Proteome

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  Subject Areas on Research

  • 14-3-3 zeta protein secreted by tumor associated monocytes/macrophages from ascites of epithelial ovarian cancer patients. 
  • A Heat Shock Protein 48 (HSP48) Biomolecular Condensate Is Induced during Dictyostelium discoideum Development. 
  • A dataset of human cornea proteins identified by Peptide mass fingerprinting and tandem mass spectrometry. 
  • A mass spectrometry-based proteomic approach to study Marek's Disease Virus gene expression. 
  • A metabolomic study of the PPARδ agonist GW501516 for enhancing running endurance in Kunming mice. 
  • A novel interface for variable flow nanoscale LC/MS/MS for improved proteome coverage. 
  • A proteomic analysis of human cilia: identification of novel components. 
  • A proteomic clock for malignant gliomas: The role of the environment in tumorigenesis at the presymptomatic stage. 
  • A proteomics approach to the identification of mammalian mitochondrial small subunit ribosomal proteins. 
  • Alterations in cerebrospinal fluid proteins in a presymptomatic primary glioma model. 
  • An extracellular biochemical screen reveals that FLRTs and Unc5s mediate neuronal subtype recognition in the retina. 
  • An inducible heat shock protein 70 small molecule inhibitor demonstrates anti-dengue virus activity, validating Hsp70 as a host antiviral target. 
  • Analysis of "old" proteins unmasks dynamic gradient of cartilage turnover in human limbs. 
  • Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles. 
  • Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. 
  • Antibody Profiling by Proteome Microarray with Multiplex Isotype Detection Reveals Overlap between Human and Aotus nancymaae Controlled Malaria Infections. 
  • Application of a label-free, gel-free quantitative proteomics method for ecotoxicological studies of small fish species. 
  • Applying technologies towards safe and effective medicines. 
  • Arabidopsis functional genomics. 
  • Bayesian analysis of signaling networks governing embryonic stem cell fate decisions. 
  • Benchmarking of dynamic Bayesian networks inferred from stochastic time-series data. 
  • Biomarkers and proteomic analysis of osteoarthritis. 
  • Building pathway clusters from Random Forests classification using class votes. 
  • Cancer immunotherapy with recombinant poliovirus induces IFN-dominant activation of dendritic cells and tumor antigen-specific CTLs. 
  • Cardiovascular Metabolomics. 
  • Cell surface glycoproteomic analysis of prostate cancer-derived PC-3 cells. 
  • Cerebrospinal fluid protein dynamic driver network: At the crossroads of brain tumorigenesis. 
  • Changes in the Adult GluN2B Associated Proteome following Adolescent Intermittent Ethanol Exposure. 
  • Characterization of the gila monster (Heloderma suspectum suspectum) venom proteome. 
  • Characterization of the ubiquitin-modified proteome regulated by transient forebrain ischemia. 
  • Chlamydia trachomatis Infection Leads to Defined Alterations to the Lipid Droplet Proteome in Epithelial Cells. 
  • Cloud-based solution to identify statistically significant MS peaks differentiating sample categories. 
  • Coagulation factor XIIIa substrates in human plasma: identification and incorporation into the clot. 
  • Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene. 
  • Comparative proteomic analysis of cell cycle-dependent apoptosis induced by transforming growth factor-beta. 
  • Comparative proteomic analysis of colon cancer cells in response to oxaliplatin treatment. 
  • Comparative proteomic analysis of differentially expressed proteins in β-aminobutyric acid enhanced Arabidopsis thaliana tolerance to simulated acid rain. 
  • Comparative proteomic analysis of proteins in response to simulated acid rain in Arabidopsis. 
  • Comparative proteomic analysis of proteins involved in cell aggregation during neural differentiation of P19 mouse embryonic carcinoma cells. 
  • Comparing human pancreatic cell secretomes by in vitro aptamer selection identifies cyclophilin B as a candidate pancreatic cancer biomarker. 
