List of works - Katrina M. Waters

A Statistical Analysis of the Effects of Urease Pre-treatment on the Measurement of the Urinary Metabolome by Gas Chromatography-Mass Spectrometry ⬇️

scientific article

A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments.

scientific article

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

scientific article published in 2024

A comprehensive collection of systems biology data characterizing the host response to viral infection.

scientific article

A network integration approach to predict conserved regulators related to pathogenicity of influenza and SARS-CoV respiratory viruses

scientific article

A statistical selection strategy for normalization procedures in LC-MS proteomics experiments through dataset-dependent ranking of normalization scaling factors.

scientific article

A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics.

scientific article published on July 2010

AHR2 mutant reveals functional diversity of aryl hydrocarbon receptors in zebrafish

scientific article

Accumulation of CD11b⁺Gr-1⁺ cells in the lung, blood and bone marrow of mice infected with highly pathogenic H5N1 and H1N1 influenza viruses

scientific article

An approach for calculating a confidence interval from a single aquatic sample for monitoring hydrophobic organic contaminants ⬇️

scientific article published on October 20, 2012

Analytics challenge---High-throughput visual analytics biological sciences

article

Annexin A2 modulates radiation-sensitive transcriptional programming and cell fate

scientific article published on 13 November 2012

Association of carcinogenic polycyclic aromatic hydrocarbon emissions and smoking with lung cancer mortality rates on a global scale.

scientific article published on 8 March 2013

Atomic Force Microscopy and Infrared Nanospectroscopy of COVID-19 Spike Protein for the Quantification of Adhesion to Common Surfaces

scientific article published on 05 October 2021

Bayesian proteoform modeling improves protein quantification of global proteomic measurements.

scientific article

Bone growth and turnover in progesterone receptor knockout mice

scientific article published on 14 February 2008

Cellular dichotomy between anchorage-independent growth responses to bFGF and TPA reflects molecular switch in commitment to carcinogenesis.

scientific article

Combination Attenuation Offers Strategy for Live Attenuated Coronavirus Vaccines

scholarly article by Vineet D. Menachery published in September 2018

Combination attenuation offers strategy for live-attenuated coronavirus vaccines

scholarly article published 28 April 2018

Combined statistical analyses of peptide intensities and peptide occurrences improves identification of significant peptides from MS-based proteomics data

scientific article

Comparative developmental toxicity of environmentally relevant oxygenated PAHs.

scientific article published on 14 May 2013

Comparative iron oxide nanoparticle cellular dosimetry and response in mice by the inhalation and liquid cell culture exposure routes

scientific article

Comparative proteomics and pulmonary toxicity of instilled single-walled carbon nanotubes, crocidolite asbestos, and ultrafine carbon black in mice

journal article published in 2011

Completing the Link between Exposure Science and Toxicology for Improved Environmental Health Decision Making: The Aggregate Exposure Pathway Framework.

scientific article published on 13 January 2016

Conserved host response to highly pathogenic avian influenza virus infection in human cell culture, mouse and macaque model systems

scientific article

Controlling the response: predictive modeling of a highly central, pathogen-targeted core response module in macrophage activation

scientific article

Coupling Genome-wide Transcriptomics and Developmental Toxicity Profiles in Zebrafish to Characterize Polycyclic Aromatic Hydrocarbon (PAH) Hazard.

scientific article published on 25 May 2019

Cytochrome P450 1b1 in polycyclic aromatic hydrocarbon (PAH)-induced skin carcinogenesis: Tumorigenicity of individual PAHs and coal-tar extract, DNA adduction and expression of select genes in the Cyp1b1 knockout mouse

scientific article

DNA microarray analysis reveals a role for lysophosphatidic acid in the regulation of anti-inflammatory genes in MC3T3-E1 cells.

scientific article published on August 2007

Data merging for integrated microarray and proteomic analysis

scientific article

Dibenzo[def,p]chrysene transplacental carcinogenesis in wild-type, Cyp1b1 knockout, and CYP1B1 humanized mice.

scientific article

Diet-induced obesity reprograms the inflammatory response of the murine lung to inhaled endotoxin

scientific article published on 7 January 2013

Differential gene expression in response to methoxychlor and estradiol through ERalpha, ERbeta, and AR in reproductive tissues of female mice.

scientific article published on September 2001

Discovery of common chemical exposures across three continents using silicone wristbands

scientific article published on 06 February 2019

Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics

scientific article

ERK oscillation-dependent gene expression patterns and deregulation by stress response

journal article published in 2014

Early life stage trimethyltin exposure induces ADP-ribosylation factor expression and perturbs the vascular system in zebrafish

scientific article

Effect of Native American fish smoking methods on dietary exposure to polycyclic aromatic hydrocarbons and possible risks to human health.

