Experience

Bioinformatician I

University of Kansas Medical Center — June 2024 to Present

Graduate Research Assistant

University of Kansas Medical Center — August 2022 to May 2024

Education

School Degree Years GPA
University of Kansas Medical Center M.S. Health Data Science 2022–2024 4.0
University of Kansas B.S. Behavioral Neuroscience 2017–2020 3.9

Publications

Published

Nrf2 Promotes Regulatory T Cell Differentiation by Reprogramming Glutamine Metabolism and Alleviates Ulcerative Colitis

Dasgupta, D., Tripathi, A., Griffard-Smith, R., Dahabieh, M.S., Islam Saif, M.S., Roy, B.C., Burt, E., Ellis, A., Sheldon, R.D., Dhorajiya, P., Umar, S., Koestler, D.C., Jones, R.G., Pyaram, K.

Science Immunology

Published

Distinguishing the significance of blood microbes in epithelial ovarian cancer

Mahoney, D.E., Chalise, P., Pei, D., Griffard-Smith, R., Home, T., Pathak, H.B., Umar, S., Godwin, A.K.

Gut Microbes Reports, 2026

Paper
Preprint

Integrative modeling of read depth and B-allele frequency improves single-cell copy number calling from targeted DNA sequencing panels

Pei, D., Griffard-Smith, R., Urrego, B.C., Schueddig, E.

bioRxiv, March 2026

Preprint
Published

Extracellular Vesicle miRNAs as Biomarkers of Asthma Severity

Prasad, C., Griffard, R., Pei, D., Haworth, S., Dhillon, N.K., Castro, M., Sundar, I.K.

Allergy, January 2026

Paper
Published

Nrf2 drives activation-driven expansion of CD4+ T cells by modulating glucose and glutamine metabolism

Tripathi, A., Dasgupta, D., Dahabieh, M.S., Griffard-Smith, R., Pant, A., Bugbee, A., Yellapu, N.K., Burt, E., Choi, B.H.Y., Ellis, A.E., Sheldon, R.D., Giri, S., Koestler, D., Jones, R.G., Yadav, V.N., Pyaram, K.

Cell Reports, September 2025

Paper
Published

Therapeutic potential of NRF2 activating drug RTA-408 in suppressing T cell effector responses and inflammatory bowel disease

Griffard-Smith, R., Dasgupta, D., Tripathi, A., Yellapu, N.K., Pyaram, K.

The Journal of Immunology, August 2025

Paper
Published

micRoclean: an R package for decontaminating low-biomass 16S-rRNA microbiome data

Griffard-Smith, R., Pei, D., Schueddig, E., Mahoney, D., Chalise, P., Koestler, D.

Frontiers in Bioinformatics, May 2025

Paper GitHub
Published

optima: an Open-source R Package for the Tapestri platform for Integrative single cell Multi-omics data Analysis

Bioinformatics, October 2023

Paper
In Progress

Fixed single-cell RNA sequencing analysis of mouse models of asthma

Griffard-Smith, R., Sundar, I., Prasad, C.

In Progress

Nextflow pipeline for 16S rRNA microbiome sequencing analysis using the guild-based method

Griffard-Smith, R. et al.

Guild Method
In Progress

Single-cell and bulk DNA-seq using Tapestri platform to identify subclones in pig kidney cyst models

Griffard-Smith, R. et al.

Presentations

Introduction to Nextflow and nf-core

Workshop — University of Kansas Medical Center, Department of Biostatistics & Data Science, Kansas City, KS — March 2026

micRoclean: an R package for decontaminating low biomass 16S-rRNA microbiome data

Presentation — Innovations in Design, Analysis, and Dissemination, Olathe, KS — April 2024

optima: an open-source R package for the Tapestri platform for integrative single cell multiomics data analysis

Poster — Innovations in Design, Analysis, and Dissemination, Olathe, KS — April 2023

Professional Training

Multi Omics NETwork Analysis Workshop (MONET)

University of Colorado Anschutz Medical Campus — June 2026

Nextflow Training Week

Seqera — November 2025

  • Certificates: Hello Nextflow, Nextflow for Genomics, Hello nf-core, Nextflow for RNA-seq

Single Cell RNA-seq Workshop

National Center for Genome Resources / New Mexico-INBRE — November 2023

Epic Cosmos Data Model Certification

Epic — June 2023

IBM Data Science Professional Certificate

Coursera — 2022

SQL for Data Science with R

edX — 2021–2022

Memberships & Affiliations

Nextflow Ambassador

Seqera — 2026 to Present

Member, American Statistical Association

2022 to Present

  • Section on Statistics in Genomics and Genetics

Board Member, Graduate Student Biostatistics Association

University of Kansas Medical Center — 2022 to 2024

Skills & Technology

Transcriptomics

  • Single-cell RNA-seq: Preprocessing and QC (Cell Ranger), dimensionality reduction and differential expression (Seurat, scanpy), pathway enrichment (GO, Reactome, Qiagen IPA)
  • Bulk RNA-seq: QC (FastQC, MultiQC), alignment (RSEM, Bowtie2), dimensionality reduction (PCA, UMAP), differential expression and pathway analysis (GO, Reactome, Qiagen IPA)
  • Spatial Transcriptomics: Visium HD (10x Genomics) - Spatial gene expression analysis, tissue segmentation, spot-level and bin-level quantification, integration with single-cell reference atlases

Genomics

  • Single-cell DNA-seq: Tapestri (MissionBio) -Preprocessing and QC (MissionBio Tapestri Insights), subclone identification via dimensionality reduction, integration with bulk DNA-seq for germline variant detection

Epigenomics

  • Reduced representation bisulfite sequencing: QC (FastQC), read trimming, genome preparation and alignment (Bismark), differential methylation analysis (methylKit)

Metagenomics

  • 16S rRNA-seq: QC (FastQC), adapter trimming (cutadapt), denoising and ASV generation (DADA2), taxonomic profiling (QIIME2), differential abundance testing (ANCOM-BC)
  • Metagenomic shotgun sequencing: QC, read trimming (Trimmomatic), taxonomic profiling (MetaPhlAn), diversity analysis and visualization (phyloseq)

Programming & Infrastructure

  • Languages: R, Python, Bash, SQL
  • Workflow Management: Nextflow, Slurm
  • Version Control: Git, GitHub