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Ecosystem in a box: Dissecting the dynamics of a defined microbial community in vitro

Deliverables

Data Management Plan

Compilation of the Open Research Data Management Plan

Publications

Single-Cell Analysis and Metabolic Modelling of Pairwise Interactions in the Gut Microbiome

Author(s): Clémence Joseph
Published in: 2023
Publisher: KU Leuven

Towards a microbial network inference and analysis platform

Author(s): Lisa Röttjers
Published in: 2021
Publisher: KU Leuven

Predicting microbial interactions with approaches based on flux balance analysis: an evaluation

Author(s): Clémence Joseph, Haris Zafeiropoulos, Kristel Bernaerts and Karoline Faust
Published in: BMC Bioinformatics, 2024, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-024-05651-7

Fast quantification of gut bacterial species in cocultures using flow cytometry and supervised classification

Author(s): Charlotte C. van de Velde, Clémence Joseph, Anaïs Biclot, Geert R. B. Huys, Vitor B. Pinheiro, Kristel Bernaerts, Jeroen Raes and Karoline Faust
Published in: ISME Communications, 2022, ISSN 2730-6151
Publisher: Springer
DOI: 10.1038/s43705-022-00123-6

Starvation responses impact interaction dynamics of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis

Author(s): Bin Liu, Daniel Rios Garza, Didier Gonze, Anna Krzynowek, Kenneth Simoens, Kristel Bernaerts, Annelies Geirnaert, Karoline Faust
Published in: The ISME Journal, 2023, ISSN 1751-7362
Publisher: Nature Publishing Group
DOI: 10.1038/s41396-023-01501-1

Metabolic models of human gut microbiota: Advances and challenges

Author(s): Daniel Rios Garza, Didier Gonze, Haris Zafeiropoulos, Bin Liu, Karoline Faust
Published in: Cell Systems, 2023, ISSN 2405-4712
Publisher: Elsevier
DOI: 10.1016/j.cels.2022.11.002

Fast and flexible analysis of linked microbiome data with mako

Author(s): Lisa Röttjers, Karoline Faust
Published in: Nature Methods, 2022, Page(s) 51-54, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-021-01335-9

Null-model-based network comparison reveals core associations

Author(s): Lisa Röttjers, Doris Vandeputte, Jeroen Raes, Karoline Faust
Published in: ISME Communications, Issue 1/1, 2021, ISSN 2730-6151
Publisher: Springer Nature
DOI: 10.1038/s43705-021-00036-w

manta: a Clustering Algorithm for Weighted Ecological Networks

Author(s): Lisa Röttjers, Karoline Faust
Published in: mSystems, Issue 5/1, 2020, ISSN 2379-5077
Publisher: Scientific Society Publisher Alliance
DOI: 10.1128/msystems.00903-19

Synthetic ecology of the human gut microbiota

Author(s): Gino Vrancken, Ann C. Gregory, Geert R. B. Huys, Karoline Faust, Jeroen Raes
Published in: Nature Reviews Microbiology, Issue 17/12, 2019, Page(s) 754-763, ISSN 1740-1526
Publisher: Nature Publishing Group
DOI: 10.1038/s41579-019-0264-8

Towards a Better Understanding of Microbial Community Dynamics through High-Throughput Cultivation and Data Integration

Author(s): Karoline Faust
Published in: mSystems, Issue 4/3, 2019, ISSN 2379-5077
Publisher: mSystems
DOI: 10.1128/msystems.00101-19

miaSim: an R/Bioconductor package to easily simulate microbial community dynamics

Author(s): Yu Gao, Yağmur Şimşek, Emma Gheysen, Tuomas Borman, Yi Li, Leo Lahti, Karoline Faust, Daniel Rios Garza
Published in: Methods in Ecology and Evolution, 2023, ISSN 2041-210X
Publisher: John Wiley and Sons Inc.
DOI: 10.1111/2041-210x.14129

Open challenges for microbial network construction and analysis

Author(s): Karoline Faust
Published in: The ISME Journal, 2021, ISSN 1751-7362
Publisher: Nature Publishing Group
DOI: 10.1038/s41396-021-01027-4

Technical versus biological variability in a synthetic human gut community

Author(s): van de Velde C, Joseph C, Simoens K, Raes J, Bernaerts K and Faust K
Published in: Gut Microbes, 2023, ISSN 1949-0976
Publisher: Landes Bioscience
DOI: 10.1080/19490976.2022.2155019

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