Trainer biographies

José Carbonell Caballero | Barcelona Supercomputing Center

José Carbonell Caballero is a postdoctoral research scientist in the Life Sciences Department at the BSC. He studied computer science at the Technical University of Valencia (UPV). Subsequently, he completed a master’s degree in biostatistics at the University of Valencia (UV), where he also conducted his PhD studies in statistics developing different mathematical models for studying genomic heterogeneity in cancer. Throughout his professional career, he has been involved in the development of many widely used computational data analysis frameworks spanning different disciplines such as quality control of sequencing data, variant calling, genome integrity assessment, chromatin dynamics and network-based analysis, among others. In recent years, he has focused his research on the development of new statistical methods for molecular pathway analysis. In particular, he focused on statistical modelling of signalling pathways, contributing new approaches to quantify pathway activity and hierarchical matrix deconvolution methods to understand sample heterogeneity in cancer.

ORCID: 0000-0002-9170-0533

Davide Cirillo | Barcelona Supercomputing Center

Davide Cirillo is the head of the Machine Learning for Biomedical Research Unit at the Life Sciences Department of the Barcelona Supercomputing Center (BSC). He received the MSc degree in Pharmaceutical Biotechnology from University of Roma ‘La Sapienza’, Italy, and the PhD degree in Biomedicine from Universitat Pompeu Fabra (UPF) and Center for Genomic Regulation (CRG) of Barcelona, Spain. His research focuses on computational methods for precision medicine with a special emphasis on machine learning, network science, and ethics of artificial intelligence. He is a member of the ELIXIR Machine Learning Focus Group, co-leads the research subgroup of BSC Bioinfo4Women initiative, and is a scientific advisor to the Swiss non-profit Women’s Brain Project. He is co-editor of the book “Sex and Gender Bias in Technology and Artificial Intelligence: Biomedicine and Healthcare Applications” (Elsevier Academic Press, 2022).

ORCID: 0000-0003-4982-4716

Javier Conejero | Barcelona Supercomputing Center

Javier Conejero is a Senior Researcher in the Workflows and Distributed Computing Team of the Computer Science Department, Barcelona Supercomputing Center (BSC), Spain. His research interest are QoS, development paradigms, parallel and distributed computation, HPC and Cloud computing. Conejero received a PhD in Advanced Computer Technologies (2014) from the University of Castilla-La Mancha (UCLM), Spain.

ORCID: 0000-0001-6401-6229

Åsmund Flobak | Norwegian University of Science and Technology – NTNU

MD at the Cancer Clinic at St Olav’s hospital, Trondheim. Associate professor at the Norwegian University of Science and Technology Senior researcher at Sintef Project leader for the ERA PerMed project OncoLogics and project leader for the RCN project PRESORT. Principal Investigator at St Olavs hospital for the clinical trial IMPRESS-Norway.

ORCiD: 0000-0002-3357-425X

Arnau Montagud | Barcelona Supercomputing Center

I am a researcher with experience in Systems Biology, Data integration, Data deconvolution, Metabolic Engineering, High-performance computing and Boolean, Metabolic and Multi-scale modelling. I am an enthusiastic collaborator who has promoted collaborations with researchers with varied backgrounds and different fields of expertise, secured funding for international pioneering projects and keenly mentored several MSc and PhD students.

ORCID: 0000-0002-7696-1241

Vincent Noël | Institut Curie

I’m a researcher at the Computational System Biology team at Institut Curie, where I have been working since 2018. My research interests concern modelling of biological systems, where I have expertise in building and analyzing models, but also developing simulation frameworks. I started working mainly on ODEs models during my PhD, then Boolean models during my second post-doc, and I am now also working on agent-based models. My main interest at the moment is to build multi-scale models with PhysiBoSS, in which cell population is described using an agent-based model with PhysiCell, and the signalling inside each cell is described using MaBoSS.

