Summary

HPC Systems Administrator at Arizona State University accelerating research through system optimization, research software engineering, user collaboration, and community education.

Education

• Computer Science (Biomedical Informatics)

  2023
  Arizona State University
• Computer Science

  2022
  Arizona State University
• Biology

  2017
  Wuhan University

Work Experience

• HPC Systems Administrator

  2024-01 -
  Accelerate research computing through system optimization and research software engineering.

  • Port bioinformatics LLMs and scientific software to Intel Gaudi2 accelerators and generate accompanying benchmark data.
  • Develop benchmarking and post-maintenance testing software for heterogeneous HPC clusters.
  • Tune workflow-management system performance and scheduling on Slurm-based HPC.
  • Refactor genomic sequencing software to modern nf-core standards, contributing to the Earth BioGenome Project.
  • Develop a large-scale Nextflow-based virus detection and discovery pipeline with the NASA OSDR Microbiome Analysis Working Group.
  • Integrate the HPC account management system with the university registration database for automated account provisioning.
  • Customize the Open OnDemand web portal to support scientific applications and agentic AI functionality.
  • Manage HPC software stacks and databases; provide real-time troubleshooting for job, software, and hardware issues.
• Graduate Research Assistant

  2022-01 - 2023-12
  Machine-learning and genomics pipelines for microbiome classification and viral surveillance.

  • Developed an explainable neural network pipeline for microbiome-based classification of COVID-19 patient samples (400 features), using a multilayer perceptron (mean AUC 0.75) with SHAP for feature importance analysis.
  • Designed a DBSCAN-based clustering workflow to establish the true-positive threshold for KrakenUniq classification output.
  • Contributed to an open-source Python package for model-agnostic feature reduction methods.
  • Served on the Arizona Department of Health Services COVID-19 Sequencing Project team; built an ETL pipeline managing sequencing data for over one-third of the Arizona patient population.
  • Built a generalizable genomic workflow that identified two novel bat coronaviruses from 250 raw samples on ASU supercomputing resources.
• Research Assistant

  2021-06 - 2022-01
  IoT sensing and real-time data dashboards for mobile weather stations.

  • Connected twelve analog and digital environmental sensors to Arduino Uno and Raspberry Pi platforms to build IoT sensor enclosures for mobile weather stations.
  • Built a real-time Adafruit data dashboard integrating MQTT, Google Drive, and SQLite for data logging and visualization.
• Research Assistant

  2020-09 - 2021-06
  Machine learning curriculum design and COVID-19 mobility modeling.

  • Designed an undergraduate machine learning curriculum (MAT 400-level) that has been taught at ASU since Fall 2021.
  • Processed 50,000 rows of U.S. population mobility data using the spectral clustering algorithm to model COVID-19 transmission patterns.
• Software Development and Testing Intern

  2020-05 - 2020-08
  Software and hardware testing for a self-driving robotic street sweeper.

  • Designed and executed software and hardware tests for a self-driving robotic street sweeper, resolving issues identified during virtual and real-world road trials.
  • Reviewed and managed testing data, providing feedback and recommendations to the R&D and Business teams.
  • Led relocation of the full test set from Chandler to Chicago, including establishing a new test environment, producing new LiDAR maps, and training personnel for ongoing operations.
• Volunteer Research Assistant

  2019-09 - 2020-01
  NLP and machine learning for gene associations and protein-sequence analysis.

  • Applied natural language processing and machine learning algorithms to find associations among genes across more than 1,700 biomedical papers, using Python and Excel.
  • Extracted and cleaned protein sequences from over 3,500 records in the NCBI database, using Biopython, Pandas, and NumPy.
  • Adapted multiple-sequence alignment, motif searching, and text-mining algorithms to cluster and identify universal features among antibody protein sequences.
• Research Assistant — ZooPhy Data Expansion Project

  2019-09 - 2019-12
  Climate-data integration for phylogeographic reconstruction of virus spread.

  • Developed the Geoname Climate Data Integration System (GCIS) for ZooPhy, supporting the reconstruction of virus spread through phylogeography.
  • Integrated NOAA GHCN temperature and precipitation data, cleaned and parsed into a PostgreSQL relational database, to enhance ZooPhy's epidemiological and phylogeographic capabilities.
  • Built a command-line interface to manage the databases.
• Research Affiliate

  2018-09 - 2019-04
  Clinical field observation and decision-support research in biomedical informatics.

  • Conducted field observations across Mayo Clinic ambulatory and ancillary care settings to analyze clinical-environment issues and observe provider–EHR interaction during migration to the Epic system, reporting findings in TOYOTA A3 problem-solving format.
  • Proposed a Clinical Decision Support System (CDSS) based on Prescription Drug Monitoring Programs (PDMPs) for patient pain management; presented as a poster speaker at the 5th Annual Mayo Clinic–ASU BMI/BMD Student Poster and Employer Networking Event (April 2019).
  • Completed a two-month intensive introduction to medical terminology, human anatomy, and physiology.
• Research Assistant

  2014-04 - 2018-01
  Cell biology and prion protein signaling research.

