Pepe Bonet Giner

Experience

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  Universidad de Granada

  Jul 2011 - Jul 2011

  Summer Scholar

  FECYT Grant for the Scientific Summer School on Mathematics for Science / Life, Science and Sport

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  Universitat Politècnica de València (UPV)

  Jun 2014 - Jul 2014

  Research Intern

  - Pure and Applied Mathematics Institute (IUMPA-UPV)- Research project Collaboration: "Bioinformatics and Synthetic Biology for Metabolic Modeling"- Group leader: Javier Urchgueia

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  Bonn University

  Jun 2015 - Aug 2015

  Research Intern

  - Pharmazeutisches Institut – Pharmazeutische Chemie I - Research project collaboration PhD student: "Antagonists screening for a Mas-related gene Receptor".- Group Leader: Dr. Christa Müller

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  Instituto de Biomedicina de Valencia IBV-CSIC

  Jan 2016 - Jul 2016

  Research Intern

  - Department of Pathology and Therapy / Molecular and Cellular. Unit of signaling pathways by nutrients.- Bachelor Thesis: "Glycogen synthesis modulation in astrocytes from Lafora disease mice models".- Grade: 10/10, Mention of Honour. - Thesis Directors: Carla Rubio Villena, María Adelaida García Gimeno & Pascual Sanz Bigorra

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  Maastricht Centre for Systems Biology (MaCSBio)

  Jul 2017 - Jun 2018

  Research Student

  Department of Data Science & Knowledge EngineeringMaster Thesis: "Improvement of Tumor Phylogenetic models: An ILP approach"Thesis Directors: Dr. Steven Kelk & Russell SchwartzGrade: 9.1/10Role: Developed a new mathematical model based on an Integer Linear Programming approach that does not follow the perfect phylogeny assumption and that takes into account copy number alterations. Prizes: Faculty of Sciences and Engineering best Master Thesis: https://www.maastrichtuniversity.nl/news/prizewinners-maastricht-universitys-43rd-dies-natalisSystems Biology best master thesis: https://www.maastrichtuniversity.nl/news/master-thesis-award-systems-biology-graduate Show less

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  Carnegie Mellon University

  Jan 2018 - Jun 2018

  Visiting Scholar

  Schwartz Lab - Department of Biological SciencesMaster Thesis: "Improvement of Tumor Phylogenetic Models: An ILP approach"Thesis Directors: Russell Schwartz & Steven KelkGrade: 9.1/10Role: Developed a new mathematical model based on an Integer Linear Programming approach that does not follow the perfect phylogeny assumption and that takes into account copy number alterations. Prizes: Faculty of Sciences and Engineering best Master Thesis & Systems Biology best master thesisKey skills: Tumor Phylogenetics | Integer Linear Programming | Mathematical Modelling Show less

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  IRB Barcelona

  Jul 2018 - May 2022

  PHD Student

  Thesis topic: Computational studies of DNA modifications and mutations in bulk and single-cell data.Thesis Director: Nuria López BigasRole: Application of machine learning techniques to improve the extraction of information from both, single-cell data to cluster cells into clones and, bulk data to detect DNA modifications. Methods developed are framed in the Bayesian statistics and deep learning fields.Key skills:Data Analysis | Cancer Genomics | Machine Learning | Data Science | Statistics | Nanopore Sequencing | Cancer Biology Show less

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  ETH Zurich

  Jan 2019 - Mar 2019

  Academic Researcher

  Academic Guest Researcher at the Department of Biosystems Science and Engineering in Basel | ETH Zurich - Niko Beerenwinkel's labRole:Development of a fully Bayesian method (BnpC) to analyze large-scale scDNA-seq datasets and to accurately determine the clonal composition and genotypes, handling noisy data and an unknown number of clones non-parametrically.Publication: https://doi.org/10.1093/bioinformatics/btaa599Presented at RECOMB2020 in the Single-Cell Genomics session: https://www.recomb2020.org/programKey skills: Bayesian Statistics | MCMC | Single-cell DNA data | Snakemake Show less

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  Universidad de Vigo

  Apr 2019 - May 2019

  Academic Researcher

  Academic Guest Researcher at the Department of Biochemistry, Genetics and Immunology.Universidad de Vigo - David Posada's lab (Phylogenomics)Role: Implementation of a Snakemake pipeline for benchmarking BnpC (developed at ETH) against state-of-the-art methods.Publication: https://doi.org/10.1093/bioinformatics/btaa599Presented at RECOMB2020 in the Single-Cell Genomics session: https://www.recomb2020.org/program

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  KTH Royal Institute of Technology

  Aug 2020 - Jan 2021

  Academic Researcher

  Academic Guest at the division of Computational Science and Technology - Largergren LabRole:Development of a deep learning framework to detect DNA modifications (In preparation)Attending a PhD course in Systems for Scalable Machine Learning (fid3024)Key skills: Deep Learning | Distributed Learning | Data Parallelism | Device Placement | Robust Learning

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  Esade

  May 2022 - now

  Academic collaborator

  I teach the following courses to bachelor and executive students: - Data Exploration Course @ Executive Master in Business Analytics (EMIBA)- Intermediate Python & AI @ BBA and GEL Bachelor Students- Advanced Python @ BBA Bachelor Students

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  Hynts Analytics

  Sept 2022 - Apr 2024

  CEO/CTO/AI Developer

  Hynts is an EdTech company that provides AI-based software to educational institutions.I developed end-to-end the following products:1. Dropout Models to predict students that will leave universities. 2. ML models to predict the grades of university access exams. 3. Management dashboards to analyze the data from the institutions. I was in charge of developing the ML models from scratch, building the web application, containerizing them using docker, and deploying them in AWS. Show less

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  TetraScience

  Apr 2024 - now

  Data Architect