Aarón D. Ramírez-Sánchez

I'm

About

I am a postdoctoral researcher aiming to contribute to cutting-edge research in medical sciences and multi-omics, with a focus on translational genomics and precision medicine. My research focus in autoimmunity, especially in Celiac Disease and Multiple Sclerosis.

Aarón D. Ramírez-Sánchez Profile Picture

Postdoctoral Researcher.

Exploring genetics elements linked to Multiple Sclerosis and Celiac Disease.

  • Current position: Postdoc
  • Affiliation: Genetics Department
  • Institution: University Medical Center Groningen
  • City: Groningen, The Netherlands
  • Age: 32
  • Degree: PhD
  • Email: aarondrs2@gmail.com
  • Birthday: 22 April 1992

I got my PhD degree at the University of Groningen in The Netherlands. At the University Medical Center Groningen's Genetics Department, under the supervision of Dr. Iris Jonkers and Dr. Sebo Withoff, I engaged in multiple collaborations to advance research in Celiac Disease, employing cutting-edge technologies such as single-cell RNA sequencing.

Currently, I am a postdoctoral fellow in Dr. Iris Jonkers' group, focusing on the study of regulatory elements associated with Multiple Sclerosis. My work contributes to the scientific understanding of complex diseases, utilizing advanced genomic techniques and collaborative research efforts.

Achievements

Throughout my career, I have achieved significant milestones in research, academia, and mentoring:

7

Manuscripts Published: Published in indexed journals, with 5 as first author.

11

Presentations: Delivered at International and National Congresses and Meetings on Immunology and Celiac Disease.

19

Lectures and Workshops: Conducted on topics such as Bulk and Single-Cell RNA Sequencing, Big Data in Immunology, and the Non-Coding Genome.

8

Students Mentored: Mentored Master’s and Bachelor’s students through research projects and academic programs.

Skills

Below is an overview of my expertise, categorized into technical skills, software proficiencies, teaching/project management capabilities, and languages.

Technical / Wet Lab Skills

  • Flow Cytometry: Design, Implementation, Analysis, and Interpretation (Conventional and Spectral Flow Cytometry; multicolor panels).
  • Bulk and Single-Cell RNA and ATAC sequencing (10X Genomics platform).
  • Tissue culture and Cell dissociation: experience with 3 primary cells, 10 inmortal cell lines, and 3 types of tissues.
  • Good laboratory practices (ISO:17025, ISO:15189 standards).
  • Molecular Biology: DNA/RNA/protein techniques (RT-qPCR, capillar electrophoresis, Western blot, etc.).
  • Genetic Engineering: human cell lines and primary cells (viral and plasmid based, CRISPR-Cas9 gene editing), bacteria and yeast (plasmid based).
  • Fluorescence Microscopy: Axio Scope, ZEISS.
  • Analytical chemistry and biochemistry.

Bioinformatics / Dry Lab Skills

  • R: Data cleaning, Plotting, Analysis, and Genomic packages.
  • Unix environment: Data cleaning and Bioinformatics workflows.
  • Familiar with version control systems: Git (GitHub), Perforce.
  • Genomics analysis tools: Bedtools, VCFtools, PLINK.
  • Genotype imputation.
  • Flow-cytometry analysis: Kaluza Analysis, FlowJo.
  • Use of biological databases (NCBI, EMBL, KEGG, SILVA, RDP, PDB).
  • Basic programming: C#, Python.
  • Other bioinformatics tools: Staden Package, Mega7.
  • Microsoft Office Suite (Word, Excel, PowerPoint) and Adobe Suite (Illustrator, Acrobat).

Teaching & Project Management

  • Designing and delivering lectures and workshops.
  • Mentoring students and junior researchers.
  • Grant writing and research proposal development.
  • Managing cross-disciplinary research projects.
  • Science communication and outreach.

Languages

Spanish (Native), English (Advanced, TOEFL iBT 99/120), German (Intermediate, B2-C1), Dutch (Basic, A1).

