About Me
Hello. My name is Arta Seyedian.
My career in tech began with a strong foundation in bioinformatics, which I approached with a biologist's background12. Over the years, I've been fortunate enough to explore various subfields and research niches, diving deep into the expansive world of bioinformatics:
- Human evolutionary genomics (unpublished study on Neandertal sQTL introgression in modern human DNA — ask me about it)
- Psychiatric and neurological transcriptomics34
- Single-cell and spatial mapping of Castleman Disease5
Currently, I'm working as a contracted Web App Developer and Bioinformatics Engineer for PEDsnet, a large, inter-institutional pediatric clinical research data-sharing consortium. My role involves setting up and customizing two instances of the open-source metadata repository DSpace to manage codesets (collections of codes used for a given clinical concept, such as diagnosis or procedure codes). These repositories enable investigators around the world to collaboratively share pediatric clinical research data.
I'm also updating, refining and optimizing already-existing computational pipelines that standardize large pediatric clinical datasets for analysis. Many of these pipelines were written years ago by developers who have since left the project, so my role involves understanding and rewriting these pipelines to ensure they are efficient and accurate. To do this, I am working with Perl, Python, Airflow and PostgreSQL to write new scripts and optimize existing ones. I am also using Docker to containerize these pipelines and ensure they are reproducible.
Skills
- R, Python, Java, SQL
- Node.js, Angular, TypeScript
- JavaScript, HTML/CSS
- ggplot2, Seurat, Bioconductor
- NumPy, pandas, ScanPy
- DESeq2, EdgeR
- Distributed Computing: Slurm, Sun Grid Engine
- Cloud: Google Cloud, AWS
- Workflow: Prefect, NextFlow, Snakemake, Airflow
- Containerization: Docker
Contact
- Email: arta[dot]seyedian[at]gmail.com
- GitHub: github.com/aseyedia
- LinkedIn: linkedin.com/in/artaseyedian
References
- Pivotal Role of Adenosine Neurotransmission in Restless Legs Syndrome. Frontiers in Neuroscience, 2018
- Pharmacological targeting of G protein-coupled receptor heteromers. Pharmacological Research, 2022
- Amygdala and anterior cingulate transcriptomes from individuals with bipolar disorder reveal downregulated neuroimmune and synaptic pathways. Nature Neuroscience, 2022
- A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex. Science, 2024
- Spatial and Single Cell Mapping of Castleman Disease Reveals Key Stromal Cell Types and Cytokine Pathways. bioRxiv, 2024