A5090227920- Single-cell and spatial transcriptomics
- Bioinformatics and Genomic Networks
- Microbial Metabolic Engineering and Bioproduction
- Cancer, Hypoxia, and Metabolism
- Gene Regulatory Network Analysis
- Gene expression and cancer classification
- Nitric Oxide and Endothelin Effects
- Metabolomics and Mass Spectrometry Studies
- Endoplasmic Reticulum Stress and Disease
- Machine Learning in Bioinformatics
- Health, Environment, Cognitive Aging
- Cancer Genomics and Diagnostics
- T-cell and B-cell Immunology
- Radiomics and Machine Learning in Medical Imaging
- Viral Infectious Diseases and Gene Expression in Insects
- Cancer-related Molecular Pathways
- Molecular Biology Techniques and Applications
- Neurobiology and Insect Physiology Research
- Bacterial Genetics and Biotechnology
- CRISPR and Genetic Engineering
- Neutrophil, Myeloperoxidase and Oxidative Mechanisms
- Redox biology and oxidative stress
- Free Radicals and Antioxidants
- Neural dynamics and brain function
- Hemoglobin structure and function
Chalmers University of Technology
2016-2024
BioInnovation Institute
2022-2024
Science for Life Laboratory
2020-2022
Princeton University
2013-2018
University of Kentucky
2015
Morehead State University
2015
Colorado State University
2009-2010
University of Pennsylvania
2006-2007
Royal Albert Edward Infirmary
2007
A database provides information on the relative abundances and locations of human proteins that are predicted to be secreted.
An open-source, genome-scale human metabolic model and a web portal to explore the are generated.
Genome-scale metabolic models (GEMs) are used extensively for analysis of mechanisms underlying human diseases and malfunctions. However, the lack comprehensive high-quality GEMs model organisms restricts translational utilization omics data accumulating from use various disease models. Here we present a unified platform that covers five major animals, including Mouse1 (Mus musculus), Rat1 (Rattus norvegicus), Zebrafish1 (Danio rerio), Fruitfly1 (Drosophila melanogaster), Worm1...
Triple negative breast cancer (TNBC) metastases are assumed to exhibit similar functions in different organs as the original primary tumor. However, studies of metastasis often limited a comparison metastatic tumors with their origin, and little is known about adaptation local environment sites. We therefore used transcriptomic data metabolic network analyses investigate whether adapt metabolism site found that adopt signature some similarity destinations. The extent adaptation, however,...
Single-cell RNA sequencing combined with genome-scale metabolic models (GEMs) has the potential to unravel differences in metabolism across both cell types and states but requires new computational methods. Here, we present a method for generating cell-type-specific from clusters of single-cell RNA-Seq profiles. Specifically, developed estimate minimum number cells required pool obtain stable models, bootstrapping strategy estimating statistical inference, faster version task-driven...
Novel therapies are undergoing clinical trials, for example, the Hsp90 inhibitor, XL888, in combination with BRAF inhibitors treatment of therapy-resistant melanomas. Unfortunately, our data show that this elicits a heterogeneous response panel melanoma cell lines including PDX-derived models. We sought to understand mechanisms underlying differential responses and suggest patient stratification strategy. Thermal proteome profiling (TPP) identified protein targets XL888 pair sensitive...
•Simplified application of enzyme usage constraints to genome-scale metabolic models with the software GECKO Light.•Estimation maximum metabolite influx into tumors at varying levels hypoxia.•Simulations tumor metabolism explain "glutamine addiction" in cancers.•Metabolic collaboration between cell types microenvironment does not increase growth. The is composed a complex mixture different interacting under conditions nutrient deprivation, but therein fully understood due difficulties...
The energy metabolism of the brain is poorly understood partly due to complex morphology neurons and fluctuations in ATP demand over time. To investigate this, we used metabolic models that estimate enzyme usage per pathway, utilization time, transportation evaluate how these parameters processes affect costs for synthesis transportation. Our show total maintenance expenditure human body depends on glycolysis mitochondrial respiration are distributed both across within cell types brain. We...
Nitric oxide (NO•) is generated by the innate immune response to neutralize pathogens. NO• and its autoxidation products have an extensive biochemical reaction network that includes reactions with iron-sulfur clusters, DNA, thiols. The fate of inside a pathogen depends on kinetic competition among many targets, critical importance infection outcomes. Due complexity network, where intermediates are short-lived at extremely low concentrations, several species can be measured, but stable...
ABSTRACT The field of metabolic modelling at the genomescale continues to grow with more models being created and curated. This comes an increasing demand for adopting common principles regarding transparency versioning, in addition standardisation efforts file formats, annotation testing. Here, we present a standardised template git-based GitHub-hosted genome-scale (GEMs) supporting both new curated ones, following FAIR (findability, accessibility, interoperability, reusability),...
Abstract Although the specific mechanism of neuronal damage in human immunodeficiency virus (HIV) ‐associated dementia is not known, a prominent role for NMDA receptor (NMDAR)‐induced excitotoxicity has been demonstrated neurons exposed to HIV‐infected/activated macrophages. We hypothesized NMDAR‐mediated activation calcium‐dependent protease, calpain, would contribute cell death by induction cyclin‐dependent kinase 5 (CDK5) activity. Using an vitro model HIV neurotoxicity, which primary rat...
The virulence of many pathogens depends upon their ability to cope with immune-generated nitric oxide (NO·). In Escherichia coli, the major NO· detoxification systems are Hmp, an dioxygenase (NOD), and NorV, reductase (NOR). It is well established that Hmp dominant system under aerobic conditions, whereas NorV dominates anaerobic conditions; however, quantitative contributions these physiologically relevant microaerobic regime remain ill defined. Here, we investigated in environments ranging...
Cell-type specific gene expression profiles are needed for many computational methods operating on bulk RNA-Seq samples, such as deconvolution of cell-type fractions and digital cytometry. However, the profile a cell type can vary substantially due to both technical factors biological differences in state surroundings, reducing efficacy methods. Here, we investigated which contribute most this variation. We evaluated different normalization methods, quantified variance explained by factors,...
The antimicrobial properties of nitric oxide (NO●) have motivated the design NO●-releasing materials for treatment and prevention infection. biological activity NO● is dependent on its delivery rate, suggesting that variable effects can result from identical payloads dosed at different rates. Using a kinetic model Escherichia coli biochemical network, we investigated relationship between payload, cytotoxicity, as indicated by duration respiratory inhibition. At low payloads, predicted...
Recombinant protein production can cause severe stress on cellular metabolism, resulting in limited titer and product quality. To investigate metabolic characteristics associated with these limitations, we compare HEK293 clones producing either erythropoietin (EPO) (secretory) or GFP (non-secretory) at different rates. Transcriptomic functional analyses indicate significantly higher metabolism oxidative phosphorylation EPO producers compared parental cells. In addition, ribosomal genes...