Job Details
Salary:
***Current Employees: If you are currently employed at any of the Universities of Wisconsin, log in to Workday to apply through the internal application process.***
Job Category:Academic Staff
Employment Type:Regular
Job Profile:Scientist III
Job Summary:
The O’Connor Lab in the Department of Pathology & Laboratory Medicine seeks a PhD-level Advanced Scientist to lead genome-resolved characterization of the wastewater and environmental virome as part of the donor-funded Lungfish surveillance program. The scientist will serve as the computational lead for detecting and characterizing known and emerging viruses from complex, low-biomass samples while managing project timelines and partner deliverables. This is an ongoing, career-track position with full benefits.
- It is anticipated that this position will be remote and requires work be performed at an offsite, non-campus work location.
Candidates who demonstrate the following knowledge, skills, and abilities will be given first consideration:
- Genome-resolved metagenomics of the viral/microbial community of complex environmental or wastewater samples with experience characterizing at least 5,000 novel viruses.
- Development and validation of both untargeted (shotgun) and targeted (probe-capture/hybrid-capture) viral sequencing workflows from low-biomass material.
- Bioinformatic pipeline development for known- and novel-pathogen detection in high-throughput sequencing data (Python and/or R; Linux/HPC).
Key Job Responsibilities:
- Attends and assists with the facilitation of scholarly events and presentations in support of continued professional development and the dissemination of research information
- Identifies, writes, or assists in developing grant opportunities, grant applications, and proposals to secure research funding
- May supervise the day-to-day activities of a research unit and staff and resolve routine personnel issues
- Leads genome-resolved metagenomic characterization of the wastewater and environmental virome, including ultra-deep untargeted (shotgun) sequencing and targeted probe-capture/hybrid-capture enrichment of priority and emerging viruses, and develops and validates the associated low-biomass nucleic-acid recovery and sequencing-library workflows
- Identifies research problems and develops highly complex research methodologies and procedures. Publishes and presents results to help advance research
- Serves as scientific and project-management lead for the wastewater virome-surveillance program — coordinating sample logistics and timelines across partner sites and funders, and supervising and mentoring a Research Specialist and junior scientific staff
- Serves as an institutional subject matter expert and liaison with key internal and external stakeholders providing expert level information and representing the interests of a specialized research area
- Collects and analyzes highly complex research data, conducts experiments and interviews, and documents results according to established policies and procedures
- Partners with the lab’s bioinformatics group and external collaborators (including the ORCHARDS team and multi-campus wastewater-surveillance networks) to co-develop and implement improved methods for low-input viral recovery, sequencing, and downstream analysis, and establishes SOPs, QC, and standardized data-return systems
- Conducts literature reviews, prepares reports and materials and, disseminates information to appropriate entities
Department:
School of Medicine and Public Health, Department of Pathology & Laboratory Medicine, O'Connor Lab
Compensation:
The starting salary for the position is $95,000 annually but is negotiable based on experience and qualifications.
Required Qualifications:
- Demonstrated expertise in genome-resolved metagenomics / metaomics of complex microbial or viral communities, including assembly, binning/classification, and genome-resolved interpretation of high-throughput sequencing data. The successful applicant will likely have a track record of characterizing at least 5,000 novel viruses from complex samples. Applicants who have not characterized at least 1,000 novel viruses will likely not be competitive for this position.
- PhD in microbiology, virology, molecular biology, genetics/genomics, environmental microbiology, or a closely related field, with an outstanding track record of peer-reviewed first- or corresponding-author publications, preprints, and conference presentations.
- Documented experience developing, benchmarking, and validating both untargeted (shotgun metagenomic) and targeted (probe-capture / hybrid-capture enrichment) high-throughput viral sequencing workflows from low-biomass or environmentally derived samples and using computational tools to assess these benchmarking experiments.
- Demonstrated experience developing or substantially adapting bioinformatic pipelines for pathogen detection and characterization in HTS data, including programming in Python and/or R and working in Linux / high-performance computing (HPC/HTC) environments.
- Experience with wastewater-based epidemiology or environmental pathogen surveillance, including sample concentration and viral-recovery methods.
- Demonstrated independent project leadership: coordinating multi-step laboratory and computational workflows, managing large sample sets, and meeting funder/stakeholder deliverables on defined timelines.
- Experience supervising or mentoring junior scientists, technical staff, and/or students.
- Track record of securing or substantially contributing to competitive research funding (e.g., lead or co-author on funded grant proposals).
- Excellent written and verbal communication and strong organizational skills.
Preferred Qualifications:
- Experience with One Health or multi-pathogen genomic surveillance (e.g., SARS-CoV-2 variant tracking, influenza A) across multi-site or multi-campus networks.
- Experience establishing or maintaining LIMS or sample-tracking systems, QC frameworks, and standardized data-return/reporting formats for partner sites and funders.
- Demonstrated cross-institutional collaboration to co-develop and implement improved laboratory and analytical methods.
- Teaching, peer-review, or formal mentoring experience.
Education:
PhD in microbiology, virology, molecular biology, genetics/genomics, environmental microbiology, or a closely related discipline is required.
How to Apply:
For the best experience completing your application, we recommend using Chrome or Firefox as your web browser. To apply for this position, select either “I am a current employee” or “I am not a current employee” under . You will then be prompted to upload your application materials.
Important: The application has only one attachment field. Upload the following documents in that field, either as a single combined file or as multiple files in the same upload area:
- Cover letter
- Resume / CV
This is a Preview Listing…
You must sign in to see the full job description, and to apply.
Manage / Upgrade this job to a Full Job Listing.
Find Your Best Opportunity
Tell them AcademicJobs.com sent you!
