Cynthia Soto-Cardinault, PhD
Founder of Arkhe Multiomics
Profile
I am a computational biologist and multi-omics data specialist with a background in computer science, molecular biology, and computational genomics.
My work focuses on transforming complex biological datasets into meaningful scientific insights through bioinformatics analysis, integrative approaches, and reproducible computational workflows.
My research experience spans plant molecular biology and human neurogenomics, with expertise in transcriptomic, epigenomic, and spatial data analysis. I am particularly interested in applying computational approaches across diverse biological systems, organisms, and research areas.
As founder of Arkhe Multiomics, I provide specialized bioinformatics consulting and technical training for researchers, laboratories, and academic institutions.
Open to international research collaborations, consulting projects, and specialized technical training.
Research Collaboration & Services
I collaborate with researchers and scientific teams seeking computational support for their omics research projects.
Omics Data Analysis & Bioinformatics Consulting
- Bulk RNA-seq: Differential expression, functional interpretation, and gene co-expression networks.
- Single-cell & single-nucleus RNA-seq: Quality control, clustering, cell-type annotation, and exploratory analysis.
- Single-cell multiome: Integrated analysis of gene expression and chromatin accessibility.
- Spatial transcriptomics: Spatial gene expression patterns and cellular organization.
- Reproducible workflows: Computational pipelines, documentation, and analytical best practices.
Projects can be tailored to specific datasets, research questions, and computational requirements.
Specialized Technical Training
Through Arkhe Multiomics, I develop and deliver hands-on bioinformatics training for research laboratories, universities, and scientific institutions.
Training activities include:
- Practical workshops using real biological datasets.
- Guided analysis with R/Python and bioinformatics tools.
- Single-cell, multiome, and spatial transcriptomics workflows.
- Training adapted to research teams and institutional needs.
The goal is to help researchers develop practical analytical skills and apply reproducible workflows to their own projects.
Have an omics dataset, a research challenge, or a team seeking computational expertise?
Research Interests
My research focuses on computational biology and high-dimensional omics data analysis, with two primary areas of interest:
- Neuroscience & Disease: Single-cell, single-nucleus, and spatial transcriptomics to investigate cellular heterogeneity and molecular organization in the human brain.
- Plant–Pathogen Interactions: Transcriptomics and gene co-expression networks to investigate plant defense mechanisms, with growing interest in single-cell and spatial transcriptomics.
I am particularly interested in integrative approaches combining transcriptomic, epigenomic, and spatial information to investigate complex biological systems.
Publications
Montgomery KD, Werner JM, Eagles NJ, Liu C, Cardinault CS, Bach SV, Chandra A, Zhang R, Maguire SE, Divecha HR, et al.
Multi-omic spatial mapping of the human habenula defines the molecular and anatomical organization of medial and lateral subregions.
bioRxiv. 2026. Preprint. DOI: 10.64898/2026.09.30.755667
Soto-Cardinault C, Childs KL, Góngora-Castillo E.
Network Analysis of Publicly Available RNA-seq Provides Insights into the Molecular Mechanisms of Plant Defense against Multiple Fungal Pathogens in Arabidopsis thaliana.
Genes (Basel). 2023 Dec 16;14(12):2223
Soto-Cardinault CG, Duarte-Aké F, De-la-Peña C, Góngora-Castillo E.
DNA Methylation and Transcriptomic Next-Generation Technologies in Cereal Genomics.
Methods Mol Biol. 2020;2072:65–84
Soto C, Ucán JP, Aguilar RA.
Diseñando entornos virtuales de aprendizaje para el análisis de la colaboración con UWE.
Abstraction & Application. 2018;20
Soto C, Menéndez V, Aguilar R.
Interoperabilidad entre el LMS Moodle y aplicaciones educativas utilizando IMS-LTI.
Revista Apertura. 2015
Soto C, Menéndez V, Aguilar R.
Methodological framework for collaborative virtual learning environments integrated with LMS.
EDULEARN14 Proceedings. 2014
Technical Expertise
My computational experience includes the analysis of transcriptomic, epigenomic, and spatial omics datasets using R, Python, and high-performance computing environments.
Core Bioinformatics Ecosystem
- Programming & environments: R, Python, Bash/Shell, Linux, HPC (SLURM/SGE), Git/GitHub.
- Single-cell & spatial analysis: Seurat, Signac, SpatialExperiment, spatialLIBD, scran, scater, bluster.
- Transcriptomics & network analysis: WGCNA, DESeq2, ggplot2, tidyverse, ComplexHeatmap.
- 10x Genomics pipelines: Cell Ranger, Cell Ranger ARC, Space Ranger.
- RNA-seq preprocessing & quantification: FastQC, Trimmomatic, STAR, HISAT2, Salmon, Kallisto, HTSeq.
I prioritize reproducibility, biological interpretation, and clear documentation, adapting computational approaches to the scientific questions and characteristics of each dataset.
Research Background & Experience
My background combines computer science, molecular biology, and computational genomics, with research experience spanning plant biology and human neuroscience.
During my PhD at the Centro de Investigación Científica de Yucatán (CICY), I investigated plant defense mechanisms using bulk RNA-seq and gene co-expression network analysis.
At the Lieber Institute for Brain Development (LIBD), I contributed to collaborative neurogenomics research integrating single-nucleus RNA-seq, chromatin accessibility, and spatial transcriptomics to investigate cellular and molecular organization in the human brain.
Today, as founder of Arkhe Multiomics, I apply this interdisciplinary experience to support research teams through omics data analysis, bioinformatics consulting, and specialized technical training.
Education
PhD in Biological Sciences
Biotechnology specialization
Centro de Investigación Científica de Yucatán (CICY), Mexico
2019–2023
MSc in Computer Science
Universidad Autónoma de Yucatán, Mexico
2013–2016
BSc in Computer Science
Universidad Autónoma de Tamaulipas, Mexico
For additional academic background and recognitions:
Let’s Collaborate
Are you working with an omics dataset, planning a bioinformatics analysis, or looking to strengthen your team’s computational skills?
I welcome inquiries from research laboratories, principal investigators, universities, and scientific institutions worldwide.
Whether you need support for a specific analysis, a collaborative research project, or specialized technical training, I would be happy to discuss your goals.
Last updated: October 2026