About me

Bio

I’m Cynthia S Cardinault, a bioinformatician passionate about bringing biology and data science together to tackle complex questions. At the Lieber Institute, my current work centers on multiome (transcriptomic and epigenomic) and spatial transcriptomics in the human brain habenula, where we are building an integrated atlas of cell-type signatures, their regulatory elements, and their spatial organization. I’m excited to see a preprint of this work coming soon.

I began my genomics career during my doctorate at CICY, studying plant–pathogen interactions in Arabidopsis. Using bulk RNA data and co-expression networks, I identified key defense gene modules against ascomycete fungi, relevant topic for food security in the face of climate change.

Before that, during my master’s degree, I researched educational technologies of the future, analyzing interoperability between the Moodle LMS and purpose-built educational applications. I study IMS-LTI–based services that strengthened connections between learning platforms.

I see bioinformatics as 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.

Scientific Open Resources | SpeakerDeck | YouTube

Presentations and public talks on bioinformatics, neuroscience and plant biology:

🎥 Walkthroughs in multiomics | YouTube Playlist
Title: LIEBER - Behind the Scenes of Spatial an Multiomic Data Analysis in Neuroscience 🧠🧬
Playlist featuring walkthroughs of my work with a focus on the human brain. Multiome pipelines like CellRanger ARC and Data-driven discussions. Thanks to PhD Collado who compiled, edited and allocated all these recordings. Youtube

📑 My SpeakerDeck | SpeakerDeck
Title: LIEBER - Slides for talks
Spatial transcriptomics and multiomics. Material used for internal talks, the R-StatClub and conferences. SpeakerDeck

🎥 Transcriptomic Analysis in Arabidopsis thaliana | YouTube Playlist | Posters
Title: CICY – Arabidopsis Pathogenesis
Compiles a set of talks and presentations in which I discussed topics in molecular biology, plant genetics, and transcriptomic analysis in Arabidopsis thaliana. YouTube

My GitHub Repo

Most of my current project repositories are private for now, but these are planned to be public next year. In the meantime, you can check out my activity and contributions from this year:
🔗 GitHub Profile – cyntsc

A recent project in action is

“My Bioinformatics Notebook”. Planned to be a growing collection with weekly updated, containing workflows, tips, and insights for scRNA-seq, scATAC-seq, multiome, and Visium spatial transcriptomics, along with plot interpretations, favorite tools, and curated references.

Here’s a preview of the expected content: Bioinformatic_Notebook

Technical Skills

The short answer: any language or package I need to get the job done. But a more detailed view: I work across R, Python (Jupyter), and Shell/Bash for high-performance, SLURM-managed workflows, with GitHub for reproducible documentation.

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 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

My Formal 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