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

Quantification of transcript isoforms at the single-cell level using SCALPEL

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.

Methanol fixation is the method of choice for droplet-based single-cell transcriptomics of neural cells

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.