A little about me...
My name is Fernando, I'm from Seville, Spain, and I'm passionate about leveraging Bioinformatics and AI to advance healthcare.
I currently lead a research group at the University of Hamburg, focusing on innovative applications of generative AI in biomedicine.
My background includes a solid base in Computer Science combined with Health Biotechnology, with a strong emphasis on data-driven approaches to drug repurposing, personalized medicine and generative AI
Work Experience
University of Hamburg | Hamburg, Germany
Junior Group Leader | October 2024 – Present (4 months)
Lead a research group focused on developing innovative methodologies in bioinformatics and biomedicine, with an emphasis on integrating generative language models (LLMs) into biomedical research.
Responsibilities:
Direct interdisciplinary research projects, ensuring alignment with strategic goals.
Supervise and mentor PhD candidates and Master's students, fostering their research skills and professional development.
Secure competitive funding for research initiatives through successful grant applications.
Publish research findings in high-impact, peer-reviewed scientific journals.
Collaborate with national and international research groups to address complex challenges in systems biology and biotechnology.
Enhance the impact and visibility of the group's scientific work through effective communication and dissemination strategies.
Lead efforts to apply network-based approaches to drug repurposing for infectious diseases under the REPO4EU framework.
Postdoctoral Researcher | January 2023 – September 2024 (1 year 9 months)
Developed and implemented network biology approaches for multi-omics data integration in disease research.
Designed and optimized advanced analysis pipelines using biological networks and machine learning techniques.
Created an advanced conversational agent (ChatDrex) for disease module identification and drug repurposing, demonstrating the practical application of AI in bioinformatics.
Conducted research on breast cancer using computational methods, focusing on identifying potential biomarkers and therapeutic targets.
Collaborated with experimental biologists to validate computational findings, bridging the gap between in silico research and experimental validation.
Published research findings in peer-reviewed journals and presented at international conferences, contributing to the advancement of the field.
Research Associate | May 2022 – January 2023 (9 months)
Focused on developing and applying network-based approaches for the analysis of multi-omics data in the context of disease research.
Designed and optimized advanced analysis pipelines, leveraging biological networks and machine learning to identify disease modules and potential drug targets.
Contributed to the development of an advanced conversational agent for disease module identification and drug repurposing.
Collaborated with interdisciplinary teams to integrate computational insights into broader biomedical research projects.
REPO4EU | Hamburg, Germany (Remote)
Bioinformatician in AI based on real data | September 2022 – Present (2 years 5 months)
Lead initiatives within the REPO4EU project focused on developing and applying network medicine approaches for drug repurposing, with a particular emphasis on infectious diseases.
Design computational pipelines integrating multi-omics data and advanced biological network analysis tools to identify disease modules and key biomarkers.
Prioritize existing drugs with therapeutic potential in the context of infectious diseases using computational methods, accelerating the drug discovery process.
Collaborate with an international consortium of researchers to implement these methodologies in personalized medicine scenarios, contributing to the development of data-driven therapeutic strategies.
Contributed to strategies for preventing efficient viral replication during the critical time window for the immune system to respond.
Delgado Chaves S.C. | Seville, Andalusia, Spain
Owner and Manager | July 2019 – Present (5 years 7 months)
Founded and manage a family-owned company specializing in commercial property rentals.
Responsible for the strategic oversight and operational management of the company, including:
Negotiating lease agreements with tenants, ensuring mutually beneficial terms.
Managing tenant relations, addressing concerns, and resolving issues promptly and effectively.
Overseeing property maintenance and ensuring compliance with all relevant safety regulations.
Administering finances, including rent collection, expense management, and tax reporting.
Making strategic decisions regarding property improvements and investments to maximize returns.
Demonstrated strong leadership, decision-making, problem-solving, adaptability, and resilience in navigating the complexities of the real estate market.
Developed entrepreneurial mindset and skills in identifying and capitalizing on opportunities for growth and improvement.
