A5009011251- Microbial Metabolic Engineering and Bioproduction
- Biofuel production and bioconversion
- Bioinformatics and Genomic Networks
- Fungal and yeast genetics research
- Health, Environment, Cognitive Aging
- Enzyme Catalysis and Immobilization
- Gene Regulatory Network Analysis
- Advanced Proteomics Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Viral Infectious Diseases and Gene Expression in Insects
- Mass Spectrometry Techniques and Applications
- Fermentation and Sensory Analysis
- Microbial Natural Products and Biosynthesis
- Process Optimization and Integration
- Photosynthetic Processes and Mechanisms
- Inorganic Fluorides and Related Compounds
- Plant biochemistry and biosynthesis
Chalmers University of Technology
2018-2025
Novo Nordisk Foundation
2019
Foundation Center
2019
An open-source, genome-scale human metabolic model and a web portal to explore the are generated.
RAVEN is a commonly used MATLAB toolbox for genome-scale metabolic model (GEM) reconstruction, curation and constraint-based modelling simulation. Here we present Toolbox 2.0 with major enhancements, including: (i) de novo reconstruction of GEMs based on the MetaCyc pathway database; (ii) redesigned KEGG-based pipeline; (iii) convergence reconstructions from various sources; (iv) improved performance, usability, compatibility COBRA Toolbox. Capabilities are here illustrated through...
Abstract Genome-scale metabolic models (GEMs) represent extensive knowledgebases that provide a platform for model simulations and integrative analysis of omics data. This study introduces Yeast8 an associated ecosystem comprehensive computational resource performing the metabolism Saccharomyces cerevisiae ––an important organism widely used cell-factory. tracks community development with version control, setting standard how GEMs can be continuously updated in simple reproducible way. We...
Abstract Genome-scale metabolic models (GEMs) have been widely used for quantitative exploration of the relation between genotype and phenotype. Streamlined integration enzyme constraints proteomics data into such was first enabled by GECKO toolbox, allowing study phenotypes constrained protein limitations. Here, we upgrade toolbox in order to enhance with any organism a compatible GEM reconstruction. With this, enzyme-constrained budding yeasts Saccharomyces cerevisiae , Yarrowia lipolytica...
Heme is an oxygen carrier and a cofactor of both industrial enzymes food additives. The intracellular level free heme low, which limits the synthesis proteins. Therefore, increasing allows increased production Using genome-scale metabolic model (GEM) Yeast8 for yeast Saccharomyces cerevisiae , we identified fluxes potentially important to synthesis. With this model, in silico simulations highlighted 84 gene targets balancing biomass production. Of those identified, 76 genes were individually...
Yeasts are known to have versatile metabolic traits, while how these traits evolved has not been elucidated systematically. We performed integrative evolution analysis investigate genomic determines trait generation by reconstructing genome-scale models (GEMs) for 332 yeasts. These GEMs could comprehensively characterize diversity and predict enzyme functionality, thereby signifying that sequence-level shaped reaction networks towards new functions. Strikingly, using GEMs, we can...
Development of efficient cell factories that can compete with traditional chemical production processes is complex and generally driven by case-specific strategies, based on the product microbial host interest. Despite major advancements in field metabolic modeling recent years, prediction genetic modifications for increased remains challenging. Here, we present a computational pipeline leverages concept protein limitations metabolism optimal combinations gene engineering targets enhanced...
Abstract RAVEN is a commonly used MATLAB toolbox for genome-scale metabolic model (GEM) reconstruction, curation and constraint-based modelling simulation. Here we present Toolbox 2.0 with major enhancements, including: (i) de novo reconstruction of GEMs based on the MetaCyc pathway database; (ii) redesigned KEGG-based pipeline; (iii) convergence reconstructions from various sources; (iv) improved performance, usability, compatibility COBRA Toolbox. Capabilities are here illustrated through...
Abstract The Saccharomycotina subphylum (budding yeasts) spans 400 million years of evolution and includes species that thrive in diverse environments. To study niche-adaptation, we identify changes gene expression three divergent yeasts grown the presence various stressors. Duplicated non-conserved genes are significantly more likely to respond stress than conserved as single-copy orthologs. Next, develop a sorting method considers evolutionary origin duplication timing assign an age each...
Abstract Genome-scale metabolic models (GEMs) have been widely used for quantitative exploration of the relation between genotype and phenotype. Streamlined integration enzyme constraints proteomics data into GEMs was first enabled by GECKO method, allowing study phenotypes constrained protein limitations. Here, we upgraded toolbox in order to enhance with any organism an available GEM reconstruction. With this, enzyme-constrained (ecModels) budding yeasts Saccharomyces cerevisiae, Yarrowia...
