A5069227992- Gene Regulatory Network Analysis
- Microbial Metabolic Engineering and Bioproduction
- RNA and protein synthesis mechanisms
- Algal biology and biofuel production
- RNA modifications and cancer
- Mathematical Biology Tumor Growth
- Single-cell and spatial transcriptomics
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- Glioma Diagnosis and Treatment
- Metabolomics and Mass Spectrometry Studies
- Photosynthetic Processes and Mechanisms
- Evolution and Genetic Dynamics
- Wound Healing and Treatments
- Protein Structure and Dynamics
- Protein Degradation and Inhibitors
- Protist diversity and phylogeny
- Microbial Community Ecology and Physiology
- Tuberculosis Research and Epidemiology
- Bacterial Genetics and Biotechnology
- Multiple Myeloma Research and Treatments
- Computational Drug Discovery Methods
- Cancer, Hypoxia, and Metabolism
- Ecosystem dynamics and resilience
University of Iceland
2021-2025
Institute for Systems Biology
2015-2023
InSysBio (Russia)
2018
SIB Swiss Institute of Bioinformatics
2013
University of Zurich
2013
ETH Zurich
2013
Universitat Pompeu Fabra
2008-2010
Microalgae have reemerged as organisms of prime biotechnological interest due to their ability synthesize a suite valuable chemicals. To harness the capabilities these organisms, we need comprehensive systems-level understanding metabolism, which can be fundamentally achieved through large-scale mechanistic models metabolism. In this study, present revised and significantly improved genome-scale metabolic model for widely-studied microalga, Chlamydomonas reinhardtii. The model, iCre1355,...
Algae accumulate lipids to endure different kinds of environmental stresses including macronutrient starvation. Although this response has been extensively studied, an in depth understanding the transcriptional regulatory network (TRN) that controls transition into lipid accumulation remains elusive. In study, we used a systems biology approach elucidate program coordinates nitrogen starvation-induced metabolic readjustments drive Chlamydomonas reinhardtii.We demonstrate starvation triggered...
Abstract The fate of diatoms in future acidified oceans could have dramatic implications on marine ecosystems, because they account for ~40% primary production. Here, we quantify resilience Thalassiosira pseudonana mid-20th century (300 ppm CO 2 ) and (1000 conditions that cause ocean acidification, using a stress test probes its ability to recover from incrementally higher amount low-dose ultraviolet A (UVA) B (UVB) radiation re-initiate growth day–night cycles, limited by nitrogen. While...
Poor prognosis and drug resistance in glioblastoma (GBM) can result from cellular heterogeneity treatment-induced shifts phenotypic states of tumor cells, including dedifferentiation into glioma stem-like cells (GSCs). This rare tumorigenic cell subpopulation resists temozolomide, undergoes proneural-to-mesenchymal transition (PMT) to evade therapy, drives recurrence. Through inference transcriptional regulatory networks (TRNs) patient-derived GSCs (PD-GSCs) at single-cell resolution, we...
SARS-CoV-2 significantly impacts the human metabolome. This study aims to evaluate predictive capability of a comprehensive module clustering approach in plasma metabolomics for identifying risk critical complications COVID-19 patients admitted intensive care units (ICUs). We conducted prospective monocenter study, gathering blood samples within 24 h ICU admission, alongside clinical, biological, and demographic patient characteristics. Subsequently, we quantified patients' metabolome using...
Glioblastoma (GBM) is a heterogeneous tumor made up of cell states that evolve over time. Here, we modeled evolutionary trajectories during standard-of-care treatment using multi-omic single-cell analysis primary sample, corresponding mouse xenografts subjected to standard care therapy, and recurrent at autopsy. We mined the data with SYstems Genetics Network AnaLysis (scSYGNAL) identify network 52 regulators mediate treatment-induced shifts in xenograft tumor-cell were also reflected...
Managing trade-offs through gene regulation is believed to confer resilience a microbial community in fluctuating resource environment. To investigate this hypothesis, we imposed environment that required the sulfate-reducer Desulfovibrio vulgaris undergo repeated ecologically relevant shifts between retaining metabolic independence (active capacity for sulfate respiration) and becoming metabolically specialized mutualistic association with hydrogen-consuming Methanococcus maripaludis...
Disruption to endothelial cell homeostasis results in an extensive variety of human pathologies that are particularly relevant major trauma. Circulating catecholamines, such as adrenaline and noradrenaline, activate adrenergic receptors triggering a potent response function. The regulation the metabolism is distinct profoundly important endothelium homeostasis. However, precise catalogue metabolic alterations caused by sustained high catecholamine levels dysfunction still underexplored....
The scale of post-transcriptional regulation and the implications its interplay with other forms in environmental acclimation are underexplored for organisms domain
Melanoma cells frequently dedifferentiate in response to inflammation which can increase responses certain cytokines. Interferon-γ (IFNγ) is an integral part of the anti-tumor immune and directly induce both differentiational changes expression immunosuppressive proteins melanoma cells. How differentiation status affects IFNγ remains unclear.
