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Model-guided Engineering of Complex Microbial Communities

Publications

metaGEM: reconstruction of genome scale metabolic models directly from metagenomes

Author(s): Francisco Zorrilla, Filip Buric, Kiran R Patil, Aleksej Zelezniak
Published in: Nucleic Acids Research, 2021, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab815

Unravelling metabolic cross‐feeding in a yeast–bacteria community using <scp> <sup>13</sup> C </scp> ‐based proteomics

Author(s): Natalia Gabrielli; Christoniki Maga‐Nteve; Eleni Kafkia; Mandy Rettel; Jakob Loeffler; Stephan Kamrad; Athanasios Typas; Kiran Raosaheb Patil
Published in: Molecular Systems Biology, Issue 1, 2023, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.202211501

Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion

Author(s): Dimitrios Konstantinidis; Filipa Pereira; Eva‐Maria Geissen; Kristina Grkovska; Eleni Kafkia; Paula Jouhten; Yongkyu Kim; Saravanan Devendran; Michael Zimmermann; Kiran Raosaheb Patil
Published in: Molecular Systems Biology, Issue 17:e10189, 2021, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.202010189

Predictive evolution of metabolic phenotypes using model-designed environments

Author(s): Jouhten, Paula; Konstantinidis, Dimitrios; Pereira, Filipa; Andrejev, Sergej; Grkovska, Kristina; Castillo, Sandra; Ghiachi, Payam; Beltran, Gemma; Almaas, Eivind; Mas, Albert; Warringer, Jonas; Gonzalez, Ramon; Morales, Pilar; Patil, Kiran R.; 0000-0003-1075-7448; 0000-0002-9125-326X; 0000-0002-0763-1679; 0000-0001-6144-2740; 0000-0002-0130-6111; 0000-0002-6166-8640
Published in: Molecular Systems Biology, Issue 2, 2022, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.202210980

Ecological modelling approaches for predicting emergent properties in microbial communities

Author(s): Naomi Iris van den Berg, Daniel Machado, Sophia Santos, Isabel Rocha, Jeremy Chacón, William Harcombe, Sara Mitri & Kiran R. Patil
Published in: Nature Ecology and Evolution, 2022, ISSN 2397-334X
Publisher: Springer Nature
DOI: 10.1038/s41559-022-01746-7

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