CV
Education
- PhD in Bioinformatics, University of Barcelona / IDIBELL, 2025
- Program for Predictive and Personalized Medicine of Cancer
- Supervisor: Dr. Mireya Plass
- Focus: Single-cell transcriptomics, isoform quantification, alternative polyadenylation
- MSc in Bioinformatics, Université Paris Diderot / Paris 7, 2019
Research Experience
- Postdoctoral Scholar (2025–Present)
- Department of Pathology, Stanford University
- Supervisor: Dr. Vivek Charu
- Research: Multi-omics data integration, spatial transcriptomics, cancer genomics
- PhD Researcher (2021–2025)
- IDIBELL Research Institute, Barcelona, Spain
- Plass Group
- Developed computational approaches for isoform quantification and differential isoform usage analysis in single-cell datasets
Technical Expertise
- Programming & Workflow Development: Nextflow, nf-core, R, Python, Linux/HPC
- Genomics Analysis: scRNA-seq, bulk RNA-seq, long-read transcriptomics, spatial transcriptomics
- Computational Methods: Isoform quantification, alternative polyadenylation analysis, fusion transcript detection
- Infrastructure: Cloud computing, HPC clusters, reproducible research environments
Honors and Awards
- Nextflow Ambassador, Seqera, 2025–Present
- FPI Predoctoral Fellowship Grant, Ministry of Science and Innovation, Government of Spain, 2021–2025
- Keystone Symposia Scholarship, Single Cell Biology: Pushing New Frontiers in the Life Sciences, April 2022
- Winner Team, Meet-U Protein Prediction Program Competition, Université Sorbonne Paris Cité, 2019
Professional Service
- Member, International Society for Computational Biology, 2023–Present
- Nextflow Ambassador, Seqera, 2025–Present
- Contributor, nf-core Community / Seqera, 2021–Present
Publications
Ake, F., Schilling, M., Fernández-Moya, S.M., Jaya Ganesh, A., et al. (2025). Quantification of transcript isoforms at the single-cell level using SCALPEL. Nature Communications, 16(1), 6402.
Gutiérrez-Franco, A., Ake, F., Hassan, M.N., Cayuela, N.C., Mularoni, L., Plass, M. (2023). Methanol fixation is the method of choice for droplet-based single-cell transcriptomics of neural cells. Communications Biology, 6(1), 522.
Projects & Software
See Software and Projects pages for detailed descriptions of research software and computational pipelines.