The interplay between nutrient-induced signaling and metabolism plays an important role in maintaining homeostasis its malfunction has been implicated many different human diseases such as obesity, type 2 diabetes, cancer, neurological disorders. Therefore, unraveling the of nutrients molecules metabolites together with their interconnectivity may provide a deeper understanding how these conditions occur. Both have extensively studied using various systems biology approaches. However, they...
Protein quantification via label-free mass spectrometry (MS) has become an increasingly popular method for predicting genome-wide absolute protein abundances. A known caveat of this approach, however, is the poor technical reproducibility, that is, how consistent predictions are when same sample measured repeatedly. Here, we proteomics data Saccharomyces cerevisiae with both biological and inter-batch triplicates, to analyze accuracy precision MS. Moreover, analyzed these metrics vary...
Abstract Development of efficient cell factories that can compete with traditional chemical production processes is complex and generally driven by case-specific strategies, based on the product microbial host interest. Despite major advancements in field metabolic modelling recent years, prediction genetic modifications for increased remains challenging. Here we present a computational pipeline leverages concept protein limitations metabolism optimal combinations gene engineering targets...
Metabolic network reconstructions have become an important tool for probing cellular metabolism in the field of systems biology. They are used as tools quantitative prediction but also scaffolds further knowledge contextualization. The yeast Saccharomyces cerevisiae was one first organisms which a genome-scale metabolic model (GEM) reconstructed, 2003, and since then 45 models been developed wide variety relevant yeasts species. A systematic evaluation these revealed that-despite this long...
It is important to understand the basis of thermotolerance in yeasts broaden their application industrial biotechnology. The capacity run bioprocesses at temperatures above 40 °C great interest but this beyond growth range most commonly used yeast species. In contrast, some such as Kluyveromyces marxianus can grow 45 or higher. Such species are valuable for direct use biotechnology and a vehicle study genetic physiological thermotolerance. previous work, we reported that evolutionarily young...
Abstract Genome-scale metabolic models (GEMs) have been widely used for quantitative exploration of the relation between genotype and phenotype. Streamlined integration enzyme constraints proteomics data into GEMs was first enabled by GECKO method, allowing study phenotypes constrained protein limitations. Here, we upgraded toolbox in order to enhance with any organism an available GEM reconstruction. With this, enzyme-constrained (ecModels) budding yeasts Saccharomyces cerevisiae , Yarrowia...
Abstract The Saccharomycotina subphylum (budding yeasts) spans more than 400 million years of evolution and includes species that thrive in many Earth’s harsh environments. Characterizing grow conditions could enable the design robust yeast strains for biotechnology. However, tolerance to stressful is a multifactorial response, which difficult understand since genes involved are as yet uncharacterized. In this work, three divergent were grown under multiple identify stress-induced genes. For...
Converting industrial side streams into value-added chemicals using microbial cell factories is of increasing interest, as such processes offer solutions to reduce waste and production costs. However, developing new, efficient for precision fermentation remains challenging due limited knowledge about their metabolic capabilities. Here, we investigate the lactose galactose metabolism non-conventional yeast Sungouiella intermedia (formerly Candida intermedia), knowledge-matching high-quality...
Abstract Protein quantification via label-free mass spectrometry (MS) has become an increasingly popular method for determining genome-wide absolute protein abundances. A known caveat of this approach is the poor technical reproducibility, i.e. how consistent estimations are when same sample measured repeatedly. Here, we proteomics data Saccharomyces cerevisiae with both biological and inter-batch triplicates, to analyze accuracy precision MS. Moreover, analyzed these metrics vary applying...
Abstract The interplay between nutrient-induced signaling and metabolism plays an important role in maintaining homeostasis its malfunction has been implicated many different human diseases such as obesity, type 2 diabetes, cancer neurological disorders. Therefore, unravelling the of nutrients molecules metabolites well their interconnectivity may provide a deeper understanding how these conditions occur. Both signalling have extensively studied using various systems biology approaches....
Abstract Development of efficient cell factories that can compete with traditional chemical production processes is complex and generally driven by case-specific strategies, based on the product microbial host interest. Despite major advancements in field metabolic modelling recent years, prediction genetic modifications for increased remains challenging. Here we present a computational pipeline leverages concept protein limitations metabolism optimal combinations gene engineering targets...