Professional summary

Bioengineer (B.S. and M.Eng., University of Illinois) with two years of full-time research experience at the bench and at the computer. At the Uniformed Services University I processed human specimens, isolated and cultured PBMCs, ran high-parameter spectral flow cytometry, and analyzed the CD4 T cell arm of a published COVID-19 immunology study. Since July 2025 I have worked as an independent researcher, reanalyzing published datasets and building tools that make sequencing analyses reproducible. I keep careful records, report results plainly (including null results), and am a co-author on two peer-reviewed papers.

Education

University of Illinois Urbana-Champaign Aug 2023 - May 2024
Master of Engineering (M.Eng.), Bioengineering Urbana, IL
University of Illinois Urbana-Champaign Aug 2019 - May 2023
Bachelor of Science (B.S.), Bioengineering. GPA 3.68/4.00 Urbana, IL
Harvard Extension School Fall 2026
CSCI E-22 Data Structures (in progress)

Professional experience

Self-directed research (Phalaena Automata, formed Mar 2026) Jul 2025 - Present
Independent Bioinformatics Researcher Frisco, TX (remote)
  • Reanalyzed a published single-cell dataset (230,000 bone marrow cells, 38 samples, eight preleukemic mutation models); re-tested the main comparisons across samples rather than individual cells, found that most of the original differences did not hold, and reported that null result.
  • Compared T cell receptor repertoires of 140 donors from a tuberculosis cohort who did or did not progress to disease, using matched permutation tests and public reference sequences, and reported the null result plainly.
  • Built Bench, a cloud platform of seven analysis pipelines for sequencing and mass spectrometry data, as its sole developer, and ran 42 published datasets through it end to end (42 of 42 completed).
  • Built a research assistant that answers questions about each analysis only from its recorded results; it passed 66 of 69 graded questions (95.7 percent) and declines questions the data cannot answer.
Uniformed Services University of the Health Sciences Oct 2024 - Jun 2025
Research Assistant, Laboratory of Pediatric Infection and Immunity Bethesda, MD · employer of record: Henry M. Jackson Foundation
  • Processed incoming human blood and nasopharyngeal specimens and ran high-parameter spectral flow cytometry (Cytek Aurora, FlowJo) alongside the bench team.
  • Isolated PBMCs by Ficoll density gradient and cultured them, extracted RNA and DNA, and immunostained cells for flow cytometry in support of the lab's immunology studies.
  • Analyzed the CD4 T cell arm of a T cell receptor study of SARS-CoV-2 vaccination and severe disease in a longitudinal military cohort (EPICC), published in Frontiers in Immunology (2025).
  • Built a CD4-specific reference set from public data, removing any sequence also found among 76.6 million pre-pandemic T cell receptor sequences, and compared clonality across four clinical groups.
Carle Foundation Hospital Sep 2023 - Jul 2024
Emergency Department Technician Urbana, IL
  • Performed EKGs, phlebotomy, urinalysis and triage support in the emergency department of a Level I trauma center, documenting in Epic, 25 hours per week alongside the M.Eng.
Sweeney Lab, Molecular and Integrative Physiology, University of Illinois Aug 2021 - Jun 2023
Undergraduate Research Assistant Urbana, IL
  • Built the lab's fiber photometry analysis application in R Shiny, replacing hours of per-session scripting; credited in the Journal of Neuroscience (2023) and still live online.
  • Analyzed single-cell RNA-seq data to characterize MC3R-expressing neurons; cryosectioned mouse brain samples and handled mice for colony upkeep and documentation.
Illini Emergency Medical Services Jan 2022 - May 2023
Emergency Medical Technician (EMT-B) Champaign, IL
  • Volunteer EMT-B providing medical coverage at university events.
Haedos Sep 2020 - Feb 2021
Coding Tutor Naperville, IL
  • Tutored students in Python, Java and JavaScript, and volunteered at Hour of Code events.
Thom Lab, Wheaton College May 2020 - Aug 2020
Research Assistant Wheaton, IL
  • Ran a meta-analysis of 54 studies (94 effect sizes) in R and produced a seven-part training series on the methods for incoming lab students.
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 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 · Google Cloud Batch · Cloud Run · Vertex AI
  • Multi-omics analysis platform built as sole developer, in closed beta. Seven Nextflow pipelines for genomics, transcriptomics, proteomics and metabolomics run on Google Cloud Batch behind a FastAPI service on Cloud Run; 42 of 42 published datasets ran end to end.
  • A results assistant (Vertex AI) answers only from each run's recorded summary; 66 of 69 graded questions passed (95.7 percent).
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.
TCR Clonality Analysis (TB progressors vs. controllers)
Python · Jupyter · pandas · NumPy · SciPy
  • Bulk TCR-beta repertoire comparison of 140 tuberculosis-cohort donors (52 progressors, 88 controllers; Musvosvi et al., Nature Medicine 2022), revised to respect the matched case-control design: one baseline sample per donor, a stratified rank test with permutations within matched sets, and rarefaction to a common sequencing depth.
  • Standardized V/J/CDR3 nomenclature to IMGT format and matched repertoires against curated IEDB and VDJdb reference clonotypes; no metric differed between groups, reported with Hodges-Lehmann effect sizes and BH adjustment as an informative null.
Fiber Photometry Web App
R · R Shiny
  • R Shiny application for fiber photometry data processing and figure generation at the Sweeney Lab, credited in a Journal of Neuroscience paper (2023) and still live online.
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
  • Course group project (BIOE 420) designing and tuning a PID controller for patient-specific anaesthetic dosing under variable drug sensitivity, with top cohort performance on steady-state error and 10% settling time.
EMG-Controlled Saxophone2023
Arduino · C/C++ · surface EMG circuitrygroup project
  • Designed the surface-EMG analog front end (instrumentation amplifier, bandpass filtering, rectification) for an Arduino system 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 Analyzed the CD4 T cell arm (Supplemental Figure 3) of this bulk TCR-beta repertoire study, building a CD4-specific reference set from public data with a pre-pandemic exclusion filter and comparing clonality and antigen specificity across four clinical groups.

