Nil Tianchen Mu

Nil Tianchen Mu

he/him

HPC Systems Administrator accelerating research through system optimization, research software engineering, and community education.

Research

Presentation

Tuning Workflow Management Systems for Shared HPC Resources

RMACC HPC Symposium

Presentation on tuning workflow-management systems and their scheduling behavior for shared, multi-tenant HPC resources.

Related paper

Presentation

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

RMACC HPC Symposium

Presentation on running HPL (Linpack) and other popular benchmarks across heterogeneous HPC clusters, and interpreting the results for capacity and performance planning.

Conference Paper

Optimizing Nextflow-based Software on Shared HPC Resources: A Case Study with make_lastz_chains (opens in a new tab)

US Research Software Engineer Association (US-RSE)

Practical lessons from supporting the make_lastz_chains genome-alignment pipeline on ASU supercomputers, where Nextflow submits many small Slurm jobs that erode a user’s Fairshare score and stretch queue waits. Covers scheduling tactics, Fairshare impact, and reliably capturing Slurm errors, aimed at researchers, RSEs, and HPC support teams.

Related talk

Journal Article

Longitudinal dynamics of the nasopharyngeal microbiome in response to SARS-CoV-2 Omicron variant and HIV infection in Kenyan women and their children (opens in a new tab)

mSystems, American Society for Microbiology

Followed the nasopharyngeal microbiome of Kenyan mothers and their children before, during, and after SARS-CoV-2 Omicron infection in a longitudinal cohort that included women living with HIV. Genomic epidemiology showed mother and child pairs carried the same rapidly spreading Omicron strain, and the cohort design separates how infection and HIV exposure each shape the airway microbiome.

Journal Article

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 (opens in a new tab)

mBio, American Society for Microbiology

Baseline genomic surveillance that tracked SARS-CoV-2 across public clinical testing, hospitals, and community wastewater in Arizona, capturing the rapid takeover by the Omicron variant of concern. Pairing the three sampling streams shows how quickly a new variant can rise to dominance in a community.

Poster

A Clinical Decision Support System Based on Prescription Drug Monitoring Programs for Patient Pain Management

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

Poster proposing a Clinical Decision Support System (CDSS) built on Prescription Drug Monitoring Programs (PDMPs) to support patient pain management, developed during a research affiliation at Mayo Clinic.

Journal Article

Prion protein is required for tumor necrosis factor alpha (TNFα)-triggered nuclear factor kappa B (NF-κB) signaling and cytokine production (opens in a new tab)

Journal of Biological Chemistry

Showed that cellular prion protein is required for TNFα-triggered NF-κB signaling and cytokine production: deleting PRNP in melanoma and pancreatic cancer cell lines silenced the response, and reintroducing it restored signaling. Mechanistically, prion protein keeps RIP1 and TRAF2 ubiquitinated by restraining the deubiquitinase CYLD. Selected as a JBC Recommended Read (Oct 2017).

Poster & Slides

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

International Genetically Engineered Machine (iGEM) 2015 Jamboree

Slides and poster presentation for Team WHU-China’s synthetic-biology project — a DNA criticality-detector circuit in E. coli designed as an automatic medicine-dosage threshold for addressing human dental caries. Awarded a Silver Medal.

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