PhD Thesis
Title: Relation between protein sequence and structure/function and the effect on clinical phenotype
Student: Gabriel Ruiz Alías
Advisors: Mireia Olivella
PhD Program: Bioinformatics
University: Universitat de Vic – Universitat Central de Catalunya (interuniversity)
Defense date: in progress
Title: Study of the relation between genotype and phenotype in glutamatergic synapse genes
Student: Sergi Soldevila Gálvez
Advisors: Mireia Olivella
PhD Program: Bioinformatics
University: Universitat de Vic – Universitat Central de Catalunya (interuniversity)
Defense date: in progress
Title: Regulatory function of piRNAs in insect oogenesis
Student: David Pujal Bau
Advisors: Josep Bau Macià and M.Dolors Piulachs Bagà (IBE)
PhD Program: Experimental Sciences and Technology
University: Universitat de Vic – Universitat Central de Catalunya
Defense date: in progress
Title: Gene expression prediction under novel conditions using ATAC-seq-informed regulons
Student: Roger Casals Franch
Advisors: Jordi Villà Freixa, Adrián López García de Lomana
PhD Program: Bioinformatics
University: Universitat de Vic – Universitat Central de Catalunya (interuniversity)
Defense date: in progress
Title: Development of a personalized multifactorial model for intestinal microbial health evaluation
Student: Meritxell Pujolassos Tanyà
Advisors: Malu Calle
PhD Program: Experimental Sciences and Technology
University: Universitat de Vic – Universitat Central de Catalunya
Defense date: in progress
Title: Working memory capacity during aging: a neurodynamical investigation.
Student: Marta Balagué
Advisors: Laura Dempere
PhD Program: Experimental Sciences and Technology
University: Universitat de Vic – Universitat Central de Catalunya
Defense date: in progress
Title: The role of glycosylation and sialylation of cell membrane receptors: linking function to molecular organization
Student: Sergi Masó Orriols
Advisors: Carlo Manzo and Joan Bertran
PhD Program: Experimental Sciences and Technology
University: Universitat de Vic – Universitat Central de Catalunya
Defense date: in progress
Title: The influence of the spatiotemporal organization of proteins of the tight junction on the permeability of the intestinal barrier
Student: Montserrat Masoliver
Advisors: Carlo Manzo
PhD Program: Experimental Sciences and Technology
University: Universitat de Vic – Universitat Central de Catalunya
Defense date: in progress
Title: Investigating The Structure-Function Changes Due to Variations In Redox Regulating Glutathione Peroxidases
Student: Nayanika Das
Advisors: Jordi Villà and V. Baladhye (Pune University)
PhD Program: Bioinformatics
University: Universitat de Vic – Universitat Central de Catalunya (interuniversity)
Defense date: in progress
Title: Inference of perturbed gene regulatory mechanisms in glioblastoma
Student: Jing Yang
Advisors: Jordi Villà and Adrián López
PhD Program: Bioinformatics
University: Universitat de Vic – Universitat Central de Catalunya (interuniversity)
Defense date: in progress
Title: Artificial Intelligence ability to predict delirium onset in ICU patients with remote computer vision (affective monitoring, motor activity patterns monitoring)
Student: Karen Márquez
Advisors: Bartomeu Ayala & Laura Dempere
PhD Program: Experimental Sciences and Technology
University: Universitat de Vic – Universitat Central de Catalunya
Defense date: in progress
Title: Deep Learning for Quantitative Microscopy
Student: J. Pineda
Advisors: Carlo Manzo and Giovanni Volpe (University of Gothenburg)
PhD Program: Physics
University: University of Gothenburg
Defense date: in progress
Title: Quantitative Analysis of Super-resolution Imaging of Exocytosys
Student: J.S. Ortiz
Advisors: Oriol Gallego and Carlo Manzo
PhD Program: Biomedicine
University: Universitat Pompeu Fabra
Defense date: in progress
Title: Chronic wound multiscale evaluation: from the molecular mechanisms to an objective clinical follow-up
Student: Marta Cullell
Advisors: Carlo Manzo and Marta Otero
PhD Program: Experimental Sciences and Technology
University: Universitat de Vic – Universitat Central de Catalunya
Defense date: May 22, 2023
Title: Network-based predictions of drug’s adverse events on druggable protein targets
Student: Cristiano Galletti
Advisors: Narcís Fernàndez
PhD Program: Bioinformatics
University: Universitat de Vic – Universitat Central de Catalunya (interuniversity)
Defense date: October 10, 2022