  • Comparison of proteomic and metabolomic profiles of mutants of the mitochondrial respiratory chain in Caenorhabditis elegans. 
  • Comprehensive molecular characterization of gastric adenocarcinoma. 
  • Connecting genetic risk to disease end points through the human blood plasma proteome. 
  • Defective innate immunity and hyperinflammation in newborn cystic fibrosis transmembrane conductance regulator-knockout ferret lungs. 
  • Delineating signal transduction pathways in smooth muscle through focused proteomics. 
  • Determination of an angiotensin II-regulated proteome in primary human kidney cells by stable isotope labeling of amino acids in cell culture (SILAC). 
  • Differential ConA-enriched urinary proteome in rat experimental glomerular diseases. 
  • Differential display of proteins involved in the neural differentiation of mouse embryonic carcinoma P19 cells by comparative proteomic analysis. 
  • Differential extraction and enrichment of human sperm surface proteins in a proteome: identification of immunocontraceptive candidates. 
  • Direct methods for detection of protein S-nitrosylation. 
  • Directional Exosome Proteomes Reflect Polarity-Specific Functions in Retinal Pigmented Epithelium Monolayers. 
  • Discovery of Age-Related Protein Folding Stability Differences in the Mouse Brain Proteome. 
  • Discovery of Tamoxifen and N-Desmethyl Tamoxifen Protein Targets in MCF-7 Cells Using Large-Scale Protein Folding and Stability Measurements. 
  • Discovery of novel targets of quinoline drugs in the human purine binding proteome. 
  • Dynamic evolution of base composition: causes and consequences in avian phylogenomics. 
  • Elucidating the Molecular Composition of Cartilage by Proteomics. 
  • Evaluation of serum protein profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry for the detection of prostate cancer: I. Assessment of platform reproducibility. 
  • Evolution of budding yeast prion-determinant sequences across diverse fungi. 
  • Evolutionary Divergence of Gene and Protein Expression in the Brains of Humans and Chimpanzees. 
  • Expanding the functional repertoire of CTD kinase I and RNA polymerase II: novel phosphoCTD-associating proteins in the yeast proteome. 
  • Exploiting the complementary nature of LC/MALDI/MS/MS and LC/ESI/MS/MS for increased proteome coverage. 
  • Exploring the mechanism of Physcomitrella patens desiccation tolerance through a proteomic strategy. 
  • Ferritin heavy chain-mediated iron homeostasis and subsequent increased reactive oxygen species production are essential for epithelial-mesenchymal transition. 
  • Frequency-dependent response of the vascular endothelium to pulsatile shear stress. 
  • G Protein-Coupled Receptor Endocytosis Confers Uniformity in Responses to Chemically Distinct Ligands. 
  • General olfactory sensitivity database (GOSdb): candidate genes and their genomic variations. 
  • Genetics, genomics, proteomics: what is a cardiologist to do? 
  • Genome-based pharmacogenetics and the pharmaceutical industry. 
  • Genomic analysis of human lung fibroblasts exposed to vanadium pentoxide to identify candidate genes for occupational bronchitis. 
  • Genomic insights into the atopic eczema-associated skin commensal yeast Malassezia sympodialis. 
  • Genomic predictors of the maximal O₂ uptake response to standardized exercise training programs. 
  • Getting more from less: algorithms for rapid protein identification with multiple short peptide sequences. 
  • Global Mapping of the Inc-Human Interactome Reveals that Retromer Restricts Chlamydia Infection. 
  • Global analysis of protein folding thermodynamics for disease state characterization. 
  • Global phosphorylation analysis of beta-arrestin-mediated signaling downstream of a seven transmembrane receptor (7TMR). 
  • Growth-Phase-Specific Modulation of Cell Morphology and Gene Expression by an Archaeal Histone Protein. 
  • Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage. 
  • Haploinsufficiency for Core Exon Junction Complex Components Disrupts Embryonic Neurogenesis and Causes p53-Mediated Microcephaly. 
