Phd in Quantitative Microbial Biosignatures and Statistical Biophysics

Introduction

UNIL is a leading international teaching and research institution, with over 5,000 employees and 17,000 students split between its Dorigny campus, CHUV and Epalinges. As an employer, UNIL encourages excellence, individual recognition and responsibility.

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NCCR GENESIS - Fully funded Phd position

The National Centre of Competence in Research NCCR Genesis is a research infrastructure project funded by SNSF focussing on exploring the emergence of life in the Universe. This interdisciplinary research infrastructure brings together physicists, earth and planetary scientists, chemists and biologists to understand the conditions and the mechanisms that enable life to emerge. Developing reliable methods to detect reliable traces of life (biosignatures) – whether through remote sensing or direct onsite measurements – requires significant innovation. These challenges demand close collaboration across physics, biology, chemistry and the earth sciences. NCCR Genesis does not aim to provide answers in all fields, but to drive innovative research and achieve decisive progress.

Details on NCCR Genesis are available on its website https://nccr-genesis.ch .

NCCR Genesis is deeply committed to equality, diversity and inclusion. Our aim is to cultivate a respectful and fair work culture with equal access to professional development and support for all. We strongly encourage applications from under-represented groups.

The Institute of Earth Sciences (ISTE) at the University of Lausanne invites applications for a PhD position in computational biosignatures and quantitative modeling within the framework of the NCCR Genesis. The successful candidate will work under the joint supervision of Alice Bosco Santos (UNIL) and Paolo De Los Rios (EPFL).

Presentation

This PhD project aims to quantify how viral perturbations of microbial metabolism translate into measurable biosignatures in low-oxygen environments.

Focusing on sulfur-cycling microbial communities (e.g., purple sulfur bacteria and associated viruses), the project will combine bioinformatics, quantitative modeling, and experimental data integration to identify key metabolic control points targeted by viruses and evaluate how their perturbation propagates through microbial and biogeochemical systems, producing detectable shifts in biosignatures (e.g., isotopic fractionation, pigment production).

Job information

Expected start date in position : fall 2026 or upon agreement

Contract length : 4 years (1+2+1)

Activity rate : 100%                     

Workplace : Institute of Earth Sciences, Faculty of Geosciences and Environment, University of Lausanne

Your responsibilities

The successful candidate will analyse multi-omics datasets, including metagenomes, metatranscriptomes, viromes, and viral auxiliary metabolic genes (AMGs), to investigate how viral infections reshape microbial metabolism. The project will involve identifying metabolic pathways (KEGG pathways) and rate-limiting reactions targeted by viruses, integrating these data into quantitative models that simulate microbial metabolic networks, quantify the impact of viral perturbations, and estimate the thresholds at which viral activity produces detectable biosignature shifts. The candidate will contribute to the interpretation of carbon and sulfur cycling in natural environments, participate in field campaigns to gain familiarity with the studied ecosystems, and have the opportunity to take part in laboratory experiments, such as gene expression analyses, to validate and parameterize the quantitative models.

Your qualifications

We are looking for a motivated candidate interested in the intersection of biology, physics, and Earth sciences, with a strong inclination toward computational approaches. You must have a MSc (or equivalent) in bioinformatics, computational biology, physics, environmental sciences, or a related field. Have a strong interest in quantitative analysis and modeling, programming skills, and the ability to work at the interface of disciplines. We are looking for a candidate that has interest in linking models to experimental data.

We are committed to fostering an equitable, diverse, and inclusive research environment. We particularly encourage applications from individuals who are underrepresented in science, including those from diverse cultural and ethnic backgrounds and those who have followed non-traditional academic paths. We believe that diversity strengthens our science and actively seek to build an inclusive and supportive team.

What the position offers you

The candidate will be based at the University of Lausanne and will collaborate closely with EPFL. The project offers a highly interdisciplinary environment at the interface of microbial ecology, physics, and Earth sciences.

We offer a nice working place in a multicultural, diverse and dynamic academic environment. Opportunities for professional training, a lot of activities and other benefits to discover.

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Contact for further information

Dr Alice Bosco Santos – E-Mail schreiben

Your application

Deadline : 20.08.2026

Please, send your full application in Word or PDF : 

• A cover letter outlining your research motivation and interests (max. 1 page);


• Your CV including academic background, previous research/publications and/or industrial experiences as well as the names and contact details of 2-3 referees;


• Copy of your diplomas.

Only applications through this website will be taken into account.

We thank you for your understanding.

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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