About me
I am a Bioinformatics Developer at the Centers for Disease Control and Prevention (CDC) and a PhD student in Bioinformatics at the Georgia Institute of Technology. I specialize in developing bioinformatics pipelines and tools, primarily using Nextflow, to support public health research and surveillance. My interests include workflow development, high-performance computing, comparative genomics, metagenomics, and machine learning applications in biology.
Outside of work and school, I enjoy skateboarding, weightlifting and playing jazz on the trombone.
Feel free to reach out via email or connect with me on GitHub!
Experience
Bioinformatics Developer, Leidos contractor
Scientific Computing and Bioinformatics, CDC/NCEZID/DIDRI/OAMD
April 2023 – Present
- Develop bioinformatics pipelines and tools, primarily in Nextflow.
- Filled in as acting team lead for the Bioinformatics Consultation Service during crucial transition periods, serving as the technical lead for all bioinformatics projects, project management, leading consultations, and participating as an interview panelist.
- Consult on bioinformatics projects across CDC.
- Service and maintain SciComp’s shared high-performance computing environments including software module maintenance and HPC jobs.
- Help desk technical support agent and administrator for CDC user community.
- Develop and deliver training seminars on Nextflow, HPC, Python, Software package management and containerization, Linux and related topics.
- Create Nextflow best practices, documentation, shared resources, and training content.
- Mentor SciComp interns and full-time staff on bioinformatics and workflow development.
Bioinformatician, Response Deployment
Multi-national monkeypox outbreak response, CDC/NCEZID/DHCPP/PRB & CDC/NCEZID/DIDRI/OAMD
July 2022 – September 2022
- Assisted in developing the monkeypox virus assembly pipeline (PolkaPox) and benchmarking host read removal.
- Developed a bioinformatics tool to resolve tandem repeats in Monkeypox genomes.
Microbiology Fellow
Oak Ridge Institute for Science and Education Fellowship, National Salmonella Reference Laboratory, CDC/NCEZID/DFWED/EDLB
July 2021 – April 2023
- Processed Salmonella isolates from state public health laboratories for routine and outbreak surveillance.
- Assayed Salmonella isolates using a variety of biochemical and serotyping methods.
- Performed whole genome sequencing using Illumina and Nanopore NGS platforms.
- Prototyped a CLIA bioinformatics pipeline for Salmonella whole genome sequence analysis.
- Investigated Salmonella antigen alleles using comparative genomics.
Clinical Laboratory Assistant
Indiana University Ball Memorial Hospital Pathology Laboratory
December 2020 – July 2021
- Operated chemistry, flow cytometry, coagulation, and urinalysis instruments.
- Performed diagnostic assays to identify fungal, viral, and bacterial pathogens in patient specimens.
- Processed all patient specimens and serviced physicians’ orders.
Education
Georgia Institute of Technology
PhD in Bioinformatics (in progress)
Projected graduation: May 2028
- Focus areas: Applied machine learning, comparative genomics, evolution, public health science, environmental science
- Relevant coursework: Machine Learning for Computational Biology, Computational Genomics, Genomics & Applied Bioinformatics, Research Ethics, Evolutionary Biology, Programming for Bioinformatics
Ball State University
B.S. in Biology, Concentration in Microbiology; Minors in Spanish & Chemistry
May 2021 — summa cum laude
- Completed microbiology-focused curriculum with minors in Spanish and chemistry.
- Conducted multiple undergraduate research projects in biochemistry, mycology, and environmental chemistry.
- Relevant coursework: Pathogenic Bacteriology, Medical Mycology, Immunology, Biochemistry, Aquatic Microbiology
Skills
Coding & Scripting: Python, Bash, R, Groovy, Nextflow
Bioinformatics & HPC: High-performance computing environments, workflow development, and
experience with hundreds of bioinformatics software tools.
Communication & Leadership: Documentation, nonviolent communication / conflict resolution,
mentoring, training seminar development and facilitation.
Languages: Fluent in Spanish.
Selected Projects
Lead Bioinformatics Developer Projects
Leidos Contractor
- Developed (Neissflow), an end-to-end Nextflow NGS pipeline for typing, AMR detection and phylogenetics of Neisseria isolates in nf-core style. In assistance to the CDC/NCHHSTP/DSTDP program.
- Developed an end-to-end Streptococcus pneumoniae typing pipeline , including quality control, in-silico serotyping, MLST, AMR detection, and phylogenetics in nf-core style. In assistance to the CDC/NCIRD/DBD/PSLB program.
- Developed an end-to-end Legionella sp. NGS pipeline for processing paired-end Illumina data, genome assemblies and NCBI SRA datasets for MLST, AMR detection, quality control and phylogenetics in nf-core style. In assistance to the CDC/NCIRD/DBD program.
