Stanford University is a leading research and teaching institution in the San Francisco Bay Area. The Department of Civil and Environmental Engineering brings together engineers, scientists and social scientists to address the sustainability of the built and natural environment, with a long-standing focus on water, health and the environment.
The Boehm Lab, in the Department of Civil and Environmental Engineering and the Woods Institute for the Environment, invites applications for a Postdoctoral Scholar in Wastewater Metagenomics and Computational Biology
WastewaterSCAN is a national infectious disease monitoring program led by Stanford University in partnership with Emory University, with Verily as laboratory partner, funded philanthropically through a gift to Stanford. The program measures pathogen nucleic acids in wastewater solids from roughly 150 sewersheds across more than 40 states, serving over 39 million people, and publishes the resulting data freely on a public dashboard for use by health departments, utilities and researchers. The panel currently spans more than a dozen targets, including SARS-CoV-2, influenza A and B, RSV, human metapneumovirus, norovirus, enterovirus D68, measles, mpox, hepatitis A, West Nile virus, Candidozyma auris, Mycobacterium tuberculosis and the carbapenemase gene blaNDM.
The program has recently established a prospective metagenomic sequencing arm. Hybrid capture metagenomic sequencing is applied to wastewater samples prospectively 3 times per week, yielding a median viral read fraction above 19% and relative abundance estimates that agree with direct digital PCR quantification of the same targets. This creates a continuously growing, genomically resolved view of pathogen diversity and dynamics across the United States, alongside the established targeted dPCR measurements.
The position
We seek a postdoctoral scholar to serve as a primary bioinformatician and computational biologist for the metagenomics arm of WastewaterSCAN. The role has two halves of equal weight. The first is stewardship of the operational sequencing pipeline that turns weekly raw sequencing output into public-health-relevant information. The second is independent, first-author research using one of the largest prospective wastewater metagenomic datasets assembled to date.
Duties will include:
- Regular quality control assessment and summary of weekly metagenomic sequencing data, and communication of anomalies to the laboratory and program teams.
- Monthly in silico primer and probe checks, evaluating existing dPCR assays against accumulating sequence data to detect mismatches arising from pathogen evolution.
- Routine screening of sequencing data against a watch list of high-consequence, emerging and re-emerging agents, and triage of candidate signals.
- Development and maintenance of bioinformatic pipelines in collaboration with academic and industry partners.
- Bioinformatics support for academic research projects across the lab and the wider program.
- Communication of results to public health stakeholders through regular meetings, and to the scientific community through conferences and symposia.
- Leading innovative longer-term research projects with metagenomic data as lead author.
Who we are looking for:
This position is not structured as a training role in bioinformatics. We are looking for someone who can assume ownership of established pipelines with minimal ramp-up, exercise independent judgement about data quality and biological plausibility, and raise the computational and virological capability of the group as a whole. The successful candidate will be teaching us as much as learning from us.
Required:
- A PhD in bioinformatics, computational biology, genomics, microbiology, virology, environmental engineering or a closely related field, completed by the start date.
- Demonstrated experience analysing high-throughput sequencing data, evidenced by first-author publications, preprints or a public code record.
- Strong programming ability in Python and/or R, fluency at the Unix command line, and competence with version control and reproducible workflow management.
- Experience working comfortably at scale: large and unwieldy data frames, high-performance computing clusters or cloud compute, and workflows that must run reliably on a fixed weekly schedule.
- Working knowledge of virology and viral genomics sufficient to judge whether a detection is biologically sensible, including familiarity with viral taxonomy, genome organisation and evolution.
- The ability to explain technical findings clearly to public health practitioners and other non-specialist stakeholders, and to work effectively within a multi-institution team.
Strong assets:
- Direct experience with metagenomic sequencing data, particularly hybrid capture or other target-enrichment approaches.
- Familiarity with environmental or wastewater matrices, or with pathogen genomic surveillance in a public health setting.
- Experience with assay design or in silico primer evaluation.
- A record of building tools or pipelines that other people went on to use.
What we offer:
The postdoctoral scholar will join a dynamic, collaborative and multidisciplinary group with state-of-the-art computational infrastructure and direct access to an unusually rich prospective dataset. The role carries genuine visibility: the successful candidate will work alongside academic collaborators at Stanford and Emory, industry partners, and public health agencies at local, state and national level, and their analyses will inform decisions taken outside the university. Stanford offers a comprehensive postdoctoral benefits package and an active postdoctoral community. Please visit https://postdocs.stanford.edu for more information on post doc compensation.
Application
Please submit your application by 1 December 2026 or sooner. Applications will be considered in the order received. Please include a letter of motivation (1 page maximum) explaining why you think you fit this position well, a CV including a publication list, a link to a public code repository if you have one, and the names and contact information of three references. The intended start date is as soon as possible, and the initial appointment is for one year.
For further information, please contact Alexandria Boehm: aboehm@stanford.edu. Applications should be submitted via email to Alexandria Boehm with the subject line: Metagenomics postdoc. Applications received by other means will not be considered.