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List of works by Carrie D Nicora

A compendium of multi-omics data illuminating host responses to lethal human virus infections

scientific article published in 2024

A highly sensitive targeted mass spectrometric assay for quantification of AGR2 protein in human urine and serum

scientific article

A systematic analysis of a deep mouse epididymal sperm proteome

scientific article published on June 2012

Addressing the challenge of soil metaproteome complexity by improving metaproteome depth of coverage through two-dimensional liquid chromatography

scholarly article by Stephen J. Callister et al published October 2018 in Soil Biology and Biochemistry

Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies.

scientific article published on 16 August 2013

An efficient method for native protein purification in the selected range from prostate cancer tissue digests.

scientific article published on December 2016

Analysis of biostimulated microbial communities from two field experiments reveals temporal and spatial differences in proteome profiles

scientific article

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

scientific article published on August 2006

Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data

scientific article published on 09 November 2020

Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements

scientific article published on 16 August 2014

Bayesian proteoform modeling improves protein quantification of global proteomic measurements.

scientific article

Broad Substrate-Specific Phosphorylation Events Are Associated With the Initial Stage of Plant Cell Wall Recognition in Neurospora crassa

scientific article published on 01 November 2019

Carrier-Assisted Single-Tube Processing Approach for Targeted Proteomics Analysis of Low Numbers of Mammalian Cells

scientific article published on 28 December 2018

Characterizing microbial community and geochemical dynamics at hydrothermal vents using osmotically driven continuous fluid samplers

scientific article published on 5 April 2013

Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation

scientific article published on 06 January 2020

Comparative Community Proteomics Demonstrates the Unexpected Importance of Actinobacterial Glycoside Hydrolase Family 12 Protein for Crystalline Cellulose Hydrolysis.

scientific article

Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes

scientific article published on 7 July 2006

Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway

scientific article published on 12 July 2016

Correction: Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants

scientific article published on 23 September 2015

Corrigendum: The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol

scientific article published on 03 October 2016

Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales

article published in the Proceedings of the National Academy of Sciences of the United States of America

Decrypting bacterial polyphenol metabolism in an anoxic wetland soil

scientific article published on 29 April 2021

Deep-Subsurface Pressure Stimulates Metabolic Plasticity in Shale-Colonizing Halanaerobium spp.

scientific article

Detection of Organohalide-Respiring Enzyme Biomarkers at a Bioaugmented TCE-Contaminated Field Site

scientific article published on 27 June 2019

Development of a biomarker for Geobacter activity and strain composition; proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI)

scientific article published on January 2011

Development of an ecophysiological model for Diplosphaera colotermitum TAV2, a termite hindgut Verrucomicrobium

scientific article published on 09 May 2013

Diacyltransferase Activity and Chain Length Specificity of Mycobacterium tuberculosis PapA5 in the Synthesis of Alkyl β-Diol Lipids

scientific article

Diurnal rhythms result in significant changes in the cellular protein complement in the cyanobacterium Cyanothece 51142.

scientific article

Dynamic Proteome Analysis of Cyanothece sp. ATCC 51142 under Constant Light

article

Ectomycorrhizal fungi enhance pine growth by stimulating iron‐dependent mechanisms with trade‐offs in symbiotic performance

scientific article published in 2023

Effects of delayed NSAID administration after experimental eccentric contraction injury – A cellular and proteomics study

scientific article (publication date: 28 February 2017)

Elucidating regulatory processes of intense physical activity by multi-omics analysis

journal article published in 2023

Endophyte-Promoted Phosphorus Solubilization in Populus

scientific article published on 21 October 2020

Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants

scientific article

Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1.

scientific article published on 19 September 2013

Exploiting the Semidestructive Nature of Gas Cluster Ion Beam Time-of-Flight Secondary Ion Mass Spectrometry Imaging for Simultaneous Localization and Confident Lipid Annotations

scientific article published on 11 November 2019

Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells

scientific article published on 06 August 2018

Fluctuations in species-level protein expression occur during element and nutrient cycling in the subsurface

scientific article

Functional diversification of maize RNA polymerase IV and V subtypes via alternative catalytic subunits

scientific article

Genome-Resolved Metaproteomics Decodes the Microbial and Viral Contributions to Coupled Carbon and Nitrogen Cycling in River Sediments

scientific article published in 2022

Genome-centric view of carbon processing in thawing permafrost

scientific article published in Nature

Genomes and secretomes of Ascomycota fungi reveal diverse functions in plant biomass decomposition and pathogenesis

scientific article published on 12 December 2019

Global proteomic analysis of the chromate response in Arthrobacter sp. strain FB24.

scientific article published in April 2009

Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle

scientific article published on 11 March 2019

In situ transformation of ethoxylate and glycol surfactants by shale-colonizing microorganisms during hydraulic fracturing

scientific article published on 26 June 2019

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

scientific article

Insights into the histology of planarian flatworm Phagocata gracilis based on location specific, intact lipid information provided by GCIB-ToF-SIMS imaging

scientific article published on 04 February 2019

Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism.

scientific article

Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations

scientific article published on 02 July 2020

Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem

article

Ion Mobility Spectrometry and the Omics: Distinguishing Isomers, Molecular Classes and Contaminant Ions in Complex Samples

scientific article published on 29 April 2019

LC-SRM-Based Targeted Quantification of Urinary Protein Biomarkers.

scientific article

Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica

scientific article

Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens

scientific article (publication date: June 2013)

Lignin induced iron reduction by novel sp., Tolumonas lignolytic BRL6-1

scientific article published on 17 September 2020

Long-gradient separations coupled with selected reaction monitoring for highly sensitive, large scale targeted protein quantification in a single analysis.

