8 documents found, page 1 of 1
Ecological dynamics of Enterobacteriaceae in the human gut microbiome across gl...
Yin, Qi; da Silva, Ana C.; Zorrilla, Francisco; Almeida, Ana S.; Patil, Kiran R.; Almeida, AlexandreGut bacteria from the Enterobacteriaceae family are a major cause of opportunistic infections worldwide. Given their prevalence among healthy human gut microbiomes, interspecies interactions may play a role in modulating infection resistance. Here we uncover global ecological patterns linked to Enterobacteriaceae colonization and abundance by leveraging a large-scale dataset of 12,238 public human gut metagenom...
Ecological modelling approaches for predicting emergent properties in microbial...
Berg, Naomi Iris van den; Machado, Daniel; Santos, Sophia Torres; Rocha, I.; Chacón, Jeremy; Harcombe, William; Mitri, Sara; Patil, Kiran R.Recent studies have brought forward the critical role of emergent properties in shaping microbial communities and the ecosystems of which they are a part. Emergent properties---patterns or functions that cannot be deduced linearly from the properties of the constituent parts---underlie important ecological characteristics such as resilience, niche expansion and spatial self-organization. While it is clear that ...
MEMOTE for standardized genome-scale metabolic model testing
Lieven, Christian; Beber, Moritz E.; Olivier, Brett G.; Bergmann, Frank T.; Ataman, Meric; Babaei, Parizad; Bartell, Jennifer A.; Blank, Lars M.Reconstructing metabolic reaction networks enables the development of testable hypotheses of an organisms metabolism under different conditions1. State-of-the-art genome-scale metabolic models (GEMs) can include thousands of metabolites and reactions that are assigned to subcellular locations. Geneproteinreaction (GPR) rules and annotations using database information can add meta-information to GEMs. GEMs with ...
Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing
Lieven, Christian; Beber, Moritz E.; Olivier, Brett G.; Bergmann, Frank T.; Ataman, Meric; Babaei, Parizad; Bartell, Jennifer A.; Blank, Lars M.An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Yeast chassis design for dicarboxylic acids production
Pereira, Filipa; Lopes, Helder; Maia, Paulo; Meyer, Britta; Konstantinidis, Dimitrios; Kafkia, Eleni; Kötter, Peter; Rocha, I.; Patil, Kiran R.
In silico design of Saccharomyces cerevisiae strains for production of industri...
Lopes, H.; Silva, P.; Patil, Kiran R.; Rocha, I.Saccharomyces cerevisiae is one of the most widely used cell factories in industrial biotechnology. However, the development of optimized yeast strains for the production of novel compounds is a costly and time-consuming process, mainly due to the unavailability of suitable chassis cells. This work was developed under the scope of the ERA-IB DeYeastLibrary project and aimed to design in silico pre-optimized str...
In silico modular design of Saccharomyces cerevisiae strains for enhanced produ...
Lopes, H.; Maia, Paulo; Patil, Kiran R.; Rocha, I.
Optflux: an open-source software platform for in silico metabolic engineering
Rocha, I.; Maia, Paulo; Evangelista, P.; Vilaça, P.; Simão Soares; Pinto, José P.; Rocha, Miguel; Nielsen, Jens; Patil, Kiran R.[Excerpt] OptFlux is an open-source, user-friendly and modular software aimed at being the reference computational tool for Metabolic Engineering (ME) applications. It allows the use of stoichiometric metabolic models for phenotype simulation and strain optimization purposes. Many different approaches have been used to aid in metabolic engineering efforts that take available models of metabolism together with m...