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).

• 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

School of Medicine and Public Health, Department of Pathology & Laboratory Medicine, O'Connor Lab

The Department of Pathology and Laboratory Medicine is dedicated to the highest quality patient care, cutting-edge and impactful research, and teaching the next generation of pathologists and scientists. We emphasize a healthy work-life balance and provide a supportive work environment committed to the growth and advancement of our members. Our vibrant clinical department integrates anatomic pathology, laboratory medicine, teaching, and a robust research enterprise, and serves the UW, American Family Children’s, VA, and other Madison hospitals. Our basic science and translational research programs have made fundamental discoveries in cell and stem cell biology, immunology, neuroscience, and infectious disease. Opportunities in education include a T32-funded PhD graduate program, pathology resident and fellowship programs, and both medical school and undergraduate curricula.

Madison, often rated as one of the best places to live in America, is built on an isthmus, surrounded by lakes. The city, campus, green spaces and urban areas are blended to create a place unlike any other.

The starting salary for the position is $95,000 annually but is negotiable based on experience and qualifications.

Employees in this position can expect to receive benefits such as generous vacation, holidays, and sick leave; competitive insurances and savings accounts; and retirement benefits. For more information, refer to the campus benefits webpage. SMPH Faculty / Academic Staff Benefits Flyer 2026

• 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.

• 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.

• 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.

• 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.

PhD in microbiology, virology, molecular biology, genetics/genomics, environmental microbiology, or a closely related discipline is required.

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 Apply Now. 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

Application reviewers will rely on these written materials to determine which applicants move forward in the process. References will be requested from final candidates. All applicants will be notified once the search concludes and a candidate is selected.

University sponsorship is not available for this position, including transfers of sponsorship and TN visas. The selected applicant will be responsible for ensuring their continuous eligibility to work in the United States on or before the effective date of appointment. This is an ongoing position that will require continuous work eligibility. If selected, you must provide proof of work authorization and eligibility to work.