Luis Fernández, Agustín Gutierrez-Gálvez, Santiago Marco, Alexandre Perera. Bioinspired Early Detection through Gas Flow Modulation in Chemo-Sensory Systems. Sensors and actuators B: Chemical Sensors and Actuators B: Chemical  (206) 538-547 (2014). Link
  33. Fernández-Albert F., Llorach R., Garcia-Aloy M, Ziyatdinov A, Andrés-Lacueva C., Perera-Lluna A. Intensity drift removal in LC/MS metabolomics by Common Variance Compensation. Bioinformatics 30(20): 2899–2905, Bioinformatics (2014). Link
  34. Fernández-Albert F., Llorach R., Andrés-Lacueva C., Perera-Lluna A. An R package to analyse LC/MS metabolomic data: MAIT (Metabolite Automatic Identification Toolkit). Bioinformatics 30(13):1937-9 (2014). Link
  35. Fernández-Albert F., Llorach R., Andrés-Lacueva C., Perera-Lluna A. Peak Aggregation as an Innovative Strategy for Improving the Predictive Power of LC-MS Metabolomic Profiles. Analytical Chemistry 86 (5), 2320–2325 (2014). Link
  36. S Marco, A Gutiérrez-Gálvez, Anders Lansner, D Martinez, JP Rospars, R Beccherelli, A Perera, Timothy Charles Pearce, PFMJ Verschure, K Persaud,
     A biomimetic approach to machine olfaction, featuring a very large-scale chemical sensor array and embedded neuro-bio-inspired computation, Microsystem Technologies 20 (4-5), 729-742 (2014). Link
  37. A Perera-Lluna, K Manivannan, P Xu, R Gutierrez-Osuna, C Benner, B.D. Russell, Automatic capacitor bank identification in power distribution systems, Electric Power Systems Research 111, 96-102 (2014). Link
  38. Ziyatdinov A., Perera A., Data simulation in machine olfaction with the R package chemosensors, PLOS One, 9 (2), e88839 , (2014).
  39. Brunel, H., Gallardo-Chacón, J.-J., Vallverdú, M., Caminal, P. & Perera, A. Effect of genetic regions on the correlation between single point mutation variability and morbidity. Computers in biology and medicine, 43 (5), 594-599 (2013). Link
  40. Jaramillo-Garzón, J.A., Gallardo-Chacón, J.J., Castellanos-Domínguez, C.G. & Perera-Lluna, A. Predictability of Gene Ontology Slim-Terms From Primary Structure Information in Embryophyta plant Proteins. BMC bioinformatics 14, 68 (2013). Link
  41. Ziyatdinov, A.; Fernandez, E.; Chaudry, A.; Marco, S.; Persaud, K.; Perera, A. A software tool for large-scale synthetic experiments based on polymeric sensor arrays. Sensors and actuators. B. Chemical.177, 596 – 604 (2013). Link
  42. Melia, U. S., Vallverdú, M., Clarià, F., Gallardo, J. J., Perera, A., & Caminal, P. Choi-Williams Distribution to Describe Coding and Non-coding Regions in Primary Transcript Pre-mRNA. Journal of Medical and Biological Engineering33(5), 504-512 (2013). Link
  43. Pairo, E., Maynou, J., Marco, S. & Perera, A. A subspace method for the detection of transcription factor binding sites. Bioinformatics 28, 1328-1335 (2012). Link
  44. Fonollosa, J.; Gutierrez-Galvez, A.; Lansner, A.; Martinez, D.; Rospars, J.; Beccherelli, R.; Perera, A.; Pearce, T.; Vershure, P.; Persaud, K.; Marco, S. Biologically Inspired Computation for Chemical Sensing. Procedia Computer Science 7, 226-227 (2011). Link
  45. Brunel, H.; Gallardo, J.; Buil, A.; Vallverdu, M.; Soria, J.; Caminal, P.; Perera, A. MISS: a non-linear methodology based on mutual information for genetic association studies in both population and sib-pairs analysis. Bioinformatics 26, 1811-1818 (2010). Link
  46. Perera, A., Pardo, A., Barrettino, D., Hierlermann, A. & Marco, S. Evaluation of fish spoilage by means of a single metal oxide sensor under temperature modulation. Sensors and Actuators B: Chemical 146, 477-482 (2010). Link
  47. Ziyatdinov, A.; Marco, S.; Chaudry, A.; Persaud, K.; Caminal, P.; Perera, A. Drift compensation of gas sensor array data by common principal component analysis. Sensors and Actuators B: Chemical 146, 460-465 (2010). Link
  48. Maynou, J., Gallardo-Chacon, J.J., Vallverdu, M., Caminal, P. & Perera, A. Computational Detection of Transcription Factor Binding Sites Through Differential Rényi Entropy. IEEE Transactions on Information Theory 56, 734-741 (2010). Link
  49. Padilla, M.; Perera, A.; Montoliu, I.; Chaudry, A.; Persaud, K.; Marco, S. Drift compensation of gas sensor array data by Orthogonal Signal Correction. Chemometrics and Intelligent Laboratory Systems 100, 28-35 (2010). Link
  50. Buil, A.; Martínez-Pérez, A.; Perera, A.; Rib, L.; Caminal, P.; Soria, J. A new gene-based association test for genome-wide association studies. The American Journal of Human Genetics 3, S130 (2009). Link
  51. Delgado E, Perera A, Vallverdú M, Caminal P, Castellanos G. Dimensionality reduction oriented toward the feature visualization for ischemia detection. IEEE Trans. Information Technology in Biomedicine 13, 4 590-598 (2009). Link
  52. Delgado-Trejos, E., Perera-Lluna, A., Vallverdu-Ferrer, M., Caminal-Magrans, P. & Castellanos-Dominguez, G. Dimensionality reduction oriented toward the feature visualization for ischemia detection. IEEE transactions on information technology in biomedicine a publication of the IEEE Engineering in Medicine and Biology Society 13, 590-598 (2009). Link
  53. Perera, A., Vallverdu, M., Claria, F., Soria, J.M. & Caminal, P. DNA binding site characterization by means of Rényi entropy measures on nucleotide transitions. IEEE Transactions on NanoBioscience 7, 133-141 (2008). Link
  54. Buil, A.; Perera, A.; Souto, R.; Peralta, J.; Almasy, L.; Vallverdu, M.; Caminal, P.; Soria, J. Searching for master regulators of transcription in a human gene expression data set. BMC proceedings 1, S81 (2007). Link
  55. Buil, A.; Perera, A.; Brunel, H.; Souto, J.; Fontcuberta, J.; Vallverdu, M.; Soria, J.; Caminal, P. Gene-phenotype association using mutual information-based cluster analysis. Genetic epidemiology.31 – 6, 618 – 618.09 (2007). Link
  56. Antonio, P.; Lourdes, C.; Cabré, J.; Perera, A.; Xavier, C.; Santiago, M. Gas measurement systems based on IEEE1451.2 standard. Sensors and Actuators B: Chemical 116, 11-16 (2006). Link
  57. Perera, A., Yamanaka, T., Gutiérrez-Gálvez, A., Raman, B. & Gutiérrez-Osuna, R. A dimensionality-reduction technique inspired by receptor convergence in the olfactory system. Sensors and Actuators B: Chemical 116, 17-22 (2006). Link
  58. Padilla, M.; Montoliu, I.; Pardo, A.; Perera, A. Feature extraction on three way enose signals. Sensors and actuators B. Chemical.116 – 1-2 ,145 – 150.07 (2006). Link
  59. Perera, A., Papamichail, N., Barsan, N., Weimar, U. & Marco, S. On-line novelty detection by recursive dynamic principal component analysis and gas sensor arrays under drift conditions. Ieee Sensors Journal 6, 770-783 (2006). Link
  60. Perera, A.; Montoliu, I.; Pardo, A.; Marco, S. Algoritmos de reconocimiento de patrones y clasificación para olfacción artificial. La Olfacción en España.pp. 325 – 352.Editorial SBI3, ISBN 84-933858-5-9 (2006). Link
  61. Teodor, S.; Santiago, M.; Perera, A.; Antonio, P.; Simone, H.; Nicolae, B. Fuzzy inference system for sensor array calibration: prediction of CO and CH4 levels in variable humidity conditions. Chemometrics and intelligent laboratory systems.64 – 2,103 – 122.11 (2002). Link
  62. Perera, A., Sundic, T., Pardo, A., Gutiérrez-Osuna, R., Marco, S. A portable electronic nose based on embedded PC technology and GNU/LINUX: Hardware, software and applications, IEEE Sensors Journal, 2 (3), 235-246 (2002). Link
  63. Arturo, O.; Santiago, M.; Perera, A.; Teodor, S.; Antonio, P.; Samitier, J. An intelligent detector based on temperature modulation of a gas sensor with a digital signal processor. Sensors and Actuators B: Chemical 78, 32-39 (2001). Link
  64. Perera, A.; Sundic, T.; Marco, S. A bio-inspired nonlinear algorithm to integrate carbon monoxide concentration aiming to fulfil international standards. Sensors and actuators B. Chemical. 69 – 3, 308 – 313.10 (2000). Link

