Metabolic Networks and Pathways

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  Subject Areas on Research

  • A general map of iron metabolism and tissue-specific subnetworks. 
  • A genome-wide association meta-analysis of circulating sex hormone-binding globulin reveals multiple Loci implicated in sex steroid hormone regulation. 
  • A guide to interrogating immunometabolism. 
  • A roadmap for interpreting (13)C metabolite labeling patterns from cells. 
  • A robust and efficient method for estimating enzyme complex abundance and metabolic flux from expression data. 
  • A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability. 
  • A targeted analysis reveals relevant shifts in the methylation and transcription of genes responsible for bile acid homeostasis and drug metabolism in non-alcoholic fatty liver disease. 
  • A transcription factor links growth rate and metabolism in the hypersaline adapted archaeon Halobacterium salinarum. 
  • A unique chromosomal rearrangement in the Cryptococcus neoformans var. grubii type strain enhances key phenotypes associated with virulence. 
  • Ablation of Sirtuin5 in the postnatal mouse heart results in protein succinylation and normal survival in response to chronic pressure overload. 
  • Advances in enzymology and related areas of molecular biology. Preface. 
  • Alterations in metabolic pathways and networks in Alzheimer's disease. 
  • Altered skeletal muscle metabolic pathways, age, systemic inflammation, and low cardiorespiratory fitness associate with improvements in disease activity following high-intensity interval training in persons with rheumatoid arthritis. 
  • An aberrant SREBP-dependent lipogenic program promotes metastatic prostate cancer. 
  • An integration of complementary strategies for gene-expression analysis to reveal novel therapeutic opportunities for breast cancer. 
  • Analysis of Homeostatic Mechanisms in Biochemical Networks. 
  • Analysis of cancer metabolism by imaging hyperpolarized nuclei: prospects for translation to clinical research. 
  • Application of a label-free, gel-free quantitative proteomics method for ecotoxicological studies of small fish species. 
  • Attenuation of the retinoblastoma pathway in pancreatic neuroendocrine tumors due to increased cdk4/cdk6. 
  • Auxin biosynthesis and storage forms. 
  • Biochemical Pathways and Myometrial Cell Differentiation Leading to Nodule Formation Containing Collagen and Fibronectin. 
  • CD8+ T cells: mechanistic target of rapamycin and eukaryotic initiation factor 2 in elite HIV-1 control. 
  • Cancer's insatiable appetite. 
  • Catabolism of exogenous lactate reveals it as a legitimate metabolic substrate in breast cancer. 
  • Caulobacter crescentus Adapts to Phosphate Starvation by Synthesizing Anionic Glycoglycerolipids and a Novel Glycosphingolipid. 
  • Cell-Type-Specific Analysis of Molecular Pathology in Autism Identifies Common Genes and Pathways Affected Across Neocortical Regions. 
  • Cellular arrays for large-scale analysis of transcription factor activity. 
  • Characterization of the usage of the serine metabolic network in human cancer. 
  • Cilia loss sensitizes cells to transformation by activating the mevalonate pathway. 
  • Comparative Evaluation of MS-based Metabolomics Software and Its Application to Preclinical Alzheimer's Disease. 
  • Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens. 
  • Comparative proteomic analysis of proteins in response to simulated acid rain in Arabidopsis. 
  • Comprehensive metabolic modeling of multiple 13C-isotopomer data sets to study metabolism in perfused working hearts. 
  • Conservation of the chitin utilization pathway in the Vibrionaceae. 
  • Convergence of genes and cellular pathways dysregulated in autism spectrum disorders. 
  • Cross-talk Between Nitrate-Nitrite-NO and NO Synthase Pathways in Control of Vascular NO Homeostasis. 
  • Cytoplasmic polyadenylation element binding protein deficiency stimulates PTEN and Stat3 mRNA translation and induces hepatic insulin resistance. 
  • Design and Analysis of Large-Scale Biological Rhythm Studies: A Comparison of Algorithms for Detecting Periodic Signals in Biological Data 
  • Differential metabolic impact of gastric bypass surgery versus dietary intervention in obese diabetic subjects despite identical weight loss. 
  • Dissecting the in vivo metabolic potential of two human gut acetogens. 
  • Dysfunctional T cell metabolism in the tumor microenvironment. 
  • Dysregulated metabolism contributes to oncogenesis. 
  • Dysregulation of fatty acid synthesis and glycolysis in non-Hodgkin lymphoma. 
