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Prof. Sofía Reyes
Associate Professor, Computational Biology
s.reyes@upm.es +34 91 900 1234 Madrid, Spain orcid.org/0000-0002-1234-5678
Research Metrics
47 Peer-reviewed publications
19 h-index (Google Scholar)
€2.1M Total grant funding
6 PhD students supervised
Research Profile

Computational biologist specialising in single-cell genomics, gene-regulatory network inference, and integrative multi-omics. ERC Starting Grant holder. Collaborative research spanning genomics centres in the US, UK, and Europe. Committed to open-source tools and reproducible computational research.

Selected Funding
ERC Starting Grant — Single-cell Regulatory Networks (SCRN) 2021 – 2026
European Research Council
  • €1.5M — Principal Investigator. Developing probabilistic models for inferring gene-regulatory networks from scRNA-seq data at scale.
Ramón y Cajal Fellowship 2019 – 2024
Spanish Ministry of Science and Innovation
  • €390K — Competitive tenure-track fellowship for outstanding early-career researchers returning to Spain.
Plan Nacional Project — Multi-omics in Cancer 2020 – 2023
AEI / MINECO (PI: Reyes)
  • €210K — Integrative analysis of transcriptomic and epigenomic alterations in colorectal cancer progression.
Academic Positions
Associate Professor, Computational Biology Sep 2022 – Present
Universidad Politécnica de Madrid (UPM), School of Computer Science
  • Lead the Computational Genomics Laboratory (12 members: 6 PhD students, 3 postdocs, 3 research engineers).
  • Teach MSc Bioinformatics (60 students/year) and coordinate the Genomics Data Science module.
  • Member of UPM Research Commission; co-organised RECOMB Satellite Workshop on Regulatory Genomics 2024.
Assistant Professor, Computational Biology Sep 2018 – Aug 2022
Universidad Politécnica de Madrid (UPM)
  • Established research group; secured ERC Starting Grant and Ramón y Cajal Fellowship in first three years.
  • Supervised 3 PhD completions; all graduates placed in postdoctoral or industry research positions.
  • Published 18 articles in this period, including first-author work in Nature Methods and Genome Biology.
Postdoctoral Research Fellow Oct 2015 – Aug 2018
Broad Institute of MIT and Harvard, Cambridge MA (Regev Lab)
  • Developed scVI-Reg, a variational autoencoder for joint dimensionality reduction and regulatory network inference (3,200+ GitHub stars).
  • Co-first author on landmark Cell Systems paper on single-cell atlas of human embryonic development.
  • Collaborated with the Human Cell Atlas consortium; contributed to data processing pipelines for 1.2M cells.
Selected Publications
Probabilistic inference of gene-regulatory networks from single-cell multi-omics data
Reyes S, Martínez A, et al. Cell Systems 15(4):312–328, 2024. DOI: 10.1016/j.cels.2024.01.004
Integrative chromatin accessibility and gene expression profiling reveals lineage-specific regulators in haematopoiesis
Reyes S*, García P*, et al. Genome Biology 24:89, 2023. DOI: 10.1186/s13059-023-02897-x (*equal contribution)
scVI-Reg: Scalable variational inference for regulatory network reconstruction from single-cell RNA-seq
Reyes S, Lopez-Bigas N, et al. Nature Methods 18:1124–1133, 2021. DOI: 10.1038/s41592-021-01168-8
A single-cell transcriptomic atlas of human embryonic development
Bloom J*, Reyes S*, et al. Cell Systems 9(3):214–228, 2019. DOI: 10.1016/j.cels.2019.06.005 (*co-first author)
Teaching & Supervision
  • MSc Bioinformatics (module coordinator)
  • Genomics Data Science (60 students/year)
  • 6 PhD students supervised (3 completed, 3 ongoing)
  • 3 postdoctoral researchers mentored
  • Undergraduate Computational Biology projects (8 supervised)
Education
PhD, Computational Biology Sep 2011 – Sep 2015
ETH Zürich — Excellent (summa cum laude equivalent) · Advisor: Prof. Gunnar Rätsch
MSc Bioinformatics Sep 2009 – Jul 2011
Universidad Autónoma de Madrid (UAM) — Distinction
BSc Biology Sep 2005 – Jun 2009
Universidad Complutense de Madrid (UCM) — First Class Honours