Professional summary

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.

Education

University of Illinois Urbana-Champaign Aug 2023 - May 2024

Master of Engineering (M.Eng.), Bioengineering Urbana-Champaign, IL

University of Illinois Urbana-Champaign Aug 2019 - May 2023

Bachelor of Science (B.S.), Bioengineering Urbana-Champaign, IL

Professional experience

Phalaena Automata Mar 2026 - Present

Founding Engineer Austin, TX

• Leading end-to-end development of a biotechnology research platform, from architecture through 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.
• Built containerized Nextflow DSL2 workflows that run on Cloud Run under least-privilege IAM, with a FastAPI ingestion layer that normalizes varied sequencing inputs.
• Validated variant-calling output against the GIAB HG002 benchmark to establish pipeline accuracy on a public ground-truth reference.

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.
• Published analyses as interactive dashboards and open project write-ups to make results explorable by non-computational audiences.
• Self-directed period spent deepening single-cell methods, pipeline engineering, and cloud architecture, culminating in founding Phalaena Automata to productionize these workflows.

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.
• Bioinformatically isolated and modeled CD4 T-cell populations using custom extraction scripts, comparing TCR repertoire usage across participants stratified by COVID-19 severity and vaccination status.
• Handled nasopharyngeal and blood specimen processing for a longitudinal respiratory infectious disease cohort.
• Performed mammalian cell culture, PCR, and microscopy in support of a longitudinal respiratory infectious disease study.
• Analyzed high-parameter spectral flow cytometry data in FlowJo, including gating strategy design, compensation, and population quantification.
• Executed molecular and cell-based assays end to end, from sample receipt and processing through staining, acquisition, and downstream analysis, bridging bench work and computational output within a single workflow.
• Presented bioinformatic findings to lab and collaborator audiences, translating repertoire analyses into figures and diagrams for non-computational stakeholders.

Carle Foundation Hospital, Emergency Department Sep 2023 - Jul 2024

Healthcare Technician Champaign, IL

• Managed patient care and diagnostic workflows on Epic EMR in a Level I Trauma Center, performing EKGs, blood collection, and urinalysis.
• Relayed information between patients and providers, rotating across triage and EKG technician roles.
• Worked across every ED functional area over roughly 1,000 hours, building direct familiarity with clinical data capture at point of care.

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 an interactive R Shiny application for fiber photometry data processing and interpretation. Its outputs contributed to a paper in The Journal of Neuroscience.
• Consolidated a multi-step manual analysis into one reactive application. Photometry processing dropped from a multi-hour scripting task per session to minutes, and lab members who do not code could run their own analyses.
• Performed mouse brain slice mounting, immunostaining, and imaging, iterating antibody concentration protocols to resolve failed staining runs.
• Used both R and Python to analyze scRNA-seq and fiber photometry data characterizing MC3R-expressing neurons in energy homeostasis.

Illini Emergency Medical Services Jan 2022 - May 2023

Emergency Medical Technician (EMT-B) Champaign, IL

• 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 LLC Sep 2020 - Feb 2021

Coding Tutor Naperville, IL

• Tutored students aged 10 to 17 in Python, Java, and JavaScript, and volunteered at interstate Hour of Code events.
• Adapted instruction to individual learning styles, using project-based builds to sustain engagement over traditional exercises.

Thom Lab, Wheaton College May 2020 - Aug 2020

Data Analyst and Research Assistant Wheaton, IL

• Led a meta-analysis across 54 studies and 94 effect sizes, designing R scripts for automated data extraction, transformation, and statistical validation.
• Produced a seven-part training video series onboarding incoming lab members on software tools and analytical workflows, from raw data to results.

Argonne National Laboratory Sep 2017 - May 2018

ESRP Intern Lemont, IL

• Explored applications of synchrotron X-ray scanning tunneling microscopy (SX-STM) for atomic-scale imaging and characterization of metallic surfaces.

Portillo's Jun 2019 - Aug 2019

Cashier Bolingbrook, IL

• Handled high-volume order processing and kitchen communication.

