What we do
EPFL

The Hatzimanikatis Group at EPFL has over 20 years of experience in academic and industrial research for the design of metabolic pathways and whole-cell industrial biocatalysis.




What We Do

EPFL (École Polytechnique Fédérale de Lausanne) was founded in 1969 and has established itself as one of the world’s best research and teaching institutions. EPFL is ranked in the top 12 institutions according to the Academic Ranking of World Universities and is ranked 11th in the world in the fields of engineering and technology in the Times Higher Education Ranking. With its 5 Schools, 2 Colleges, 27 Institutes, 350 laboratories, it is Europe’s most cosmopolitan technical university with students, professors and staff from over 120 nations. It has over 10,000 students (including 2,000 PhDs). EPFL offers 13 complete study programs at the Bachelor and Master levels in engineering, basic sciences, computer and communication sciences, life sciences, civil engineering, architecture and the environment. With both a Swiss and international calling, it is therefore guided by a constant wish to open up; its missions of teaching, research and innovation impact various circles: universities and engineering schools, developing and emerging countries, secondary schools and gymnasiums, industry and economy, political circles and the general public.

The Laboratory of Computational Systems Biotechnology (LCSB) at EPFL consists of 18 researchers working on cellular process modeling, large-scale computations, and data analysis, with the aim to develop mathematical models and novel methods of mathematical and computational analysis for systems biology, metabolic engineering, and the prediction of novel biotransformations. LCSB researchers have pioneered the development of computational methods for the prediction of novel biotransformations; the construction of databases for enzyme-based hypothetical reactions; and the development of retrobiosynthesis workflows for the identification and reconstruction of enzyme-based pathways for the production of target molecules from biochemical intermediates and living organisms. LCSB has also pioneered the development of methods for biochemical network thermodynamics. These methods allow the estimation of the thermodynamic properties and thermodynamic feasibility of every known and novel biochemical reaction. Furthermore, LCSB has developed cutting-edge computational methods for systematic and efficient construction and analysis of large-scale and genome-scale dynamic nonlinear models of metabolism. Using these methods, LCSB researchers have constructed models for E. coli, S. cerevisiae, P. putida, P. falciparum and human cells, which account for the thermodynamic and kinetic properties of metabolic pathways and can be used for bioenergetics studies and the identification of rate-limiting steps in the absence of complete kinetic information on the pathway enzymes.

LCSB has been a partner in many European and Swiss multi-investigator projects: SynPath, RobustYeast, DD-DecaF, NEMO etc. The methods developed by LCSB have been also used by leading chemical, food, materials and synthetic biology companies: DuPont, Total, Cargill, BP, DSM, Nestlé, Amyris, and Gevo.

EPFL's key contributions to the ShikiFactory100 project are in computational bioretrosynthesis, and dynamic and hybrid stoichiometric-kinetic modelling for target refining. They are important contributors to Work Package 2: Retrosynthesis & Enumeration, and Work Package 5: In silico Metabolic Engineering. 

The Principal Investigator for EPFL in the ShikiFactory100 project is Prof. Vassily Hatzimanikatis. 

Find out more about EPFL here.



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Partners

SilicoLife
SilicoLife

Braga, Portugal

SilicoLife
SilicoLife designs optimised microorganisms and novel pathways for industrial biotech applications.
EPFL
EPFL

Vaud, Switzerland

EPFL
EPFL was founded in 1969 and has established itself amongst the world’s best research and teaching institutions.
DTU
DTU

Copenhagen, Denmark

DTU
Technical University of Denmark (DTU) is recognised internationally in the areas of technology and natural sciences.
EMBL
EMBL

Heidelberg, Germany

EMBL
EMBL is Europe’s flagship laboratory for life sciences.
DSM
DSM

Delft, Netherlands

DSM
DSM is a global science-based company active in health, nutrition and materials.
University of Manchester
University of Manchester

Manchester, United Kingdom

University of Manchester
The University of Manchester is the largest single-site university in the UK, with research strengths across all scientific disciplines.
University of Minho
UMinho

Braga, Portugal

University of Minho
The University of Minho has expertise in the development of algorithms and computational tools for metabolic engineering.
Universidade NOVA de Lisboa
NOVA

Lisbon, Portugal

Universidade NOVA de Lisboa
Universidade NOVA de Lisboa is the youngest of Lisbon's state universities.
c-LEcta
c-LEcta

Leipzig, Germany

c-LEcta
c-LEcta specializes on the discovery, optimization and production of enzymes and engineered strains for the production of proteins and small molecules.
GalChimia
GalChimia

La Coruña, Spain

GalChimia
GalChimia is a service provider focused in the field of synthetic organic chemistry.
NNFCC
NNFCC

York, United Kingdom

NNFCC
NNFCC has over 17 years of experience in supporting the development of bio-based chemicals and products.
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