Universidad Pablo de Olavide | Seville, Andalusia, Spain
Predoctoral Researcher | February 2020 – April 2022 (2 years 2 months)
Conducted research under the supervision of Drs. Francisco A. Gómez-Vela and Federico Divina, focusing on the development and application of novel computational methods for gene network reconstruction to enhance biomedical research.
Leveraged multi-omics data and ensemble techniques to build robust gene co-expression networks (GCNs), aiming to unravel the complex molecular mechanisms underlying diseases.
Developed and implemented algorithms for gene network reconstruction using conditional expression data.
Streamlined the analysis of next-generation sequencing (NGS) data to identify new omics-phenotype associations.
Coordinated interdisciplinary research efforts, bridging computational and life sciences.
Mentored Master's and Bachelor's students in bioinformatics research techniques.
Contributed to the development of EnGNet, an innovative tool that leverages ensemble strategies to reconstruct robust GCNs, facilitating the interpretation of complex biological networks for the discovery of disease modules and mechanisms.
Actively participated in lab meetings, contributing to the generation of new research ideas and the refinement of existing projects.
Applied systems biology and data science approaches to improve the understanding of diseases.
Research Assistant in Bioinformatics | September 2017 – February 2020 (2 years 6 months)
Worked within the DATAI UPO research group under the supervision of Prof. Dr. Francisco A. Gómez-Vela.
Focused on leveraging computational approaches to understand complex biological systems, with an emphasis on:
Designing new algorithms for gene co-expression network reconstruction using transcriptomic data.
Applying these algorithms to investigate the impact of drug-mediated topoisomerase inhibition on gene regulatory networks.
Performing in-depth reviews of state-of-the-art methods for network reconstruction, contributing to the development of improved methodologies.
Developing a foundational pipeline for basic co-expression network reconstruction, setting the stage for more advanced research in subsequent years.
Internships
I.E.S. Las Encinas | Valencina de la Concepción, Spain
Professor of Biology and Geology | April 2021 – May 2021 (2 months)
Developed and delivered a teaching unit in Geology, utilizing innovative pedagogical approaches.
Implemented the Content and Language Integrated Learning (CLIL) methodology to enhance student engagement and understanding.
Studied and addressed the special educational needs of students, adapting teaching materials and methods accordingly.
Incorporated digital tools and task-based learning to create a dynamic and interactive learning environment.
Conducted a socio-metric study of diversity within the classroom to foster a more inclusive and supportive learning atmosphere.
Andalusian Center for Developmental Biology | Seville, Spain
Postgraduate Researcher | September 2019 – July 2020 (11 months)
Worked within the research group of Dr. María Dolores Martín-Bermudo, focusing on the mechanisms that regulate changes in cell morphology and migration.
Conducted a systematic examination of possible concurrent cancer-causing mutations that enhance tumorigenesis in Drosophila melanogaster.
Generated mutant flies for genes of interest using CRISPR-Cas9 and other molecular biology tools.
Performed dissection of larval wing discs for the quantification of cell migration and invasion using confocal microscopy.
cicCartuja - Scientific Research Centre | Seville, Spain
Research Assistant | February 2018 – March 2018 (2 months)
Worked within the research group of Dr. Ignacio Luque-Romero, focusing on aminoacyl tRNA synthetases and translation.
Investigated genomic fragility in the cyanobacterium Anabaena.
Performed computational analysis of tRNA groups in the genomes of cyanobacteria.
Contributed to the research conducted at the Institute of Plant Biochemistry and Photosynthesis (IBVF), a joint center of the Spanish National Research Council (CSIC) and the University of Seville (US).
Ruhr-Universität Bochum | Bochum, Germany
Research Assistant | June 2017 – July 2017 (2 months)
Worked within the research group of Dr. Linda Weiss, investigating genomic plasticity and differential gene expression in inducible defense systems in Daphnia pulex.
Dissected daphnia brains for immunostaining and quantification of brain growth.
Contributed to the development of a methodology for automated cell counting in 3D in stacks of confocal microscopy images.