Title: Bioinformatic tools to understand the structure-function relationships in membrane protein
Student: Adrián García Recio
Advisors: Mireia Olivella and Arnau Cordomí
PhD Program: Bioinformatics
University: Universitat de Vic – Universitat Central de Catalunya (interuniversity)
Defense date: February 09, 2022
Title: Development of a framework for the computational design and evolution of enzymes
Student: Martin Floor
Advisors: Jordi Villà-Freixa, Luís Agulló
PhD Program: Bioinformatics
University: Universitat de Vic – Universitat Central de Catalunya (interuniversity)
Defense date: January 04, 2022
Title: Producció d’antígens recombinants de Toxoplasma Gondii en soques Escherichia coli editades genèticament. Industrial PhD at Spinreact SAU (Toyobo Group) and Universitat de Vic-Universitat Central de Catalunya
Student: Adrià Redondo Jiménez
Advisors: Joan Bertran
PhD Program: Industrial Doctorate / Experimental Sciences and Technology
University: Universiat de Vic – Universitat Central de Catalunya
Defense date: November 20, 2020
Title: Refining and improving a next-generation sequencing gene panel for clinical diagnosis of hereditary hematologic diseases and development of bioinformatic tools for biomedical analysis. Industrial PhD at Whole Genics SL and Institut d’Investigacions Josep Carreras contra la Leucèmia and Universitat de Vic-Universitat Central de Catalunya
Student: Beatriz Cadenas Sevilla
Advisors: M.Luz Calle, Mayka Sanchez, Christian Tornador
PhD Program: Industrial Doctorate / Experimental Sciences and Technology
University: Universiat de Vic – Universitat Central de Catalunya
Defense date: November 12, 2019
Qualification: Excel.lent Cum Laude
Title: Research on Graph-based Visual Scene Representation and its Applications
Student: Lijuan Xu
Advisors: Xiaopeng Hu & Laura Dempere
PhD Program: Experimental Sciences and Technology
University: Dalian University of Technology
Defense date: October 28, 2019
Title: Development of Bioinformatic Tools for the Study of Membrane Proteins
Student: Eduard Mayol
Advisors: Mireia Olivella and Arnau Cordomí
PhD Program: Bioinformatics
University: Universitat de Vic – Universitat Central de Catalunya (interuniversity)
Defense date: June 2019
Title: Statistical methods for the analysis of microbiome compositional data in HIV studies
Student: Javier Rivera Pinto
Advisors: M.Luz Calle, Marc Noguera
PhD Program: Experimental Sciences and Technology
University: Universiat de Vic – Universitat Central de Catalunya
Defense date: November 30, 2018
Qualification: Excel.lent Cum Laude
Title: Proposal, evaluation and application of two new methodologies for genetic profiling in association studies
Student: Víctor Urrea
Advisor: M.Luz Calle
PhD Program: Systems Biology
Department: Systems Biology Department
University: Universitat de Vic – Universitat Central de Catalunya
Defense date: April 22, 2015
Qualification: Excel.lent
Title: Development of a multiscale protocol for the study of energetic of protein dynamics
Student: Nils Jan Daniel Drechsel
Advisor: Jordi Villà-Freixa
University: Universitat Pompeu Fabra
Defense date: 2013
Title: Interval-censored semi-competing risks data: a novel approach for modelling bladder cancer.
Student: Nuria Porta Bleda
Advisors: Guadalupe Gómez (UPC) and M.Luz Calle (Uvic)
PhD Program: Programa de doctorado en Estadística e IO
Department: Departamento de Estadística e Investigación Operativa
University: Universitat Politècnica de Catalunya
Defense date: July 27, 2010
Qualification: Excel.lent Cum Laude
Title: El transporte de arginina en macrófagos.! Respuesta a activación, proliferación y GM-CSF
Student: Lorena Martín Jaular
Advisors: Manuel Palacín, Joan Bertran
University: Universitat de Barcelona
Defense date: October 03, 2006
Title: Caracterització estructural i funcional del transportador d’aminoàcids heterodimèric rBAT/bo,+AT
Student: Núria Reig i Bolaño
Advisors: Manuel Palacín, Joan Bertran
University: Universitat de Barcelona
Defense date: January 31, 2003
Final Master & Bachelor Thesis
Master Thesis
Title: Energia lliure d’activació en les variants enzimàtica en la transaminació del mecanisme molecular de formació de la sitagliptina
Student: J. Solà
Advisor: J. Villà
Master program: Química Aplicada
University:Universitat Nacional d’Educació a Distància
Date: 2022
Title: Incoporation of Alphafold in the development of a new protocol for enzyme design
Student: J. González
