Name

Karoline Faust

Address

Microbial Systems Biology
Laboratory of Molecular Bacteriology
Department of Microbiology, Immunology and Transplantation
Rega institute, 7th floor, Room 7.A130
KU Leuven
Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium

E-mail

karoline.faust(at)kuleuven.be

KU Leuven

ORCiD

Publons

ResearchGate

Loop

10/2016 to present

Assistant Professor in microbiological bioinformatics at KU Leuven

10/2013 to 9/2016

FWO grant prolongation for post-doctoral position with Prof. Raes
Topic: "Exploration of microbial community dynamics by metagenomic time series analysis, community model development and validation"

10/2010 to 9/2013

FWO grant for post-doctoral position with Prof. Raes
Topic: "Development of computational approaches for the prediction and analysis of species interaction networks from metagenomics data"

2/2010 to 9/2010

Post-doctoral position in the Research Group of Bioinformatics and (Eco)-Systems Biology headed by Prof. Raes

February 12th, 2010

Public PhD defense at ULB (pdf)

September 8th, 2006

DEA in Bioinformatics at ULB (pdf)

12/2005 to 1/2010

PhD in the laboratory "Bioinformatique des Génomes et des Réseaux" (BiGRe) at ULB (Brussels)
Topic: "Inferring metabolic pathways from clusters of co-expressed genes in yeast."
Supervisor: Prof. Jacques van Helden

September 15th, 2005

Diplom in Biology at Humboldt University, Berlin (pdf)
(equivalent to Master, qualifies recipient for PhD)

12/2004 to 9/2005

Diplomarbeit with the Sers group (Charite university hospital) and the Institute for Theoretical Biology (Humboldt University)
Title: "Effects of Oncogenic Ras on Gene Expression: Clustering of Microarray Data and Screening for Potential Serum Response Factor Targets"
Supervisors: PD Dr. Christine Sers, Prof. Hanspeter Herzel

2003 to 2004

Additional subject (Zusatzfach):
Applied computer science at Humboldt University (Berlin)

2002 to 2003

Study of Biology at University of York (UK)
(Undergraduate courses)

1999 to 2002

Study of Biology at Humboldt University (Berlin)
Major subject: Biochemistry
Minor subjects: Microbiology, Theoretical biology

Faust K
Microbial Consortium Design Benefits from Metabolic Modeling
TIBTECH 37(2), 123-125 (2018)
Spotlight, not peer-reviewed

Joossens M, Faust K, Gryp T, Nguyen ATL, Wang J, Eloot S, Schepers E, Dhondt A, Pletinck A, Vieira-Silva S, Falony G, Vaneechoutte M, Vanholder R, Van Biesen W, Huys GRB, Raes J, Glorieux G
Gut microbiota dynamics and uraemic toxins: one size does not fit all Gut, Accepted (2018)

D'hoe K*, Vet S*, Faust K*+, Moens F, Falony G, Gonze D, Lloréns-Rico V, Gelens L, Danckaert J, De Vuyst L*, Raes J*+
Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community eLife 7, e37090 (2018)

Röttjers L and Faust K
From hairballs to hypotheses - biological insights from microbial networks
FEMS Microbiology Reviews 42, 761-780 (2018)

Ma B, Zhao K, Lv X, Su W, Dai Z, Gilbert JA, Brookes PC, Faust K, Xu J
Genetic correlation network prediction of forest soil microbial functional organization The ISME Journal 12, 2492-2505 (2018)

Gonze D, Coyte KZ, Lahti L, Faust K, Microbial communities as dynamical systems
Current Opinion in Microbiology 44, 41-49 (2018)

Faust K+, Bauchinger F, Laroche B, de Buyl S, Lahti L, Washburne AD, Gonze D, Widder S+, Signatures of ecological processes in microbial community time series
Microbiome 6, 120 (2018)

Vet S, de Buyl S, Faust K, Danckaert J, Gonze D, Lendert G
Bistability in a system of two species interacting through mutualism as well as competition: chemostat vs. Lotka-Volterra equations
PLoS ONE, 13(6), e0197462 (2018)

