open positions

Research and software engineer in Bioinformatics

https://genev.unige.ch/research/laboratory/Jan-Pawlowski

A research and software engineer position (50 % to 100%) is available in the Department of Genetics and Evolution, University of Geneva, as part of a Swiss National Science Foundation project. The hosting laboratory is specialized in molecular ecology and evolution of microbial eukaryotes and is currently involved in several projects aiming at development of new environmental genomics tools for environmental biomonitoring.

Objectives: The position will focus on the maintenance and the development of new features for a bioinformatic pipeline that is routinely-used in our lab. These new functionality would come from newly published, state-of-art bioinformatics methods and from the custom development of new methods that the successful candidate would conduct.

Rationale: Marine ecosystems are threatened by the rapid expansion of industrial activities. Solutions could emerge from the development of innovative tools based on the monitoring of biological communities in order to detect and measure the specificity and the magnitude of environmental impacts. The implementation of genomics technologies into routine biomonitoring by regulating agencies is highly depending on the standardization and ease-of-use of these new tools. This prompts for the development of informatic solutions that would efficiently integrate, store, query and mine the genomics data for the generation of monitoring reports.  

What we propose: We offer an attractive position in a dynamic interdisciplinary team composed of marine biologists, molecular ecologists and computer scientists. The successful candidate will have the opportunity to participate in national and international research projects as well as in scientific publications. 

Required and preferred qualifications. We are looking for a highly motivated and autonomous candidate interested in informatics and software development.

Applicants are expected to have:

  • A strong background in programming (C, C++, Python) and experience in software development, preferentially using web technologies (JavaScript, SQL or other database technologies), preferentially applied to bioinformatics and pipeline design and development.
  • Experience in high-throughput sequencing data analysis (metabarcoding and/or metatranscriptomics and/or metagenomics).
  • Experience in microbial ecology is a plus but not mandatory.

Mode of application. To apply, please send an email to Jan Pawlowski (jan.pawlowski@unige.ch) and Tristan Cordier (tristan.cordier@unige.ch) containing a short letter of motivation, a detailed CV (including a brief description of research interests, previous employments and publication list), and contact details of at least two references (letters of recommendation are optional).

Job starts As soon as possible

Post-Doc Bioinformatics / Environmental Genomics

https://genev.unige.ch/research/laboratory/Jan-Pawlowski

A postdoc position (50 % to 100%) is available in the Department of Genetics and Evolution, University of Geneva, as part of a Swiss National Science Foundation project. The hosting laboratory is specialized in molecular ecology and evolution of microbial eukaryotes and is currently involved in several projects aiming at development of new environmental genomics tools for environmental biomonitoring.

Objectives: The position will focus on adapting and developing algorithms and statistical methods for the processing and data mining of high-throughput DNA sequencing data applied to the detection and quantitative assessment of environmental biodiversity responses to pollution in aquatic ecosystems. A part of the position will be dedicated to the maintenance of bioinformatics tools already developed and routinely used in our lab.

Rationale: Aquatic ecosystems are threatened by the rapid expansion of industrial activities. Solutions could emerge from the development of innovative tools based on the monitoring of biological communities in order to detect and measure the specificity and the magnitude of environmental impacts. Although multiple dimensions of the information delivered by high-throughput DNA sequencing technologies show great promise, many others remain unexplored. Hence, the development of powerful algorithms and robust statistical analyses are required to comprehend and fully exploit patterns of biodiversity changes and ensure fast and reliable assessments.

Required and preferred qualifications. We are looking for a highly motivated and autonomous researcher interested in bioinformatics and environmental genomics.

Applicants are expected to have:

  • Experience in high-throughput sequencing data analysis (metabarcoding and/or metatranscriptomics and/or metagenomics). 


  • Experience in statistic tools applied to microbial ecology 


  • A background in programming (C, C++, Python, JavaScript, node.js), 
preferentially applied to bioinformatics and pipeline design and development. 


  • Proficiency in descriptive/inferential biostatistics and/or machine learning (R, Python or MATLAB). 
Mode of application. To apply, please send an email to Jan Pawlowski (jan.pawlowski@unige.ch) and Tristan Cordier (tristan.cordier@unige.ch) containing a short letter of motivation, a detailed CV (including a brief description of research interests, previous employments and publication list), and contact details of at least two references (letters of recommendation are optional). 
Job starts September 2018. The initial appointment is for a year, possibility of extension for a second year.

3D Animations and Interactive Virtual Reality of Animal Development 
and Evolution: Position for a Computer Graphics Scientist in Switzerland


In the context of a multidisciplinary study combining mathematical modelling, physics-based numerical simulations, and biology, we offer one position for an outstanding, highly motivated, and creative computer scientist with Autodesk Maya and Unreal Engine 4 experience to produce animations, ultra-realistic interactive VR applications and educational software for teaching recently-discovered physical and biological processes generating Life’s complexity and diversity. These developments will be targeted to all levels of education and outreach, from the general public to university students to the physics-of-biology academic research community. Good written and verbal communication skills in the English language are mandatory.