Advisor: J. Villà
Master program: Msc in Omics Data Analysis
University: Universitat de Vic – Universitat Central de Catalunya
Date: 2022
Title: Seguiment de l’activitat de la plaga Helicoverpa armigera amb raspberry pi
Student: C. Pernazza
Advisor: J. Bau
Master program: Protecció Integrada de Conreus
University: Universitat de Lleida
Date: 2022
Title: Producció de proteïnes recombinants a partir de substrats crus amb Pichia pastoris
Student: J. M. Navarro i J. Vendrell
Advisor: X. Garcia
Master program: Biotecnologia Avançada
University: Universitat de Auntònoma de Barcelona
Date: 2022
Title: Evaluating the polygenicity of brain structure features using Compositional Data Analysis
Student: P. Genius
Advisor: M. Calle
Master program: Msc in Omics Data Analysis
University: Universitat de Vic – Universitat Central de Catalunya
Date: 2021
Title: A nested sampling algorithm for quantifying protein copy number in super-resolution microscopy
Student: T. Kosuta
Advisor: C. Manzo
Date: 2021
Title: A deep learning approach for the quantification of molecular organization from single-molecule localization microscopy
Student: S. Noé
Advisor: C. Manzo
Master program: Msc in Omics Data Analysis
University: Universitat de Vic – Universitat Central de Catalunya
Date: 2021
Title: Application of convolutional neural network for protein counting and localization photographed by super-resolution microscopy
Student: I. Meic
Advisor: C. Manzo
Date: 2020
Title: Integration of omics and non-omics data in pancreatic cancer research
Student: P. Alarcón
Advisor: M. Calle and N. Malats (CNIO, Madrid)
Master program: Msc in Omics Data Analysis
University: Universitat de Vic – Universitat Central de Catalunya
Date: 2019
Title: MetKMR: a flexible package for the discovery of differentially methylated regions via a Kernel regression sliding-window approach on DNA methylation data and the integration of transcriptomic data
Student: R. Barral
Advisor: M. Calle
Master program: Msc in Omics Data Analysis
University: Universitat de Vic – Universitat Central de Catalunya
Date: 2019
Title: Omics Child gut microbiome diversity and pollutant exposure to heavy metals and organochlorines
Student: S. Prérez
Advisor: M. Calle
Master program: Msc in Omics Data Analysis
University: Universitat de Vic – Universitat Central de Catalunya
Date: 2019
Title: Analysis of α5β1 integrin diffusion with single-particle tracking
Student: J. Ivcevic
Advisor: C. Manzo
Date: 2019
Title: Identification of Blattella germanica piRNAs
Student: N. Llonga
Advisor: J. Bau (codirigit amb IBE, projecte piRNAs)
Master program: Msc in Omics Data Analysis UVic-UCC
University: Universitat de Vic – Universitat Central de Cataluya
Date: 2018
Title: Modelling GPCR homodimers using molecular dynamics simulations
Student: A. Garcia-Recio
Advisor: M. Olivella
Master program: Msc in Omics Data Analysis
University: Universitat de Vic – Universitat Central de Cataluya
Date: 2018
Title: Efecte de la velocitat especifica de creixement en la producció de Lip-1 de Candida rugosa en Pichia pastoris sota l’efecte del promotor AOX1
Student: A. Gasset
Advisor: X. Garcia
Master program: Biotecnologia Avançada
University: Universitat Auntònoma de Barcelona
Date: 2018
Title: Effect of modification in the gene sequence of Rhizopus oryzae lipase expressed in Pichia pastoris in the production and downstream bioprocess
Student: P. Gonzalez
Advisor: X. Garcia
Master program: Biotecnologia Avançada
University: Universitat Auntònoma de Barcelona
Date: 2018
Title: StP: a web server to predict pathogenesis of non-synonymous single nucleotide polymorphisms in membrane proteins
Student: I. Reina
Advisor: M. Olivella
Master program: Msc in Omics Data Analysis UVic-UCC
University: Universitat de Vic – Universitat Central de Cataluya
Date: 2017
Title: Producción de lipasas recombinantes bajo el promotor PAOX1 en la factoría celular Pichia pastoris
Student: M. Sicilia
Advisor: X. Garcia
Master program: Biotecnologia Avançada
University: Universitat Autònoma de Barcelona
Date: 2017
Title: CRL1 recombinant production in Pichia pastoris regulated by the constitutive GAP promoter in fed-batch cultures
Student: M. Sanchez
Advisor: X. Garcia
Master program: Biotecnologia Avançada
University: Universitat Autònoma de Barcelona
Date: 2017
Title: Implementation of an R package for the detection of differentially methylated regions through a Kernel regression sliding-window approach