Resume

I am a dedicated Postdoctoral Researcher specializing in Multi-omics and Translational Genomics, with a strong focus on Autoimmune Diseases such as Multiple Sclerosis and Celiac Disease. My expertise spans Molecular Biology, Bioinformatics, Single-Cell Sequencing, and Project Management. Throughout my career, I have published in high-impact journals, mentored students, and contributed to advancing our understanding of Complex Diseases.

Summary

Aarón D. Ramírez-Sánchez

Postdoctoral researcher with expertise in multi-omics, autoimmune diseases, and single-cell sequencing. I value collaboration, take a thoughtful and dedicated approach to research, and enjoy contributing to impactful scientific advancements.

  • aarondrs2@hotmail.com

Education

PhD

2017 - 2024

Genetics Department, University Medical Center Groningen, Groningen, The Netherlands

Supervisor: Iris Jonkers and Sebo Withoff

Project: Molecular Mapping of Celiac Disease: A Journey from Biomarkers to Tissues.

  • Identified potential biomarkers for Celiac Disease.
  • Developed methods for processing, storing, and dissociating gut biopsies.
  • Designed and implemented antibody panels for flow cytometry analysis.
  • Prepared and analyzed bulk-RNA, single-cell RNA, and ATAC-seq libraries.
  • Disseminated results in congresses, international meetings, and scientific journals.
  • Contributed to grant writing and supervised one master’s student.

Graduate in Genomic Biotechnology

2009 - 2014

School of Biological Sciences, Universidad Autónoma de Nuevo León (UANL), Mexico

Specialization in Genetic Engineering, Bioinformatics, Systems Biology, Bio-business, Development and Technology Transfer, Industrial and Agricultural Biotechnology.

Top GPA (Overall GPA: 94.3/100).

Academic exchange program DAAD

2013 - 2014

Georg-August Universität Göttingen, Germany

Master level subjects: General and Applied Microbiology, Molecular Biology and Agricultural Biotechnology, Reproductive Biotechnology and Genome Analysis, Application of Markers in Plant Breeding.

Professional and Scientific Experience

Postdoctoral Researcher

2021 - Present

Genetics Department, University Medical Center Groningen, Groningen, The Netherlands

Supervisor: Iris Jonkers

Project: Fine Mapping of Genetics Associated to Multiple Sclerosis.

  • Selected GWAS-associated variants linked to Multiple Sclerosis.
  • Optimized cell culture and transfection protocols for MS-relevant cell lines.
  • Generated libraries to analyze ~30,000 potential gene regulatory elements.
  • Supervised four master’s students and three bachelor’s students.

Head of Bioprocesses Laboratory

2016

Vitagenesis SA de CV, Monterrey, Mexico

  • Coordinated and supervised training, services, and R&D projects.
  • Developed and implemented enzyme detection methods, hemagglutination assays, primer walking sequencing, and qPCR for microorganism identification.
  • Improved molecular identification methods.
  • Preparing and implementing protocols to obtain ISO:17025 and ISO:15189.
  • Coordinated submission of four grants to CONACYT.

Research Assistant

2015

Vitagenesis SA de CV, Monterrey, Mexico

  • Optimized genetic construct designs and yeast identification methods.
  • Coordinated provisional R&D projects.
  • Contributed to the submission of two projects to CONACYT and private entities.

Internship

2014

Vector Laboratory, Dept. of Neurology, University of Göttingen, Germany

Supervisor: Sebastian Kügler

Project: Cytotoxicity Determination of Fluorescent Proteins and AAV Construction.

  • Designed and constructed adeno-associated virus (AAV) vectors for inducible expression/repression in neurons.
  • Performed electroporation, transduction, and fluorescence microscopy.
  • Managed primary cortical neuronal cultures and conducted digital image analysis.

Internship

2012 - 2013

Gene and Cell Therapy Laboratory, CIDICS, UANL, Monterrey, Mexico

Supervisor: Iván Alberto Marino Martínez

Project: Design and Construction of Adenoviral Vectors for Tumor Cell Line Transduction.