Candidates must have a master’s degree in computer science and strong expertise in:
-Development and optimization of ultra-realistic VR graphics in Unreal Engine (and possibly Unity);
-3D modeling, point cloud and mesh processing, surface reconstruction, texturing and animation;
-C/C++ and GPU programming and optimization of 3D graphics rendering.
Interests and skills in artificial life, evolutionary algorithms, deep-learning, neural networks, image processing/analysis, pattern recognition and robotics are useful additional assets. 

Candidates must have a master’s degree in computer science. The position is available at the level of a PhD student position or at the level of Research Scientist (requiring a PhD degree or at least 3 years of professional experience).

The University of Geneva (UNIGE) is world-renowned for its research and is among the top 1% best universities in the world. Research Scientists and PhD students are remunerated according to the standards of UNIGE, which are very generous when compared to other international programs.

Geneva is an international city occupying a privileged geographical situation with its beautiful lake and the close-by Alps.

References: A Living Mesoscopic Cellular Automaton Made of Skin Scales. Nature 544: 173-179 (2017); Bifurcation Analysis of Reaction Diffusion Systems on Arbitrary Surfaces. Bulletin of Mathematical Biology (2017); Photonic Crystals Cause Active Colour Change in Chameleons. Nature Communications 6: 6368 (2015); R2OBBIE-3D, a Fast Robotic High-Resolution System for Quantitative Phenotyping of Surface Geometry and Colour-Texture. PlosOne 10(6): e0126740 (2015) ; Crocodile Head Scales Are Not Developmental Units But Emerge from Physical Cracking. Science 339, 78-81 (2013).

The position description is also available at https://www.lanevol.org/jobs 

How to Apply
Candidates must send their application — in the form of a single PDF file including a brief letter of interest, a CV, as well as contact information (not support letters) of two to three persons of reference — to: Prof. Michel Milinkovitch (michel.Milinkovitch@unige.ch). The position description is also available at https://www.lanevol.org/jobs 

Physics-Based Numerical Simulations of Animal Development 
and Evolution: Position for a Computer Scientist 
in Switzerland

n the context of a multidisciplinary study combining mathematical modeling and physics-based numerical simulations of biology experiments, we offer one position for an outstanding, highly motivated, and creative computer scientist to investigate the interactions between physical (mechanics, reaction-diffusion) and biological (cell signaling, proliferation) processes that generate and constrain Life’s complexity and diversity. He/she will develop high performance numerical simulations that will require strong mathematical and programming skills. In this academic research position, you will join a multidisciplinary team of physicists, mathematicians, computer scientists and biologists, and you will apply your creative talent to uncover the self-organizational processes that generate complexity during morphogenesis and evolution. Good written and verbal communication skills in the English language are mandatory. Other specific requirements are strong expertise in:
-Physics: mechanics of elastic solids and mechanics of fluids, reaction-diffusion;
-C/C++ and GPU programming, including performance optimization;
-3D reconstruction, point cloud and mesh processing, surface reconstruction.
Interests and skills in other coding languages, artificial life, evolutionary algorithms, deep-learning, neural networks, image processing/analysis, pattern recognition, cellular automata, and robotics are useful additional assets.

Candidates must have a master’s degree in computer science. The position is available at the level of a PhD student position or at the level of Research Scientist (requiring a PhD degree or at least 3 years of professional experience). 

The University of Geneva (UNIGE) is world-renowned for its research and is among the top 1% best universities in the world. Research Scientists and PhD students are remunerated according to the standards of UNIGE, which are very generous when compared to other international programs.

Geneva is an international city occupying a privileged geographical situation with its beautiful lake and the close-by Alps.

References: A Living Mesoscopic Cellular Automaton Made of Skin Scales. Nature 544: 173-179 (2017); Bifurcation Analysis of Reaction Diffusion Systems on Arbitrary Surfaces. Bulletin of Mathematical Biology (2017); Photonic Crystals Cause Active Colour Change in Chameleons. Nature Communications 6: 6368 (2015); R2OBBIE-3D, a Fast Robotic High-Resolution System for Quantitative Phenotyping of Surface Geometry and Colour-Texture. PlosOne 10(6): e0126740 (2015) ; Crocodile Head Scales Are Not Developmental Units But Emerge from Physical Cracking. Science 339, 78-81 (2013).

The position description is also available at https://www.lanevol.org/jobs 

How to Apply
Candidates must send their application — in the form of a single PDF file including a brief letter of interest, a CV, as well as contact information (not support letters) of two to three persons of reference — to: Prof. Michel Milinkovitch (michel.Milinkovitch@unige.ch). The position description is also available at https://www.lanevol.org/jobs