Publication
Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models
Publications associées (36)
Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities
Microorganisms are a key component in the chain of life. They are essential for agriculture, produce a large proportion of oxygen, and play a central role in the cycle of elements. Microorganisms are widely used in the production of food and alcoholic beve ...
EPFL2024The microbial genomics of glacier-fed streams: adaptations to an extreme ecosystem
Glacier-fed streams are the cold, ultra-oligotrophic, and unstable streams that are fed by glacial meltwater. Despite these extreme conditions, they harbour a diverse and abundant microbial diversity that develops into biofilms, covering the boulders and s ...
EPFL2024Modeling, analysis, and design of complex biological networks
Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...
EPFL2023Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics
We report a droplet microfluidic method to target and sort individual cells directly from complex microbiome samples and to prepare these cells for bulk whole-genome sequencing without cultivation. We characterize this approach by recovering bacteria spike ...
2022Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter
Christof Holliger, Julien Maillard, Aline Sondra Adler, Marco Pagni, Simon Marius Jean Poirier
Complete genomes can be recovered from metagenomes by assembling and binning DNA sequences into metagenome assembled genomes (MAGs). Yet, the presence of microdiversity can hamper the assembly and binning processes, possibly yielding chimeric, highly fragm ...
WILEY2022Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium
Rizlan Bernier-Latmani, Karin Lederballe Meibom, Karen Elda Viacava Romo, Nicolas Louis Maurice Jacquemin, Matthew Charles Reid, Jiangtao Qiao
Soil microbiomes harbor unparalleled functional and phylogenetic diversity and are sources of novel metabolisms. However, extracting isolates with a targeted function from complex microbiomes is not straightforward, particularly if the associated phenotype ...
2022Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater
Rizlan Bernier-Latmani, Emma Bell
While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provi ...
NATURE RESEARCH2021Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN
Vassily Hatzimanikatis, Meriç Ataman, Maria Masid Barcon
Altered metabolism is associated with many human diseases. Human genome-scale metabolic models (GEMs) were reconstructed within systems biology to study the biochemistry occurring in human cells. However, the complexity of these networks hinders a consiste ...
2020redLips: a comprehensive mechanistic model of the lipid metabolic network of yeast
Vassily Hatzimanikatis, Sofia Tsouka
Over the last decades, yeast has become a key model organism for the study of lipid biochemistry. Because the regulation of lipids has been closely linked to various physiopathologies, the study of these biomolecules could lead to new diagnostics and treat ...
OXFORD UNIV PRESS2020Optimization methods and objective functions for analysis of metabolic network models
Computational studies of metabolism aim to systematically analyze the metabolic behaviour of biological systems in different conditions. Genome-scale metabolic network models (GEMs) capture the connection between elements of the network by applying stoichi ...
EPFL2020