You can also find my papers at some conferences in my google scholar website.

Thesis

I have advised several PhD students, which just defended:

  • Helena Brunel. Genetic association analysis of complex diseases through information theoretic metrics and linear pleiotropy. Defended on 14/11/2013 at Universitat Politècnica de catalunya
  • Jorge Alberto Jaramillo Garzón. Protein function prediction with semi-supervised classification based on evolutionary multi-objective optimization, Defended on 25/11/2013 at the Universidad Nacional de Colombia. This thesis was coadvised with Dr. German Castellanos from the same university.
  • Andrey Ziyatdinov, Biomimetic Setup for Chemosensor-Based Machine olfaction. Defended on 4/12/2014 at Universitat Politècnica de Catalunya.
  • Francesc Fernandez, Machine Learning Methods for the automated analysis of metabolomic data. Defended on 30/10/2014 at Universitat Politècnica de Catalunya.
  • Erola Pairó,   Detection of Transcription Factor Binding Sites by Means of Multivariate Signal Processing Techniques. Defended on 21/07/2015 at Universitat de Barcelona. This thesis was coadvised with Dr. Santiago Marco from the same university.
  • Joan Maynou, Computational representation and discovery of transcription factor binding sites. Defended on 01/02/2016 at Universitat Politècnica de Catalunya.
  • Giovana Gavidia, Study of Longitudinal Neurodegeneration Biomarkers to Support the Early Diagnosis of Alzheimer’s Disease. Defended on 20/03/2018 at Universitat Politècnica de Catalunya.
  •  Samir Kanaan. Multiview pattern recognition methods for data visualization, embedding and clustering.  Defended on 22/09/2017 at Universitat Politècnica de Catalunya.
  • Sergio Pixart, “Statistical Normalisation of Network Propagation Methods for Computational biology” , by Sergio Picart, 23/7,2020. The defense was performed online due to the sars-cov-2 pandemic and published in here.

Currently, the PhD students working with me are:

  • Sergio Picart
  • María Maqueda
  • Pol Solà
  • Àngela López
  • Jon Garrido