  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 Built the R Shiny fiber photometry analysis application used to process the paper's photometry recordings, and analyzed data.

Skills

Laboratory
human specimen processing (blood, nasopharyngeal), PBMC isolation (Ficoll density gradient) and culture, RNA and DNA extraction, immunostaining of cells for flow cytometry, spectral flow cytometry (Cytek Aurora, FlowJo), cryosectioning of mouse brain samples, mouse handling and colony upkeep
Genomics & omics analysis
single-cell RNA-seq (Cell Ranger, Seurat, Scanpy, Harmony, SingleR), bulk RNA-seq differential expression, TCR repertoire analysis (immunoSEQ, IMGT, IEDB/VDJdb), germline variant calling (BWA-MEM2, GATK HaplotypeCaller, DeepVariant, SnpEff), proteomics (MSFragger, Percolator, MaxLFQ), metabolomics (OpenMS)
Languages
Python (pandas, NumPy, SciPy, statsmodels, Scanpy, FastAPI), R (tidyverse, Seurat, edgeR/limma, Shiny, ggplot2), Bash, SQL (BigQuery), TypeScript/React, PyTorch (foundations, in progress)
Pipelines & infrastructure
Nextflow DSL2, Docker, conda/mamba, Git and GitHub Actions CI, pytest, Quarto, Google Cloud (Batch, Cloud Run, Cloud Storage, Firestore, Vertex AI, IAM)
Statistics
sample-level and pseudobulk inference, permutation and rank-based tests, multiple-testing correction, survival analysis (Cox, Kaplan-Meier), meta-analysis (metafor), retrieval-augmented LLM tooling with schema-constrained outputs
Clinical
EKG, phlebotomy, urinalysis, triage, Epic EMR, REDCap, Illinois EMT-B

Certifications

  • Google Cloud Professional Data Engineer (Dec 2025 - Dec 2027)
  • IBM Data Science Professional Certificate
  • Illinois EMT-B license

Honors & awards

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