About me | Bio

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I’m a passionate data scientist who loves bringing together biology, statistics, and computer science to tackle complex biological questions.

I began my Ph.D. in Biological Sciences in 2018 at the Centro de Investigación Científica de Yucatán (CICY), where I studied Arabidopsis thaliana under the guidance of Dra. Elsa Gongora. Using public bulk RNA-seq datasets from plants infected by ascomycete fungi, a widespread pathogen responsible for major crop losses worldwide, I identified key defense gene modules linked to food security and agricultural resilience.

Earlier, in 2013, I completed my master’s degree in Computer Sciences, focusing on IMS-LTI–based services that strengthened connections between learning platforms and educational applications. My thesis earned first place in the Computing Category of the XXIX National Contest of Computer Science (ANIEI, 2016). This early experience in computing sparked my lasting enthusiasm for the fast-growing field of artificial intelligence in bioinformatics.

At the Lieber Institute for Brain Development (LIBD), my current work focuses on data-driven analyses of the human brain habenula. Together with Kelsey Montgomery and under the leadership of Dr. Kristen Maynard and Dr. Leonardo Collado-Torres, our team aims to characterize habenular cell subpopulations, canonical and novel gene markers, and candidate regulatory elements, all within their spatial context. Our integrative approach combines cutting-edge single-cell and spatial technologies, including multiome (snRNA-seq + snATAC-seq) and spatial transcriptomics (Visium and Visium HD). We look forward to sharing our preprint soon!

I could list the many tools, platforms, and workflows I’ve mastered, but honestly, bioinformatics moves at bullet-train speed, staying connected and curious is what truly matters. Bioinformatics is a borderless field, unconstrained by species, languages, or methods. I’m driven to contribute to projects that advance human health, agriculture, and other global challenges. If you’d like to collaborate or share ideas, don’t hesitate to reach out. I’m always open to meaningful conversations and projects where my skills can help answer complex biological questions.

Technical Skills

Any language or package I need to get the job done. I work across R, Python (Jupyter), and Shell/Bash for high-performance, SLURM-managed workflows, with GitHub for reproducibility.

My toolkit includes:

  • 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 Pipleines: Cell Ranger, Cell Ranger ARC, Space Ranger
  • RNA-seq preprocessing & assembly tools: FastQC, Trimmomatic, STAR, HISAT2, Salmon, Kallisto, HTSeq
  • AI-assisted workflows: ChatGPT, Gemini and Co-Pilot for accelerating analysis and problem-solving

My 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. doi: 10.3390/genes14122223. PMID: 38137044; PMCID: PMC10743233 Link

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. [doi: 10.1007/978-1-4939-9865-4_7. PMID: 31541439] Book-chapter

Soto, C., Ucán, J. P., & Aguilar, R. A. (2018). Diseñando entornos virtuales de aprendizaje para el análisis de la colaboración con UWE. Abstraction & Application, 20, 55–67. México. ISSN:2007-2635

Soto, C., Menéndez, V. y Aguilar, R. (2015) Interoperabilidad entre el LMS Moodle y aplicaciones educativas de propósito específico utilizando servicios del IMS-LTI. Revista Apertura. Vol. 7 No. 2. Índice de Revistas Mexicanas de Investigación Científica y Tecnológica. ISSN:2007-1094

Soto, C., Menéndez, V & Aguilar, R. (2014) Methodological framework for the development of virtual environments for collaborative-ludic sceneries and integration to learning management systems. Proceedings of the International Conference on Education and New Learning Technologies (Edulearn 2014).Julio 7-9. Spain: Barcelona. pp. 2534-2540. ISBN: 978-84-6170557-3 / ISSN: 2340-1117. Indexed in Web Of Science. EDULEARN14

Education

  • Doctor in Biology Sciences
    Biotechnology Specialist
    Thesis: “Análisis de redes de coexpresión RNA-Seq para identificar patrones genéticos consenso en Arabidopsis en respuesta a la infección por hongos ascomycetes”
    Centro de Investigación Científica de Yucatán, Yucatán, Mx.
    CONACYT 552999
    January 2019 - January 2023

  • Master in Computer Science
    Thesis: “Modelo para el Análisis de la Interacción en Entornos Virtuales de Aprendizaje Colaborativo”
    Universidad Autónoma de Yucatán, Yucatán, Mx.
    CONACYT 552999
    September 2013 - May 2016

  • Bachelor in Computer Science
    Universidad Autónoma de Tamaulipas, Tamaulipas, Mx.
    January 1993 - January 1997