Projects

Bench @ Phalaena AutomataMar 2026 - Present

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.

Preleukemia scRNA-seq Analysis (mouse HSPC landscapes)Sep 2025 - Oct 2025

R · Python · Quarto · R Shiny · Seurat · Harmony · Scanpy

• Revised scRNA-seq analysis of 38 mouse bone-marrow HSPC samples spanning eight preleukemic mutation models (Isobe et al., Cell Genomics 2023): emptyDrops cell calling, per-sample adaptive QC with doublet removal, Harmony integration, and SingleR annotation against a mouse HSPC atlas, each stage a rendered Quarto document.
• Tested composition (propeller) and differential expression (pseudobulk edgeR) with the mouse as the replicate, added CellRank fate mapping, and tested the paper's PLPS and Stem11 signatures against overall survival in 151 TCGA-LAML patients with age-adjusted Cox models; most of the original pipeline's significant findings did not hold.
• Built an interactive R Shiny dashboard for exploring the results.

AML Bulk RNA-seq Differential Expression (TCGA-LAML vs. GTEx)

Nextflow · Python

• Nextflow bulk RNA-seq differential-expression pipeline comparing TCGA-LAML against GTEx whole blood, checking that canonical AML markers separate the two cohorts. Includes an interactive volcano plot.

Spatial Transcriptomics Deconvolution (10x Visium breast cancer)

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

• Nine-stage Nextflow DSL2 pipeline mapping cell types into tissue space from a 10x Visium breast-cancer section (3,798 spots) against a 100,064-cell annotated scRNA-seq reference, covering QC, shared-gene-space normalization, signature construction, per-spot deconvolution, and spatially variable genes.
• Implemented per-spot deconvolution as non-negative least squares with inverse-mean gene weighting to keep the fit from collapsing onto high-expression immune signatures under cross-platform reference shift, recovering the expected tumor composition with cancer epithelium leading in 2,201 of 3,798 spots.
• Computed spatially variable genes by a from-first-principles Moran's I on a symmetric kNN spot graph, vectorized across genes with a seeded permutation test, identifying 949 significant genes that resolve into epithelial, stromal, and immune compartments.
• Validated with an offline demo mode that synthesizes a toy section with planted spatial cell-type proportions and self-checks recovery to 0.008 mean absolute error against known truth.
• Source on GitHub

TCR Clonality Analysis (TB progressors vs. controllers)2022

Python · Jupyter · tcrdist3 · pandas · SciPy

• Reproducible TCR-beta repertoire workflow comparing TB progressors against controllers (Musvosvi et al., Nature Medicine 2022), revised to respect the matched case-control design: one baseline sample per donor, a stratified rank test within matched sets, and rarefaction to a common sequencing depth.
• 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, reported with Hodges-Lehmann effect sizes, bootstrap confidence intervals, and BH adjustment across metrics.

Fiber Photometry Web App

R · R Shiny

• R Shiny application for fiber photometry data processing and figure generation at the Sweeney Lab. Its outputs were used in a Journal of Neuroscience paper.

R Meta-Analysis Walkthrough

R

• Seven-part video walkthrough of an end-to-end meta-analysis in R, produced as a lab onboarding resource.

PID Controller for Anaesthetic Dosing2023

MATLAB · Simulinkgroup project

• Designed and tuned a PID controller for patient-specific anaesthetic dosing under variable drug sensitivity, achieving top cohort performance in steady-state error and 10% settling time.

EMG-Controlled Saxophone2023

Arduino · C/C++ · surface EMG circuitrygroup project

• Built a surface-EMG analog front end with instrumentation amplifier, bandpass filtering, and rectification, paired with an Arduino driving servo motors over saxophone keys. Exhibited at the 2023 Engineering Open House as an assistive prosthetic concept.

