Carrie D. Nicora

Publications

• Urinary Virome Perturbations in Kidney Transplantation
  Frontiers in Medicine. 2018  |   Pubmed ID: 29725592
• Optimization for Peptide Sample Preparation for Urine Peptidomics
  Methods in Molecular Biology (Clifton, N.J.). Apr, 2018  |   Pubmed ID: 29623538
• Salmonella-Mediated Inflammation Eliminates Competitors for Fructose-Asparagine in the Gut
  Infection and Immunity. May, 2018  |   Pubmed ID: 29483291
• Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction
  Metabolites. Jan, 2018  |   Pubmed ID: 29342073
• MERS-CoV and H5N1 Influenza Virus Antagonize Antigen Presentation by Altering the Epigenetic Landscape
  Proceedings of the National Academy of Sciences of the United States of America. Jan, 2018  |   Pubmed ID: 29339515
• Multiplexed Targeted Mass Spectrometry Assays for Prostate Cancer-associated Urinary Proteins
  Oncotarget. Nov, 2017  |   Pubmed ID: 29254211
• LC-SRM-Based Targeted Quantification of Urinary Protein Biomarkers
  Methods in Molecular Biology (Clifton, N.J.). Nov, 2017  |   Pubmed ID: 29116567
• Sulfide Generation by Dominant Microorganisms in Hydraulically Fractured Shales
  MSphere. Jul-Aug, 2017  |   Pubmed ID: 28685163
• Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in
  MBio. 06, 2017  |   Pubmed ID: 28634240
• Targeted Quantification of Functional Enzyme Dynamics in Environmental Samples for Microbially Mediated Biogeochemical Processes
  Environmental Microbiology Reports. Oct, 2017  |   Pubmed ID: 28618201
• Phycobilisome Truncation Causes Widespread Proteome Changes in Synechocystis Sp. PCC 6803
  PloS One. 2017  |   Pubmed ID: 28253354
• Effects of Delayed NSAID Administration After Experimental Eccentric Contraction Injury - A Cellular and Proteomics Study
  PloS One. 2017  |   Pubmed ID: 28245256
• MPLEx: a Method for Simultaneous Pathogen Inactivation and Extraction of Samples for Multi-omics Profiling
  The Analyst. Jan, 2017  |   Pubmed ID: 28091625
• New Roles in Hemicellulosic Sugar Fermentation for the Uncultivated Bacteroidetes Family BS11
  The ISME Journal. 03, 2017  |   Pubmed ID: 27959345
• An Efficient Method for Native Protein Purification in the Selected Range from Prostate Cancer Tissue Digests
  Chinese Clinical Oncology. Dec, 2016  |   Pubmed ID: 28061542
• Proteome Remodeling in Response to Sulfur Limitation in " Pelagibacter Ubique"
  MSystems. Jul-Aug, 2016  |   Pubmed ID: 27822545
• Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes
  MSystems. May-Jun, 2016  |   Pubmed ID: 27822530
• MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses
  MSystems. May-Jun, 2016  |   Pubmed ID: 27822525
• The Fungal Cultivar of Leaf-cutter Ants Produces Specific Enzymes in Response to Different Plant Substrates
  Molecular Ecology. Nov, 2016  |   Pubmed ID: 27696597
• The Abundant Marine Bacterium Pelagibacter Simultaneously Catabolizes Dimethylsulfoniopropionate to the Gases Dimethyl Sulfide and Methanethiol
  Nature Microbiology. 05, 2016  |   Pubmed ID: 27573103
• Comparative Community Proteomics Demonstrates the Unexpected Importance of Actinobacterial Glycoside Hydrolase Family 12 Protein for Crystalline Cellulose Hydrolysis
  MBio. 08, 2016  |   Pubmed ID: 27555310
• Unambiguous Metabolite Identification in High-throughput Metabolomics by Hybrid 1D H NMR/ESI MS Approach
  Magnetic Resonance in Chemistry : MRC. Dec, 2016  |   Pubmed ID: 27539910
• Conservation of Protein Abundance Patterns Reveals the Regulatory Architecture of the EGFR-MAPK Pathway
  Science Signaling. 07, 2016  |   Pubmed ID: 27405981
• Mining the Human Urine Proteome for Monitoring Renal Transplant Injury
  Kidney International. 06, 2016  |   Pubmed ID: 27165815
• Multi-omics Analysis Reveals Regulators of the Response to Nitrogen Limitation in Yarrowia Lipolytica
  BMC Genomics. Feb, 2016  |   Pubmed ID: 26911370