scientific article published on 19 September 2013

MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape

scientific article published on 16 January 2018

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

scientific article published on 10 May 2016

MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling

scientific article published on 16 January 2017

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

scientific article

Metabolite, Protein, and Lipid Extraction (MPLEx): A Method that Simultaneously Inactivates Middle East Respiratory Syndrome Coronavirus and Allows Analysis of Multiple Host Cell Components Following Infection

scientific article published on 01 January 2020

Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens

scientific article

Mining the human urine proteome for monitoring renal transplant injury

scientific article published on 04 March 2016

Moisture modulates soil reservoirs of active DNA and RNA viruses

scientific article published on 26 August 2021

Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes

scientific article

Multi 'omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone

scientific article published on 17 June 2018

Multi omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone

article

Multi-Omic Dynamics Associate Oxygenic Photosynthesis with Nitrogenase-Mediated H2 Production in Cyanothece sp. ATCC 51142

scientific article

Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica

scientific article

Multiomics resolution of molecular events during a day in the life of Chlamydomonas

article published in the Proceedings of the National Academy of Sciences of the United States of America

Multiplexed targeted mass spectrometry assays for prostate cancer-associated urinary proteins

scientific article published on 9 October 2017

New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11

scientific article published on 13 December 2016

Optimization for Peptide Sample Preparation for Urine Peptidomics

scientific article published on 01 January 2018

Optimization for peptide sample preparation for urine peptidomics

scientific article published on 25 February 2014

Perturbations in the urinary exosome in transplant rejection

scientific article

Phosphoproteome profiling of human skin fibroblast cells in response to low- and high-dose irradiation

scientific article published in May 2006

Phycobilisome truncation causes widespread proteome changes in Synechocystis sp. PCC 6803

scientific article

Production of ent-kaurene from lignocellulosic hydrolysate in Rhodosporidium toruloides

scientific article published on 05 February 2020

Protein and microRNA biomarkers from lavage, urine, and serum in military personnel evaluated for dyspnea

scientific article

Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass

scientific article (publication date: 2013)

Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation

scientific article published on 28 August 2009

Proteome Remodeling in Response to Sulfur Limitation in "Candidatus Pelagibacter ubique".

scientific article published on 12 July 2016

Proteome analysis of Borrelia burgdorferi response to environmental change

scientific article

Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome

scientific article

Proteomic Insights into Phycobilisome Degradation, A Selective and Tightly Controlled Process in The Fast-Growing Cyanobacterium Synechococcus elongatus UTEX 2973

scientific article published on 16 August 2019

Proteomic analysis of stationary phase in the marine bacterium "Candidatus Pelagibacter ubique".

scientific article

Proteomic and transcriptomic analyses of "Candidatus Pelagibacter ubique" describe the first PII-independent response to nitrogen limitation in a free-living Alphaproteobacterium

scientific article

Proteomic detection of non-annotated protein-coding genes in Pseudomonas fluorescens Pf0-1.

scientific article

Proteomic profiles of five strains of oxygenic photosynthetic cyanobacteria of the genus Cyanothece

scientific article published on 4 June 2014

Proteomics informed by transcriptomics identifies novel secreted proteins in Dermacentor andersoni saliva.

scientific article published on 7 August 2014

Rare Earth Elements Alter Redox Balance in 20Z

scientific article published on 27 November 2018

Re-routing of Sugar Catabolism Provides a Better Insight Into Fungal Flexibility in Using Plant Biomass-Derived Monomers as Substrates

scientific article published on 08 March 2021

Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells

scientific article published on 21 October 2020

Salmonella-Mediated Inflammation Eliminates Competitors for Fructose-Asparagine in the Gut.

scientific article

Sensitive targeted quantification of ERK phosphorylation dynamics and stoichiometry in human cells without affinity enrichment

scientific article

Simple sodium dodecyl sulfate-assisted sample preparation method for LC-MS-based proteomics applications

scientific article published on 2 March 2012

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.

scientific article published on 26 March 2015

Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II

scientific article

Suite of activity-based probes for cellulose-degrading enzymes

scientific article (publication date: 19 December 2012)

Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales

scientific article

Synthetic Soil Aggregates: Bioprinted Habitats for High-Throughput Microbial Metaphenomics

scientific article published on 30 April 2022

Tandem Mass Tag Labeling Facilitates Reversed-Phase Liquid Chromatography-Mass Spectrometry Analysis of Hydrophilic Phosphopeptides

scientific article published on 28 August 2019

Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes

scientific article published on 15 June 2017

The MPLEx Protocol for Multi-omic Analyses of Soil Samples

scientific article published on 30 May 2018

The Specific Carbohydrate Diet and Diet Modification as Induction Therapy for Pediatric Crohn's Disease: A Randomized Diet Controlled Trial

scientific article published on 06 December 2020

The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol.

scientific article

The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates

scientific article

The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation

scientific article

The identification of novel potential injury mechanisms and candidate biomarkers in renal allograft rejection by quantitative proteomics

scientific article published on 12 December 2013

Time-course analysis of the Shewanella amazonensis SB2B proteome in response to sodium chloride shock

scientific article published on 29 June 2011

Transcriptional and translational regulatory responses to iron limitation in the globally distributed marine bacterium Candidatus pelagibacter ubique

scientific article

Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea.

scientific article published on 4 September 2008

Trauma-associated human neutrophil alterations revealed by comparative proteomics profiling

scientific article published on 22 May 2013

Trypsin-catalyzed oxygen-18 labeling for quantitative proteomics

scientific article published on 01 January 2011

Urinary Virome Perturbations in Kidney Transplantation.

scientific article

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