Peer-reviewed publications

1. Patterns of restricted TCR usage following SARS-CoV-2 vaccination and severe disease

   Parsons E, Lu Z, Richard SA, Zelkoski A, Le J, Palanikumar N, Nguyen P, Alba C, Sukumar G, Rosenberger J, Zhang X, Burgess TH, Colombo R, Mende K, Berjohn C, Epsi N, Agan BK, Tribble D, Lindholm DA, Dalgard CL, Pollett SD, Malloy AMW, and EPICC COVID-19 Cohort Study Group. Patterns of restricted TCR usage following SARS-CoV-2 vaccination and severe disease. Frontiers in Immunology. 2025;16:1576903. doi:10.3389/fimmu.2025.1576903

   doi:10.3389/fimmu.2025.1576903

   Contribution Bioinformatically isolated and modeled CD4 T-cell populations using custom data extraction scripts to analyze TCR repertoires.

2. Paraventricular Thalamic MC3R Circuits Link Energy Homeostasis with Anxiety-Related Behavior

   Cho D, O'Berry K, Possa-Paranhos IC, Butts J, Palanikumar N, Sweeney P. Paraventricular Thalamic MC3R Circuits Link Energy Homeostasis with Anxiety-Related Behavior. The Journal of Neuroscience. 2023 Sep 6;43(36):6280-6296. doi:10.1523/JNEUROSCI.0704-23.2023. PMID: 37591737. PMCID: PMC10490510.

   doi:10.1523/JNEUROSCI.0704-23.2023· PMID 37591737· PMC10490510

   Contribution Developed an interactive R Shiny application for fiber photometry data processing and visualization used in the publication.

Skills

Languages

Python, R, SQL, Bash, MATLAB, JavaScript, TypeScript, HTML/CSS

Frameworks

FastAPI, React, R Shiny, Jekyll

Workflow & reproducibility

Nextflow (DSL2), Docker, Git, containerization, CI, conda, pytest, reproducible pipelines

Cloud & infrastructure

Google Cloud Platform, Cloud Run, Vertex AI, IAM, cloud-native architecture, data engineering

Genomics & sequencing

genomics, transcriptomics, proteomics, metabolomics, 10x Genomics, variant calling, bulk RNA-seq, differential expression, GIAB/HG002 benchmarking, GATK4, HaplotypeCaller, joint genotyping, BWA-MEM, HISAT2, samtools, bcftools, featureCounts, fastp, seqtk, FASTQ/BAM/VCF, pydeseq2, DESeq2, GO over-representation analysis, spatial transcriptomics (computational), 10x Visium, cell-type deconvolution

Single-cell & spatial

Seurat, Scanpy, Cell Ranger, tcrdist3, UMAP, clustering, pseudotime, trajectory inference, anchor-based integration, reference-guided annotation, AnnData, Squidpy

ML & AI

PyTorch, machine learning, LLM/RAG architecture, dimensionality reduction

Statistics & analysis

meta-analysis, survival analysis, statistical validation, SciPy, pandas, NumPy, scikit-learn, negative-binomial modeling, hypergeometric enrichment, multiple-testing correction, permutation testing, non-negative least squares, spatial autocorrelation (Moran's I)

Laboratory

spectral flow cytometry (Cytek Aurora), FlowJo, flow panel design, compensation, gating strategy, PCR, qPCR, mammalian cell culture, aseptic technique, immunostaining, immunohistochemistry, fluorescence microscopy, tissue sectioning and slide mounting, PBMC and biospecimen processing, nasopharyngeal and blood specimen handling, 10x Genomics library prep support, biosafety and specimen chain-of-custody, laboratory documentation

Clinical research

Epic EMR, clinical data capture, patient-facing workflows, IRB-context human-subjects research, longitudinal cohort study support, participant biosample and metadata handling, HIPAA-context data handling, EKG, phlebotomy, urinalysis

Domain

immune repertoire analysis, computational immunology, reproducible research, regulatory and safety awareness

Certifications

• Google Cloud Professional Data Engineer (Dec 2025 - Dec 2027)
• IBM Data Science Professional Certificate

Honors & awards

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

Standardized exam scores

Standardized exam scores with percentile and date taken

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