Carrie D. Nicora

Biological Sciences Division, Pacific Northwest National Laboratory

Affiliated withPacific Northwest National Laboratory

Research Area

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 31	2018

Other Publications

Article	Year
Phosphoproteome profiling of human skin fibroblast cells in response to low- and high-dose irradiation. Journal of proteome research\| PubMed ID: 16674116	2006
Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes. Journal of microbiological methods\| PubMed ID: 16828186	2006
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 culture... Journal of proteome research\| PubMed ID: 16889416	2006
Proteomic analysis of stationary phase in the marine bacterium "Candidatus Pelagibacter ubique". Applied and environmental microbiology\| PubMed ID: 18469119	2008
Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II. Molecular cell\| PubMed ID: 19110459	2009
Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation. Applied and environmental microbiology\| PubMed ID: 19717633	2009
Proteomic detection of non-annotated protein-coding genes in Pseudomonas fluorescens Pf0-1. PloS one\| PubMed ID: 20041161	2009
Transcriptional and translational regulatory responses to iron limitation in the globally distributed marine bacterium Candidatus pelagibacter ubique. PloS one\| PubMed ID: 20463970	2010
Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome. The ISME journal\| PubMed ID: 20613792	2011
Analysis of biostimulated microbial communities from two field experiments reveals temporal and spatial differences in proteome profiles. Environmental science & technology\| PubMed ID: 21058662	2010
Proteome analysis of Borrelia burgdorferi response to environmental change. PloS one\| PubMed ID: 21072190	2010
Development of a biomarker for Geobacter activity and strain composition; proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI). Microbial biotechnology\| PubMed ID: 21255372	2011
Diurnal rhythms result in significant changes in the cellular protein complement in the cyanobacterium Cyanothece 51142. PloS one\| PubMed ID: 21364985	2011
Trypsin-catalyzed oxygen-18 labeling for quantitative proteomics. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 21604114	2011
Dynamic Proteome Analysis of Cyanothece sp. ATCC 51142 under Constant Light. Journal of proteome research\| PubMed ID: 22060561	2012
Simple sodium dodecyl sulfate-assisted sample preparation method for LC-MS-based proteomics applications. Analytical chemistry\| PubMed ID: 22339560	2012
Time-course analysis of the Shewanella amazonensis SB2B proteome in response to sodium chloride shock. Scientific reports\| PubMed ID: 22355544	2011
Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens. The ISME journal\| PubMed ID: 22378535	2012
A systematic analysis of a deep mouse epididymal sperm proteome. Biology of reproduction\| PubMed ID: 23115268	2012
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\| PubMed ID: 23142082	2012
Suite of activity-based probes for cellulose-degrading enzymes. Journal of the American Chemical Society\| PubMed ID: 23176123	2012
Fluctuations in species-level protein expression occur during element and nutrient cycling in the subsurface. PloS one\| PubMed ID: 23472107	2013
Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens. Applied and environmental microbiology\| PubMed ID: 23584789	2013
Trauma-associated human neutrophil alterations revealed by comparative proteomics profiling. Proteomics. Clinical applications\| PubMed ID: 23589343	2013
Development of an ecophysiological model for Diplosphaera colotermitum TAV2, a termite hindgut Verrucomicrobium. The ISME journal\| PubMed ID: 23657364	2013
Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies. Proteomics\| PubMed ID: 23776032	2013
Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. PloS one\| PubMed ID: 23894306	2013
Long-gradient separations coupled with selected reaction monitoring for highly sensitive, large scale targeted protein quantification in a single analysis. Analytical chemistry\| PubMed ID: 24004026	2013
A highly sensitive targeted mass spectrometric assay for quantification of AGR2 protein in human urine and serum. Journal of proteome research\| PubMed ID: 24251762	2014
Proteomic and transcriptomic analyses of "Candidatus Pelagibacter ubique" describe the first PII-independent response to nitrogen limitation in a free-living Alphaproteobacterium. mBio\| PubMed ID: 24281717	2013
The identification of novel potential injury mechanisms and candidate biomarkers in renal allograft rejection by quantitative proteomics. Molecular & cellular proteomics : MCP\| PubMed ID: 24335474	2014
Optimization for peptide sample preparation for urine peptidomics. Clinical proteomics\| PubMed ID: 24568099	2014
Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer. The ISME journal\| PubMed ID: 24621521	2014
