Data Scientist II

The O’Connor Lab is searching for a Data Scientist II. The successful applicant will help develop, design, organize, and conduct research projects under the supervision of Dr. O'Connor and senior scientists in the lab. They will contribute to projects across the lab but work predominantly on the Lungfish project, which focuses on advancing environmental pathogen monitoring with virus metagenomic sequencing.

The Data Scientist will use workflow orchestration tools such as Nextflow or Snakemake to develop robust, reproducible data analysis workflows that can run on a variety of computational platforms, including local servers, UW-Madison CHTC HTC and HPC resources, and commercial on-demand cloud computing clusters. Data analysis tools developed in this position are shared publicly via GitHub, so demonstrated experience documenting and deploying robust analysis tools is essential. Visible experience with AI-assisted data exploration, analysis, visualization, and reporting is strongly preferred.The successful applicant will also be responsible for mentoring and advising students and staff on computational analysis of genomic data, and presenting and publishing this data. Therefore, outstanding communication skills are required. 

• 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:
  • Programming experience in Python, R, and Nextflow
  • Version control with Git and collaborative open source software development experience
  • Data visualization and presentation experience, ideally including reporting via web deployment and also via public speaking e.g. at conferences
  • Track record of identifying and pursuing interesting problems in complex datasets
  • Can operate across multiple compute environments and technology stacks
  • Data transfer and management with command-line utilities and services like Globus
  • Strong competency with AI assistive technologies, e.g., coding agents

• Composes and assembles reproducible workflows and reports to clearly articulate patterns to researchers and/or administrators

• Documents approaches to address research questions and contributes to the establishment of reproducible research methodologies and analysis workflows

• Prepares data sets for analysis including cleaning/quality assurance, transformations, restructuring, and integration of multiple data sources

• Independently identifies and implements appropriate data science techniques to find data patterns and answer research questions chosen by the lead researcher including data visualization, statistical analysis, machine learning, and data mining

• Mentor less computationally experienced lab staff and collaborators in robust and reproducible data analysis

• Liaise with stakeholders including but not limited to collaborators, other research staff, and IT staff to generate, maintain, backup, and publicly disseminate raw and interpreted laboratory data

• Organizes and automates project steps for data preparation and analysis

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

The  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.

, 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$92,228 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; retirement benefits. For more information, refer to the campus benefits webpage. SMPH Faculty /Academic Staff Benefits Flyer 2026

• At least three years of experience working with genomic data sets in a research laboratory
• At least one year of experience performing laboratory research involving high throughput nucleic acid sequencing
• Experience with data science methods (programming, algorithms, deep learning)
• Demonstrated experience developing reproducible and flexible scientific workflows with orchestration platforms such as Nextflow or Snakemake
• Excellent written and verbal scientific communication skills
• Documented experience using GitHub to disseminate research pipelines to the broader scientific community
• Demonstrated ability to work independently and collaborate with other scientists, as well as mentor other researchers learning computational data analysis
• Strong organization and prioritization skills

• Knowledge of statistics
• Understanding of pathogen genomics
• Experience in an academic research laboratory
• Familiarity with manuscript and research grant preparation
• Understanding of laboratory data management systems such as LabKey Server

Master’s Degree preferred; focus in genomics or bioinformatics preferred

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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. Failure to submit the required documents will result in no longer being considered for the position.

 • Cover letter required
 • Resume required

Your cover letter should address how your training and experience aligns with the required and preferred qualifications listed above and should provide links to public Github repositories or other demonstrations of previous work products. 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 (i.e. a citizen or national of the United States, a lawful permanent resident, a foreign national authorized to work in the United States without the need of an employer sponsorship) on or before the effective date of appointment. This position is an ongoing position that will require continuous work eligibility. If you are selected for this position you must provide proof of work authorization and eligibility to work. 

Tia Seguin, tia.seguin@wisc.edu, 608-263-3731

Relay Access (WTRS): 7-1-1. See RELAY_SERVICE for further information.