Muller EL, Faust K, Widder S, Herold M, Martinez Arbas S, Wilmes P
Using metabolic networks to resolve ecological properties of microbiomes Current Opinion in Systems Biology 8, 73-80 (2018)

Parente E, Zotta T, Faust K, De Filippis F, Ercolini D
Structure of association networks in food bacterial communities Food Microbiology 73, 49-60 (2018)

Gonze D, Lahti L, Raes J, Faust K
Multi-stability and the origin of microbial community types The ISME Journal 11, 2159-2166 (2017)

Wang H, Wei Z, Mei L, Gu J, Yin S, Faust K, Raes J, Deng Y, Wang Y, Shen Q, Yin S
Combined use of network inference tools identifies ecologically meaningful bacterial associations in a paddy soil Soil Biology and Biochemistry 105, 227-235 (2017)

Pérez-Valera E, Goberna M, Faust K, Raes J, García C, Verdú M
Fire modifies the phylogenetic structure of soil bacterial co-occurrence networks Environmental Microbiology 19, 317-327 (2016)

Faust K and Raes J, CoNet app: inference of biological association networks using Cytoscape. F1000 5:1519, Cytoscape apps Channel 5, 1519 (2016)

Faust K and Raes J, Host-microbe interaction: Rules of the game for microbiota. Nature News & Views (2016), not peer-reviewed

Günther S, Faust K, Schumann J, Harms H, Raes J, Müller S
Species-sorting and mass-transfer paradigms control managed natural metacommunities. Environmental Microbiology 18, 4862-4877 (2016)

Bálint M, Bahram M, Eren AM, Faust K, Fuhrman J, Lindahl B, O'Hara R, Opik M, Sogin M, Unterseher M, Tedersoo L
Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes. FEMS Microbiology Reviews fuw017 (2016)

Falony G*, Joossens* M, Vieira-Silva* S, Wang* J, Darzi Y, Faust K, Kurilshikov A, Bonder, MJ, Valles-Colomer M, Vandeputte D, Tito RY, Chaffron S, Rymenans L, Verspecht C, Sutter LD, Lima-Mendez G, D'hoe K, Jonckheere K, Homola D, Garcia R, Tigchelaar EF, Eeckhaudt L, Fu J, Henckaerts L, Zhernakova A, Wijmenga C, Raes J
Population-level analysis of gut microbiome variation. Science 352 (6285), 560-564 (2016)

Mattiello F, Verbist B, Faust K, Raes J, Shannon WD, Bijnens L, Thas O
A Web Application for Sample Size and Power Calculation in Case-Control Microbiome Studies. Bioinformatics 32, 2038-2040 (2016)

Weiss S, Van Treuren W, Lozupone C, Faust K, Friedman J, Deng Y, Xia LC, Xu ZZ, Ursell L, Alm EJ, Birmingham A, Cram JA, Fuhrman JA, Raes J, Sun F, Zhou J, Knight R
Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. The ISME Journal 10, 1669-1681 (2016)

Edwards RA, McNair K, Faust K, Raes J, Dutilh B
Computational approaches to predict bacteriophage-host relationships. FEMS Microbiology Reviews fuv048 (2015)

Faust K, Lima Mendez G, Lerat J-S, Sathirapongsasuti JF, Knight R, Huttenhower C, Lenaerts T and Raes J
Cross-biome comparison of microbial association networks. Frontiers in Microbiology 6, 01200 (2015)