Proteomic profiles of five strains of oxygenic photosynthetic cyanobacteria of the genus Cyanothece. Journal of proteome research\| PubMed ID: 24846609	2014
The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation. Environmental microbiology reports\| PubMed ID: 24992538	2014
Proteomics informed by transcriptomics identifies novel secreted proteins in Dermacentor andersoni saliva. International journal for parasitology\| PubMed ID: 25110293	2014
Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements. Molecular & cellular proteomics : MCP\| PubMed ID: 25129695	2014
Functional diversification of maize RNA polymerase IV and V subtypes via alternative catalytic subunits. Cell reports\| PubMed ID: 25284785	2014
Bayesian proteoform modeling improves protein quantification of global proteomic measurements. Molecular & cellular proteomics : MCP\| PubMed ID: 25433089	2014
Sensitive targeted quantification of ERK phosphorylation dynamics and stoichiometry in human cells without affinity enrichment. Analytical chemistry\| PubMed ID: 25517423	2015
Perturbations in the urinary exosome in transplant rejection. Frontiers in medicine\| PubMed ID: 25593928	2014
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\| PubMed ID: 25813043	2015
Diacyltransferase Activity and Chain Length Specificity of Mycobacterium tuberculosis PapA5 in the Synthesis of Alkyl β-Diol Lipids. Biochemistry\| PubMed ID: 26271001	2015
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\| PubMed ID: 26317212	2015
Multi-Omic Dynamics Associate Oxygenic Photosynthesis with Nitrogenase-Mediated H2 Production in Cyanothece sp. ATCC 51142. Scientific reports\| PubMed ID: 26525576	2015
Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism. Cell host & microbe\| PubMed ID: 26867183	2016
Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica. BMC genomics\| PubMed ID: 26911370	2016
Mining the human urine proteome for monitoring renal transplant injury. Kidney international\| PubMed ID: 27165815	2016
Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway. Science signaling\| PubMed ID: 27405981	2016
Unambiguous metabolite identification in high-throughput metabolomics by hybrid 1D H NMR/ESI MS approach. Magnetic resonance in chemistry : MRC\| PubMed ID: 27539910	2016
Comparative Community Proteomics Demonstrates the Unexpected Importance of Actinobacterial Glycoside Hydrolase Family 12 Protein for Crystalline Cellulose Hydrolysis. mBio\| PubMed ID: 27555310	2016
The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol. Nature microbiology\| PubMed ID: 27573103	2016
The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates. Molecular ecology\| PubMed ID: 27696597	2016
MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses. mSystems\| PubMed ID: 27822525	2016
Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes. mSystems\| PubMed ID: 27822530	2016
Proteome Remodeling in Response to Sulfur Limitation in " Pelagibacter ubique". mSystems\| PubMed ID: 27822545	2016
New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11. The ISME journal\| PubMed ID: 27959345	2017
An efficient method for native protein purification in the selected range from prostate cancer tissue digests. Chinese clinical oncology\| PubMed ID: 28061542	2016
MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling. The Analyst\| PubMed ID: 28091625	2017
Effects of delayed NSAID administration after experimental eccentric contraction injury - A cellular and proteomics study. PloS one\| PubMed ID: 28245256	2017
Phycobilisome truncation causes widespread proteome changes in Synechocystis sp. PCC 6803. PloS one\| PubMed ID: 28253354	2017
Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes. Environmental microbiology reports\| PubMed ID: 28618201	2017
Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in . mBio\| PubMed ID: 28634240	2017
Sulfide Generation by Dominant Microorganisms in Hydraulically Fractured Shales. mSphere\| PubMed ID: 28685163	2017
LC-SRM-Based Targeted Quantification of Urinary Protein Biomarkers. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 29116567	2017
Multiplexed targeted mass spectrometry assays for prostate cancer-associated urinary proteins. Oncotarget\| PubMed ID: 29254211	2017
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\| PubMed ID: 29339515	2018
Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction. Metabolites\| PubMed ID: 29342073	2018
Salmonella-Mediated Inflammation Eliminates Competitors for Fructose-Asparagine in the Gut. Infection and immunity\| PubMed ID: 29483291	2018
Optimization for Peptide Sample Preparation for Urine Peptidomics. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 29623538	2018
Urinary Virome Perturbations in Kidney Transplantation. Frontiers in medicine\| PubMed ID: 29725592	2018