Research Methods To Software
Translate evolving scientific methods into maintainable applications, workflows, and interfaces that research teams can operate repeatedly.
10+ years
Research software experience
Statewide
HIV sequencing surveillance workflows
NIH-funded
Researcher-facing NGS platforms
Co-author
Multiple peer-reviewed publications
Featured Research Software
Systems for sequencing research, lab operations, and public-health reporting.
These projects are strongest when evaluated as research infrastructure: they connect scientists, specimens, files, computational pipelines, review workflows, and downstream reporting.
Lead Project
Phylodynamics
Phylodynamics is an end-to-end scientific software platform that unified specimen management, laboratory workflows, computational analysis, and public-health reporting for statewide HIV sequencing research.
Problem
Spreadsheet tracking, manual file workflows, and slow handoffs made it harder to preserve data integrity and move sequencing results through the surveillance process.
System
Automated specimen tracking, processing watchers, searchable review records, repeat-sampling states, and downstream handoff to existing public-health databases.
Impact
Improved data integrity, reduced turnaround time, and supported statewide HIV surveillance workflows used for public-health reporting.
Role
Application architecture, scientific workflow automation, operational support, and translation between researchers, lab staff, and infrastructure constraints.
Website is access protected and the repository is private.
NIH-Funded Platform
Primer ID
Primer ID is a researcher-facing NGS platform that lets users submit, validate, process, and retrieve sequencing workflows through a Next.js application backed by GCP storage and SLURM-based HPC processing.
The platform connects signed uploads for multi-gigabyte sequence files, database-backed submission parameters, cluster queue initialization, and result delivery for OGV, drug resistance, intactness, and splicing workflows.
- Next.js researcher interface for complex submission setup.
- Private GCP bucket uploads using resumable signed URLs.
- SLURM workload management for memory-intensive pipeline runs.
- Docker setup for replication studies and continued research.
- Integrated with
GitHub/ViralSeq/viral_seqandGitHub/veg/ogv-datingpipelines.
Additional Research Work
Supporting tools across pipelines, visualization, and grant-stage prototypes.
viral_seq
Open-source sequencing pipelines used with Primer ID workflows for alignment, mutation analysis, and repeatable research processing.
- Supports the computational side of researcher-facing NGS submission workflows.
- Designed for repeatable execution in research environments where inputs, parameters, and analysis methods must remain auditable.
FigTree
Research software work focused on visual inspection and interpretation of phylogenetic outputs.
- Fits the broader phylodynamics workflow: researchers need reliable ways to move from processed sequence data into interpretable relationships.
- Relevant to institutions evaluating software that supports computational biology, visualization, and analysis review.
Epitope Analysis Tool
Grant proposal prototype for interdisciplinary comparison of viral antibody, patient, and sequence data.
- Converted an early whiteboard concept into a structured prototype for immunology and virology collaboration.
- Balanced speed, cost, and research uncertainty by keeping the architecture lean while still clarifying the future data model.
Technical Capabilities
Practical infrastructure for scientific computing.
I am strongest in applied environments where researchers need an engineer who can understand the method, build the workflow, and keep the system reliable as the science changes.
Publications
Peer-reviewed research impact.
I am a co-author on multiple publications connected to sequencing research, Primer ID methods, and HIV surveillance.
Zhou S, Hill CS, Clark MU, Sheahan TP, Baric R, Swanstrom R.
Primer ID Next-Generation Sequencing for the Analysis of a Broad Spectrum Antiviral Induced Transition Mutations and Errors Rates in a Coronavirus Genome.
Bio Protoc. 2021 Mar 5;11(5):e3938. doi: 10.21769/BioProtoc.3938.
Zhou S, Sizemore S, Moeser M, Zimmerman S, Samoff E, Mobley V, Frost S, Cressman A, Clark M, Skelly T, Kelkar H, Veluvolu U, Jones C, Eron J, Cohen M, Nelson JAE, Swanstrom R, Dennis AM.
Near Real-Time Identification of Recent Human Immunodeficiency Virus Transmissions, Transmitted Drug Resistance Mutations, and Transmission Networks by Multiplexed Primer ID-Next-Generation Sequencing in North Carolina.
J Infect Dis. 2021 Mar 3;223(5):876-884. doi: 10.1093/infdis/jiaa417.
Zhou S, Hill CS, Spielvogel E, Clark MU, Hudgens MG, Swanstrom R.
Unique Molecular Identifiers and Multiplexing Amplicons Maximize the Utility of Deep Sequencing To Critically Assess Population Diversity in RNA Viruses.
ACS Infectious Diseases. doi: 10.1021/acsinfecdis.2c00319.
Zhou S, Long N, Moeser M, Hill CS, Samoff E, Mobley V, Frost S, Bayer C, Kelly E, Greifinger A, Shone S, Glover W, Clark M, Eron J, Cohen M, Swanstrom R, Dennis AM.
Use of Next Generation Sequencing in a State-Wide Strategy of HIV-1 Surveillance: Impact of the SARS-CoV-2 Pandemic on HIV-1 Diagnosis and Transmission.
J Infect Dis. 2023 Jun 7. doi: 10.1093/infdis/jiad211.
Selected Earlier Work
Useful breadth, kept secondary to research software.
Data Visualization And Effects
Three.js, React Fiber, Observable, and chart-driven interfaces used to explore simulation, motion, and scientific outputs.
notesy.app
A Next.js writing application used to sharpen product design, authentication, realtime editing, and performance work.
Sheet Music Creator
A freelance PWA for drag-and-drop sheet music creation, PDF output, and offline-friendly client workflows.