CV

Summary

10+ years building cloud-native systems across genomics, healthcare, and AI. 1 first-author and 6 co-authored peer-reviewed publications with 125+ citations.

Work Experience

• Senior Backend & Cloud Engineer

  Feb 2024 - Present
  Egen.ai

  Applied ML Systems. Technology services through cloud, data, AI, and platforms.

  • Built an automated data pipeline migration tool with an internal developer API for healthcare and precision medicine workloads on GCP.
  • Built a Twilio-based testing framework to automatically generate all mood and user behavior call combinations for a Voice AI system, replacing manual script configuration.
  • Hardened CI/CD pipelines, code quality gates, and security standards for a US financial client — catching production issues earlier and reducing error-prone contributions across the team.
  • Developed GCP Agents and A2A orchestration via MCP/ADK for a pharma & biotech corporation.
• Senior Software Engineer

  Mar 2022 - Feb 2024
  Illumina, Inc.

  Genetic analysis technologies: personalized medicine, disease research, drug development.

  • Evaluated privacy-preserving data sharing solutions to reduce friction from restrictive genomic data policies.
  • Built machine learning pipelines on Illumina Connected Analytics (ICA), HPC, and AWS.
  • Designed and optimized Snowflake-based data models for genomics and GWAS pipelines.
  • Co-authored a pending patent in applied bioinformatics and genomic data processing.
• Bioinformatics Engineer

  Oct 2018 - Feb 2022
  Cancer Research Center of Toulouse (CRCT)

  Translational cancer research center in Toulouse, focused on oncology and systems biology.

  • Designed reproducible ML pipelines for multi-omics analysis of pancreatic and lung cancer, scaled across cancer types.
  • 1 first-author and 6 co-authored peer-reviewed publications with 125+ citations in oncology and systems biology.
  • Built GARDEN-NET, a web tool for 3D chromatin interaction analysis, still in active use — published in Nucleic Acids Research.
• Research Engineer

  Jul 2017 - May 2018
  Spanish National Supercomputing Center (BSC)

  European HPC center hosting the MareNostrum supercomputer.

  • Developed a platform for AQuAS to analyze health outcomes and quality indicators through an interactive geospatial map.
  • Automated server setup testing and reproducibility for the Elixir/OpenEBench European HPC infrastructure.
• Research Technician

  Nov 2016 - Jun 2017
  Spanish National Cancer Research Center (CNIO)

  Spain's national cancer research institute, focused on molecular oncology.

  • Developed a reproducible workflow to identify mutation clusters in protein structures, including web-based visualization.
  • Contributed to the European OpenMinTeD NLP/text-mining project, developing services and APIs for biomedical text analysis.

Education

• Master in Bioinformatics and Computational Biology

  May 2016
  Instituto de Salud Carlos III

  Master's Thesis: Structure-PPi v2.0: Module for Annotating Cancer-Related Single-Nucleotide Variants at Protein-Protein Interfaces.
• Computer Engineering (Information Technologies)

  Sep 2015
  Universidad Complutense de Madrid

  Bachelor's Thesis: Computer Vision Adapted to Optical Coherence Tomographies.

Expertise

Portfolio

• Invention: ML Pipeline for Genome-Wide Association Studies (Patent)

  2024
  Co-authored a patent (US20240120024A1) for a machine learning approach that significantly improves causal gene identification in GWAS.
  
• GARDEN-NET & ChAseR: 3D Chromatin Interaction Networks

  2020
  Developed an R package and a web-based visualization tool for the analysis and integration of epigenomic data within 3D chromatin networks.
  
• AQuAS: Health System Observatory Visualization Platform

  2017
  Developed an interactive geospatial platform for the Catalan Agency for Health Quality and Evaluation (AQuAS) to visualize and analyze regional health system indicators.
  
• Structure-PPi v2.0

  2016
  Module for annotating cancer-related single-nucleotide variants at protein-protein interfaces.
  
• Computer Vision adapted to Optical Coherence Tomographies (Bachelor's Thesis)

  2015
  Developed an automated image processing algorithm using Python and OpenCV to measure uvea thickness and monitor uveitis evolution in OCT scans.
  

Publications

• Machine learning pipeline for genome-wide association studies (Patent)

  2024
  Field, Y., Ulirsch, J. C., Malangone, C., Madrid-Mencia, M., et al. (2024). "Machine learning pipeline for genome-wide association studies." U.S. Patent Application No. 18/483,313 (Publication No. US20240120024A1).
• STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells

  2021
  Richart, L., Lapi, E., Pancaldi, V., Cuenca-Ardura, M., Carrillo-de-Santa Pau, E., Madrid-Mencía, M., ... & Real, F. X. (2021). "STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells." Nucleic Acids Research, 49(19), 11005-11021.
• Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks

  2020
  Madrid-Mencía, M., Raineri, E., Cao, T. B. N., & Pancaldi, V. (2020). "Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks." Nucleic Acids Research, 48(8), 4066-4080.
• Single-Cell Virtual Cytometer allows user-friendly and versatile analysis and visualization of multimodal single cell RNAseq datasets

  2020
  Pont, F., Tosolini, M., Gao, Q., Perrier, M., Madrid-Mencía, M., Huang, T. S., ... & Fournié, J. J. (2020). "Single-Cell Virtual Cytometer allows user-friendly and versatile analysis and visualization of multimodal single cell RNAseq datasets." NAR Genomics and Bioinformatics, 2(2), lqaa025.
• Insights on TAM formation from a Boolean model of macrophage polarization based on in vitro studies

  2020
  Marku, M., Verstraete, N., Raynal, F., Madrid-Mencía, M., Domagala, M., Fournié, J. J., ... & Pancaldi, V. (2020). "Insights on TAM formation from a Boolean model of macrophage polarization based on in vitro studies." Cancers, 12(12), 3664.
• Cytidine deaminase resolves replicative stress and protects pancreatic cancer from DNA-targeting drugs

  2024
  Lumeau, A., Bery, N., Francès, A., Gayral, M., Labrousse, G., Ribeyre, C., ... Madrid-Mencía, M., ... & Cordelier, P. (2024). "Cytidine deaminase resolves replicative stress and protects pancreatic cancer from DNA-targeting drugs." Cancer Research, 84(7), 1013-1028.
• Low replicative stress triggers cell-type specific inheritable advanced replication timing

  2021
  Courtot, L., Bournique, E., Maric, C., Guitton-Sert, L., Madrid-Mencía, M., Pancaldi, V., ... & Bergoglio, V. (2021). "Low replicative stress triggers cell-type specific inheritable advanced replication timing." International Journal of Molecular Sciences, 22(9), 4959.
• DoriTool: a bioinformatics integrative tool for post-association functional annotation

  2017
  Martín-Antoniano, I., Alonso, L., Madrid, M., Lopez de Maturana, E., & Malats, N. (2017). "DoriTool: a bioinformatics integrative tool for post-association functional annotation." Public Health Genomics, 20(2), 126-135.

Teaching

• Text Mining for Bioinformatics

  2017
  Instituto de Salud Carlos III (ISCIII)

  Role: Graduate Course

  Designed and delivered an intensive 15-hour module on Text Mining and Natural Language Processing (NLP) within the Master in Bioinformatics and Computational Biology program.