Curriculum Vitae

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Summary

Data Scientist with 3 years of experience at the Pacific Northwest National Laboratory. Specializing in representation learning and graph modeling for multi-omics data analysis, host-microbe interactions, microbial metabolism modeling, and applying machine learning and generative AI to biological sequence data. Ph.D. experience in clinical microbiology studying the effect of antibiotics on the gut microbiome of healthy individuals.

Skills

Programming Languages

Python R Bash/Shell SQL

Machine Learning & AI

PyTorch scikit-learn PyGeometric Generative Models

Bioinformatics

Metagenomics Transcriptomics Metabolomics Genome-scale Modeling

R Packages

ggplot2 tidyverse DESeq2 randomForest

Python Libraries

COBRApy pandas numpy BioPython

Pipeline Development

Nextflow Snakemake Docker

Cloud & DevOps

AWS Git/GitHub GitLab CI/CD SLURM

NGS Tools

Bowtie2 SAMtools FeatureCounts CarveMe Smetana

Experience

Data Scientist

2025 — Present

Pacific Northwest National Laboratory, Richland, WA

AI/ML for Complex Systems

  • Co-Principle investigator developing neurosymbolic/knowledge graphs for biological discovery
  • Biological investment advisor for the PNNL autonomy initiative
  • Current work blends multi-agent systems engineering, NER, and context graphs/world models for biological reasoning.

Post-Doctoral Research Associate

2022 — 2025

Pacific Northwest National Laboratory, Richland, WA

Multi-omic computational biology research

  • Applying generative models for inferring protein characteristics from sequence
  • Genome scale modeling for identifying microbe-microbe interactions using in silico synthetic communities
  • Spatial multi-omic analyses estimating the effect of environmental stress on microbial communities in soil
  • Building computational tools for identifying bacteriophage auxiliary metabolic genes in the human virome

Pivot 314 Intern - Data Scientist

Aug 2021 — Sept 2021

Pluton Biosciences, St. Louis, MO

AWS pipeline development for metagenomics

  • Developed an Amazon Web Services (AWS) pipeline for detecting differential gene abundance in soil metagenomes
  • Multi-node parallel batch job structure and integrated multiple tools into a multi-container application stack

Research Fellow

2013 — 2016

Harvard Medical School, Boston, MA

Aging research in C. elegans

  • Large scale experiments measuring thermotolerance and lifespan in C. elegans
  • Used automated image-analysis device developed in-house
  • Measured effect of small molecule inhibitors of respiration and metabolism

Education

Ph.D. in Computational Biology

2016 — 2022

Washington University in St. Louis School of Medicine, St. Louis, MO

Thesis: System shock: Using -omics data to characterize biological remodeling in the microbiome, resistome, and transcriptome of bacteria

Advisor: Gautam Dantas

B.S. in Biology

2008 — 2012

University of Massachusetts Amherst, Amherst, MA

Thesis: Secondary metabolites in floral nectar reduce parasite infections in bumblebees

Advisor: Lynn Adler

Awards & Honors

  • Deep Learning 4 Science Participant and Poster Presentation — Lawrence Berkeley National Laboratory (2025)
  • National Microbiome Data Collaborative Ambassador — NMDC
  • Pivot 314 Fellow — Washington University Graduate Center (2021)
  • T32 NIH Ruth L. Kirschstein National Research Training Grant Fellowship — NIH
  • Initiative for Maximizing Student Development (IMSD) — NIH
  • NSF Summer Research Experience for Undergraduates — National Science Foundation
  • Outstanding Abstract Award — American Society of Microbiology (2019)