  • Dysregulation of multiple metabolic networks related to brain transmethylation and polyamine pathways in Alzheimer disease: A targeted metabolomic and transcriptomic study. 
  • Effect of carbon source addition on toluene biodegradation by an Escherichia coli DH5alpha transconjugant harboring the TOL plasmid. 
  • Effects of a block in cysteine catabolism on energy balance and fat metabolism in mice. 
  • Electrical stimulation increases hypertrophy and metabolic flux in tissue-engineered human skeletal muscle. 
  • Environmental conditions influence the plant functional diversity effect on potential denitrification. 
  • Estrogen pathway polymorphisms in relation to primary open angle glaucoma: an analysis accounting for gender from the United States. 
  • Ethanol metabolism modifies hepatic protein acylation in mice. 
  • Evolution of flux control in the glucosinolate pathway in Arabidopsis thaliana 
  • Evolution of flux control in the glucosinolate pathway in Arabidopsis thaliana. 
  • Feeding strategy shapes gut metagenomic enrichment and functional specialization in captive lemurs. 
  • Fine tuning of immunometabolism for the treatment of rheumatic diseases. 
  • From genotype to phenotype: systems biology meets natural variation. 
  • Functionality of the TOL plasmid under varying environmental conditions following conjugal transfer. 
  • GAIP interacting protein C-terminus regulates autophagy and exosome biogenesis of pancreatic cancer through metabolic pathways. 
  • Gene Expression of Haloferax volcanii on Intermediate and Abundant Sources of Fixed Nitrogen. 
  • Gene loss and parallel evolution contribute to species difference in flower color. 
  • Genes, Pathways, and Mechanisms Involved in the Virulence of Mucorales. 
  • Genetic networks of liver metabolism revealed by integration of metabolic and transcriptional profiling. 
  • Genetic variants in PDSS1 and SLC16A6 of the ketone body metabolic pathway predict cutaneous melanoma-specific survival. 
  • Genetic variants in TKT and DERA in the nicotinamide adenine dinucleotide phosphate pathway predict melanoma survival. 
  • Genetic variants in glutamine metabolic pathway genes predict cutaneous melanoma-specific survival. 
  • Genetic variants in the folate metabolic pathway genes predict cutaneous melanoma-specific survival. 
  • Genome Analyses of >200,000 Individuals Identify 58 Loci for Chronic Inflammation and Highlight Pathways that Link Inflammation and Complex Disorders. 
  • Genomic acquisition of a capsular polysaccharide virulence cluster by non-pathogenic Burkholderia isolates. 
  • Genomic erosion and extensive horizontal gene transfer in gut-associated Acetobacteraceae. 
  • Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. 
  • Genomics and Transcriptomics Analyses of the Oil-Accumulating Basidiomycete Yeast Trichosporon oleaginosus: Insights into Substrate Utilization and Alternative Evolutionary Trajectories of Fungal Mating Systems. 
  • GlpR Is a Direct Transcriptional Repressor of Fructose Metabolic Genes in Haloferax volcanii. 
  • Glucose transporter 1-mediated glucose uptake is limiting for B-cell acute lymphoblastic leukemia anabolic metabolism and resistance to apoptosis. 
  • Glutamine metabolism during aerial mycelium growth of Neurospora crassa. 
  • Glyco-engineering in Archaea: differential N-glycosylation of the S-layer glycoprotein in a transformed Haloferax volcanii strain. 
  • HNF4α regulates sulfur amino acid metabolism and confers sensitivity to methionine restriction in liver cancer. 
  • Heterogeneity of tumor-induced gene expression changes in the human metabolic network. 
  • Hierarchical regulation of mRNA partitioning between the cytoplasm and the endoplasmic reticulum of mammalian cells. 
  • Homeostasis and dynamic stability of the phenotype link robustness and plasticity. 
  • Hypothesis-independent pathway analysis implicates GABA and acetyl-CoA metabolism in primary open-angle glaucoma and normal-pressure glaucoma. 
  • Identification of Metabolic Changes in Ileum, Jejunum, Skeletal Muscle, Liver, and Lung in a Continuous I.V. Pseudomonas aeruginosa Model of Sepsis Using Nontargeted Metabolomics Analysis. 
  • Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders. 
  • In vivo luminescent imaging of NF-κB activity and NF-κB-related serum cytokine levels predict pain sensitivities in a rodent model of peripheral neuropathy. 
  • Incorporation of extracellular fatty acids by a fatty acid kinase-dependent pathway in Staphylococcus aureus. 
  • Indoxyl sulfate, a gut microbiome-derived uremic toxin, is associated with psychic anxiety and its functional magnetic resonance imaging-based neurologic signature. 
