Publications


Find publications on Google Scholar.
2018

Röttjers L and Faust K
Can we predict keystones?
Nature Reviews Microbiology, Accepted (Correspondence) (Nature Reviews Microbiology)
Original article by Banerjee and colleagues here
Reply by Banerjee and colleagues here

Faust K
Microbial Consortium Design Benefits from Metabolic Modeling
TIBTECH, Accepted (Spotlight) (ScienceDirect)
Original article by Xu and colleagues here

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 (Gut)

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, Accepted (eLife)

Röttjers L and Faust K
From hairballs to hypotheses - biological insights from microbial networks
FEMS Microbiology Reviews, Accepted (Oxford Academic)

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, Accepted (The ISME Journal)

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

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, Accepted (BMC)

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, Accepted (PLoS ONE)

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

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 (ScienceDirect)

2017

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

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 (ScienceDirect)

2016

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 (Wiley)

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

Faust K and Raes J
Host-microbe interaction: Rules of the game for microbiota.
Nature 534, 182-183 (News & Views) (Nature)
Original article by Bashan and colleagues here

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 (Wiley)

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 40, 686-700 (pubmed)

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) (Science)

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) (pubmed)

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) (The ISME Journal)

2015

Edwards RA, McNair K, Faust K, Raes J, Dutilh B
Computational approaches to predict bacteriophage-host relationships.
FEMS Microbiology Reviews 40, 258-272 Editor's choice (pubmed)

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 (Frontiers in Microbiology)

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) (Science)

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) (ScienceDirect)

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) (Wiley)

2013

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.
The ISME Journal 7, 1678-1695 (2013) (The ISME Journal)

2012

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

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) (PLoS Computational Biology)

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

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

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) (Genome Research)

2011

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

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

2010

Faust K
Doctoral thesis
Development, assessment and application of bioinformatics tools for the extraction of pathways from metabolic networks (pdf)

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

2009

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) (Pubmed)

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

2008

Faust K, Callut J, Dupont P, van Helden J.
Inference of pathways from metabolic networks by subgraph extraction
Proceedings of the second International Workshop on Machine Learning in Systems Biology 2008. (pdf)

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). (Pubmed)

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

2005

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

+: co-corresponding author
*: co-first/co-last author