Doctorate in Life Science Complexity
Oct 2014 - Dec 2018
Sorbonne Université (Paris, France)
French universities do not award honors or grades for a PhD thesis.
Master in Life Sciences
Sep 2013 - Jun 2014
École Normale Supérieure (Paris, France)
Mention: Bien
Bachelor in Genomic Sciences
Aug 2008 - Jun 2012
Universidad Nacional Autónoma de México (Cuernavaca, Mexico)
Mention: Honors
Zenith Therapeutics (Basel, Switzerland)
Aug 2025 - Mar 2026
Senior Scientist, Computational Biologist
Supported gene target identification in oncology and autoimmune indications by analyzing public bulk and single-cell RNA-seq from patient samples.
Curated data from public resources (e.g. BioGRID, literature and genomic databases).
Designed modular and reproducible pipelines for genomic data processing and QC, enabling rapid iteration and reuse across projects.
Ridgeline Discovery (Basel, Switzerland)
Jan 2025 - May 2025
Scientist, Computational Biologist
Led cross-functional projects integrating genomics and bioinformatics to prioritize therapeutic targets and mechanisms of action for oncology and autoimmune indications across four portfolio companies.
Supported discovery of targets for advanced therapeutic modalities (degrader-antibody conjugates, molecular glues, monoclonal antibodies) by analyzing transcriptomics and perturbation screens, and integrating public resources for target annotation.
Developed and optimized scalable pipelines for CRISPR screen analysis for two companies.
Regularly presented results and strategic recommendations to managers, senior scientists and cross-functional stakeholders, aligning computational insights with portfolio decisions.
Mentored colleagues in workflow development, version control and best practices.
Analyzed pre-clinical data from non-human primates to identify potential confounding factors and refine study design and interpretation.
Cimeio Therapeutics (Basel, Switzerland)
Nov 2022 - Dec 2024
Scientist, Computational Biologist
Developed NGS analysis pipelines for short- and long-read data, including pooled CRISPR screens.
Reduced Amp-seq analysis turnaround form 3 days to ~4 hours by implementing the workflow as a Nextflow DSL2 pipeline on HPC environments, enabling technicians with basic command-line skills to run analyses independently and accelerating decisions on sgRNA prioritization.
Gained in-depth expertise in sgRNA off-target prediction and participated in the interpretation of NGS and optical genome mapping to de-risk guides across multiple CRISPR therapeutic programs.
Built pipelines for variant calling and interpretation to assess CRISPR/Cas9 editing efficiency, on-target performance and off-target risk.
Delivered automated reporting solutions and acted as technical lead for data interpretation in cross-functional collaborations, ensuring FAIR compliant, reproducible analyses.
Communicated results in internal seminars to colleagues in the research and manufacturing teams, including students, technicians, scientists and directors.
Mentored colleagues in data analysis and the usage of digital tools.
Collaborated with other data scientist on the design of a target validation analytics platform, defining data requirements, analysis workflow and technical specifications (project de-prioritized before implementation).
European Molecular Biology Laboratory EMBL (Heidelberg, Germany)
Jun 2019 - Aug 2022
EU-funded Postdoctoral Fellow
Performed allele-specific analyses to study transcriptional regulators of genes that escape the process of X chromosome inactivation in mouse and the impact of LINE1 expression.
Designed and developed 6 fully FAIR-compliant bioinformatics pipelines to process genomics data and extract information for downstream analyses (RNA-seq, DNA-seq, ChIP-seq, ATAC-seq, CUT&RUN), now adopted by lab members; the RNA-seq pipeline was further integrated into the EMBL genomics platform for routine use.
Organized and curated large-scale, multi-omics datasets, enabling robust integrative analysis across platforms.
Prepared libraries for next-generation sequencing (ATAC-seq, CUT&RUN).
Trained and supervised junior researchers in both bioinformatics and NGS library preparation, ensuring reproducible practices and knowledge transfer.
Wrote grant applications for a Marie Skłodowska-Curie (Horizon 2020) individual fellowship and an EMBO postdoctoral fellowship.
Contributed to 4 publications (2 published, 1 pre-print and 1 in preparation) and presented research at 2 international conferences and 1 outreach event.
Gained hands-on experience in tissue culture of mouse embryonic stem cells and neural progenitor cells.
Institut Curie (Paris, France)
Oct 2014 - Mar 2019
| PhD Fellow | Bridging Postdoctoral Fellow |
Conceptualized and managed projects in the gene regulation field.
Analyzed functional genomics data (RNA-seq, ChIP-seq, ATAC-seq, Hi-C) to characterize enhancers and investigate the role of an architectural protein in zebrafish.
Acquired skills in library preparation (ChIP-seq, ATAC-seq).
Pioneered the generation of zebrafish knock-in alleles using the CRISPR/Cas9 genome editing technique to obtain an endogenously tagged protein, overcoming the need to generate custom antibodies.
Communicated results in 2 first-author publications, internal seminars and conferences.
Collaborated in 2 projects that resulted in 2 co-authored publications.
Genomics & NGS
Data processing, QC, visualization, comparative analysis, and biological interpretation for Amp-seq (Illumina and PacBio platforms), ATAC-seq, ChIP-seq, CUT&RUN, DNA-seq, Hi-C, bulk/single-cell RNA-seq.
Variant calling from short- and long-read sequencing data (GATK, freebayes, bcftools, pbsv).
Experienced with genome browsers and 3D-genome tools (IGV, Juicebox, HiGlass, pyGenomeTracks).
Library preparation of ATAC-seq, ChIP-seq and CUT&RUN.
CRISPR-based technologies
Analysis of pooled CRISPR screens, including guide quantification and hit calling.
sgRNA off-target prediction and interpretation of off-target profiling methods (GUIDE-seq, DISCOVER-seq, CHANGE-seq, Optical Genome Mapping).
