selected publications
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academic article
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article
- A new class of IMP dehydrogenase with a role in self-resistance of mycophenolic acid producing fungi
- Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion
- Antibiotics-induced monodominance of a novel gut bacterial order
- Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks
- BioMet Toolbox: genome-wide analysis of metabolism
- Bioactivity assessment of natural compounds using machine learning models based on drug target similarity
- Bioactivity assessment of natural compounds using machine learning models trained on target similarity between drugs
- CRISPRi screens reveal genes modulating yeast growth in lignocellulose hydrolysate
- CRISPRi screens reveal genes modulating yeast growth in lignocellulose hydrolysate
- Computational tools for modeling xenometabolism of the human gut microbiota
- Conjugative transposition of the vancomycin resistance carrying Tn1549 : enzymatic requirements and target site preferences
- Contribution of Network Connectivity in Determining the Relationship between Gene Expression and Metabolite Concentration Changes
- Do genome-scale models need exact solvers or clearer standards?
- Draft Genome Sequence of Corynebacterium kefirresidentii SB, Isolated from Kefir.
- Draft Genome Sequences of Three Novel Low-Abundance Species Strains Isolated from Kefir Grain.
- Ecological modelling approaches for predicting emergent properties in microbial communities
- Emergence of stable coexistence in a complex microbial community through metabolic cooperation and spatio-temporal niche partitioning
- Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering
- Evolutionary programming as a platform for in silico metabolic engineering
- Extensive impact of non-antibiotic drugs on human gut bacteria.
- Fast automated reconstruction of genome-scale metabolic models for microbial species and communities
- Fast automated reconstruction of genome-scale metabolic models for microbial species and communities.
- Fluctuating Environment Can Negate Cheater Success Due to Speed-Agility Trade-Off
- Flux coupling and transcriptional regulation within the metabolic network of the photosynthetic bacterium Synechocystis sp PCC6803
- Freeing Yeast from Alcohol Addiction (Just) to Make (It) Fat Instead.
- Global transcriptional and physiological responses of Saccharomyces cerevisiae to ammonium, L-alanine, or L-glutamine limitation
- Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3
- Glycolytic flux-signaling controls mouse embryo mesoderm development
- Hap4 is not essential for activation of respiration at low specific growth rates in Saccharomyces cerevisiae
- Highly parallelized laboratory evolution of wine yeasts for enhanced metabolic phenotypes
- Identification of Metabolic Engineering Targets through Analysis of Optimal and Sub-Optimal Routes
- Impact of Stoichiometry Representation on Simulation of Genotype-Phenotype Relationships in Metabolic Networks
- Improved vanillin production in baker's yeast through in silico design
- Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory
- Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes
- Integration of metabolome data with metabolic networks reveals reporter reactions
- Involvement of a Natural Fusion of a Cytochrome P450 and a Hydrolase in Mycophenolic Acid Biosynthesis
- Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae.
- Metabolic Network Topology Reveals Transcriptional Regulatory Signatures of Type 2 Diabetes
- Metabolic anchor reactions for robust biorefining
- Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community.
- Metabolic dependencies drive species co-occurrence in diverse microbial communities.
- Metabolic interactions in microbial communities: untangling the Gordian knot.
- Metabolic memory underlying minimal residual disease in breast cancer
- Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes
- Metabolic shifts in residual breast cancer drive tumor recurrence
- Model-guided identification of gene deletion targets for metabolic engineering in Saccharomyces cerevisiae.
- Multimodal interactions of drugs, natural compounds and pollutants with the gut microbiota
- Multiplexed electron microscopy by fluorescent barcoding allows screening for ultrastructural phenotype
- Natural computation meta-heuristics for the in silico optimization of microbial strains
- Oncogenic memory underlying minimal residual disease in breast cancer
- Operation of a TCA cycle subnetwork in the mammalian nucleus
- OptFlux: an open-source software platform for in silico metabolic engineering
- Optimal fed-batch cultivation when mass transfer becomes limiting
- Overexpression of O-methyltransferase leads to improved vanillin production in baker's yeast only when complemented with model-guided network engineering
- PHUSER (Primer Help for USER): a novel tool for USER fusion primer design
- Polarization of microbial communities between competitive and cooperative metabolism
- Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours
- Proteomic characterization of extracellular vesicles produced by several wine yeast species
- Random sampling of elementary flux modes in large-scale metabolic networks
- Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium
- Saccharomyces cerevisiae metabolism in ecological context
- Single-cell transcriptomics identifies CD44 as a marker and regulator of endothelial to haematopoietic transition
- Systems Biology Perspectives on Minimal and Simpler Cells
- The metabolic background is a global player in Saccharomyces gene expression epistasis
- The metabolic response of heterotrophic Arabidopsis cells to oxidative stress
- Towards a mechanistic understanding of reciprocal drug–microbiome interactions
- Towards standards for human fecal sample processing in metagenomic studies.
- Uncovering transcriptional regulation of metabolism by using metabolic network topology
- Use of genome-scale microbial models for metabolic engineering
- Versatile Enzyme Expression and Characterization System for Aspergillus nidulans, with the Penicillium brevicompactum Polyketide Synthase Gene from the Mycophenolic Acid Gene Cluster as a Test Case
- Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow.
- Yeast metabolic chassis designs for diverse biotechnological products
- metaGEM: reconstruction of genome scale metabolic models directly from metagenomes