  • Influence of threonine metabolism on S-adenosylmethionine and histone methylation. 
  • Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types. 
  • Integrated proteomics and metabolomics suggests symbiotic metabolism and multimodal regulation in a fungal-endobacterial system. 
  • Integrative metabolomics-genomics approach reveals key metabolic pathways and regulators of Alzheimer's disease. 
  • Interplay of Auxin and Cytokinin in Lateral Root Development. 
  • Investigating the Role of Class I Adenylate-Forming Enzymes in Natural Product Biosynthesis. 
  • Lactic acidosis triggers starvation response with paradoxical induction of TXNIP through MondoA. 
  • Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways. 
  • Lessons From the Studies of a CC Bond Forming Radical SAM Enzyme in Molybdenum Cofactor Biosynthesis. 
  • Leveraging insights into cancer metabolism-a symposium report. 
  • MYC-Driven Small-Cell Lung Cancer is Metabolically Distinct and Vulnerable to Arginine Depletion. 
  • Mammalian Synthetic Biology: Engineering Biological Systems. 
  • Manganese-based superoxide dismutase mimics modify both acute and long-term outcome severity in a Drosophila melanogaster model of classic galactosemia. 
  • Mathematical analysis of the regulation of competing methyltransferases. 
  • Merging pharmacometabolomics with pharmacogenomics using '1000 Genomes' single-nucleotide polymorphism imputation: selective serotonin reuptake inhibitor response pharmacogenomics. 
  • Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci. 
  • Metabolic Network Analysis Reveals Altered Bile Acid Synthesis and Metabolism in Alzheimer's Disease. 
  • Metabolic Networks and Metabolites Underlie Associations Between Maternal Glucose During Pregnancy and Newborn Size at Birth. 
  • Metabolic Teamwork in the Stem Cell Niche. 
  • Metabolic cross-talk allows labeling of O-linked beta-N-acetylglucosamine-modified proteins via the N-acetylgalactosamine salvage pathway. 
  • Metabolic cycling in control of glucose-stimulated insulin secretion. 
  • Metabolic decisions in development and disease-a Keystone Symposia report. 
  • Metabolic division of labor in microbial systems. 
  • Metabolic dysfunctions in the kynurenine pathway, noradrenergic and purine metabolism in schizophrenia and bipolar disorders. 
  • Metabolic network failures in Alzheimer's disease: A biochemical road map. 
  • Metabolic pathway alterations that support cell proliferation. 
  • Metabolic profiling of patients with schizophrenia. 
  • Metabolic reprogramming towards aerobic glycolysis correlates with greater proliferative ability and resistance to metabolic inhibition in CD8 versus CD4 T cells. 
  • Metabolism of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) by human CYP1B1 genetic variants. 
  • Metabolomic Signatures for Drug Response Phenotypes: Pharmacometabolomics Enables Precision Medicine. 
  • Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers. 
  • Molecular pathways: the metabolic regulator estrogen-related receptor α as a therapeutic target in cancer. 
  • Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals. 
  • One-carbon metabolism and epigenetics: understanding the specificity. 
  • PHGDH amplification and altered glucose metabolism in human melanoma. 
  • Pathway for lipid A biosynthesis in Arabidopsis thaliana resembling that of Escherichia coli. 
  • Pathway-based identification of SNPs predictive of survival. 
  • Pathways-driven sparse regression identifies pathways and genes associated with high-density lipoprotein cholesterol in two Asian cohorts. 
  • Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. 
  • PharmGKB summary: methotrexate pathway. 
  • Pharmacometabolomics reveals racial differences in response to atenolol treatment. 
  • Phosphatidylcholine Biosynthesis in Mitis Group Streptococci via Host Metabolite Scavenging. 
  • Phosphatidylglycerol homeostasis in glycerol-phosphate auxotrophs of Staphylococcus aureus. 
  • Polyphasic characterization of four soil-derived phenanthrene-degrading Acidovorax strains and proposal of Acidovorax carolinensis sp. nov. 
  • Potentially functional genetic variants in PLIN2, SULT2A1 and UGT1A9 genes of the ketone pathway and survival of nonsmall cell lung cancer. 
  • Pretreatment metabotype as a predictor of response to sertraline or placebo in depressed outpatients: a proof of concept. 
  • Programmed evolution for optimization of orthogonal metabolic output in bacteria. 
  • Prostatic alpha-linolenic acid (ALA) is positively associated with aggressive prostate cancer: a relationship which may depend on genetic variation in ALA metabolism. 