Education
Doctor of Philosophy (PhD), Bioinformatics | Summa Cum Laude (highest grade)
Universidad Pablo de Olavide, Seville, Spain | February 2020 – January 2023
Thesis: "Design of New Algorithms for Gene Network Reconstruction Applied to In Silico Modeling of Biomedical Data"
Supervisors: Dr. Francisco A. Gómez Vela and Dr. Federico Divina
Key Findings/Contributions:
Developed EnGNet, a novel algorithm combining ensemble approaches and greedy optimization for improved gene co-expression network generation.
Demonstrated that ensemble methods significantly enhance the robustness and reliability of gene co-expression network inference.
Enabled the identification of disease modules and mechanisms directly from data through novel algorithmic approaches.
Contributed to the understanding of gene network dynamics and their application in complex disease research.
Published in peer-reviewed journals and presented at international conferences.
Developed a patent based on the EnGNet algorithm.
Skills: Bioinformatics, Systems Biology, Data Mining, Algorithm Development, Genetic Network Reconstruction, Gene Co-Expression Networks, Gene Expression Analysis, Biomarker Discovery, Disease Mechanisms, Transcriptomics, SARS-CoV-2, Immune Response, Viral Infections, Precision Medicine, Data Science, Big Data, High-Performance Computing (HPC), CUDA, Multi-Omics Integration, Python, JAVA, Mentorship, Scientific Communication, Grant Writing.
Master of Science (MSc), Advanced Bioinformatics Analysis
Universidad Pablo de Olavide, Seville, Spain | 2018 – 2020
Grade: 9.14/10 | Thesis Grade: 9.6/10
Specialization: Advanced statistical and computational methods for analyzing biological data.
Skills: Molecular Sequence Handling, R Programming, Linux, High-Performance Computing, Biological Problem Solving, Genomic Data Analysis, NGS, Gene Expression, Regulation, Genome Annotation, Experimental Design, Advanced Programming, Protein Structure, Gene Networks, Data Science, Big Data, Gene Co-Expression Networks, Immune Response, Viral Infections, Host-Pathogen Mechanisms, Key Genes, Biological Pathways
Master of Science (MSc), Health Biotechnology
Universidad Pablo de Olavide, Seville, Spain | 2018 – 2020
Grade: 9.56/10 | Thesis Grade: 9.8/10
Specialization: Cell Therapy
Skills: Health Biotechnology, Disease Genetics, Cancer, Aging, Degenerative Diseases, Autoimmune Diseases, Metabolic Diseases, Cardiovascular Risks, Rare Diseases, Pathology Analysis, Genomics, Fluorescent Techniques, Animal Models, Nanotechnology, Tissue Regeneration, Tissue Bioengineering, Entrepreneurship, Technology Transfer, Omics, Biomedicine, Genetic Networks, Cell Proliferation, Metastasis, CRISPR/Cas9, Drosophila, Molecular Biology
Master's Degree in Higher Education
Universidad Pablo de Olavide, Seville, Spain | October 2020 – June 2021
Specialization: Bilingual, Multilingual, and Multicultural Education
Grade: 8.81/10 | Thesis Grade: 9.9/10
Skills: Content and Language Integrated Learning (CLIL), Task-Based Learning, Curriculum Design, Assessment, Diversity and Inclusion, Educational Technology, Sociometry, Communication, Teamwork, Teacher Reflection, Lesson Planning, Continuous Learning, Curiosity, Motivation for Teaching.
Bachelor of Science (BSc), Biotechnology (Bilingual)
Universidad Pablo de Olavide, Seville, Spain | 2014 – 2018
Grade: 8.82/10
Skills: RNA Extraction, qPCR, Gel Electrophoresis, RNA Sequencing (RNA-Seq), Microarrays, Differential Gene Expression Analysis, Phylogenetic Analysis, Population Genetics, Sequence Alignment, Laboratory Techniques, Scientific Method, Data Analysis, Bilingual Proficiency (English/Spanish).