Lima Mendez G*, Faust K*, Henry N*, Decelle J, Colin S, Carcillo F, Chaffron S, Ignacio-Espinosa J, Roux S, Vincent F, Bittner L, El Darzi Y, Wang J, Audic S, Berline L, Bontempi G, Cabello A, Coppola L, Cornejo-Castillo F, d'Ovidio F, De Meester L, Ferrera I, Garet-Delmas M, Guidi L, Lara E, Pesant S, Royo-Llonch M, Salazar G, Sánchez P, Sebastian M, Souffreau C, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans coordinators, Gorsky G, Not F, Ogata H, Speich S, Stemmann L, Weissenbach J, Wincker P, Acinas S, Sunagawa S, Bork P, Sullivan M, Karsenti E, Bowler C, de Vargas C, Raes J
Determinants of community structure in the global plankton interactome. Science 348 (6237), (2015)

Faust K*, Lahti L*, Gonze D, de Vos W, Raes J
Metagenomics meets time series analysis: unraveling microbial community dynamics. Current Opinion in Microbiology 25, 56-66 (2015)

Navarrete AA, Tsai SM, Mendes LW, Faust K, Hollander M, Cassman NA, Raes J, Veen JA, Kuramae EE
Soil microbiome responses to the short-term effects of Amazonian deforestation. Molecular Ecology 24 (10), 2433-2448 (2015)

Hingamp P, Grimsley N, Acinas SG, Clerissi C, Subirana L, Poulain J, Ferrera I, Sarmento H, Villar E, Lima-Mendez G, Faust K, Sunagawa S, Claverie J-M, Moreau H, Desdevises Y, Bork P, Raes J, de Vargas C, Karsenti E, Kandels-Lewis S, Jaillon O, Not F, Pesant S, Wincker P and Ogata H
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. ISME 7, 1678-1695 (2013)

Faust K, Raes J. Microbial interactions: from networks to models. Nature Review Microbiology 10, 538-550 (2012)

Faust K*, Sathirapongsasuti, JF*, Izard J, Segata N, Gevers G, Raes J*, Huttenhower C*. Microbial Co-occurrence Relationships in the Human Microbiome. PLoS Computational Biology 8 (7), e1002606 (2012)

The Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214 (2012)

The Human Microbiome Project Consortium. A framework for human microbiome research. Nature 486, 215-221 (2012)

Lozupone C, Faust K, Raes J, Faith JJ, Frank DN, Zaneveld J, Gordon JI, Knight R. Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts. Genome Research 22, 1974-1984 (2012)

Faust K, van Helden J. Predicting Metabolic Pathways by Sub-network Extraction. Book chapter 7 in "Bacterial Molecular Networks", edited by van Helden, J., Toussaint A. and Thieffry, D., volume 804 in series "Methods in Molecular Biology" (2011)

Faust K, Croes D, van Helden J. Prediction of metabolic pathways from genome-scale metabolic networks. BioSystems, 105 (2), 109-121 (2011)

Faust K, Dupont P, Callut J, van Helden J. Pathway discovery in metabolic networks by subgraph extraction. Bioinformatics, 26 (9), 1211-1218 (2010)

Faust K, Croes D, van Helden J. In response to "Can sugars be produced from fatty acids? A test case for pathway analysis tools". Bioinformatics, 25 (23), 3202-3205 (2009)

Faust K, Croes D, van Helden J. Metabolic path finding using RPAIR annotation. Journal of Molecular Biology 388 (2), 390-414 (2009)

Brohée S, Faust K, Lima-Mendez G, Vanderstocken G, van Helden J. Network Analysis Tools: from biological networks to clusters and pathways. Nature protocols 3 (10), 1616-1629 (2008)

Brohée S, Faust K, Lima-Mendez G, Sand O, Janky R, Vanderstocken G, van Helden J. NeAT: A toolbox for the analysis of biological networks, clusters, classes and pathways. Nucleic Acids Research 36, W444-W451 (2008)

Lazarus D, Faust K, Popova-Goll I. New species of prunoid radiolarians from the Antarctic Neogene. Journal of Micropalaeontology, 24 (2), 97-121 (2005)

16-18th September 2019

Summer school on Microbial Community Modeling. Main organizer. Lecture: Introduction to qualitative metabolic modelling. Leuven, Belgium.

