Naraen Palanikumar

Bioinformatics engineer · Cloud architect · Frisco, TX

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Professional summary

Bioinformatics engineer with 4+ years of experience building scalable platforms for lab research. Proficient in designing Nextflow pipelines, Google Cloud architectures, and bioinformatics workflows. Proven track record of optimizing data analysis for peer-reviewed publications and deploying production-grade bioinformatics solutions on Google Cloud, while leveraging AI to automate complex data interpretation and accelerate scientific discovery.

Education

University of Illinois - Urbana-Champaign Aug 2023 - May 2024
Master of Engineering (M.Eng.), Biomedical Engineering Urbana-Champaign, IL
University of Illinois - Urbana-Champaign Aug 2019 - May 2023
Bachelor of Science (B.S.), Biomedical Engineering Urbana-Champaign, IL

Professional experience

Phalaena Automata Mar 2026 - Present
Founding Engineer Austin, TX, USA
  • 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 + LLM architecture to automate unstructured data interpretation pipelines and accelerate the sequence-to-insight loop.
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, leveraging a professional data engineer certification from Google Cloud.
Malloy Lab @ Uniformed Services University of the Health Sciences Oct 2024 - Jun 2025
Research Assistant Bethesda, MD, USA
  • 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.
Carle Foundation Hospital - Emergency Department Sep 2023 - Jul 2024
Healthcare Technician Champaign, IL, USA
  • Managed patient care and diagnostic workflows on Epic EMR in a Level I Trauma Center, performing critical tasks including EKGs, blood collection, and urinalysis.
  • Facilitated information flow between patients and providers, rotating across triage and specialized EKG technician roles.
Sweeney Lab @ University of Illinois at Urbana-Champaign 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 and launched an interactive web application using R Shiny to streamline fiber photometry data processing and interpretation, contributing to published research in The Journal of Neuroscience.
Illini Emergency Medical Services Jan 2022 - May 2023
Emergency Medical Technician (EMT-B) Champaign, IL, USA
  • Provided immediate medical response and direct patient care at university athletic and cultural events.
  • Maintained meticulous incident records and managed essential medical equipment across shifts.
Haedos Sep 2020 - Feb 2021
Coding Tutor Naperville, IL, USA
  • Tutored students aged 10 to 17 in Python, Java, and JavaScript, and volunteered at several interstate Hour of Code events.
Thom Lab @ Wheaton College May 2020 - Aug 2020
Data Analyst and Research Assistant Wheaton, IL, USA
  • Led a meta-analysis across 54 studies, designing R scripts for automated data extraction, transformation, and statistical validation.
  • Produced a seven-part training video series to onboard incoming lab members on software tools and analytical workflows.
Portillo's Jun 2019 - Aug 2019
Cashier Bolingbrook, IL, USA
  • Facilitated high-volume order processing and kitchen communication while developing strong customer service skills.
Argonne National Laboratory Sep 2017 - May 2018
ESRP Intern Lemont, IL, USA
  • Explored applications of SX-STM technology for atomic-scale imaging and characterization of metallic surfaces.

Projects & outside experience

Bench @ Phalaena Automata | Python, FastAPI, React, Nextflow, Docker, GCP, Vertex AI Mar 2026 - Present
  • Building a production omics platform that ingests varied sequencing data into a centralized API and runs containerized Nextflow workflows on Cloud Run with strict IAM. Integrates a tool-augmented RAG loop over Vertex AI to cross-reference output results with PubMed for accelerated insights.
  • Link to project
AML scRNA-seq Analysis | R, Python, R Shiny, Seurat, Scanpy Sep 2025 - Oct 2025
  • Built a reproducible scRNA-seq pipeline on 38 public AML patient samples, performing QC, anchor-based integration, and reference-guided cell-type annotation to characterize pre-leukemic populations. Extended with pseudotime, fate mapping, and survival analysis of PLPS/Stem11 signatures against NCI clinical data and deployed findings via an interactive R Shiny dashboard.
  • Link to project
TCR Clonality Analysis | Python, Jupyter, tcrdist3, pandas, SciPy 2022
  • Built an end-to-end reproducible TCR-β repertoire workflow comparing TB progressors vs. controllers. Standardized V/J/CDR3 nomenclature to IMGT format and cross-referenced experimental repertoires against curated IEDB and VDJdb reference sets to compute total and antigen-specific clonality metrics.
  • Link to project
PID Controller for Anaesthetic Dosing | MATLAB, Simulink May 2023
Group project
  • Helped design and tune a PID controller for patient-specific anaesthetic dosing under variable drug sensitivity, achieving top cohort performance in steady-state error and 10% settling time.
  • Link to project
EMG Saxophone | Arduino, C/C++, surface EMG circuitry Apr 2023
Group project
  • Helped build a surface-EMG analog front end (instrumentation amplifier, bandpass, rectification) paired with an Arduino that drives servo motors over saxophone keys. Exhibited at the 2023 Engineering Open House as an assistive prosthetic concept.
  • Link to project

Skills

  • Programming & Data Science: Python, R, SQL, MATLAB, JavaScript, TypeScript, HTML/CSS, React, Bash
  • Bioinformatics & Genomics: Bioinformatics, Genomics, Transcriptomics, Proteomics, Metabolomics, 10x Genomics, Nextflow
  • Cloud & Infrastructure: Google Cloud Platform, FastAPI, Data Engineering, Cloud-Native Architecture, Docker
  • AI & Machine Learning: Machine Learning, PyTorch, Clustering, UMAP, LLM/RAG Architecture, Vertex AI
  • Laboratory: flow cytometry, PCR, biological sample processing

Peer-reviewed publications

Patterns of restricted TCR usage following SARS-CoV-2 vaccination and severe disease Oct 2025
Frontiers in Immunology
  • Bioinformatically isolated and modeled specific CD4 T-cells using custom data extraction scripts to analyze TCR repertoires.
Paraventricular Thalamic MC3R Circuits Link Energy Homeostasis with Anxiety-Related Behavior Sep 2023
The Journal of Neuroscience
  • Developed an interactive R Shiny application for fiber photometry data processing and visualization used in the publication.

Certifications

  • Google Cloud Professional Data Engineer
  • IBM Data Science Professional

Honors & awards

  • National Merit Scholarship Finalist - Feb 2019
  • National AP Scholar - May 2019
  • USA Biology Olympiad Semifinalist - Apr 2018

Standardized exam scores

Exam Score Percentile Date
MCAT 521 / 528 98th Jan 2024
ACT 35 / 36 99th Jul 2018
SAT 1550 / 1600 99th Apr 2018