  • Conducted in silico and experimental genetic engineering.
  • Handled tissue and cell culture techniques.

Research Projects

In this section you can find a selection of the research projects I have been working in the last years.

  • All
  • Multiple Sclerosis
  • Celiac Disease
  • RNA
  • Epigenetics
  • Gene Regulation
  • Gut
  • PBMC
  • Cells
Mapping Regularoty elements in Multiple Sclerosis
Studying the transcriptomic landscape of epithelial lining in Celiac Disease
Immunopathogenesis of Celiac Disease
Single-cell transcriptomic landscape in onset of Celiac Disease
Single-cell transcriptomic landscape in onset of Celiac Disease
Single-Cell dissociation methods for gut tissue

Publications

Below is a list of my peer-reviewed publications, showcasing my contributions to scientific research. First author publications papers indicated by *

  • Ramírez-Sánchez, A. D.*, Tan, I. L., Gonera-de Jong, B. C., Visschedijk, M. C., Jonkers, I., & Withoff, S. (2020). Molecular biomarkers for celiac disease: Past, present and future. International Journal of Molecular Sciences, 21(22), 8528.
  • Bakker, O. B., Ramírez-Sánchez, A. D.*, Borek, Z. A., et al. (2021). Potential impact of celiac disease genetic risk factors on T cell receptor signaling in gluten-specific CD4+ T cells. Scientific Reports, 11(1), 9252.
  • Ramírez-Sánchez, A. D.*, Chu, X., Modderman, R., et al. (2022). Single-cell RNA sequencing of peripheral blood mononuclear cells from pediatric celiac disease patients suggests potential pre-seroconversion markers. Frontiers in Immunology, 13, 843086.
  • Uniken Venema, W. T., Ramírez-Sánchez, A. D.*, et al. (2022). Gut mucosa dissociation protocols influence cell type proportions and single-cell gene expression levels. Scientific Reports, 12(1), 9897.
  • Moerkens, R., Mooiweer, J., Ramírez-Sánchez, A. D., et al. (2024). An iPSC-derived small intestine-on-chip with self-organizing epithelial, mesenchymal, and neural cells. Cell Reports, 43(7).
  • Ramírez-Sánchez, A. D.*, Zühlke, S., Aguirre-Gamboa, R., et al. (2024). Gene expression and eQTL analysis reflect the heterogeneity in the inflammatory status of the duodenal epithelial lining in celiac disease. bioRxiv, 2024-02.
  • Moerkens, R., Mooiweer, J., Smits, E., Berg, M., Ramirez Sanchez, A. D., et al. (2024). Intestine-on-chip enhances nutrient and drug metabolism and maturation of iPSC-derived intestinal epithelial cells relative to organoids and Transwells. bioRxiv, 2024-06.

Other Interests

Variety's the very spice of life, That gives it all its flavor.

-William Cowper

Videogames

My biggest hobby is both playing and developing videogames—activities that I deeply enjoy and draw energy from. I play everything, from highly popular games to hidden gems.

Boardgames

I started with boardgames like any other activity, but I was quickly drawn to them because of their complexity, fun, and the memorable moments they create with friends. My favorites are chess and deck-building games.

Reading

One of my greatest pleasures is reading about all kinds of topics, from fiction to non-fiction. I am especially immersed in the sci-fi genre but would never turn down a classic.

Music

I enjoy every aspect of music, from listening to great artists to exploring my own self through this beautiful language. I primarily play the guitar, with some knowledge of piano and bass. I also have personal projects composing and producing my own pieces.

Philosophy

One of my most recent interests is philosophy. It started as a pandemic hobby, but it has stayed and become a meaningful part of my life.

Cooking

As a Mexican, food is essential to life—not just as a way to keep us alive but as a way to truly live a good life. Experimenting with flavors, creating new combinations, and bringing happiness to loved ones through these creations is an experience worth savoring.

Contact

If you have further interest in having a conversation with me to discuss one of the several topics I enjoy, feel free to contact me.

Location:

Antonius Deusinglaan 1, 9713AV, Groningen, N.L.