14-19 July 2019

Gordon Research Conference in Applied and Environmental Microbiology: Shaping the Earth's Microverse Invited oral presentation: "Emergent Behavior in a Synthetic Gut Community". Mount Holyoke College, USA.

20-24 June 2019

ASM Microbe 2019. Invited oral presentation: "Signatures of ecological processes in microbial community time series". San Francisco, USA.

26-30 May 2019

15th Symposium on Bacterial Genetics and Ecology. Invited oral presentation: "Mechanisms behind alternative community types (and how to distinguish them)". Lisbon, Portugal.

20-22 May 2019

Microbiome & Probiotics series: Europe. Invited oral presentation: "Insights from synthetic gut communities". Rotterdam, The Netherlands.

8th Feburary 2019

IB2 seminar. Invited oral presentation: "Emergent behaviour in a synthetic gut community". Brussels, Belgium.

4th February 2019

Aarhus University, Department of Bioscience. Invited oral presentation: "Principle, problems and applications of microbial network inference ". Aarhus, Danmark.

23-25th January 2019

Microbiota Data Analysis Workshop. Invited tutorial on: "Microbial network inference and analysis" (lecture and practicals, together with Lisa Röttjers). Zurich, Switzerland.

18th December 2018

Seminar at IBENS. Invited oral presentation: "Emergent behaviour in a synthetic gut community". Paris, France.

19th November 2018

Microbial Population Dynamics and Time Series Methods, Experiments and Data workshop. Invited oral presentation: "Signatures of ecological processes in microbial community time series." Ghent, Belgium.

10th October 2018

Seminar at C3BI at the Max Planck Institute for Plant Breeding Research (MPIPZ). Invited oral presentation: "From hairballs to hypotheses - what can we learn from microbial networks?" Cologne, Germany.

4th October 2018

Seminar at C3BI at the Pasteur Institute. Invited oral presentation: "Signatures of ecological processes in microbial community time series". Paris, France.

15-19th September 2018

ERS International Congress. Invited oral presentation: "What can we learn from microbial networks?" Paris, France.

12-17th August 2018

17th International Symposium on Microbial Ecology (ISME). Poster (418A): "Emergent behaviour in a synthetic gut community". Leipzig, Germany.

12th March 2018

Think tank: Host-microbiome research. Invited oral presentation: "Signatures of ecological processes in microbial community time series". Amsterdam, The Netherlands.

28th February-6th March 2018

Advanced Lecture Course on Systems Biology. Invited to contribute to the "Understanding Microbes" symposium, topic: "Microbial network inference and analysis". Innsbruck, Austria.

13-14th February 2018

The Netherlands Ecology Meeting. Co-organizer of session: " MICROBIAL ECOLOGY; Community composition and dynamics". Presentation: "Exploring the dynamics of a synthetic gut community". Lunteren, The Netherlands.

24th November 2017

Bangor University Seminar. Invited oral presentation: "From sequencing data to community structure: Network analysis of the TARA Oceans data". Bangor, UK.

11-13th September 2017

Summer school on ecological network inference and analysis. Main organizer. Microbial network inference tutorial. Leuven, Belgium.

6-11th August 2017

Ecological Society Annual Meeting. Invited oral presentation: "Multi-stability in host-associated microbial communities" Portland, US.

2nd June 2017

Journée Réseaux du GDR Génomique Environnementale. Keynote speaker: "On the origin of microbial community types." Nantes, France.

16th May 2017

Young Investigators Research Day. Keynote speaker: "Microbial Systems Biology." Kiel, Germany.

3rd May 2017

Pasteur Institute Seminars. Invited oral presentation: "Modelling the dynamics of a synthetic gut community." Paris, France.

13-17th March 2017

CIFAR-Gordon & Betty Moore Foundation Workshop: "Message in a bottle" - Chemical Symbiotic Interactions in the Oceans. Invited oral presentation: "From sequencing data to community structure: Network analysis of the TARA Oceans data." Eilat, Israel.

24-25th October 2016

Safety of Microbial Reprofiling Workshop. Invited oral presentation: "From microbial networks to community models." Bedford, UK.

