O'Connor Lab Scientist

University of Wisconsin Madison•Madison, WI

21h•Onsite

About The Position

We are seeking a PhD-level Scientist to join the O'Connor Lab's environmental surveillance team and lead a new study conducted in collaboration with the laboratory of Dr. Jonathan Temte, founder of the Oregon Child Absenteeism due to Respiratory Disease Study (ORCHARDS) program at UW–Madison. ORCHARDS investigates the causes of child absenteeism from school, and the addition of household air sampling provides a new window onto respiratory viral transmission within the home. During the 2026–2027 school year, paired clinical swab and air samples will be collected from participants with respiratory viral infections across up to 200 households and delivered to our laboratory for intake, processing, sequencing, and analysis. The successful candidate will serve as the scientific and project management lead for the study. Responsibilities include coordinating and executing sample processing for both clinical swabs and air samples, running downstream molecular biology assays, and analyzing data to identify the respiratory pathogens present in each participating household. A central technical responsibility is the design, optimization, and validation, from scratch, of digital PCR (dPCR) assays to quantify pathogen nucleic acids in air and clinical samples across each household's 8-day study window. The scientist will also work closely with external collaborators (including the ORCHARDS team and our internal bioinformatics group) to refine and implement improved techniques for low-input air-sample sequencing and downstream analysis. Scientific work is performed under the guidance of the principal investigators and in partnership with senior lab scientists and the broader environmental surveillance team. In addition to bench and method-development work, the scientist will manage the day-to-day operations of the study, tracking thousands of samples through multi-step workflows, maintaining timelines and deliverables for our donor-funded program, and supervising a Research Specialist to be hired subsequently. The scientist will also contribute to data analysis, manuscript preparation, and other lab projects as needed, and will maintain rigorous records and documentation. Regular work with human clinical swab samples is expected.

Requirements

A PhD in a molecular biology discipline (cellular/molecular biology, virology, genetics, or a closely related field) is required
Documented experience developing and independently running medium-to-high-throughput molecular assays
Demonstrated project management experience
A track record of method development from scratch
A history of productive collaboration with internal and external partners to advance laboratory techniques
Documented hands-on experience performing molecular biology experiments at the bench, including nucleic acid extraction, library preparation, and PCR-based workflows
1–3 years of experience developing molecular biology assays (dPCR, qPCR) from scratch, including assay design, optimization, validation, and troubleshooting
Experience with high-throughput molecular biology workflows and high-volume weekly sample processing
Demonstrated project management experience, including coordinating multi-step laboratory workflows, tracking large sample sets, and meeting deliverables on defined timelines
Demonstrated experience collaborating with internal and external partners to develop and implement improved laboratory techniques
Experience working with and analyzing large datasets
Excellent written and verbal communication skills and strong organizational skills
Willingness and ability to work with human clinical swab samples that may contain respiratory pathogens
Must provide a valid driver's license
Employment is conditional pending the results of a Pre-hire Driver Authorization Check

Nice To Haves

Experience managing or mentoring undergraduate researchers or technician-level staff
Experience with next-generation sequencing of low-input or environmentally derived samples (e.g., air, wastewater, surface swabs)
Prior experience in respiratory virology, viral genomics, or a public-health or environmental surveillance laboratory setting
Familiarity with sequencing bioinformatics pipelines, including experience interpreting and reporting sequencing data
Demonstrated experience collaborating with external partners or multi-institutional teams to develop and implement improved laboratory methods
Track record of peer-reviewed publications, preprints, or conference presentations
Experience drafting progress reports or deliverables for funders (private donors, foundations, or granting agencies)
Experience establishing or maintaining laboratory SOPs, quality control systems, or sample tracking systems (e.g., LIMS)

Responsibilities

Develops, optimizes, and validates novel molecular biology assays from scratch including digital PCR (dPCR) assays for quantifying pathogen nucleic acids in low-input environmental and clinical samples and establishes standard operating procedures for adoption by the lab
Manages day-to-day operations of the HouseholdPath study, including coordinating sample logistics across partner sites, tracking 3,000–5,000 samples through multi-step molecular workflows, maintaining study timelines and deliverables for a private donor, and supervising a Research Specialist
Designs and maintains quality control, data tracking, and reporting systems for the environmental surveillance program, ensuring end-to-end sample integrity and timely data return to participating sites and funders
Collects and analyzes research data, conducts experiments and interviews, and documents results according to established policies and procedures under general supervision and limited responsibility
Attends and assists with the facilitation of scholarly events and presentations in support of continued professional development and the dissemination of research information
Assists with the identification of research problems and the development of research methodologies and procedures
Serves as a main point of contact and liaison with internal and external stakeholders providing information and representing the interests of a specialized research area
Partners with external collaborators (including the ORCHARDS team and the lab's bioinformatics group) to co-develop and implement improved techniques for air-sample sequencing, nucleic acid recovery, and downstream analysis
Conducts literature reviews, prepares reports and materials, and disseminates information to appropriate entities
Writes or assists in developing grant applications and proposals to secure research funding