  • Human cornea proteome: identification and quantitation of the proteins of the three main layers including epithelium, stroma, and endothelium. 
  • Hybrid origin of SIV in chimpanzees. 
  • Hyperphosphorylated C-terminal repeat domain-associating proteins in the nuclear proteome link transcription to DNA/chromatin modification and RNA processing. 
  • Identification of Protease Specificity by Combining Proteome-Derived Peptide Libraries and Quantitative Proteomics. 
  • Identification of an elaborate complex mediating postsynaptic inhibition. 
  • Identification of four proteins from the small subunit of the mammalian mitochondrial ribosome using a proteomics approach. 
  • Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching. 
  • In vivo proximity proteomics of nascent synapses reveals a novel regulator of cytoskeleton-mediated synaptic maturation. 
  • Initial sequencing and analysis of the human genome. 
  • Initial sequencing and comparative analysis of the mouse genome. 
  • Integrating Pharmacoproteomics into Early-Phase Clinical Development: State-of-the-Art, Challenges, and Recommendations. 
  • Integrative Omics: Harnessing the Proteome to Maximize the Potential of the Genome. 
  • Is age a key factor contributing to the disparity between success of neuroprotective strategies in young animals and limited success in elderly stroke patients? Focus on protein homeostasis. 
  • LASIK surgery of granular corneal dystrophy type 2 patients leads to accumulation and differential proteolytic processing of transforming growth factor beta-induced protein (TGFBIp). 
  • Large-Scale Analysis of Breast Cancer-Related Conformational Changes in Proteins Using SILAC-SPROX. 
  • Large-scale proteomics and phosphoproteomics of urinary exosomes. 
  • Layers of regulation of cell-cycle gene expression in the budding yeast Saccharomyces cerevisiae. 
  • Little Cigars are More Toxic than Cigarettes and Uniquely Change the Airway Gene and Protein Expression. 
  • Longitudinal study of differential protein expression in an Alzheimer's mouse model lacking inducible nitric oxide synthase. 
  • Metabolomics Standards Workshop and the development of international standards for reporting metabolomics experimental results. 
  • Metabolomics applied to diabetes research: moving from information to knowledge. 
  • Metaprotein expression modeling for label-free quantitative proteomics. 
  • Mitochondrial acetylome analysis in a mouse model of alcohol-induced liver injury utilizing SIRT3 knockout mice. 
  • Mixed peptide sequencing and the FASTF/FASTS algorithms. 
  • Molecular biologist's guide to proteomics. 
  • Multivariate proteomic analysis of murine embryonic stem cell self-renewal versus differentiation signaling. 
  • Mutual information in random Boolean models of regulatory networks. 
  • Nasopharyngeal Protein Biomarkers of Acute Respiratory Virus Infection. 
  • New secrets behind bone metastasis. 
  • Noise-limited frequency signal transmission in gene circuits. 
  • Novel breast cancer biomarkers identified by integrative proteomic and gene expression mapping. 
  • Organization of enzyme concentration across the metabolic network in cancer cells. 
  • Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer. 
  • Phosphoproteome analysis in yeast. 
  • Phosphoproteome analysis of capacitated human sperm. Evidence of tyrosine phosphorylation of a kinase-anchoring protein 3 and valosin-containing protein/p97 during capacitation. 
  • Phosphoproteomic profiling of human myocardial tissues distinguishes ischemic from non-ischemic end stage heart failure. 
  • Physiological Genomics: Who we are and where we're going. 
  • Post-transcriptional operons and regulons co-ordinating gene expression. 
  • Probabilistic Disease Classification of Expression-Dependent Proteomic Data from Mass Spectrometry of Human Serum 
  • Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry. 
  • Proteome analysis by mass spectrometry. 
  • Proteome analysis of human sebaceous follicle infundibula extracted from healthy and acne-affected skin. 
  • Proteome reference maps of the Lotus japonicus nodule and root. 
  • Proteome-Wide Characterization of Phosphorylation-Induced Conformational Changes in Breast Cancer. 