  • Proteomic analysis of mitochondrial-associated ER membranes (MAM) during RNA virus infection reveals dynamic changes in protein and organelle trafficking. 
  • Quantifying Competition among Mitochondrial Protein Acylation Events Induced by Ethanol Metabolism. 
  • Quantitative H2S-mediated protein sulfhydration reveals metabolic reprogramming during the integrated stress response. 
  • Quantitative proteome analysis of colorectal cancer-related differential proteins. 
  • Rapid and weight-independent improvement of glucose tolerance induced by a peptide designed to elicit apoptosis in adipose tissue endothelium. 
  • Red blood cell folate concentrations and polyglutamate distribution in juvenile arthritis: predictors of folate variability. 
  • Remodeling of the Acetylproteome by SIRT3 Manipulation Fails to Affect Insulin Secretion or β Cell Metabolism in the Absence of Overnutrition. 
  • Reprogramming of cellular metabolic pathways by human oncogenic viruses. 
  • SIRT5 regulates the mitochondrial lysine succinylome and metabolic networks. 
  • Similarities and Distinctions of Cancer and Immune Metabolism in Inflammation and Tumors. 
  • Sleep and metabolism: role of hypothalamic neuronal circuitry. 
  • SnapShot: Immunometabolism. 
  • Sphingolipid Metabolic Pathway Impacts Thiazide Diuretics Blood Pressure Response: Insights From Genomics, Metabolomics, and Lipidomics. 
  • Structural and functional analyses of microbial metabolic networks reveal novel insights into genome-scale metabolic fluxes. 
  • Targeting One Carbon Metabolism with an Antimetabolite Disrupts Pyrimidine Homeostasis and Induces Nucleotide Overflow. 
  • Testosterone Pathway Genetic Polymorphisms in Relation to Primary Open-Angle Glaucoma: An Analysis in Two Large Datasets. 
  • Testosterone in prostate cancer: the Bethesda consensus. 
  • The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. 
  • The Molecular Link from Diet to Cancer Cell Metabolism. 
  • The Primary Effect on the Proteome of ARID1A-mutated Ovarian Clear Cell Carcinoma is Downregulation of the Mevalonate Pathway at the Post-transcriptional Level. 
  • The Trait Repertoire Enabling Cyanobacteria to Bloom Assessed through Comparative Genomic Complexity and Metatranscriptomics. 
  • The evolution of control and distribution of adaptive mutations in a metabolic pathway 
  • The impact of cellular metabolism on chromatin dynamics and epigenetics. 
  • The reacquisition of biotin prototrophy in Saccharomyces cerevisiae involved horizontal gene transfer, gene duplication and gene clustering. 
  • The role of the de novo pyrimidine biosynthetic pathway in Cryptococcus neoformans high temperature growth and virulence. 
  • The tangled circuitry of metabolism and apoptosis. 
  • The virulence factor urease and its unexplored role in the metabolism of Cryptococcus neoformans. 
  • Thermodynamic constraints on the regulation of metabolic fluxes. 
  • Thyroid hormone stimulates hepatic lipid catabolism via activation of autophagy. 
  • Transcriptional Regulation in Archaea: From Individual Genes to Global Regulatory Networks. 
  • Trehalose pathway as an antifungal target. 
  • Two distinct N-glycosylation pathways process the Haloferax volcanii S-layer glycoprotein upon changes in environmental salinity. 
  • Understanding metabolism with flux analysis: From theory to application. 
  • Unprecedented loss of ammonia assimilation capability in a urease-encoding bacterial mutualist. 
  • Upregulated heme biosynthesis increases obstructive sleep apnea severity: a pathway-based Mendelian randomization study. 
  • Use of pathway information in molecular epidemiology. 
  • Using Strand Displacing Polymerase To Program Chemical Reaction Networks. 
  • Using isotopic tools to dissect and quantitate parallel metabolic pathways. 
  • Utility of routine laboratory testing in management of chronic urticaria/angioedema. 
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  Keywords of People

  • Ferguson, P. Lee, Associate Professor of Civil and Environmental Engineering, Civil and Environmental Engineering
  • Hirschey, Matthew, Associate Professor of Medicine, Cell Biology
  • Liu, Yutao, Adjunct Assistant Professor in the Department of Medicine, Medicine, Medical Genetics
  • Pang, Herbert, Adjunct Assistant Professor in the Department of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics
  • Schmid, Amy K., David M. Goodner Associate Professor, Duke Science & Society