Functional genomics of Plasmodium falciparum using metabolic modelling and analysis

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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 ...

Microorganisms are essential for life on Earth, performing key roles in numerous biological processes. Their influence extends across a wide spectrum, from human health and ecological balance to advancements in biotechnology and industrial applications. Th ...

Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint ...

BackgroundIt is generally accepted that most evolutionary transformations at the phenotype level are associated either with rearrangements of genomic regulatory elements, which control the activity of gene networks, or with changes in the amino acid conten ...

Infectious diseases continue to pose a substantial burden on global populations, requiring innovative broad-spectrum prophylactic and treatment alternatives. Here, we have designed modular synthetic polymer nanopartides that mimic functional components of ...

All cells need to be able to sense their environment, and adapt their metabolism, growth and cell division appropriately. In this study, I examined the response of Schizosaccharomyces pombe to a change in the carbon source and how that affects cytokinesis. ...

The discovery of a drug requires over a decade of intensive research and financial investments – and still has a high risk of failure. To reduce this burden, we developed the NICEdrug.ch resource, which incorporates 250,000 bioactive molecules, and studied ...

Modelling and analysis of biological systems is crucial in order to quantitatively explain and predict their behaviour. The importance of modelling in systems biology becomes even more evident when tackling complex, large systems. Approaches that rely on ...

In a context of rapid global change, one of the key components for the survival of species is their genetic evolutionary potential for adaptation. Many methods have been developed to identify genetic variants underpinning adaptation to climate, but few too ...

Advances in single-cell genomics now enable large-scale comparisons of cell states across two or more experimental conditions. Numerous statistical tools are available to identify individual genes, proteins or chromatin regions that differ between conditio ...

Organoids allow the recapitulation of intestinal homeostasis and cancerogenesis in vitro; however, RNA sequencing (RNA-seq)-based methods for drug screens are missing. We develop targeted organoid sequencing (TORNADO-seq), a high-throughput, high-content d ...

The advancements in genome editing techniques over the past years have rekindled interest in rational metabolic engineering strategies. While Metabolic Control Analysis (MCA) is a well-established method for quantifying the effects of metabolic engineering ...

Author summary During development, enhancer sequences tightly regulate the spatio-temporal expression of target genes often located hundreds of kilobases away. This complex process is made possible by the folding of chromatin into domains, which are separa ...

Neuroscience incorporates knowledge from a range of scales, from single molecules to brain wide neural networks. Modeling is a valuable tool in understanding processes at a single scale or the interactions between two adjacent scales and researchers use a ...

Epstein–Barr virus (EBV) is one of the most common viruses latently infecting humans. Little is known about the impact of human genetic variation on the large inter-individual differences observed in response to EBV infection. To search for a potential imp ...

It was recently demonstrated that nonpersistent radicals can be generated in frozen solutions of metabolites such as pyruvate by irradiation with UV light, enabling radical-free dissolution dynamic nuclear polarization. Although pyruvate is endogenous, the ...

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 ...

The Eukaryotic Promoter Database (EPD), available online at https://epd.epfl.ch, provides accurate transcription start site (TSS) information for promoters of 15 model organisms plus corresponding functional genomics data that can be viewed in a genome bro ...

Background Low-density (LD)Plasmodiuminfections are missed by standard malaria rapid diagnostic tests (standard mRDT) when the blood antigen concentration is below the detection threshold. The clinical impact of these LD infections is unknown. This study i ...

MORN (Membrane Occupation and Recognition Nexus) repeat proteins have a wide taxonomic distribution, being found in both prokaryotes and eukaryotes. Despite this ubiquity, they remain poorly characterised at both a structural and a functional level compare ...

Functional genomics of Plasmodium falciparum using metabolic modelling and analysis

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Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities

Optimality principles for the analysis of biological processes across scales: From enzyme kinetics to microbiome dynamics

Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN

Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

Potent Virustatic Polymer-Lipid Nanomimics Block Viral Entry and Inhibit Malaria Parasites In Vivo

Metabolic regulation of cytokinesis in Schizosaccharomyces pombe

NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism

Modelling the Intracellular Environment under Uncertainty, from Post-translational Modification to Metabolic Networks

Spatial areas of genotype probability: Predicting the spatial distribution of adaptive genetic variants under future climatic conditions

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High-content, targeted RNA-seq screening in organoids for drug discovery in colorectal cancer

Constraint-based metabolic control analysis for rational strain engineering

Induction of a chromatin boundary in vivo upon insertion of a tad border

A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience

The influence of human genetic variation on Epstein–Barr virus sequence diversity

Radical-free hyperpolarized MRI using endogenously occurring pyruvate analogues and UV-induced nonpersistent radicals

Optimization methods and objective functions for analysis of metabolic network models

EPD in 2020: enhanced data visualization and extension to ncRNA promoters

Clinical relevance of low-densityPlasmodium falciparumparasitemia in untreated febrile children: A cohort study

Structures of three MORN repeat proteins and a re-evaluation of the proposed lipid-binding properties of MORN repeats