  • Proteome-Wide Structural Biology: An Emerging Field for the Structural Analysis of Proteins on the Proteomic Scale. 
  • Proteome-wide analysis reveals widespread lysine acetylation of major protein complexes in the malaria parasite. 
  • Proteome-wide muscle protein fractional synthesis rates predict muscle mass gain in response to a selective androgen receptor modulator in rats. 
  • Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae. 
  • Proteomic Analysis of Primary Human Airway Epithelial Cells Exposed to the Respiratory Toxicant Diacetyl. 
  • Proteomic analysis and identification of new biomarkers and therapeutic targets for invasive ovarian cancer. 
  • Proteomic analysis of S-nitrosylation and denitrosylation by resin-assisted capture. 
  • Proteomic analysis of human bronchoalveolar lavage fluid after subsgemental exposure. 
  • Proteomic analysis of hyperoxia-induced responses in the human choriocarcinoma cell line JEG-3. 
  • Proteomic analysis of mitochondrial-associated ER membranes (MAM) during RNA virus infection reveals dynamic changes in protein and organelle trafficking. 
  • Proteomic analysis of mitotic RNA polymerase II reveals novel interactors and association with proteins dysfunctional in disease. 
  • Proteomic analysis of pulmonary edema fluid and plasma in patients with acute lung injury. 
  • Proteomic analysis of the NOS2 interactome in human airway epithelial cells. 
  • Proteomic analysis of the soluble fraction from human corneal fibroblasts with reference to ocular transparency. 
  • Proteomic analysis of urinary extracellular vesicles reveal biomarkers for neurologic disease. 
  • Proteomic and immunologic analyses of brain tumor exosomes. 
  • Proteomic characterization of the cellular response to nitrosative stress mediated by s-nitrosoglutathione reductase inhibition. 
  • Proteomic investigation of the ventral rat hippocampus links DRP-2 to escitalopram treatment resistance and SNAP to stress resilience in the chronic mild stress model of depression. 
  • Proteomic profiling of cerebrospinal fluid identifies prostaglandin D2 synthase as a putative biomarker for pediatric medulloblastoma: A pediatric brain tumor consortium study. 
  • Proteomic profiling of nuclei from native renal inner medullary collecting duct cells using LC-MS/MS. 
  • Proteomics-based identification of differentially-expressed proteins including galectin-1 in the blood plasma of type 2 diabetic patients. 
  • Quantifying Competition among Mitochondrial Protein Acylation Events Induced by Ethanol Metabolism. 
  • Quantitative proteome analysis of colorectal cancer-related differential proteins. 
  • Quantitative proteomics reveals metabolic and pathogenic properties of Chlamydia trachomatis developmental forms. 
  • Rapid identification of monospecific monoclonal antibodies using a human proteome microarray. 
  • Recent advances for measurement of protein synthesis rates, use of the 'Virtual Biopsy' approach, and measurement of muscle mass. 
  • Reducing mass degeneracy in SAR by MS by stable isotopic labeling. 
  • Regulation of MicroRNA Machinery and Development by Interspecies S-Nitrosylation. 
  • Regulation of iron transport related genes by boron in the marine bacterium Marinobacter algicola DG893. 
  • Remodeling of the Acetylproteome by SIRT3 Manipulation Fails to Affect Insulin Secretion or β Cell Metabolism in the Absence of Overnutrition. 
  • Reprioritization of biofilm metabolism is associated with nutrient adaptation and long-term survival of Haemophilus influenzae. 
  • Residual dipolar couplings: synergy between NMR and structural genomics. 
  • Reverse engineering gene regulatory networks. 
  • Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome. 
  • Ring finger protein 121 is a potent regulator of adeno-associated viral genome transcription. 
  • S-nitrosothiols and the S-nitrosoproteome of the cardiovascular system. 
  • SILAC-MS Based Characterization of LPS and Resveratrol Induced Changes in Adipocyte Proteomics - Resveratrol as Ameliorating Factor on LPS Induced Changes. 
