Sequencing Research Associate - 137577 jobs in United States
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San Diego Supercomputer Center · 17 hours ago

Sequencing Research Associate - 137577

positionSan Diego, CA
timeContract
remoteOnsite
seniorityMid Level
money$70K/yr - $112K/yr

The San Diego Supercomputer Center is part of the UC San Diego School of Medicine, focusing on research and clinical missions. The Sequencing Research Associate will optimize and execute a targeted next-generation sequencing workflow for Mycobacterium tuberculosis drug-resistance profiling, involving lab procedures and quality control.

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Comp. & Benefits

Responsibilities

Optimize and execute a proprietary targeted next-generation sequencing (tNGS) workflow for culture-free Mycobacterium tuberculosis (Mtb) drug-resistance profiling using novel low complexity chemistry
Process clinical research specimens per standard operating procedures (SOPs)
Prepare indexed libraries
Perform bead clean-ups
Run library QC (qPCR)
Pool libraries
Operate benchtop sequencers (e.g., Illumina iSeq100)
Complete basic run-level QC with handoff to the bioinformatics team
Meticulous written documentation
Reagent/primer inventory management
Routine equipment maintenance and calibration
Contributions to SOPs and training materials
Interface with clinical and data teams to ensure collaboration, turnaround time, and data integrity for a multi-site domestic study

Qualification

Multiplex PCRSequencing library preparationIllumina sequencersQuality control (qPCR)Primer-pool balancingLaboratory information systemsMeticulous documentationClear communicationOrganizational skillsProblem-solving mindset

Required

Hands-on experience with multiplex polymerase chain reaction (PCR)
Routine instrument maintenance and calibration; ability to follow service schedules, document activities, and minimize downtime
Experience with sequencing library preparation and quality control: electrophoresis gels and qPCR; ability to interpret yield and melt-curve results
Experience with primer-pool balancing and coverage-uniformity troubleshooting (identify dropouts/over-representation; adjust primer concentrations, or clean-up conditions)
Sequencing run-level quality interpretation: read per-amplicon depth tables/plots, percent reads mapped, control behavior, and basic coverage metrics; organize outputs for bioinformatics review
Meticulous documentation in a lab notebook; accurate reagent/lot tracking, instrument IDs, deviations, and corrective actions
Clear written and verbal communication; ability to follow standard operating procedures (SOPs), escalate anomalies promptly, and collaborate with bioinformatic, clinical, and data teams
Strong organizational skills to manage multiple project components on fixed timelines; ability to support occasional evening/weekend runs to meet turnaround goals
Problem-solving mindset with attention to detail; ability to anticipate consumable needs, stage materials, and maintain readiness in a high-throughput environment
Reagent/primer inventory management and lot-qualification workflows (receiving checks, certificates of analysis, storage logs, expiration control)
Spreadsheet skills for QC tracking and per-amplicon trend logs; comfort importing/exporting run metrics and generating simple charts/tables

Preferred

Design and execution of small, structured optimization experiments (e.g., limited factorial “DoE-lite” for annealing/extension and bead ratios); ability to summarize findings with accept/reject recommendations
Familiarity with primer design and assessment tools (e.g., Primer3, BLAST, IDT OligoAnalyzer) for basic in-silico checks (specificity, dimer/hairpin risk)
Biosafety Level-2 (BSL-2) biosafety cabinet practices with potentially infectious human materials; compliance with Environment, Health & Safety (EH&S) requirements and personal protective equipment (PPE) use
Proficiency operating Illumina benchtop sequencers (e.g., iSeq100): run setup, loading, basic monitoring, and shutdown
Experience with laboratory information systems (e.g., laboratory information management system—LIMS) or structured file/metadata handoffs; attention to data integrity
Experience with Mycobacterium tuberculosis diagnostic reference testing, genomics of resistance, clinical samples

Company

San Diego Supercomputer Center

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SDSC enables science and engineering discoveries through advances in computational science and data-intensive, high-performance computing.
dateFounded in 1985
location
La Jolla, California, USA
people-size201-500 employees
web-link
http://www.sdsc.edu/

Funding

Current Stage
Growth Stage
Total Funding
unknown
Key Investors
National Science Foundation
2024-12-05Grant

Leadership Team

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Ilkay Altintas
Division Director, Cyberinfrastructure and Convergence Research and Education
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