Naraen Palanikumar

Bioinformatics engineer with 3+ years of research and engineering experience spanning wet-lab sample processing, single-cell and repertoire analysis, and cloud-native pipeline engineering. Two peer-reviewed co-authorships, and a record of building tools researchers actually use.

Now Building Bench at Phalaena Automata. Google Cloud 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 · Cloud Run · Vertex AI

Production omics platform ingesting varied sequencing data into a centralized API and running containerized Nextflow workflows on Cloud Run under strict IAM. Tool-augmented RAG loop over Vertex AI cross-referencing pipeline output against PubMed and public catalogs for accelerated interpretation.

Bioinformatics portfolio

AML transcriptomics: single-cell + bulk RNA-seq

R · Python · R Shiny · Seurat · Scanpy

Two complementary acute myeloid leukemia projects: a single-cell pipeline characterizing pre-leukemic populations (R Shiny dashboard) and a Nextflow bulk RNA-seq differential-expression pipeline (interactive volcano).

Bioinformatics portfolio

Germline variant calling: GATK short-variant pipeline (Nextflow)

Nextflow · GATK4 · BWA-MEM · samtools · bcftools · fastp · Python

A reproducible Nextflow DSL2 pipeline taking raw Illumina short reads through the GATK germline best-practice path — BWA-MEM alignment, duplicate marking, HaplotypeCaller joint genotyping, hard-filtering, and consequence annotation — to a filtered cohort VCF, validated on a synthetic cohort with planted variants and wired to benchmark against the GIAB HG002 truth set.

Bioinformatics portfolio

Spatial transcriptomics: Visium breast-cancer cell-type deconvolution (Nextflow)

Nextflow · Python · scanpy · anndata · squidpy · SciPy · scikit-learn

A reproducible Nextflow DSL2 pipeline that takes a 10x Visium breast-cancer section plus a matched scRNA-seq atlas and maps cell types back into tissue space: per-spot NNLS deconvolution and spatially variable genes, rendered as interactive figures.

Experience

Phalaena Automata Mar 2026 - Present

Founding Engineer Austin, TX

Spearheading end-to-end development of a biotechnology research accelerator platform, managing the product lifecycle from initial architecture to cloud deployment. Developing full-stack AI-centric infrastructure on Google Cloud, integrating RAG and LLM architecture to automate unstructured data interpretation pipelines and accelerate the sequence-to-insight loop.
Independent Research & Development Jul 2025 - Mar 2026

Bioinformatics Engineer (Independent Projects) Remote

Built end-to-end single-cell and bulk RNA-seq analyses on public oncology datasets, covering QC, integration, cell-type annotation, trajectory inference, and survival analysis. Developed cloud-native, containerized bioinformatics pipelines for high-throughput omics workflows, applying Google Cloud Professional Data Engineer practices to reproducible research infrastructure.
Malloy Lab, Uniformed Services University of the Health Sciences Oct 2024 - Jun 2025

Research Assistant Bethesda, MD

Processed study participant biosamples and metadata for downstream high-throughput processing using flow cytometry and scRNA-seq. Led bioinformatics analysis to extract and analyze CD4 T-cell repertoires from scTCR-seq data, contributing to published research in Frontiers in Immunology.
Sweeney Lab, University of Illinois Urbana-Champaign Aug 2021 - Jun 2023

Undergraduate Research Assistant Champaign, IL

Analyzed complex scRNA-seq datasets using Cell Ranger and Seurat to uncover metabolism-associated neural circuits and rare cell populations. Built and launched an interactive R Shiny application to streamline fiber photometry data processing and interpretation, contributing to published research in The Journal of Neuroscience.

Full CV, publications, and skills →