Naraen Palanikumar
Founding engineer, Phalaena Automata

Naraen Palanikumar

Bioinformatics AI engineer and cloud architect, building production omics platforms and applied AI for biological data.

Now Building Bench at Phalaena Automata. Consulting on single-cell pipelines.

About

I build production-grade analytical platforms for genomics, with a focus on cloud-native architecture and applied AI. As founding engineer at Phalaena Automata, I lead the technical development of Bench, an omics analysis platform that ingests sequencing data into a centralized API, runs containerized Nextflow workflows on Google Cloud, and uses a tool-augmented RAG loop over Vertex AI to interpret results against PubMed and public catalogs.

Before founding Phalaena Automata, I worked on CD4 T-cell repertoire analysis at USUHS, single-cell sequencing in the Sweeney Lab at UIUC, and a handful of clinical and emergency-response roles. My peer-reviewed work covers TCR usage in SARS-CoV-2 vaccination and paraventricular thalamic circuits.

Explore my portfolio, read my CV, or get in touch if you'd like to collaborate.

Selected projects

Phalaena Automata

Bench

Python · FastAPI · React · Nextflow · Docker · GCP · Vertex AI

Production omics platform that ingests sequencing data (FASTA, FASTQ, VCF, 10x) into a centralized API, runs containerized Nextflow workflows on Cloud Run with strict IAM, and integrates a tool-augmented RAG loop over Vertex AI to cross-reference results with PubMed.

Research portfolio

TCR and scRNA-seq workflows

Python · tcrdist3 · R · Seurat · Shiny

End-to-end reproducible workflow for TCR repertoire analysis with tcrdist3, alongside preleukemia scRNA-seq clustering in R and Seurat. Interactive R Shiny dashboard deployed to shinyapps.io.

Experience

  • Founding engineer, Phalaena Automata
    Remote · Mar 2026 – Present

    Leading end-to-end technical development of a multi-tenant omics SaaS on Google Cloud. Architecting scalable bioinformatics workflows, full-stack cloud-native AI infrastructure, and LLM-augmented interpretation pipelines.

  • Independent bioinformatics consultant
    Remote · Jul 2025 – Present

    Consulting on single-cell sequencing pipelines and metabolic pathway analysis. Building cloud-native workflows for high-throughput omics research teams.

  • Bioinformatics research assistant, Malloy Lab
    USUHS · Bethesda, MD · Oct 2024 – Jun 2025

    Led bioinformatic analysis of CD4 T-cell repertoires investigating respiratory infectious diseases. Optimized high-throughput processing for scRNA-seq and flow cytometry, with results published in Frontiers in Immunology.

  • Research assistant, Sweeney Lab
    UIUC · Champaign, IL · Aug 2021 – Jun 2023

    Analyzed scRNA-seq with Cell Ranger and Seurat to surface metabolism-associated neural circuits. Built an interactive R Shiny app for fiber photometry, co-authored in The Journal of Neuroscience.