  • Designed and conducted cell-biology and BSL-2 animal experiments, including the handling of infectious materials; co-authored a paper published in the Journal of Biological Chemistry (2017).
  • Studied how GPI anchor system genes regulate the formation of PrP in AsPC-1 cells.
  • Showed that PrP responds to the TNFα-triggered NF-κB signaling pathway by preventing the deubiquitinase activity of CYLD on RIP1 and TRAF2 (published).
  • Investigated how PrP expression influences the establishment of Herpes Simplex Virus Type 1 latency.
  • Techniques: fluorescence microscopy, UV-Vis spectrophotometry, RT-PCR/qPCR/PCR, CRISPR/Cas9, molecular cloning, SDS-PAGE, Native PAGE, Western blot, Co-IP, IP, and ELISA.
• Team Leader / Slides & Poster Speaker

  2014-01 - 2015-09
  Synthetic-biology team lead; Silver Medal at the iGEM 2015 Jamboree.

  • Led a synthetic-biology project constructing a DNA criticality-detector circuit in E. coli as an automatic medicine-dosage threshold for addressing human dental caries.
  • Awarded a Silver Medal at the iGEM 2015 Jamboree.

Skills

Publications

• Longitudinal dynamics of the nasopharyngeal microbiome in response to SARS-CoV-2 Omicron variant and HIV infection in Kenyan women and their children

  2025
  mSystems, American Society for Microbiology

  A longitudinal study of how the nasopharyngeal microbiome responds to SARS-CoV-2 Omicron infection and HIV status in Kenyan women and their children.

  View Publication
• Baseline Sequencing Surveillance of Public Clinical Testing, Hospitals, and Community Wastewater Reveals Rapid Emergence of SARS-CoV-2 Omicron Variant of Concern in Arizona, USA

  2023
  mBio, American Society for Microbiology

  Genomic surveillance across clinical testing, hospitals, and community wastewater capturing the rapid emergence of the SARS-CoV-2 Omicron variant of concern in Arizona.

  View Publication
• Prion protein is required for tumor necrosis factor alpha (TNFα)-triggered nuclear factor kappa B (NF-κB) signaling and cytokine production

  2017
  Journal of Biological Chemistry

  Prion protein is required for TNFα-triggered NF-κB signaling by preventing the deubiquitinase activity of CYLD on RIP1 and TRAF2. JBC Recommended Reads, Oct 2017.

  View Publication
• Provisioning a Large-Scale AI Platform Composed of Intel Gaudi2 Accelerators at Arizona State University

  2026
  PEARC (Practice and Experience in Advanced Research Computing)

  A case study on standing up and operating a large-scale AI platform built on Intel Gaudi2 accelerators. Long paper.

  View Publication
• Ten Practices for Refactoring Scientific Pipelines to nf-core DSL2 on Shared Slurm HPC

  2026
  US-RSE

  Ten practical recommendations for refactoring scientific pipelines to nf-core DSL2 on shared, Slurm-based HPC. Long paper.

  View Publication
• Optimizing Nextflow-based Software on Shared HPC Resources: A Case Study with make_lastz_chains

  2025
  US-RSE

  A case study on optimizing Nextflow-based software for shared HPC resources using the make_lastz_chains pipeline. Long paper.

  View Publication

Presentations

• HPL (Linpack) and Other Popular Benchmarks on Heterogeneous HPC Clusters

  2026
  RMACC HPC Symposium

  Boulder, CO, USA
• Tuning Workflow Management Systems for Shared HPC Resources

  2026
  RMACC HPC Symposium

  Boulder, CO, USA
• A Clinical Decision Support System Based on Prescription Drug Monitoring Programs for Patient Pain Management

  2019
  5th Annual Mayo Clinic–ASU BMI/BMD Student Poster and Employer Networking Event

  Phoenix, AZ, USA

  Poster.
• A DNA Criticality-Detector Circuit in E. coli for Automatic Medicine-Dosage Thresholds

  2015
  International Genetically Engineered Machine (iGEM) 2015 Jamboree

  Boston, MA, USA

  Poster & slides, Team WHU-China. Silver Medal.

Teaching

• Undergraduate Machine Learning Curriculum (MAT 400-level)

  2021
  Arizona State University, School of Mathematical and Statistical Sciences

  Role: Undergraduate course

  Designed a MAT 400-level machine learning curriculum taught at ASU since Fall 2021.
• Certified Instructor, The Carpentries

  2024
  The Carpentries

  Role: Workshops

  Teaching foundational computing and data skills to researchers through hands-on workshops.
• Mentor — Tuning Workflow Management Systems on HPC

  2026
  Cyberinfrastructure Community-wide Mentorship Network (CCMNet)

  Role: Mentorship

  Led a mentorship project on tuning workflow-management systems on HPC.

Languages

• English

  Full professional
• Chinese

  Native / bilingual