Doctorate of Philosophy of Science: Cell and Molecular Biology

May 2023

Colorado State University, Fort Collins, CO

Master of Science Degree: Microbiology/Immunology

May 2019

Colorado State University, Fort Collins, CO

International TEFOL Certification

August 2017

Australian Vietnam School of English, Ho Chi Minh City, Vietnam

Bachelor of Science Degree: Mathematics and Biotechnology (Computer Science Minor)

May 2017

Minnesota State University Mankato, Mankato, MN

Microbial Ecosystems Lab

June 2023 – July 2024

Research Scientist

Colorado State University, Fort Collins CO

Full-Time: 40+ Hours/Week

Bioinformatics Pipeline Engineer

• • Spearheaded the development of DRAM2 (Distilled and Refined Annotation of Metabolism) and COMET (CustOmizable Metagenome-assembled-genome Extraction Toolkit) software pipelines.
• • Designed software to scale seamlessly from tens to thousands of input samples, effectively utilizing tens to thousands of CPUs.
• • Engineered version-controlled pipelines in Nextflow, integrating Singularity, Docker, and Conda dependencies.
• • Implemented pipelines for high-performance computing clusters, utilizing job schedulers (SLURM).
• • Optimized data analysis workflows to enhance computational efficiency and accuracy.
• • Ensured robust and scalable bioinformatics solutions through rigorous testing and validation.
• • Documented pipelines rigorously in various formats (GitHub, ReadTheDocs).

• • Communicated and collaborated with the DSRI Riviera HPC cluster administrators to streamline data analysis processes.
• • Presented DRAM software at the Undergraduate Research Poster Session, showcasing innovative bioinformatics tools.
• • Liaised with DSRI Riviera server administrators to ensure optimal configuration for lab computing needs.
• • Contributed to software development on the DSRI Riviera server, enhancing computational training workshops and data management practices.
• • Engaged in CoSMic Network activities to drive the development and integration of advanced bioinformatics tools.

• • Mentored a first-year PhD student, providing guidance on computational framework development and coursework.
• • Supported lab members with troubleshooting assistance and strategic problem-solving.
• • Facilitated the use of bioinformatic tools across various lab projects, promoting best practices in genomic data analysis.
• • Collaborated on impactful projects with the Department of Energy, Dr. Tiffany Weir, Dr. Susan De Long, NIH, Department of Energy, The Ohio State University, demonstrating leadership in bioinformatics and practical applications of genomic research.

U.S. Department of Agriculture (USDA)

June 2019 – August 2020

Agricultural Research Service (ARS) Research Participation Program Fellow

Colorado State University, Fort Collins CO

PhD Candidate, Abdo Lab, Colorado State University

Full-Time: 40+ Hours/Week

Bioinformatics Pipeline Developer

• • Developed Reads2Resistome, an integrated bioinformatics pipeline for bacterial DNA data analysis, accommodating both short and long-read sequencing data.
• • Engineered software to scale efficiently on HPCs: processing tens to thousands of input samples.
• • Streamlined the assembly of high-quality bacterial genomes and analyses such as antimicrobial resistance gene and virulence factor identification.
• • Enhanced the utility of individual tools by combining them into a cohesive software package capable of processing tens to hundreds of bacterial genomic samples simultaneously.
• • Documented data processes through process diagrams and step-by-step tutorials available on GitHub.
• • Managed a sustainable, user-friendly software application using Python, R, Bash, Singularity, and Nextflow, suitable for high-performance computing environments.
• • Implemented data governance practices, developing standards, maintaining metadata, and ensuring data consistency.
• • Benchmarked the data tool using standardized genetic data, significantly reducing quality control and analysis time.

• • Hosted and taught an informational and tutorial-based session on Reads2Resistome for USDA-ARS scientists.
• • Communicated effectively with ARS scientists to develop and execute a hands-on tutorial on the SCINET CERES high-performance computing infrastructure.
• • Highlighted Reads2Resistome in the October 2020 USDA-ARS SCINET newsletter.

• • Tracked modifications in soil microbial communities and their impact on functional capabilities across different land uses and soil types in Paragominas, Brazil.
• • Assessed data quality, performed filtering and trimming of low-quality sequences, and conducted taxonomic classification and metagenomic assembly.
• • Measured diversity within and between samples using alpha and beta diversity metrics in R, utilizing packages such as vegan, phyloseq, and metagenomseq.

