Naraen Palanikumar
Founding engineer, Phalaena Automata

Naraen Palanikumar

Bioinformatics engineer with 4+ years of experience building scalable platforms for lab research, spanning Nextflow pipelines, Google Cloud architectures, and applied AI for biological data.

Now Building Bench at Phalaena Automata. Google Cloud Certified Professional Data Engineer.

About

Founding engineer at Phalaena Automata, leading end-to-end development of Bench, a production omics 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 cross-reference results with PubMed and public catalogs.

Prior work spans CD4 T-cell repertoire analysis at USUHS, single-cell sequencing and an interactive R Shiny tool at the Sweeney Lab at UIUC, and clinical and emergency-response roles. Peer-reviewed contributions cover restricted TCR usage following SARS-CoV-2 vaccination (Frontiers in Immunology) and paraventricular thalamic MC3R circuits (The Journal of Neuroscience).

Browse the portfolio, read the CV, or get in touch to collaborate.

Selected projects

Phalaena Automata

Bench

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

Production omics platform ingesting varied sequencing data into a centralized API and running containerized Nextflow workflows on Cloud Run with strict IAM. Integrates a tool-augmented RAG loop over Vertex AI to cross-reference output against PubMed for accelerated insights.

Bioinformatics portfolio

AML scRNA-seq & TCR clonality

R · Python · Seurat · Scanpy · tcrdist3 · Shiny

Reproducible scRNA-seq pipeline across 38 public AML patient samples, characterizing pre-leukemic populations with pseudotime, fate mapping, and PLPS/Stem11 survival analysis, deployed as an R Shiny dashboard. Companion TCR-β workflow compares clonality between TB progressors and controllers.

Experience

  • Phalaena Automata Mar 2026 - Present
    Founding Engineer Austin, TX, USA

    Spearheading end-to-end development of a biotechnology research accelerator, managing the product lifecycle from initial architecture to cloud deployment. Developing full-stack AI-centric infrastructure on Google Cloud, integrating RAG + LLM architecture to automate unstructured data interpretation.

  • Independent Jul 2025 - Feb 2026
    Bioinformatics Consultant Remote

    Consulted on single-cell sequencing pipelines, metabolic pathway analysis, and cellular heterogeneity queries to provide scalable workflows for research teams. Applied cloud-native bioinformatics pipelines built for high-throughput omics research.

  • Malloy Lab @ USUHS Oct 2024 - Jun 2025
    Research Assistant Bethesda, MD, USA

    Led bioinformatics analysis to extract and analyze CD4 T-cell repertoires from scTCR-seq data, contributing to published research in Frontiers in Immunology. Processed study participant biosamples and metadata for downstream flow cytometry and scRNA-seq.

  • Sweeney Lab @ UIUC Aug 2021 - Jun 2023
    Undergraduate Research Assistant Champaign, IL, USA

    Analyzed complex scRNAseq datasets using Cell Ranger and Seurat to uncover metabolism-associated neural circuits and rare cell populations. Built an interactive R Shiny web app for fiber photometry data processing, contributing to published research in The Journal of Neuroscience.