About me | Bio
Profile
I am a multi-omics data specialist and founder of El Arkhe.
My work sits at the intersection of bioinformatics, statistics, and molecular biology, where I focus on translating large-scale genomics data into meaningful and interpretable insights.
I am particularly interested in bridging research, training, and scientific communication.
Research Interests
My work focuses on developing classical and AI-assisted frameworks to interpret high-dimensional biological data, with an emphasis on:
- Neurological diseases through single-cell and spatial transcriptomics
- Plant host–pathogen interactions using bulk transcriptomics, with growing interest in single-cell and spatial transcriptomics in plants
Through El Arkhe – Multiomics, I provide training and consulting in omics technologies, supporting researchers in building analytical capacity and reproducible workflows.
In parallel, El Arkhe – Cuentos Moleculares focuses on accessible scientific communication, connecting molecular biology with broader cultural contexts.
Technologies & approaches of interest
- Single-cell transcriptomics (scRNA-seq)
- Chromatin accessibility and regulatory genomics (scATAC-seq)
- Multiome data integration (RNA + ATAC)
- Spatial Resolved Transcriptomics (SRT)
My journey into molecular biology (2013–2026)
Early training in computer science (2013–2016)
In 2013, I completed a Master’s degree in Computer Science under the guidance of Dr. Raúl Aguilar, where I designed an IMS-LTI–based service model to strengthen interoperability between learning platforms and educational applications. My thesis received first place in the Computing Category at the XXIX National Contest of Computer Science (ANIEI, 2016).
This early experience in computing, together with a summer research program at Texas A&M University, sparked my long-term interest in applying computational methods and artificial intelligence to biological problems.
Transition into molecular biology (2018–2023)
In 2018, I began my Ph.D in Biological Sciences at the Centro de Investigación Científica de Yucatán (CICY) under the supervision of Dr. Elsa Góngora. My research focused on Arabidopsis thaliana and plant defense responses against fungal pathogens. Using public bulk RNA-seq datasets, I identified gene co-expression modules associated with plant immunity, contributing to the understanding of molecular defense mechanisms relevant to food security and agricultural resilience.
This period strengthened my commitment to the intersection of computational methods and biology, while connecting me with a vibrant and collaborative bioinformatics research community.
Neurogenomics research at LIBD (2023–2025)
At the Lieber Institute for Brain Development (LIBD), my work focused on data-driven analyses of the human brain habenula, a small but functionally critical structure involved in reward processing and neuropsychiatric disorders.
As part of a collaborative research team led by Dr. Leonardo Collado-Torres and Dr. Kristen Maynard, we investigated habenular cellular diversity and candidate regulatory elements within their spatial context.
Our integrative approach combined advanced technologies including:
- single-nucleus RNA-seq
- snATAC-seq multiome
- spatial transcriptomics (Visium)
This stage represented one of the most formative periods in my development as a computational biologist working at the intersection of genomics and neuroscience.
Current work — El Arkhe (2025–present)
I currently lead El Arkhe, an initiative focused on advancing training, consulting, and scientific communication in multi-omics.
Through El Arkhe – Multiomics, I design and deliver specialized training programs in single-cell, multiome, and spatial transcriptomics, supporting researchers in building analytical capacity and reproducible workflows.
In parallel, El Arkhe – Cuentos Moleculares explores scientific communication through accessible, interdisciplinary formats that connect molecular biology with culture and storytelling.
This stage reflects a transition toward leadership, education, and the development of scalable scientific programs in multi-omics.
Technical Skills in Computational Biology and Bioinformatics
A typical day includes:
- Reading scientific literature
- Coding in R and Python (Jupyter)
- Working with Shell/Bash in HPC environments (SLURM/SGE/GPU/local)
- Maintaining reproducible workflows with GitHub
I continuously explore new tools and technologies that can enhance my work, but I am not a tool collector. I prefer to master a few widely used tools that allow me to remain flexible and adaptable.
My key strengths include staying organized, maintaining focus, and adapting to new tools and methods as required by the research questions I address.
I enjoy sharing knowledge and learning from others, and I am always looking for ways to contribute to the scientific community through my work and collaborations.
Core bioinformatics ecosystem
- R packages: Seurat, Signac, SpatialExperiment, spatialLIBD, scran, scater, bluster, WGCNA, DeconvoBuddies, dendextend, ComplexHeatmap, ggplot2, tidyverse
- Technologies & data types: scRNA-seq, scATAC-seq, multiome, Visium spatial transcriptomics
- 10x Genomics pipelines: Cell Ranger, Cell Ranger ARC, Space Ranger
- RNA-seq preprocessing & quantification: FastQC • Trimmomatic • STAR • HISAT2 • Salmon • Kallisto • HTSeq
- AI-assisted workflows: ChatGPT • GitHub Copilot for accelerating analysis and problem-solving
Publications
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
Education
Doctor in Biological Sciences
Biotechnology specialization
Centro de Investigación Científica de Yucatán (CICY), México
2019 – 2023
Master in Computer Science
Universidad Autónoma de Yucatán, México
2013 – 2016
Bachelor in Computer Science
Universidad Autónoma de Tamaulipas, México
Training & Honors
A summary of my academic background and recognitions:
Updated on March 2026