• Integrated Omics Analysis of Pathogenic Host Responses During Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism
  Cell Host & Microbe. Feb, 2016  |   Pubmed ID: 26867183
• Multi-Omic Dynamics Associate Oxygenic Photosynthesis with Nitrogenase-Mediated H2 Production in Cyanothece Sp. ATCC 51142
  Scientific Reports. Nov, 2015  |   Pubmed ID: 26525576
• Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus Gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants
  PloS One. 2015  |   Pubmed ID: 26317212
• Diacyltransferase Activity and Chain Length Specificity of Mycobacterium Tuberculosis PapA5 in the Synthesis of Alkyl β-Diol Lipids
  Biochemistry. Sep, 2015  |   Pubmed ID: 26271001
• Subunit Compositions of Arabidopsis RNA Polymerases I and III Reveal Pol I- and Pol III-specific Forms of the AC40 Subunit and Alternative Forms of the C53 Subunit
  Nucleic Acids Research. Apr, 2015  |   Pubmed ID: 25813043
• Sensitive Targeted Quantification of ERK Phosphorylation Dynamics and Stoichiometry in Human Cells Without Affinity Enrichment
  Analytical Chemistry. Jan, 2015  |   Pubmed ID: 25517423
• Perturbations in the Urinary Exosome in Transplant Rejection
  Frontiers in Medicine. 2014  |   Pubmed ID: 25593928
• Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements
  Molecular & Cellular Proteomics : MCP. Dec, 2014  |   Pubmed ID: 25433089
• Functional Diversification of Maize RNA Polymerase IV and V Subtypes Via Alternative Catalytic Subunits
  Cell Reports. Oct, 2014  |   Pubmed ID: 25284785
• Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements
  Molecular & Cellular Proteomics : MCP. Aug, 2014  |   Pubmed ID: 25129695
• Proteomics Informed by Transcriptomics Identifies Novel Secreted Proteins in Dermacentor Andersoni Saliva
  International Journal for Parasitology. Nov, 2014  |   Pubmed ID: 25110293
• The Fungus Gardens of Leaf-cutter Ants Undergo a Distinct Physiological Transition During Biomass Degradation
  Environmental Microbiology Reports. Aug, 2014  |   Pubmed ID: 24992538
• Proteomic Profiles of Five Strains of Oxygenic Photosynthetic Cyanobacteria of the Genus Cyanothece
  Journal of Proteome Research. Jul, 2014  |   Pubmed ID: 24846609
• Metabolic Interdependencies Between Phylogenetically Novel Fermenters and Respiratory Organisms in an Unconfined Aquifer
  The ISME Journal. Jul, 2014  |   Pubmed ID: 24621521
• Optimization for Peptide Sample Preparation for Urine Peptidomics
  Clinical Proteomics. Feb, 2014  |   Pubmed ID: 24568099
• The Identification of Novel Potential Injury Mechanisms and Candidate Biomarkers in Renal Allograft Rejection by Quantitative Proteomics
  Molecular & Cellular Proteomics : MCP. Feb, 2014  |   Pubmed ID: 24335474
• A Highly Sensitive Targeted Mass Spectrometric Assay for Quantification of AGR2 Protein in Human Urine and Serum
  Journal of Proteome Research. Feb, 2014  |   Pubmed ID: 24251762
• Proteomic and Transcriptomic Analyses of "Candidatus Pelagibacter Ubique" Describe the First PII-independent Response to Nitrogen Limitation in a Free-living Alphaproteobacterium
  MBio. Nov, 2013  |   Pubmed ID: 24281717
• Long-gradient Separations Coupled with Selected Reaction Monitoring for Highly Sensitive, Large Scale Targeted Protein Quantification in a Single Analysis
  Analytical Chemistry. Oct, 2013  |   Pubmed ID: 24004026
• Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass
  PloS One. 2013  |   Pubmed ID: 23894306
• Amino Acid Treatment Enhances Protein Recovery from Sediment and Soils for Metaproteomic Studies
  Proteomics. Oct, 2013  |   Pubmed ID: 23776032
• Development of an Ecophysiological Model for Diplosphaera Colotermitum TAV2, a Termite Hindgut Verrucomicrobium
  The ISME Journal. Sep, 2013  |   Pubmed ID: 23657364
• Trauma-associated Human Neutrophil Alterations Revealed by Comparative Proteomics Profiling
  Proteomics. Clinical Applications. Aug, 2013  |   Pubmed ID: 23589343
