Scientist III — Wastewater Virome Genomic Surveillance

Universities of Wisconsin•Madison, WI

4d•Remote

About The Position

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.

Requirements

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.

Nice To Haves

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.

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