  • SILAC-pulse proteolysis: A mass spectrometry-based method for discovery and cross-validation in proteome-wide studies of ligand binding. 
  • SUMO proteomics to decipher the SUMO-modified proteome regulated by various diseases. 
  • Scanning Quadrupole Data-Independent Acquisition, Part A: Qualitative and Quantitative Characterization. 
  • Sequence heuristics to encode phase behaviour in intrinsically disordered protein polymers. 
  • Simultaneous generation of aptamers to multiple gamma-carboxyglutamic acid proteins from a focused aptamer library using DeSELEX and convergent selection. 
  • Small ubiquitin-like modifier 3-modified proteome regulated by brain ischemia in novel small ubiquitin-like modifier transgenic mice: putative protective proteins/pathways. 
  • Solid-phase capture for the detection and relative quantification of S-nitrosoproteins by mass spectrometry. 
  • StableIsotope Labeling with Amino Acids in Cell Culture (SILAC)-based strategy for proteome-wide thermodynamic analysis of protein-ligand binding interactions. 
  • Systemic surfaceome profiling identifies target antigens for immune-based therapy in subtypes of advanced prostate cancer. 
  • Targeted Proteomics of Human Metapneumovirus in Clinical Samples and Viral Cultures. 
  • Targeted proteomic profiling of renal Na(+) transporter and channel abundances in angiotensin II type 1a receptor knockout mice. 
  • Tetracycline treatment targeting Wolbachia affects expression of an array of proteins in Brugia malayi parasite. 
  • The Diacetyl-Exposed Human Airway Epithelial Secretome: New Insights into Flavoring-Induced Airways Disease. 
  • The Human Eye Proteome Project: perspectives on an emerging proteome. 
  • The NOESY Jigsaw: Automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data 
  • The SNO-proteome: causation and classifications. 
  • The anatomy of microbial cell state transitions in response to oxygen. 
  • The ciliary proteome database: an integrated community resource for the genetic and functional dissection of cilia. 
  • The emerging complexity of the vertebrate cilium: new functional roles for an ancient organelle. 
  • The human cornea proteome: bioinformatic analyses indicate import of plasma proteins into the cornea. 
  • The metabolomics standards initiative. 
  • The protein expression landscape of the Arabidopsis root. 
  • The proteome of seed development in the model legume Lotus japonicus. 
  • The purinome, a complex mix of drug and toxicity targets. 
  • The somatic genomic landscape of glioblastoma. 
  • The spider hemolymph clot proteome reveals high concentrations of hemocyanin and von Willebrand factor-like proteins. 
  • Thermodynamic analysis of protein-ligand interactions in complex biological mixtures using a shotgun proteomics approach. 
  • Transcriptional profiling of Alzheimer blood mononuclear cells by microarray. 
  • Use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses. 
  • Vagal nerve stimulation modifies neuronal activity and the proteome of excitatory synapses of amygdala/piriform cortex. 
  • Visual annotation of the gene database. 
  • p300-Mediated Lysine 2-Hydroxyisobutyrylation Regulates Glycolysis. 
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  Keywords of People

  • Ferguson, P. Lee, Associate Professor of Civil and Environmental Engineering, Civil and Environmental Engineering
  • Garman, Katherine Schuver, Associate Professor of Medicine, Medicine, Gastroenterology
  • Hartemink, Alexander J., Professor in the Department of Computer Science, Biology
  • Hirschey, Matthew, Associate Professor, Pharmacology & Cancer Biology
  • McCall, Shannon Jones, Associate Professor of Pathology, Pathology
  • Milano, Carmelo Alessio, Professor of Surgery, Surgery, Cardiovascular and Thoracic Surgery
  • Pang, Herbert, Adjunct Assistant Professor in the Department of Biostatistics and Bioinformatics, Biostatistics & Bioinformatics
  • Sampson, John Howard, Robert H., M.D. and Gloria Wilkins Professor of Neurosurgery, in the School of Medicine, Immunology