Single-cell Regulatory Networks
Probabilistic models for inferring gene-regulatory networks from scRNA-seq data at scale.
€1.5M from the European Research Council
Associate Professor · Computational Biology · Madrid
Sofía Reyes
A computational biologist working on single-cell genomics, gene-regulatory network inference and integrative multi-omics — and an ERC Starting Grant holder.
- 47peer-reviewed publications
- 19h-index (Google Scholar)
- €2.1Mtotal grant funding
- 6PhD students supervised
Research
Funded projects and the lab
Three funded awards, the laboratory she leads, and work with the wider genomics community.
Multi-omics in Cancer
Integrative analysis of transcriptomic and epigenomic alterations in colorectal cancer progression.
€210K national project
Ramón y Cajal Fellowship
A competitive tenure-track fellowship for outstanding early-career researchers returning to Spain.
€390K fellowship
Computational Genomics Laboratory
The laboratory she leads as Associate Professor: 6 PhD students, 3 postdocs and 3 research engineers.
12 members
Human Cell Atlas pipelines
Collaborated with the Human Cell Atlas consortium, contributing to its data processing pipelines.
Pipelines for 1.2M cells
RECOMB Satellite Workshop on Regulatory Genomics
Co-organised the 2024 satellite workshop, alongside her service on the UPM Research Commission.
Software in focus
scVI-Reg
Regulatory network reconstruction from single-cell RNA-seq, at scale
Question
How to reconstruct gene-regulatory networks from single-cell RNA-seq data in a scalable way.
Approach
scVI-Reg, a variational autoencoder that performs dimensionality reduction and regulatory network inference jointly.
Outcome
Published in Nature Methods (2021) with Sofía as first author; the tool has 3,200+ GitHub stars.
Selected publications
Four of forty-seven
Each first-authored or joint-first-authored.
- Probabilistic inference of gene-regulatory networks from single-cell multi-omics dataCell Systems · 2024
- Integrative chromatin accessibility and gene expression profiling reveals lineage-specific regulators in haematopoiesisGenome Biology · 2023
- scVI-Reg: Scalable variational inference for regulatory network reconstruction from single-cell RNA-seqNature Methods · 2021
- A single-cell transcriptomic atlas of human embryonic developmentCell Systems · 2019
Teaching & supervision
Students and trainees
All three of her PhD graduates so far went on to postdoctoral or industry research positions.
- MSc Bioinformatics — Genomics Data Science module (coordinator)60 a year
- PhD students supervised6 · 3 completed
- Postdoctoral researchers mentored3
- Undergraduate computational biology projects8 supervised
A computational biologist committed to open-source tools and reproducible computational research.
Sofía trained in biology and bioinformatics in Madrid and took her PhD at ETH Zürich before a postdoc at the Broad Institute of MIT and Harvard. She joined Universidad Politécnica de Madrid in 2018, secured an ERC Starting Grant and a Ramón y Cajal Fellowship in her first three years, and became Associate Professor in 2022. Her collaborations span genomics centres in the US, the UK and Europe.
- Based inMadrid, Spain
- InstitutionUPM, School of Computer Science
- LeadsComputational Genomics Laboratory
- ResearchSingle-cell genomics, regulatory networks, multi-omics
- ServiceUPM Research Commission
Positions & education
Career path
- Sep 2022 — Present
Associate Professor, Computational Biology
Universidad Politécnica de Madrid, School of Computer Science
Leads the Computational Genomics Laboratory; teaches on the MSc Bioinformatics.
- Sep 2018 — Aug 2022
Assistant Professor, Computational Biology
Universidad Politécnica de Madrid
Established the research group; 18 articles in this period, including first-author work in Nature Methods and Genome Biology; 3 PhD completions.
- Oct 2015 — Aug 2018
Postdoctoral Research Fellow
Broad Institute of MIT and Harvard, Cambridge MA (Regev Lab)
Developed scVI-Reg; co-first author on a Cell Systems single-cell atlas of human embryonic development.
- Sep 2011 — Sep 2015
PhD, Computational Biology
ETH Zürich
Excellent (summa cum laude equivalent). Advisor: Prof. Gunnar Rätsch.
- Sep 2009 — Jul 2011
MSc Bioinformatics
Universidad Autónoma de Madrid
Distinction.
- Sep 2005 — Jun 2009
BSc Biology
Universidad Complutense de Madrid
First Class Honours.
Contact
Get in touch
s.reyes@upm.es
- Madrid, Spain
- +34 91 900 1234
- orcid.org/0000-0002-1234-5678
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