ORCID: 0000-0003-3448-291X

Henrik Nortamo | CSC

HPC expert at CSC – IT Center for Science in finland, working on everything from digital twins, quantum computer integration and generic computing environment development to webinterfaces for HPC and user documentation.

Thaleia Ntiniakou | Barcelona Supercomputing Center

She is a computer scientist and master holder of Electrical and computer engineering. Currently working as a research engineer at the computational biology lab of the Barcelona Supercomputing Center. Her present work involves the parallelization of the MPI version of Physicell and the development of a benchmark on agent-based simulating software for multicellular systems.

Miguel Ponce de León | Barcelona Supercomputing Center

Miguel Ponce-de-Leon is an established researcher at Alfonso’s Valencia Lab (Barcelona Supercomputing Center). He got his bachelor’s degree in biophysics and a master’s in bioinformatics. In 2011 he moved to Spain where he did his PhD in metabolic reconstruction and modelling at the Universidad Complutense de Madrid. In 2017 he moved to Barcelona where he started working as a postdoc at the Barcelona Supercomputing Center. His current lines of research are in computational systems biology where his work focuses on developing multi-scale simulations and HPC workflows for model exploration.

ORCID: 0000-0002-7496-844X

Pablo Rodriguez-Mier | Heidelberg University

Upon completing his PhD in Computer Science and Artificial Intelligence at the University of Santiago de Compostela (Spain), he shifted his research focus to merge two areas of interest: biomedicine and informatics. As a postdoctoral researcher at the Food Toxicology Research Center of the French National Institute for Agricultural Research (INRAE) in Toulouse, he contributed to a project funded by the French National Cancer Institute (INCA). His primary responsibility involved developing novel computational methods to analyze metabolic dysregulations in cancer caused by mutations in the p53 gene and key target genes, integrating prior biological knowledge with experimental data. This experience provided him with extensive expertise in mathematical modeling for metabolism, as well as linear and discrete optimization. Subsequently, he joined the Saez-Rodríguez group at Heidelberg University as a Postdoctoral Researcher, aiming to address certain technical and methodological challenges associated with existing methods for causal inference of signaling networks. His work was conducted within the context of the European project PerMedCoE, which seeks to enhance current methodologies and prepare them for pre-exascale computing. This advancement would facilitate large-scale modeling using omics data for personalized medicine.

ORCID: 0000-0002-4938-4418

Marco Ruscone | Institut Curie

Marco Ruscone is a trained physicist from the University of Turin. He did his master internship at Institut Curie and shortly after obtained his degree in Physics of complex systems for biology. He continues his training as a Ph.D. student at Institut Curie under the supervision of Dr. Laurence Calzone, Dr. Vincent Noel, and Dr. Andrei Zinovyev. His work mainly focuses on the development of a multiscale model of cancer cell invasion using PhysiBoSS. He presented his work at different conferences like ISMB 2020 (online), ECCB 2022 (Sitges, Spain), and INSERM/JSPS 2022 (Yamaguchi, Japan) and attended multiple workshops and hackathons on agent-based modeling and cancer invasion.

ORCID: 0000-0002-7607-0203

Dénes Turei | Heidelberg University

I started off as a freshwater ecologist, then changed to bioinformatics in my PhD. Doing my PhD at Semmelweis University of Budapest, I created signalling pathway databases, a topic that I continued working on in my postdoc. I received an EIPOD postdoc fellowship in 2014, and started to work in the group of Julio Saez-Rodriguez in Cambridge and at Anne-Claude Gavin in EMBL Heidelberg. I developed a comprehensive integrated database to support the modelling and analysis activities in our group. In the Gavin group I created a software for lipidomics LC MS/MS data processing and analysis. In the group of Christoph Merten, also in EMBL, I developed methods for an ex vivo microfluidics combinatorial drug screening. Since then, I still work with Julio Saez-Rodriguez at the Heidelberg University Hospital, and my main activity is scientific software development, especially in the field of databases.

ORCID: 0000-0002-7249-9379