Everardo Castañeda
Los Angeles,CA
Summary
Bioinformaticist with 4+ years of experience analyzing high-dimensional genomic and proteomic data from human clinical samples at Children’s Hospital Los Angeles. Extensive hands-on work in spatial transcriptomics and proteomics (GeoMx DSP), RNA-seq differential expression, unsupervised clustering, and multi-omics integration across cancer and translational pathology studies. I work fluently across R, Python, SQL, and clinical data systems such as Cerner Command Language and MPages, and I love partnering closely with physicians, clinicians, researchers, and informatics partners to shape analyses that are biologically meaningful and clinically relevant. I’m driven by a collaborative approach to bioinformatics that values patience and careful study design. with the goal of turning complex data into insights that can ultimately support our patients.
Overview
7
7
years of professional experience
Work History
Research Assistant & Bioinformaticist
Children's Hospital Los Angeles
Los Angeles, CA
11.2021 - Current
- Leading research and data analysis on spatially resolved transcriptomic data of diffuse hemispheric gliomas with H3 G34 mutations; identified presence of interneuron lineage markers and tumor invasiveness by conducting and employing differential expression analysis, gene set enrichment analysis (GSEA) and single sample GSEA, large throughput dimensional reduction techniques, unsupervised hierarchical clustering, statistical testing, and multi-dimensional visualization for an 18,000 gene target cohort.
- Co-leading spatially resolved proteomic analyses of human placental tissue using GeoMx DSP, delineating trophoblast and endothelial compartments via morphology markers (CK7, CD34) and identifying compartment-specific protein signatures through differential expression analysis, high-dimensional statistical modeling, unsupervised clustering, and multi-dimensional visualization across clinically annotated samples.
- Collaborating on a data analytics pipeline for multi-omics research of choroid plexus tumors (CPT); merged and performed correlation analysis on datasets from multiple -omics sources, NGS sequencing panels, methylation arrays, and magnetic resonance spectroscopy to categorize tumor grades, and further validated findings by writing whole-slide imaging analysis scripts to incorporate automated histologic grading, and assisted in creating a machine-learning classifier to predict CPT subtypes.
- Supported spatial transcriptomic analysis of Wilms tumor using an 18,000-gene RNA panel by designing and curating morphology-defined ROIs across multiple tumor compartments (blastema, epithelial, stromal, glomerular, tubular, nephrogenic rest, anaplastic), enabling compartment-resolved downstream differential and high-dimensional analyses.
- Led the design, construction, and implementation of a patient health information de-identifying portal (DIDNet) for the Pathology department using a SQL database and PHP backend; streamlined tracking of cross-departmental patient information at a clinical, research, and sample level and reduced user error through a modernized and engaging frontend and accompanying workflow.
- Co-leading the design and development of a clinical data management web application for the Pathology department at CHLA, utilizing Next.js and Django. This application empowers pathologists to query, sort, and filter complex clinical datasets, including pathology reports, histology, molecular data, and digital slide images through a modern UI/UX approach. By providing an intuitive dashboard, the platform supports advanced search capabilities and data interactions tailored to meet diverse clinical and research objectives.
- Designed and implemented a Cerner MPage–based Nutrition TPN clinic laboratory dashboard, integrating clinical lab data via CCL and Javascript to provide clinicians with an intuitive view of abnormal trends, test recency, and patient status, improving clinical decision support, data accessibility, and workflow efficiency.
- Leading the design and development of the Billing Operations Portal Hub (BOPH) for the Pathology department. Building a robust internal tool using Next.js and SQL to streamline and centralize billing processes and research fund tracking. Currently developing the application to include secure user authentication, notification system, and advanced filtering features, to enable the biorepository team to monitor fund allocations, project statuses, and billing cycles in real-time-improving transparency, accuracy, and operational efficiency.
- Designed and delivered an approachable coding and computer science fundamentals course for physicians and clinical research coordinators, empowering colleagues to automate repetitive Excel tasks with VBA and retrieve data more confidently using SQL, reducing manual errors, improving efficiency, and easing reliance on IT support.