- Modified an existing nf-core amplicon pipeline to support amplicon taxonomic classification of Borellia amplicon reads from tick surveillance samples. In assistance to the CDC/NCEZID/DVBD/BDB program.
Bioinformatics Consultant/Support Projects
Leidos Contractor
- (TOSTAS) Toolkit for Open Sequence Triage, Annotation and DAtabase Submission.
- amplicon tick surveillance pipeline) in assistance of CDC/NCEZID/DVBD/BDB
- (aquascope) processes SARS-CoV-2 wastewater samples to determine relative variant abundance.
- SARS-CoV-2 variant calling pipeline in assistance of CDC/NCIRD/CORVD program.
- nf-pass whole genome sequence analysis pipeline in assistance of CDC/NCIRD/DVD program.
- Beta-tester of AMD’s Nextflow Tower instance in support of CDC/NCEZID/DIDRI/OAMD program.
- Bacterial whole-genome sequence analysis pipelines in assistance of CDC/NCEZID/DFWED/EDLB program.
- UPDX eukaryotic parasite detection pipeline in support of CDC/NCEZID/DPDM/LSDB program.
- Transitioning a Fast Fourier Tranform model for estimating the disease burden of antibiotic-resistant infections from R to GPU-accelerated Python libraries for a large-scale analysis.
Bioinformatics Research Projects
PhD Student Researcher
- Elucidated the species boundaries of Microbial Eukaryotes using Average Nucleotide Identity (ANI) and comparative genomics, improving taxonomic classification methods for applications in ecological research and pathogen detection.
- Investigated metagenomic and biochemical trends in the Chattahoochee River associated with wastewater, including taxonomic shifts and antibiotic resistance gene prevalence.
Infrastructure and Operations Projects
Leidos Contractor
- Developed the best practice production Nextflow configuration file for CDC’s HPC compute cluster for all production pipelines and Nextflow trainings.
- Assisted in managing and performing the migration of system modules during the HPC cluster OS upgrade.
- Constructed a storage optimization plan and performed in-depth storage review to optimize resource usage.
- Developed documentation for various software management and HPC best practices.
Presentations & Events
CDC Hack-a-thon 2023
Facilitator
Office of Advanced Molecular Detection (OAMD), CDC
- Served as developer and facilitator for Nextflow incubation projects.
- Created starter Nextflow pipelines.
AMD Days Conference, CDC 2023
Oral & Poster Presenter
Office of Advanced Molecular Detection (OAMD), CDC
- Presented a 10-minute oral talk and poster on benchmarking read-mapping tools for use-case optimization and reproducibility in public health research.
- Developed a Python script for performance metric calculations and a Nextflow workflow to automate the benchmarking protocol.
Publications
Patterns of genomic deletions in monkeypox virus during the 2022 outbreak in the United States
Nature Communications
2025
View Publication
Gigante, C.M., McGrath, D., Sukkestad, S., Hetrick, E., et al. Patterns of genomic deletions in monkeypox virus during the 2022 outbreak in the United States. Nature Communications 16, 8942 (2025).
Research Experience
Kostas Bioinformatics Research Lab, Georgia Institute of Technology
PhD Student Researcher
Fall 2023 – Present
- Project 1: Investigating metagenomic trends in the Chattahoochee River associated with wastewater treatment facility byproducts using comparative genomics.
- Project 2: Evaluating the species boundaries of Microbial Eukaryotes using Average Nucleotide Identity and comparative genomics.
Emil Biochemistry Research Lab, Ball State University
Undergraduate Research Assistant
August 2020 – December 2020
- Computationally designed oligonucleotides using NUPACK for binary light-up aptameric sensors (BLAS).
Bernstein Mycology Research Lab, Ball State University
Undergraduate Research Assistant
October 2019 – May 2020
- Performed quantitative biofilm assays on Candida albicans for future application of expansion microscopy on biofilms.
Zahran Environmental Chemistry Research Lab, Ball State University
Undergraduate Research Assistant
December 2018 – August 2019
- Developed protocols for synthesizing copper nanoparticles that photodegrade persistent organic pollutants (e.g., PCBs) and embedding them in polymeric membranes for nanoparticle recovery.
- Completed 2019 summer student internship program (CRISP) project on assessing a CuO2 nanoparticle synthesis protocol for degrading organic pollutants via photoactivation.
- Presented project findings to chemistry faculty and interns.
Volunteering
Hammond Sanitary District Wastewater Treatment Facility
Volunteer Laboratory Assistant
December 2019
- Performed wastewater chemical analyses and sample processing, including phosphorus, pH, total Kjeldahl nitrogen, suspended solids, and biochemical / chemical oxygen demand.