Experience establishing transgenic zebrafish lines.
Programming & software engineering
R/Bioconductor (expert); Bash (expert); Python (intermediate); awk.
Workflow development with Nextflow; containerization with Docker; basic exposure to Kubernetes.
Version control with git/GitHub.
Linux/Unix and HPC environments.
Machine learning
Supervised and unsupervised methods (regression, classification, clustering, dimensionality reduction).
Basic experience with convolutional neural networks.
Data management & reproducibility
Pipeline optimization and benchmarking.
Traceable and reproducible analyses (Jupyter notebooks, RMarkdown).
Adherence to FAIR principles and systematic documentation for collaborative projects.
Spanish (Native)
English (Fluent)
French (Fluent)
German (B2, Telc certificate)
Russian (Basic)
Marie Skłodowska-Curie Actions - Individual Fellowship
Feb 2020
European Union’s Horizon 2020
Complementary Fellowship for Graduate Studies
2015
Secretaría de Ciencia, Tecnología e Innovación (Seciti), Government of Mexico City
PhD Program Fellowship
Jan 2012
Vienna BioCenter (VBC), Austria (kindly declined).
Organizer and speaker
Oct 2022
Annual event of the Heidelberg International Professional Women’s Forum in the context of the Frauen Wirtschafts Tage BW (> 90 registrations), Heidelberg, Germany.
Assistant organizer
Sep 2018
International 1st course on Computational Systems Biology of Cancer at the Institut Curie, Paris, France.
Main organizer
Apr 2018
First European LCG-UNAM Symposium (31 participants and 3 keynote speakers) at the Centre for Mexican Studies UNAM-France and the Mexican House of the Cité International Universitaire de Paris.
PhD student supervision
Apr 2025 - Dec 2025
Supervised Anna Françoise Lucienne Le Breton at the Gulbenkian Institute for Molecular Medicine in ChIP-seq data analysis as part of an article revision.
Bioinformatics
Nov 2022 - Mar 2026
Provided day-to-day mentoring to senior scientists at Cimeio Therapeutics, Ridgeline Discovery and Zenith Therapeutics on workflow development, Linux, R programing, Kubernetes.
Developed internal training materials and reusable code templates to standardize and scale statistical analysis and visualization at Cimeio Therapeutics, Ridgeline Discovery and Zenith Therapeutics.
Technician supervision
Jun 2023 - Dec 2025
Trained Sophie Lackner at Cimeio Therapeutics in command-line usage and Amp-seq analysis using a custom Nextflow pipeline I developed.
Technician supervision
Nov 2021 - Jan 2022
Trained Isabel Rall at EMBL in NGS library preparation for ATAC-seq and CUT&RUN.
Master student supervision
Jan 2021 - Jun 2021
Supervised Léna Clerquin at EMBL in bioinformatics analysis, tissue culture and molecular biology techniques.
Outreach
Aug 2021
Jury at the 7th National Science Fair organized by the Mexican PAUTA program.
Outreach
May 2021
Transcriptional regulation of the inactive X chromosome - Virtual talk given to Mexican high school students (~60 participants) from “Colegio Ceyca” in Mexico City.
Teaching
Sep 2017
Trainer during the bioinformatics sessions on small RNA-seq analysis of the international course Analysis of NonCoding RNAs quaerite et invenietis at the EMBL Heidelberg.
Open Studies
May 2025 - Jan 2026
Applied Data Science - Machine Learning, EPFL, Switzerland
Course
Nov 2025
Kommunikation bei Demenz - short course at the Volkshochschule beider Basel
Workshop
Feb 2022
Empowerment Tools for Leading Sustainably - Heidelberg International Professional Women’s Forum.
Course
Jul 2021
Motivate & inspire your team, EMBL Heidelberg.
Course
Jul 2021
Conflict & Difficult Conversations, EMBL Heidelberg.
Summer School
Jun 2021
EMBL Corporate Summer School, Heidelberg.
Alzheimer’s Disease International 37th Global Conference
Apr 2026
Lyon, France - attendee
Alzheimer’s Disease International 36th Global Conference
Apr 2024
Kraków, Poland - online attendee
Alzheimer’s Disease International 35th Global Conference
Jun 2022
London, UK - online attendee
Journal
[1] Pérez-Rico YA, Le Breton A., Bousard A, Misikova LH, Mulugeta E, de Almeida SF, Muotri AR, Heard E, Gendrel AV. “Transcriptional perturbation of LINE-1 elements reveals their cis-regulatory potential.” bioRxiv doi: 10.1101/2024.02.20.581275.
[2] Hauth A, Panten J, Kneuss E, Picard C, Servant N, Rall I, Pérez-Rico YA, Clerquin L, Servaas N, Villacorta L, Jung F, Luong C, Chang HY, Zaugg JB, Stegle O, Odom DT, Loda A, Heard E. “Escape from X inactivation is directly modulated by levels of Xist non-coding RNA.” Nat Cell Biol. 2025 Dec 15. doi: 10.1038/s41556-025-01823-6.
[3] Pérez-Rico YA, Barillot E, Shkumatava A. “Demarcation of Topologically Associating Domains Is Uncoupled from Enriched CTCF Binding in Developing Zebrafish.” iScience. 2020 May 22;23(5):101046. doi: 10.1016/j.isci.2020.101046.
Book Chapter
[4] Collombet S, Pérez-Rico YA, Ancelin K, Servant N, Heard E. “Bioinformatic Analysis of Single-Cell Hi-C Data from Early Mouse Embryo.” Methods Mol Biol. 2021;2214:295-316. doi: 10.1007/978-1-0716-0958-3_20.
ORCID
Full list of publications available in ORCID.
