Postdoctoral position in environmental DNA and autonomous biodiversity monitoring

Introduction

UNIL is a leading international teaching and research institution, with over 5,000 employees and 15,500 students split between its Dorigny campus, CHUV and Epalinges. As an employer, UNIL encourages excellence, individual recognition and responsibility.

Presentation

The Group of Prof. Nadir Alvarez is proposing a Postdoctoral (Premier Assistant) position in museomics, environmental genomics and molecular ecology at the Department of Ecology and Evolution, University of Lausanne, Switzerland. The postdoc will join a dynamic team working mainly on environmental DNA (eDNA) methods for autonomous aquatic biodiversity monitoring, in the framework of the Innosuisse-funded AquaDecode project, in partnership with the EPFL-based startup Decode NAture. AquaDecode aims to develop a fully integrated, field-deployable DNA analysis system, combining sampling, molecular processing, sequencing, and real-time data analysis. The Postdoctoral project will focus on system-level integration and deployment of field-compatible DNA workflows, bridging molecular biology, microengineering, and real-world environmental monitoring.For more information, see https://applicationspub.unil.ch/interpub/noauth/php/Un/UnPers.php?PerNum=1107109&LanCode=37&menu=coord

The Alvarez group has a strong track record in museomics and environmental genomics. Pioneering work on hybridisation capture from historical and ancient specimens has enabled genomic studies on degraded DNA from historical collections, including butterfly population genomics across the 20th century among other topics. In conservation genomics, the group integrates population genomic data with species conservation, and actively contributes to strengthening partnerships between researchers and conservation practitioners across Switzerland and Europe

More recently, the group has expanded into environmental DNA (eDNA) population genomics, developing an enrichment-based nuclear eDNA capture method that opens new avenues for population-level studies directly from water samples, while advocating the use of natural history collections for improved eDNA reference databases and developing a roadmap on scaling up aquatic eDNA population genetics.

Job information

Expected start date in position: 01.06.2026

Contract length: 24 months (duration of the Innosuisse AquaDecode project)

Activity rate: 80%

Workplace: Lausanne-Dorigny

Annual gross salary: 66 KCHF – 74 KCHF at 80% (equivalent 83 KCHF – 93 KCHF 100%)

Your responsibilities

The research project will be defined together with the group leader based on the Postdoc interests and competences in the field of environmental DNA (eDNA) molecular workflows, autonomous biodiversity monitoring, and applied conservation genomics, in the framework of the Innosuisse-funded AquaDecode project, developed in partnership with DecodeNAture, an EPFL-affiliated start-up. Most of his/her time will be dedicated to research, but a contribution to teaching is expected, including the possibility of supervising master students. The job description stipulates:

70% Personal research

25% Participation to teaching activities and master student supervision

5% Maintenance of lab equipment or other institutional tasks.

AquaDecode aims to build the first fully autonomous eDNA monitoring station, integrating water sampling, molecular amplification (and possibly DNA capture), nanopore sequencing, and cloud-based reporting into a single field-deployable device. A functional autonomous water sampler (CoWaS) already exists; the main challenge is to integrate the complete molecular workflow on board, from Recombinase Polymerase Amplification (RPA) through to batch nanopore sequencing with real-time data transmission. Environmental DNA technologies offer the potential for universal and standardised biodiversity monitoring; AquaDecode aims to make this operational through continuous, autonomous surveillance. The applied conservation dimension is significant: the platform can enable early detection of invasive species, monitoring of pathogen loads in aquaculture and agricultural irrigation systems, and wastewater surveillance for public health.

Research & Development

The postdoctoral researcher will lead the advanced molecular developments of the project: (i) optimising multiplex RPA assays for diverse taxonomic barcodes (COI, 16S, 18S, etc.) from low-concentration aquatic eDNA; (ii) exploring RT-RPA for RNA virus detection; (iii) evaluating hybridisation capture with synthetic probe panels as a high-risk, high-reward complement to RPA; (iv) optimising nanopore library preparation and adaptive sequencing for on-device deployment; and (v) contributing to the bioinformatics pipeline for real-time species identification.

Beyond molecular method development, the postdoc will: i) lead the integration of the AquaDecode system from sampling to sequencing and data generation, in close coordination with DecodeNAture; ii) Design and implement robust, automated, and field-compatible workflows, ensuring reliability under real-world conditions; iii) Develop and optimise interfaces between hardware, molecular workflows, and sequencing technologies (Oxford Nanopore); iv) Translate experimental protocols into deployable and scalable system components; v) Coordinate field deployments across diverse aquatic environments (lakes, rivers, torrents, and potentially groundwater and aquifers); vi) Contribute to scientific publications and technical documentation.

Supervision & Teaching

The postdoc will co-supervise the doctoral student working on the project, as well as Master students and interns, and contribute to the coordination and mentoring of junior researchers within the team.

Your qualifications

We are seeking to recruit someone with the following profile:

Essential:

• PhD in molecular ecology, environmental genomics, bioengineering, microengineering, bioinformatics, or a related field


• Hands-on experience with microengineering and/or molecular biology workflows (experience in applied experimental systems, not purely theoretical)


• Demonstrated skills in eDNA metabarcoding or metagenomics are an asset


• Proficiency in bioinformatics and programming (Python, R, or equivalent)


• Ability to work across disciplines and coordinate with engineering and data science teams


• Strong autonomy and problem-solving skills

Highly desirable:

• Experience with isothermal amplification (RPA, LAMP) or hybridisation capture methods


• Experience with microfluidics, system integration, or applied R&D prototyping


• Familiarity with field deployment of molecular biology platforms


• Experience in startup or translational research environments

The applicants should have a strong ability to work in a team as doctoral students are involved in the project

Interpersonal skills

• Strong ownership and ability to drive research objectives forward autonomously


• Ability to coordinate across disciplines (molecular biology, engineering, bioinformatics)


• Leadership and coordination skills, including co-supervision of doctoral and master students


• Excellent communication skills and ability to engage with diverse stakeholders (academia, agencies, industry)

What the position offers you

• Work at the interface of academic research and startup innovation, contributing to a real-world environmental genomics platform with direct societal impact


• Be part of a dynamic and interdisciplinary team combining molecular biology, engineering, and data science, in close collaboration with DecodeNAture and Swiss environmental partners


• An inspiring setting at the University of Lausanne, on the shores of Lake Geneva with views of the Alps, in a department where research activities and seminars are conducted in English


• Direct involvement in a project connected to real ecosystems, with opportunities for fieldwork across Swiss aquatic environments


• Access to state-of-the-art molecular biology and sequencing facilities, and a strong network across academia, industry, and environmental stakeholders


• Being part of a campus offering a broad range of topics, producing a rich intellectual and social life. Although French is the common language in Lausanne region, the department research activities and seminars are conducted in English. The campus is located on the shore of the Geneva Lake, with the view on the Alps.

Contact for further information

For further information please contact Prof. Nadir Alvarez: E-Mail schreiben

Your application

Deadline to apply: 27.04.2026

Formal applications should include:

- a cover letter detailing your research interests, experience and motivation for applying;

- your CV;

- a copy of your PhD certificate;

- the names of two or three referees.

To receive full consideration, application documents should be uploaded online through the University of Lausanne recruitment platform.

Review of applications will begin immediately.

Additional information

UNIL is committed to:
•    equality, diversity and inclusion within its community;
•    ensuring an open and respectful environment that is conducive to personal development;
•    offering working conditions that facilitate work-life balance;
•    supporting early career researchers.
 

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