Alexandre Perera Lluna

alex1Welcome to my site. My name is Alexandre Perera Lluna, sometimes Alex Perera. I am a researcher at 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.

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:

  1. 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
  2. J Maynou, E Pairó, S Marco, A Perera (2015) Sequence information gain based motif analysis, BMC bioinformatics 16 (1), 1. Link.
  3. Vizoso, M., Puig, M., Carmona, F. J., Maqueda, M., Velásquez, A., Gomez, A., … & Alcaraz, J. (2015). Aberrant DNA methylation in Non Small Cell Lung Cancer associated fibroblasts. Carcinogenesis, In Press. Link
  4. Ziyatdinov, A., & Perera, A. (2015). Synthetic benchmarks for machine olfaction: Classification, segmentation and sensor damage. Data in Brief, 3, 126-130. Link
  5. 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
  6. 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
  7. 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 (2014). Link
  8. 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 (2014). Link
  9. 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
  10. 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
  11. 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
  12. 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
  13. Ziyatdinov A., Perera A., Data simulation in machine olfaction with the R package chemosensors, PLOS One, 9 (2), e88839 , (2014).
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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.

Currently, the PhD students working with me are:

  • Sergio Picart
  • María Maqueda
  • Samir Kanaan
  • Giovana Gavidia