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.

Reading Oathbringer by Brandon Sanderson. More on the shelf.

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, check out my gallery or log entries, 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 transcriptomics

R · Python · Seurat · Scanpy · Nextflow · R Shiny

Two complementary AML projects: a single-cell pipeline characterizing pre-leukemic populations across 38 patient samples (pseudotime, fate mapping, PLPS/Stem11 survival) as an R Shiny dashboard, and a Nextflow bulk RNA-seq differential-expression pipeline on TCGA-LAML vs. GTEx with an interactive volcano.

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.