Student: Carlos Martínez
Advisor: M. L. Calle
Master program: MsC in Omics Data Analysis
University: Universitat de Vic
Date: 27-9-2016
Title: Gene Set Analysis for improving genetic association studies
Student: Natàlia Vilor
Advisor: M. L. Calle
Master program: MsC in Omics Data Analysis
University: Universitat de Vic
Date: 29-1-2014
Title: Analysis of the mitochondrial DNA of schizophrenia patients by next generation sequencing
Student: Marta Rodríguez
Advisor: M. Luz Calle, Lourdes Martorell
Master program: MsC in Omics Data Analysis
University: Univsersitat de Vic
Date: 29-1-2014
Title: Chimp negative control for selective pressure in humans
Student: Núria Morató
Advisor: Jordi Planas, Josep M. Serrat
Master program: MsC in Omics Data Analysis
University: Universitat de Vic
Date: 29-1-2014
Title: Computational toolbox towards evolutionary domain mapping of membrane proteins
Student: Alba Crespi
Advisor: Mireia Olivella, Alex Peràlvarez
Master program: MsC in Omics Data Analysis
University: Universitat de Vic
Date: 29-1-2014
Title: Effect of nitrotyrosination on the reactivity of triosephosphate isomerase
Student: Guillaume Noel
Advisor: Jordi Villà
Master program: MsC in Bioinformatics of Health Sciences
University: Universitat Pompeu Fabra
Date: 2013
Title: Métodos de selección de variables en estudios de asociación genética. Aplicación a un estudio de genes candidatos en Enfermedad de Parkinson
Student: Pilar Cacheiro
Advisor: Carmen Cadarso Suárez (Univ. Santiago de Compostela), M. Luz Calle Rosingana (Univ. de Vic), M.Jesús Sobrido Gómez (Fundación Pública Galega de Medicina Xenómica).
Master program: Máster en Técnicas Estadísticas e Investigación Operativa University: Universidade de Santiago de Compostela
Date: Junio de 2011
Mark: 10
Title: Eficient genome-wide two-locus epistasis testing in disease association testing with censored traits
Student: Thomas Leysen
Advisor: M.Luz Calle (Univ. de Vic), Kristel van Steen (Univ. de Liège)
University: Universitat de Vic – Université de Liège
Department: Biologia de Sistemes
Date: Setembre de 2011
Mark: 8
Title: Gene expression and disease-associated genes in the human brain
Student: Marta Cullell
Advisor: Jordi Planas, Josep M. Serrat
Master program: Màster en Biotecnologia Molecular
University: Universitat de Barcelona
Date: July 2010
Mark: 9.5
Title: Tau leap methods extended stability regions for biochemical kinetics
Student: Pau Rué
Advisor: Jordi Villà
Master program: MsC in Bioinformatics of Health Sciences
University: Universitat Pompeu Fabra
Date: 2009
Title: Molecular Dynamics simulations on the Ras protein family: alignment of the essential movements
Student: Tiziano Gállo Cassarino
Advisor: Jordi Villà
Master program: MsC in Bioniformatics of Health Sciences
University: Universitat Pompeu Fabra
Date: 2009
Title: Modelling cardiac tissue Hybrid Automata
Student: V. Carapella
Advisor: Jordi Villà
Master program: MsC in Bioinformatics of Health Sciences
University: Universitat Pompeu Fabra
Date: 2009
Title: Detección de interacciones genéticas asociadas a enfermedades complejas. Aplicación al cáncer de vejiga.
Student: Víctor Urrea Gales
Advisor: M.Luz Calle
Master program: Màster en Estadística i Investigació Operativa
University: Universitat Politècnica de Catalunya
Date: February 2009
Mark: 10 (MH)
Title: The Random Forest methodology applied to a bladder cancer study.
Student: Julie Lauren
Advisor: M.Luz Calle
University-Center: INSA. Toulouse
Date: September 2008
Bachelor Thesis
Title: Combined biostatistics and bioinformatics analyses to
identify epigenetically regulated host factors associated
with control of HIV disease progression
Student: Laura Ordeig
Advisor: Christian Brander, Marta Ruiz, M.L. Calle,
Degree: Grau en Biotecnologia
University: Universitat de Vic
Date: Setembre-2015
Title: Susceptibilitat genètica al càncer gàstric: caracterització de les interaccions de sogon ordre entre gens i variants identificades en l’estudi epic-eurgast
Student: Núria Ros
Advisor: M.L. Calle, Núria Sala
Degree: Grau en Biotecnologia
University: Universitat de Vic
Date: 20-6-2013
Title: Susceptibilidad genética y riesgo de hemorragia digestiva asociada al consumo de aines, aspirina y otros antiagregantes plaquetarios
Student: Patricia Carrera
Advisor: M.L. Calle
Degree: Grau en estadística aplicada
University: Universitat Autònoma de Barcelona – Universitat de Vic
Date: 7-9-2013