• • Effectively communicated with the program director, committee members, and my advisor to develop a comprehensive research proposal investigating bovine mastitis diagnosis, treatment, and prevention.
• • Authored a National Institutes of Health (NIH) grant proposal, clearly defining the specific aims and objectives, and successfully defended the proposal to a committee of academic and governmental researchers.
• • Developed an experimental design that included a detailed sampling scheme, proper use of controls, and a robust data management plan, ensuring the reliability and reproducibility of the research.
• • Hypothesized and investigated that bedding material in cowsheds acts as a primary environmental reservoir for mastitis-associated pathogens and antimicrobial resistance genes, through extensive literature review and innovative research techniques.
• • Outlined and implemented specific techniques such as temporal sample collection in state-of-the-art dairy farms with automated milking systems, high-throughput chromosomal conformation capture (Hi-C) on metagenomic samples, and metatranscriptomic sequencing to analyze the presence and abundance of antimicrobial resistance genes.

• • Automated data retrieval from GenBank and NCBI’s BioProject for nearly 800 bacterial isolates, facilitating a comprehensive investigation of pathogenic Escherichia coli isolates.
• • Standardized data to ensure unbiased results and maintained isolate metadata consistency.
• • Performed additional data analysis using Python, Bash, and the Reads2Resistome pipeline, including quality control and phylogenetic analysis.
• • Documented all processes and results to ensure reproducibility and transparency.
• • Conducted phylogenetic analysis to understand the evolutionary relatedness of bacterial isolates, using Snippy to identify single nucleotide polymorphisms (SNPs) and RAxML for phylogenetic tree construction.
• • Utilized a Linux high-performance computing environment, running the phylogenetic analysis over 70 days using 64 CPU nodes, and performed bootstrapping to assess nodal support.
• • Communicated findings effectively to other analysts and collaborators, highlighting the prevalence of antimicrobial resistance in E. coli isolates from both poultry agricultural and human clinical sources.
• • Highlighted the need for ongoing monitoring of antimicrobials of high importance to human medicine in poultry agriculture to mitigate their impact on human health.

• • Developed and executed educational lectures for graduate students on bacterial metagenomics, genome assembly, and RNA-sequencing analysis.
• • Designed learning materials and tutorials available on GitHub to facilitate student learning.
• • Taught taxonomic classification of bacterial shotgun metagenomic sequencing data, bacterial genome assembly, and RNA-sequencing analysis using tools like FastQC, Trimmomatic, Kraken2, DESeq2, GAGE, GGPlot2, and Tidyverse.

National Institutes of Health (NIH)

August 2020 – August 2022

T32 Training Program Fellow

Colorado State University, Fort Collins CO

PhD Candidate, Abdo Lab, Colorado State University

Full-Time: 40+ Hours/Week

DNA Extraction and Sequencing Specialist

• • Extracted DNA and prepared next-generation sequencing libraries for over 300 bacterial isolates, including commensal and pathogenic species such as Escherichia coli, Enterococcus, Staphylococcus, Salmonella, and Campylobacter.
• • Communicated effectively with my advisor and ARS collaborators to develop and execute protocols for large-scale bacterial DNA sequencing.
• • Designed, developed, and implemented standard operating procedures for DNA extraction and library preparation, ensuring consistency in data output.
• • Recorded and documented extensive details of DNA concentrations and sequencing quality, providing comprehensive results to analysts and collaborators.
• • Utilized the Reads2Resistome pipeline for further data analysis, employing programming languages such as Python, R, Bash, Nextflow, and Singularity.

• • Collaborated with a Mycobacterium tuberculosis research group to develop an RNA sequencing analysis pipeline for gene expression data.
• • Engaged with the principal investigator and wet-lab researchers to gather data requirements and facilitate analysis.
• • Created and maintained data collection tools and developed a comprehensive data pipeline in R.
• • Performed detailed analyses and generated reports on differential expression of regulatory pathways subjected to different drug treatments.
• • Ensured data consistency through routine checks and documented all processes, utilizing packages like DESeq2, GAGE, GGPlot2, and Tidyverse for analysis and visualization.