Coding Tutor
The Coder School
Berkeley, CA
09.2020 - 12.2021
- Participated as a coding mentor for students interested in learning coding through personalized computer science projects.
- Taught students how to code in Python, C#, and C++ as well as provided daily feedback to students and parents on how to improve projects and understanding of coding concepts.
Undergraduate Research Assistant
Dr. Meng Lab - USC Viterbi School of Engineering
Los Angeles, CA
05.2019 - 08.2021
- Co-lead a finite element modeling (FEM) project focused on optimizing the structural mechanics and microfluidic design of the Meng Lab's Parylene C neural probe array, a biomedical microelectromechanical device designed for simultaneous targeted drug delivery and deep hippocampal recording.
- Used COMSOL to both design the integration and microfabrication of microfluidic channels into the existing neural probe array for targeted drug delivery, and to investigate and quantify stress-strain distributions and buckling during neural probe hippocampal insertion.
Education
Bachelor of Science - Bioengineering
University of California, Berkeley
Berkeley, CASkills
Programming Languages & Frameworks:
- R
- Python
- MATLAB
- C#
Bioinformatics & Data Tools:
- GeoMx DSP NGS Data Analysis Pipeline
- QuPath
- COMSOL Multiphysics
Backend & Databases:
- Cerner Command Language (CCL)
- SQL
- Cerner Bedrock
- AWS
- Firebase
- Docker
Web Development:
- JavaScript/TypeScript
- HTML/CSS
- Tailwind CSS
- Nextjs
- React Native
- PHP
DevOps & Deployment:
- GitHub
- Azure DevOps
- Vercel
Laboratory:
- GeoMx NGS Protocol
- Biological Specimen Inventory System (BSI)
- RNAscope
- H&E Staining
- Immunostaining
- FFPE Deparaffinization
- Cell Culturing
- Organoid Culturing
- Autoclave
- Microscopy
Office/Communication:
- Microsoft Teams
- OneDrive
- Word
- Excel
- Powerpoint
Publications
- Murad Alturkustani, Adam D Walker, Everardo A Castañeda, Jennifer A Cotter, Utility of OLIG2 immunostaining in pediatric brain tumors with embryonal morphology, Journal of Neuropathology & Experimental Neurology, 83, 12, 12/01/24, 1039-1046, https://doi.org/10.1093/jnen/nlae082
- Cotter, J. A., Markowitz, A. L., Everardo Castañeda, Yen, C.-Y., Ostrow, D., Hawes, D., Ji, J., CNS methylation classifiers may misclassify normal developing cerebellar cortex as medulloblastoma, Acta Neuropathologica, 149, 1, 01/01/25, 66-66, https://doi.org/10.1007/s00401-025-02907-1
- Alexander L Markowitz, Jolee Suddock, Everardo Castaneda, Jianling Ji, Ashley Margol, Benita Tamrazi, Stefan Bluml, Jennifer A Cotter, PATH-06. An integrative multi-modal diagnostic approach to pediatric choroid plexus tumors, Neuro-Oncology, 26, Supplement_4, 06/01/24, 0, https://doi.org/10.1093/neuonc/noae064.709
Languages
- Fluent in English
- Fluent in Spanish
Presentations And Awards
- "Digital Spatial Profiling of H3 G34-mutant Gliomas Reveals Interneuron Gene Signatures and Potential Markers of Invasiveness", Poster Presentation, American Association of Neuropathologists, June 2024, Olympic Valley, California (R13 Travel Award - 2nd Place)
- "Berkeley Freshman Scholarship", June 2017 , Berkeley, California
References
References available upon request.
Timeline
Research Assistant & Bioinformaticist
Children's Hospital Los Angeles
11.2021 - Current
Coding Tutor
The Coder School
09.2020 - 12.2021
Undergraduate Research Assistant
Dr. Meng Lab - USC Viterbi School of Engineering
05.2019 - 08.2021
Bachelor of Science - Bioengineering
University of California, Berkeley