4th September 2016

European Conference on Computational Biology (ECCB), Pre-Meeting on Recent Computational Advances in Metagenomics (RCAM). Keynote speaker: "Network inference meets metagenomics: challenges, tools and evaluations." Den Haag, The Netherlands.

17-18th March 2016

Applied Bioinformatics in Life Sciences. Poster: "Inference, analysis and validation of a marine plankton network." Leuven, Belgium.

8-11th March 2016

Visualizing Biological Data VIZBI 2016. Invited oral presentation: "Ecological network visualization." Heidelberg, Germany.

25-26th February 2016

Simons Foundation: First Workshop on Challenges in Microbiome Data Analysis. Invited oral presentation: "On the removal of environmentally driven microbial associations." New York, USA.

10-11th December 2015

Next Generation Sequencing Symposium. Invited oral presentation: "Inference, validation and analysis of marine planktonic interactions with the TARA Oceans data." Helsinki, Finland.

6th November 2015

Symposium: Ecology and evolution in microbial communities. Invited oral presentation: "Network science meets metagenomics: what can we learn from microbial association networks?" Lausanne, Switzerland.

12-17th July 2015

Gordon research conference: Ecological & Evolutionary Genomics. Invited oral presentation: "Network inference meets metagenomics: challenges, tools and applications." Biddeford, USA.

31st-2nd April 2015

5th International Human Microbiome Congress. Poster: "Time-varying network construction with CoNet". Luxembourg City, Luxembourg.

29th Jan 2015

8th Finnish Gut Day. Invited oral presentation: "Metagenomics Meets Network Inference - What Can We Learn From Microbial Networks?". Helsinki, Finland.

10-12th Nov 2014

Meta-Omics and Bioinformatics in Microbial Ecology workshop. Invited oral presentation: "Microbial Interactions: From Network to Models". Piracicaba, Brazil.

8-11th Sep 2014

3S Biology Summer School. Invited tutorial on: "Inference and analysis of microbial association networks" (2h). Trento, Italy. [URL]

24-30th August 2014

15th International Symposium on Microbial Ecology. Invited oral presentation: "Comparative analysis of co-occurrence networks across biomes". Seoul, South Korea.

2nd April 2014

Metagenomics Approaches and Data Analysis course. Invited session on microbial association network construction (3h). Nijmegen, The Netherlands. [URL]

19th March 2014

Seminar at the CUBE, University of Vienna. Invited oral presentation: "Inference of microbial association networks from metagenomic data - challenges, tools and results". Vienna, Austria.

9-10th Dec 2013

Benelux Bioinformatics Conference 2013. Poster: "Comparative Analysis of Biome-Specific Microbial Association Networks". Brussels, Belgium. [F1000]

22nd Nov 2013

IB2 seminar. Oral presentation: "Inference of microbial association networks from metagenomic data - challenges, tools and results". Brussels, Belgium.

4th October 2013

CMC Symposium 2013. Keynote speaker: "Microbial interactions: from networks to models". Copenhagen, Denmark.

26-29 June 2013

SocBiN 2013. Invited oral presentation: "Detection of microbial relationships from metagenomics data using network inference". Torun, Poland.

6-7 March 2013

Gordon & Betty Moore workshop on incorporating -omics data into models. Invited oral presentation: "Detecting microbial relationships using network inference techniques". Miami, USA.

5-6 Feb 2013

Netherlands Annual Ecology Meeting. Poster: "CoNet - a co-occurrence Network inference tool". Lunteren, The Netherlands. [pdf]

3-4 Dec 2012

Networks in Biodiversity Research Workshop. Invited oral presentation: "Detecting bacterial associations in the human microbiome". Berlin, Germany. [pdf]

7-12 October 2012

Bertinoro Computational Biology 2012. Invited oral presentation: "Detecting bacterial associations in the human microbiome". Bertinoro, Italy. [pdf]

19-24 August 2012

14th International Symposium on Microbial Ecology (ISME). Poster: "CoNet - a Co-occurrence Network inference tool". Copenhagen, Danmark. [pdf]

18-20 April 2012

VIB seminar. Oral presentation: "Microbial co-occurrence relationships in the human microbiome". Blankenberge, Belgium. [pdf]

28-30 March 2012

MICROME training workshop. Invited teacher for session: "Predicting operons, regulons and metabolic pathways from bacterial genomes". Marseille, France.

