Lab of Microbial Systems Biology

Research

The main interest of this lab is to explore microbial community structure and dynamics in silico and in vitro. We therefore work at the boundary of microbial ecology, systems biology and bioinformatics. If you are interested, please have a look at our ERC project.

People

Karoline Faust

Daniel Rios Garza

Postdoc

Bin Liu

Postdoc

Charlotte van de Velde

PhD student

Clémence Joseph

PhD student

Anna Krzynowek

PhD student

Co-supervisors: Ellen Decaestecker
and Dirk Springael

Pallabita Saha

PhD student

Co-supervisor: Kristel Bernaerts

Mathias Bonal

Co-supervised PhD student

Main supervisor: Isabelle George

Wannes Nauwynck

Co-supervised PhD student

Main supervisor: Nico Boon

Tinh Van Nguyen

Co-supervised PhD student

Main supervisor: Dirk Springael

Master students/Visitors

Haris Zafeiropoulos
Yu Gao
Vladislav Vlasov

Alumni

Sam Röttjers (PhD student, 2017-2021, now at Biome Makers)
Emma Gheysen (Master student, 2021)
Tine Logghe (Master student, 2021)
William Roberts-Sengier (Master student, 2020)
Xinyi Cao (Visiting PhD student, 2020)
Jule Freudenthal (Online visiting PhD student, Spring 2020)
Susana Martinez Arbas (Visiting PhD student, Autumn 2017)
Leandro Nascimento Lemos (Visiting PhD student, Autumn 2017)
Lyu Su (Visiting PhD student, Autumn 2017)
Ina Deutschmann (Visiting PhD student, Spring 2017)
Hajar Fauzan Ahmad (Visiting PhD student, Spring 2017)
Nguyen Thi Loan Anh (Visiting Postdoc, 2017)
Eduardo Pérez Valera (Visiting PhD student, 2014/2015)
Aria Hahn (Visiting PhD student, 2014/2015)

Publications

See top publications.

Tool Development

CellScanner

Flow cytometry data analysis

Mako

Network meta-analysis

Anuran

Network comparison

Manta

Network clustering

seqgroup

Microbial sequencing data analysis

seqtime

Microbial community simulation

CoNet

Microbial network inference

Teaching

Events

Upcoming events

ISME18

Past events

Below are pictures from our lab day 2022.

Escape room

Lab day (25th May 2022)
School on Microbial Time Series Analysis (2nd-4th Nov 2021)
Summer School on Microbial Community Modeling (16-18 Sep 2019)
Dynamics of Biological Systems (2-4 May 2018)
Session on Microbial Systems Biology
Netherlands Annual Ecology Meeting (13-14 Feb 2018)
Session on Microbial Ecology: Community composition and dynamics
Summer School on Ecological Network Inference And Analysis (11-13 Sep 2017)

Guest speakers

Gail Rosen "Discovery of Microbial Community Structure and Interactions through Machine Learning" (29th June 2022)
Christian von Mering "STRING and MicrobeAtlas - new developments for microbiologists" (26th October 2021)
Modeling microbial ecology series - Hilje Doekes (17th August 2021)
Modeling microbial ecology series - Veronika Dubinkina (6th April 2021)
Research seminar by Christoph Ratzke (15th December 2020)
Maxime Fajgenblat "Modelling adaptational regime shifts in populations using spatially and genetically explicit Lotka-Volterra models" (6th October 2020)
Bin Ma "Exploring Soil Microbiomes from a Network Perspective" (17th June 2019)
Hein Sprong "Eco-epidemiology of Lyme borreliosis" (29th June 2018)

Vacancies

Spontaneous applications

If you are interested to join the lab as a PhD student or postdoctoral researcher or as a visiting student, please send your CV and motivation letter to: karoline.faust(at)kuleuven.be

Available positions

Currently no position available.

Contact

Address

Laboratory of Molecular Bacteriology
Department of Microbiology, Immunology and Transplantation (Rega Institute)
KU Leuven
Rega institute, 7th floor (Room 7.B142)
Bus: 1028
Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium

Email

karoline.faust(at)kuleuven.be

Phone

+32-16-322698