Ricardo O. Ramirez-Flores
My expertise lies at the intersection of computational biology, molecular biology, and biomedicine. My work focuses on developing computational methods that integrate -omics data at multiple scales—bulk, single-cell, and spatial—to investigate how cells are organized within tissues and how this organization changes in disease. A key area of my research is performing meta-analyses of -omics studies from independent patient cohorts, which I believe strengthens the reliability of identifying molecular biomarkers.
I began my academic career in the Saez-Rodriguez group in 2015 as a Bachelor intern, continuing my PhD studies within the same group. Currently, I am a Staff Scientist at EMBL-EBI, where I am expanding my research on gene regulatory mechanisms driving multicellular responses, with a growing emphasis on understanding host-microbiome interactions.
0000-0003-0087-371X Research Interests
I’m interested in understanding how the cells in our bodies work together to form tissues and how this organization changes during disease. By combining different types of data—such as bulk, single-cell, and spatial omics—I study how the structure of tissues impacts what individual cells do, and how individual cell behavior can affect the larger tissue. My goal is to understand how changes in one part of a tissue can influence the whole system. I believe that a multicellular functional perspective of single-cell data could promote the emergence of novel analysis strategies that could synergize the knowledge of the fields of mathematical physiology, ecology, and systems biology. I also explore whether different diseases or perturbations lead to similar changes in tissues, which helps us better understand how cells respond to stress or damage. For the same reason, I have also focused on systemic meta-analyses of distinct patient cohorts and etiologies to provide consensus transcriptional signatures that serve as references for future studies.
Professional Career
| 2024-Present: Staff Scientist, European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI) | |
| 2023-2024: Postdoctoral Researcher, Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine & Heidelberg University Hospital, Germany. | |
| 2019-2023: PhD Candidate, Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine & Heidelberg University Hospital, Germany. | |
| 2016-2017: Research Assistant, Microbiology and Cell Science Department, University of Florida, USA. | |
| 2015-2016: Trainee, JRC-COMBINE, RWTH Aachen University, Germany. | |
| 2015-2015: Research Assistant, Center for Genomic Sciences, UNAM, Mexico. |
Education
| 2019-2023: PhD summa cum laude in Natural Sciences, Heidelberg University, Germany | |
| 2017-2018: Specialist in Applied Statistics, National Autonomous University of Mexico, Mexico | |
| 2012-2016: B.Sc. in Genomics, National Autonomous University of Mexico, Mexico |