A5026633794- Microbial Metabolic Engineering and Bioproduction
- Bioinformatics and Genomic Networks
- Metabolomics and Mass Spectrometry Studies
- Erythrocyte Function and Pathophysiology
- Gene Regulatory Network Analysis
- Blood groups and transfusion
- Neonatal Health and Biochemistry
- Blood transfusion and management
- RNA and protein synthesis mechanisms
- Pharmacogenetics and Drug Metabolism
- Genomics and Phylogenetic Studies
- Viral Infectious Diseases and Gene Expression in Insects
- Computational Drug Discovery Methods
- Protein Structure and Dynamics
- Biofuel production and bioconversion
- Adipose Tissue and Metabolism
- CRISPR and Genetic Engineering
- Enzyme Catalysis and Immobilization
- Mitochondrial Function and Pathology
- Genetic Associations and Epidemiology
- Scientific Computing and Data Management
- RNA modifications and cancer
- Hemoglobinopathies and Related Disorders
- Gut microbiota and health
- Epigenetics and DNA Methylation
Sinopia Biosciences (United States)
2015-2020
University of California, San Diego
2010-2017
Abt Associates (Nepal)
2016
La Jolla Bioengineering Institute
2010-2014
Enzo Life Sciences (United States)
2011
University of San Diego
2010
Genome sequences of the Chinese hamster and six ovary cell lines provide a resource to aid in improving production recombinant proteins. (CHO) cells, first isolated 1957, are preferred host for many therapeutic Although genetic heterogeneity among CHO has been well documented, systematic, nucleotide-resolution characterization their genotypic differences stymied by lack unifying genomic cells. Here we report 2.4-Gb draft genome sequence female hamster, Cricetulus griseus, harboring 24,044...
Abstract Background Genome-scale metabolic reconstructions provide a biologically meaningful mechanistic basis for the genotype-phenotype relationship. The global human network, termed Recon 1, has recently been reconstructed allowing systems analysis of physiology and pathology. Utilizing high-throughput data, 1 tailored to different cells tissues, including liver, kidney, brain, alveolar macrophage. These models have shown utility in study medicine. However, no integrated between tissues...
Abstract Rapid growth in size and complexity of biological data sets has led to the ‘Big Data Knowledge’ challenge. We develop advanced integration methods for multi-level analysis genomic, transcriptomic, ribosomal profiling, proteomic fluxomic data. First, we show that pairwise primary omics reveals regularities tie cellular processes together Escherichia coli : number protein molecules made per mRNA transcript ribosomes required translated molecule. Second, genome-scale models, based on...
Article26 June 2012Open Access Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation Aarash Bordbar Department Bioengineering, University California San Diego, La Jolla, CA, USA Search for more papers by this author Monica L Mo Ernesto S Nakayasu Pacific Northwest National Laboratory, Richland, WA, Alexandra C Schrimpe-Rutledge Young-Mo Kim Thomas O Metz Marcus B Jones J. Craig Venter Institute, Rockville, MD, Bryan Frank Richard D Smith Scott N...
Abstract The increasing availability of metabolomics data necessitates novel methods for deeper analysis and interpretation. We present a flux balance method that allows the computation dynamic intracellular metabolic changes at cellular scale through integration time-course absolute quantitative metabolomics. This approach, termed “unsteady-state analysis” (uFBA), is applied to four systems: three one steady-state as negative control. uFBA FBA predictions are contrasted, found be more...
Biological systems are inherently hierarchal and multiscale in time space. A major challenge of biology is to describe biological as a computational model, which can be used derive novel hypothesis drive experiments leading new knowledge. The constraint-based reconstruction analysis approach has been successfully applied metabolism the macromolecular synthesis machinery assembly. Here, we present first integrated stoichiometric model for Escherichia coli K12 MG1655, describes...
BACKGROUND There has been interest in determining whether older red blood cell (RBC) units have negative clinical effects. Numerous observational studies shown that RBC are an independent factor for patient mortality. However, recently published randomized trials no difference of outcome patients receiving old or fresh RBCs. An overlooked but essential issue assessing unit quality and ultimately designing the necessary is a metric what constitutes unit. STUDY DESIGN AND METHODS Twenty were...
BACKGROUND Red blood cells (RBCs) are thought to have a relatively simple metabolic network compared other human cell types. Recent proteomics reports challenge the notion that RBCs mere hemoglobin carriers with limited activity. Expanding our understanding of RBC metabolism has key implications in many biomedical areas, including transfusion medicine. STUDY DESIGN AND METHODS In‐gel digestion coupled mass spectrometric analysis approaches were combined state‐of‐the‐art tracing experiments...
Abstract Malignant transformation is often accompanied by significant metabolic changes. To identify drivers underlying these changes, we calculated flux states for the NCI60 cell line collection and correlated variance between of lines with their other properties. The analysis revealed a remarkably consistent structure high metabolism. three primary uptake pathways, glucose, glutamine serine, are each characterized features: (1) metabolite sufficient stoichiometric requirement to sustain...
Abstract Background The development of high-throughput technologies capable whole cell measurements genes, proteins, and metabolites has led to the emergence systems biology. Integrated analysis resulting omic data sets proved be hard achieve. Metabolic network reconstructions enable complex relationships amongst molecular components represented formally in a biologically relevant manner while respecting physical constraints. In silico models derived from such can then queried or...
Altered metabolism in cancer cells has been viewed as a passive response required for malignant transformation. However, this view changed through the recently described metabolic oncogenic factors: mutated isocitrate dehydrogenases (IDH), succinate dehydrogenase (SDH), and fumarate hydratase (FH) that produce oncometabolites competitively inhibit epigenetic regulation. In study, we demonstrate silico predictions of have potential to dysregulate controls nine types by incorporating massive...
Computational models based on recent maps of the RBC proteome suggest that mature erythrocytes may harbor targets for common drugs. This prediction is relevant to storage in blood bank, which impact small molecule drugs or other xenometabolites deriving from dietary, iatrogenic, environmental exposures ("exposome") alter erythrocyte energy and redox metabolism and, so doing, affect red cell quality posttransfusion efficacy. To test this prediction, here we provide a comprehensive...
COnstraint-Based Reconstruction and Analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental data quantitative prediction physicochemically biochemically feasible phenotypic states. The COBRA Toolbox is comprehensive software suite interoperable methods. It has found widespread applications in biology, biomedicine, biotechnology because its functions can be flexibly combined to implement tailored protocols any biochemical network. Version 3.0...