Abstract Early evolution of mutualism is characterized by big and predictable adaptive changes, including the specialization interacting partners, such as through deleterious mutations in genes not required for metabolic cross-feeding. We sought to investigate whether these early improve cooperativity manifesting synergistic epistasis between genomes mutually species. Specifically, we have evolutionary trajectories syntrophic interactions Desulfovibrio vulgaris (Dv) with Methanococcus...
Summary Microbial populations can withstand, overcome and persist in the face of environmental fluctuation. Previously, we demonstrated how conditional gene regulation a fluctuating environment drives dilution condition‐specific transcripts, causing population Desulfovibrio vulgaris Hildenborough (DvH) to collapse after repeatedly transitioning from sulfate respiration syntrophic conditions with methanogen Methanococcus maripaludis . Failure DvH successfully transition contributed this model...
Adaptive prediction is a capability of diverse organisms, including microbes, to sense cue and prepare in advance deal with future environmental challenge. Here, we investigated the timeframe over which adaptive emerges when an organism encounters environment novel structure. We subjected yeast laboratory evolution repetitive, coupled exposures neutral chemical (caffeine), followed by sublethal dose toxin (5-FOA), interspersed requirement for uracil prototrophy counter-select mutants that...
When organisms encounter an unfavorable environment, they transition to a physiologically distinct, quiescent state wherein abundant transcripts from the previous active growth continue persist, albeit their transcription is downregulated. In order generate proteins for new physiological state, we hypothesized that translation machinery must selectively translate upregulated in intracellular milieu crowded with considerably higher abundance state. Here, have analyzed genome-wide changes...
Mesenchymal stromal cells (MSCs) are multipotent post-natal stem with applications in tissue engineering and regenerative medicine. MSCs can differentiate into osteoblasts, chondrocytes, or adipocytes, functional differences during osteogenesis accompanied by metabolic changes. The temporal dynamics of these shifts have not yet been fully characterized suspected to be important for therapeutic such as optimization. Here, our goal was characterize the that occur osteogenesis. We profiled five...
Abstract Motivation: A common problem in understanding a biochemical system is to infer its correct structure or topology. This topology consists of all relevant state variables—usually molecules and their interactions. Here we present method called topological augmentation this statistically rigorous systematic way from prior knowledge experimental data. Results: Topological starts simple model that unable explain the data augments by adding new terms capture behavior. process guided...
Abstract Despite recent advancements in the treatment of multiple myeloma (MM), nearly all patients ultimately relapse and many become refractory to lines therapies. Therefore, we not only need ability predict which are at high risk for disease progression but also a means understand mechanisms underlying their risk. Here, report transcriptional regulatory network (TRN) MM inferred from cross-sectional multi-omics data 881 that predicts how 124 chromosomal abnormalities somatic mutations...
The ability of Mycobacterium tuberculosis (Mtb) to adopt heterogeneous physiological states underlies its success in evading the immune system and tolerating antibiotic killing. Drug tolerant phenotypes are a major reason why (TB) mortality rate is so high, with over 1.8 million deaths annually. To develop new TB therapeutics that better treat infection (faster more completely), systems-level approach needed reveal complexity network-based adaptations Mtb. Here, we report predictive model...
Data-Independent Acquisition (DIA) is a mass spectrometry-based method to reliably identify and reproducibly quantify large fractions of target proteome. The peptide-centric data analysis strategy employed in DIA requires priori generated spectral assay libraries. Such libraries allow extract quantitative targeted approach have been for human, mouse, zebrafish, E. coli few other organisms. However, library the extreme halophilic archaeon Halobacterium salinarum NRC-1, model organism that...
Various molecular interaction networks have been claimed to follow power-law decay for their global connectivity distribution. It has proposed that there may be underlying generative models explain this heavy-tailed behavior by self-reinforcement processes such as classical or hierarchical scale-free network models. Here, we analyze a comprehensive data set of protein-protein and transcriptional regulatory in yeast, an Escherichia coli metabolic network, gene activity profiles different...
Burn wound healing is a complex process orchestrated through successive biochemical events that span from weeks to months depending on the depth of wound. Here, we report an untargeted metabolomics discovery approach capture metabolic changes during deep partial-thickness (DPT) and full-thickness (FT) burn wounds in porcine model. The could be described with six seven distinct trajectories for DPT FT wounds, respectively. Arginine histidine metabolism were most affected pathways healing,...
Abstract The ability of Mycobacterium tuberculosis (Mtb) to adopt heterogeneous physiological states, underlies its success in evading the immune system and tolerating antibiotic killing. Drug tolerant phenotypes are a major reason why (TB) mortality rate is so high, with over 1.8 million deaths annually. To develop new TB therapeutics that better treat infection (faster more completely), systems-level approach needed reveal complexity network-based adaptations Mtb. Here, we report...