Student Researcher

August 2018 May 2019

Colorado State University, Fort Collins CO

Borlee Lab, Infectious Disease Research Center

Part-time: 30 Hours/Week

$13/Hour

Bacterial Colonization Researcher

• • Genetically engineered bacteria with a fluorescent marker to successfully colonize the gut of Aedes aegypti mosquitoes, aiming to prevent the spread of specific viruses.
• • Developed data standardization and standard operating procedures for bacterial feeding, dissection, and imaging using confocal microscopy.
• • Collaborated with analysts to gather data requirements, ensuring data consistency with a control mosquito colony.
• • Produced fluorescent images and quantitative measurements of labeled bacterial species within mosquito guts.
• • Implemented data standards and management solutions for the care of mosquito colonies and confocal microscope imaging.

• • Communicated with Pebble Labs to develop and execute the engineering of new bacterial genetic information using bioinformatics and microbiological techniques.
• • Analyzed DNA sequencing data of the fluorescence gene cassette, identifying base pair deletions affecting fluorescence.
• • Generated diagrams and visual maps of bacterial genetic information to communicate improvements to Pebble Labs.
• • Constructed a new plasmid with the correct fluorescence gene cassette and transformed it into the bacterial species of interest, enhancing imaging efficiency.

Camas Incorporated, Le Center, MN

June 2016 - June 2017

Research and Development/Quality Control Position

Le Sueur, MN

Part-time: 35 Hours/Week

$12/Hour

Microbial Identification Specialist

• • Created and improved data collection protocols for disease detection and diagnosis in food-producing animals.
• • Performed bacterial isolation, culturing, identification, and sample collection from various biological and environmental samples (e.g., swine, dairy, cattle).
• • Dissected deceased animal specimens, collected organ samples, and used plating methods to isolate potentially disease-causing microorganisms.
• • Identified the genus and species of pathogenic microorganisms and performed qPCR to identify virulence factors.

• • Enhanced the efficiency of biochemical detection processes for testing and quality control of company products.
• • Conducted quality control testing and documented extensive written and visual reports.
• • Tested the performance of company products on client samples, generating comprehensive documentation.
• • Optimized standard operating procedures, increasing the number of samples processed from small scale (1-2 samples) to large scale (96-well and 384-well: 8-12 samples).
• • Collaborated with coworkers to gather data requirements and ensure accurate quality control testing using biochemical detection methods such as ELISA and qPCR.

Front Range Microbiome Symposium 2024

• • First Place 12-minute talk
• • Presentation: "DRAM2: Empowering Microbiome Exploration with Advanced MultiOmics Analytics for Ecosystem-Specific Profiling"
• • Recognized for innovative contributions to microbiome research and exceptional presentation skills.

College of Veterinary Medicine and Biomedical Science Research Day 2022

• • 1st Place Poster Presentation
• • Title: "Occurrence and Persistence of Food-Borne Pathogens in Peanut Hull-Based Litter under Antibiotic-Free Broiler Chicken Production"
• • Awarded for excellence in presenting and communicating scientific research, demonstrating significant impact on the field of veterinary microbiology.

October 2020 USDA-ARS SCINet Newsletter

• • Featured Highlight: Reads2Resistome Software Pipeline
• • The Reads2Resistome tool was spotlighted as a cutting-edge bioinformatics software for analyzing bacterial genetic sequencing data.
• USDA-ARS SCINet Newsletter - October 2020

Graduate Student Poster Presentation, Rocky Mountain ASM 2019

• • 2nd Place Poster Presentation
• • Title: "Antibiotic-Free Chicken Production: A Characterization of the Bacterial Resistome"
• • Recognized for exceptional research and presentation on antimicrobial resistance in poultry production.

Excellence in Student Teaching and Tutoring in Computer Science 2013-2017

• • Minnesota State University Mankato (Dr. Dean Kelley: dean.kelley@mnsu.edu)
• • Provided extensive tutoring in Computer Science courses including Introduction to Programming I and II, Algorithmic Structures, and Operating Systems.
• • For 4 years, worked as a tutor and teaching assistant, holding tutoring hours, grading assignments, and assisting students with weekly programming projects, earning recognition for outstanding teaching and mentorship.