• Leucoagaricus Gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-cutter Ant Fungus Gardens
  Applied and Environmental Microbiology. Jun, 2013  |   Pubmed ID: 23584789
• Fluctuations in Species-level Protein Expression Occur During Element and Nutrient Cycling in the Subsurface
  PloS One. 2013  |   Pubmed ID: 23472107
• Suite of Activity-based Probes for Cellulose-degrading Enzymes
  Journal of the American Chemical Society. Dec, 2012  |   Pubmed ID: 23176123
• In Vitro Transcription Activities of Pol IV, Pol V, and RDR2 Reveal Coupling of Pol IV and RDR2 for DsRNA Synthesis in Plant RNA Silencing
  Molecular Cell. Dec, 2012  |   Pubmed ID: 23142082
• A Systematic Analysis of a Deep Mouse Epididymal Sperm Proteome
  Biology of Reproduction. Jun, 2012  |   Pubmed ID: 23115268
• Metagenomic and Metaproteomic Insights into Bacterial Communities in Leaf-cutter Ant Fungus Gardens
  The ISME Journal. Sep, 2012  |   Pubmed ID: 22378535
• Simple Sodium Dodecyl Sulfate-assisted Sample Preparation Method for LC-MS-based Proteomics Applications
  Analytical Chemistry. Mar, 2012  |   Pubmed ID: 22339560
• Analisi Dinamica Proteome Di Cyanothece SP. ATCC 51142 Sotto Luce Costante
  Journal of Proteome Research. Feb, 2012  |   Pubmed ID: 22060561
• Time-course Analysis of the Shewanella Amazonensis SB2B Proteome in Response to Sodium Chloride Shock
  Scientific Reports. 2011  |   Pubmed ID: 22355544
• Trypsin-catalyzed Oxygen-18 Labeling for Quantitative Proteomics
  Methods in Molecular Biology (Clifton, N.J.). 2011  |   Pubmed ID: 21604114
• Ritmi Diurni Causare Cambiamenti Significativi in Complemento in Cyanobacterium Cyanothece 51142 Proteina Cellulare
  PloS One. 2011  |   Pubmed ID: 21364985
• Development of a Biomarker for Geobacter Activity and Strain Composition; Proteogenomic Analysis of the Citrate Synthase Protein During Bioremediation of U(VI)
  Microbial Biotechnology. Jan, 2011  |   Pubmed ID: 21255372
• Proteome Insights into the Symbiotic Relationship Between a Captive Colony of Nasutitermes Corniger and Its Hindgut Microbiome
  The ISME Journal. Jan, 2011  |   Pubmed ID: 20613792
• Proteome Analysis of Borrelia Burgdorferi Response to Environmental Change
  PloS One. Nov, 2010  |   Pubmed ID: 21072190
• Analysis of Biostimulated Microbial Communities from Two Field Experiments Reveals Temporal and Spatial Differences in Proteome Profiles
  Environmental Science & Technology. Dec, 2010  |   Pubmed ID: 21058662
• Transcriptional and Translational Regulatory Responses to Iron Limitation in the Globally Distributed Marine Bacterium Candidatus Pelagibacter Ubique
  PloS One. May, 2010  |   Pubmed ID: 20463970
• Proteomic Detection of Non-annotated Protein-coding Genes in Pseudomonas Fluorescens Pf0-1
  PloS One. Dec, 2009  |   Pubmed ID: 20041161
• Proteogenomic Monitoring of Geobacter Physiology During Stimulated Uranium Bioremediation
  Applied and Environmental Microbiology. Oct, 2009  |   Pubmed ID: 19717633
• Subunit Compositions of the RNA-silencing Enzymes Pol IV and Pol V Reveal Their Origins As Specialized Forms of RNA Polymerase II
  Molecular Cell. Jan, 2009  |   Pubmed ID: 19110459
• Proteomic Analysis of Stationary Phase in the Marine Bacterium "Candidatus Pelagibacter Ubique"
  Applied and Environmental Microbiology. Jul, 2008  |   Pubmed ID: 18469119
• Application of the Accurate Mass and Time Tag Approach to the Proteome Analysis of Sub-cellular Fractions Obtained from Rhodobacter Sphaeroides 2.4.1. Aerobic and Photosynthetic Cell Cultures
  Journal of Proteome Research. Aug, 2006  |   Pubmed ID: 16889416
• Comparison of Aerobic and Photosynthetic Rhodobacter Sphaeroides 2.4.1 Proteomes
  Journal of Microbiological Methods. Dec, 2006  |   Pubmed ID: 16828186
• Phosphoproteome Profiling of Human Skin Fibroblast Cells in Response to Low- and High-dose Irradiation
  Journal of Proteome Research. May, 2006  |   Pubmed ID: 16674116