Senior Computational Biologist

Senior Computational Biologist

Carlos Simón Foundation | Valencia, Spain |

Are you an experienced computational biologist who wants to leverage cutting-edge multi-omics technologies, advanced computational approaches and machine learning to transform women's health?

At the Carlos Simón Foundation, we work at the forefront of reproductive medicine and women’s health, and we are looking for a scientist to lead the computational work of our flagship project, DECIDUA.

As Senior Computational Biologist, you will lead advanced bioinformatics, machine-learning and computational modeling analyses, develop novel analytical methods, and contribute to the Foundation's broader strategy for the management, integration and reuse of omics data.

About the Position

The Carlos Simón Foundation is seeking an experienced Senior Computational Biologist to lead advanced computational analyses across major research programs in reproductive and women’s health.

The successful candidate will play a key role in DECIDUA, a flagship research project integrating single-cell, spatial, multi-omic and liquid-biopsy data, while contributing to the Foundation's broader computational research strategy.

Key Accountabilities and Responsibilities

• Lead the computational strategy and execution of DECIDUA, setting priorities, milestones and quality standards together with the Principal Investigator.
• Integrate and analyze large-scale sc/snRNA-seq, spatial transcriptomic and multi-omic datasets.
• Identify cell states, molecular programs and biological signatures through advanced computational and integrative analyses.
• Develop and validate advanced computational and predictive models using molecular and clinical datasets.
• Develop reproducible computational pipelines and contribute to the Foundation's strategy for management, harmonization and reuse of omics datasets.
• Work closely with biologists, clinicians and senior investigators; mentor junior computational and technical staff; lead dissemination of results and support the Foundation’s researchers in publications.

Required Skills and Experience

• PhD in Bioinformatics, Computational Biology, Statistics, Computer Science or another quantitative discipline, plus 5+ years of relevant postdoctoral or industry experience (exceptional MSc candidates considered).
• Proven track record analyzing large-scale sc/snRNA-seq data, including multi-dataset integration and batch correction (e.g., Cell Ranger, CellBender, Seurat or Scanpy, Harmony, scDblFinder).
• Deep understanding of several areas of modern NGS bioinformatics (bulk RNA-seq, ATAC-seq, spatial transcriptomics, multi-omic integration) and experience in trajectory inference or network-based modeling.
• Strong foundation in biostatistics and machine learning (penalized regression, tree-based and boosting models, nested cross-validation, calibration, SHAP), with experience building predictive models on clinical or biomarker data.
• Fluency in R (Bioconductor, RMarkdown) and Python (Pandas, NumPy); proficiency with Linux and/or cloud HPC environments and shell scripting.
• Solid understanding of molecular and cell biology.
• Demonstrated ability to lead analytical projects and mentor junior scientists.

Desirable Skills

• Reproducible pipelines (Snakemake or Nextflow), good software practices and fluency with git; experience in a lower-level language (Rust, C++, Java).
• Mechanistic or logical modeling (e.g., Boolean networks, MaBoSS, ODE-based models) and hybrid mechanistic–machine-learning (“digital twin”) approaches.
• Experience with plasma cell-free RNA, liquid-biopsy or other transcriptomic biomarker data from clinical cohorts.
• Familiarity with GWAS and LD-score regression.
• Knowledge of endometrial, reproductive or placental biology.

Personal Qualities

• Excellent communication skills: able to explain algorithms and statistical methods to non-technical stakeholders such as clinicians and biologists.
• Ability to network, influence and collaborate, balancing the needs of multiple stakeholders.
• Independence in setting priorities, breaking down complex problems into actionable steps, and proposing innovative ideas.

What We Offer

• A leadership role with scientific ownership of the computational program of a flagship project in women’s health research.
• A multidisciplinary environment with access to unique datasets and well-characterized prospective cohorts.
• A competitive salary package based on skills and experience; hybrid work mode.
• Opportunities to publish, present internationally, supervise junior researchers and build a long-term career within the Foundation.

About the Carlos Simón Foundation for Research in Women’s Health

The Carlos Simón Foundation is a non-profit organization located in Valencia (Spain), founded and directed by Professor Carlos Simón, professor at the University of Valencia and renowned clinical researcher in obstetrics and gynecology.

The Foundation is part of the INCLIVA Health Research Institute, jointly established with the University of Valencia and the Hospital Clínico of Valencia.

We are a multidisciplinary team of more than 40 professionals working to create a world in which women's health pathologies affecting the uterus are no longer a barrier to quality of life and reproductive desire.

Our main activity is biomedical research in reproductive medicine and women’s health, and its clinical application.