19-21 March 2012

International Human Microbiome Congress. Recipient of travel grant. Poster: "Prediction of microbial relationships from metagenomic data sets." Paris, France. [pdf]

12-13 Dec 2011

Benelux Bioinformatics Conference (BBC). Poster: "Prediction of bacterial relationships in the human microbiome." Luxembourg city, Luxembourg. [pdf]

9-13 March 2011

International Human Microbiome Congress. Poster: "From Parts Lists to Ecosystem Networks: Development of a 2nd Generation Toolkit for Meta-Omics Analysis." Vancouver, Canada. [pdf]

15 Oct 2010

Workshop: ICSB 2010 IOMPA. Oral presentation: "Predicting metabolic pathways from functionally linked genes." Edinburgh, UK. [pdf]

26-29 Sept 2010

European Conference of Computational Biology (ECCB) 2010. Chair of Technology Track session TT4-6. Poster: "Predicting metabolic pathways from bacterial operons and regulons." Gent, Belgium. [pdf]

26-30 Oct 2009

Workshop: "Metabolic Pathways Analysis 2009." Leiden, The Netherlands.

7-11 Sept 2009

Workshop: "Summer School on Metabolomics and Metabolic Networks." Leuven, Belgium.

15-16 Dec 2008

Benelux Bioinformatics Conference. Poster: "Discovery of metabolic pathways using graph algorithms." Maastricht, The Netherlands. [pdf]

13 Sept 2008

Machine Learning in Systems Biology (MLSB) Conference. Oral presentation: "Metabolic Pathway inference using Random Walks and Shortest-Paths Algorithms." Brussels, Belgium. [pdf]

14-21 June 2008

Summer School: "Biological Networks: Evolution, Interaction and Computation." Lipari, Italy.

12-13 Nov 2007

Benelux Bioinformatics Conference (BBC). Oral presentation: "Inference of pathways from metabolic networks by subgraph extraction." Leuven, Belgium. [pdf]

10-12 Sept 2007

Integrative Bioinformatics Workshop. Poster: "Improved metabolic path finding using RPAIR annotation." Gent, Belgium. [pdf]

7-11 May 2007

Workshop: "Complexity of Biological networks." Evry, France.

2014-current

seqtime - R package for the analysis of sequencing data time series and the simulation of community dynamics
http://hallucigenia-sparsa.github.io/seqtime/

2010-2015

CoNet - Cytoscape plugin for building co-occurrence networks
http://systemsbiology.vub.ac.be/conet/

2007-2008

Contribution to NeAT - Path finding and pathway extraction
http://embnet.ccg.unam.mx/rsa-tools/index_neat.html

Computer Science

Java:

• course: Programmation Java: advanced topics (Technofutur, 2007)
• course: Web applications: servlet & JSP (Technofutur, 2008)
• course: Enterprise Java Beans 3.0 (Technofutur, 2008)
• IDE: Eclipse

Other general purpose languages:

• Perl (intermediate)
• C++ (basic)

Statistical languages:

• R (good)
• Matlab (basic)

Good knowledge of HTML/CSS and PHP
Basic knowledge in bash, Latex and SQL
Experience with Windows, UNIX and Mac OS

Languages

English (good)

• Cambridge Certificate in Advanced English (2003, Grade A)
• TOEFL (2001, 233 out of 300 points)

French (good)

• Kamer voor Handel en Nijverheid van Brussel, Frans Module 3.2

Dutch (intermediate)

• Mobyus, Level 4 (B1)

Miscellaneous