scientific article published on 27 June 2012

Enabling high-throughput data management for systems biology: the Bioinformatics Resource Manager

scientific article

Estrogen Regulation of a Transforming Growth Factor-β Inducible Early Gene That Inhibits Deoxyribonucleic Acid Synthesis in Human Osteoblasts* ⬇️

scientific article published on March 1, 1998

Estrogen regulation of human osteoblast function is determined by the stage of differentiation and the estrogen receptor isoform.

scientific article

Expanding on Successful Concepts, Models, and Organization

scientific article published on 10 August 2016

Genetic and epigenetic changes in chromosomally stable and unstable progeny of irradiated cells

scientific article

Host regulatory network response to infection with highly pathogenic H5N1 avian influenza virus

scientific article

How Adverse Outcome Pathways Can Aid the Development and Use of Computational Prediction Models for Regulatory Toxicology

scientific article published on 19 December 2016

Impaired transcriptional response of the murine heart to cigarette smoke in the setting of high fat diet and obesity

scientific article

Implications of Bioremediation of Polycyclic Aromatic Hydrocarbon-Contaminated Soils for Human Health and Cancer Risk.

scientific article

Improved quality control processing of peptide-centric LC-MS proteomics data

scientific article

Influenza-Omics and the Host Response: Recent Advances and Future Prospects

scientific article

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

scientific article

Integration of data systems and technology improves research and collaboration for a superfund research center.

scientific article

Integrative transcriptomic and proteomic analysis of osteocytic cells exposed to fluid flow reveals novel mechano-sensitive signaling pathways

scientific article

Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models

scientific article

Ligand-Specific Transcriptional Mechanisms Underlie Aryl Hydrocarbon Receptor-Mediated Developmental Toxicity of Oxygenated PAHs.

scientific article

Localization of a polyunsaturated fatty acid response region in stearoyl-CoA desaturase gene 1.

scientific article published on November 1997

MERS-CoV Accessory ORFs Play Key Role for Infection and Pathogenesis

scientific article published on 22 August 2017

MERS-CoV NSP16 necessary for IFN resistance and viral pathogenesis

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

scientific article published on 16 January 2018

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

scientific article published on 16 January 2017

Macrophage responses to silica nanoparticles are highly conserved across particle sizes

scientific article published on 10 December 2008

Mechanism-Based Classification of PAH Mixtures to Predict Carcinogenic Potential

scientific article

Mechanisms of severe acute respiratory syndrome coronavirus-induced acute lung injury

scientific article published on 06 August 2013

Middle East Respiratory Syndrome Coronavirus Nonstructural Protein 16 Is Necessary for Interferon Resistance and Viral Pathogenesis

scientific article published on 15 November 2017

Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis

scientific article published on 15 November 2017

Network analysis of epidermal growth factor signaling using integrated genomic, proteomic and phosphorylation data

scientific article

P-Mart: Interactive Analysis of Ion Abundance Global Proteomics Data

scientific article published on 06 February 2019

Pathogenic influenza viruses and coronaviruses utilize similar and contrasting approaches to control interferon-stimulated gene responses.

scientific article

Phenotypically anchored transcriptome profiling of developmental exposure to the antimicrobial agent, triclosan, reveals hepatotoxicity in embryonic zebrafish

scientific article

Phosphoproteomics profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing radiation

scientific article

Proteome and computational analyses reveal new insights into the mechanisms of hepatitis C virus-mediated liver disease posttransplantation

scientific article

Proteomic analysis reveals down-regulation of surfactant protein B in murine type II pneumocytes infected with influenza A virus.

scientific article published on 15 May 2015

Quantitative phosphoproteome analysis of lysophosphatidic acid induced chemotaxis applying dual-step (18)O labeling coupled with immobilized metal-ion affinity chromatography.

scientific article published on 12 September 2008

Quantitative phosphoproteomics identifies filaggrin and other targets of ionizing radiation in a human skin model.

scientific article

Quantitative proteomic analysis of mitochondrial proteins reveals prosurvival mechanisms in the perpetuation of radiation-induced genomic instability.

scientific article

Regulation of gene expression and subcellular protein distribution in MLO-Y4 osteocytic cells by lysophosphatidic acid: Relevance to dendrite outgrowth

scientific article

Regulation of hepatic stearoyl-CoA desaturase gene 1 by vitamin A

scientific article published on 01 February 1997

Relative Influence of Trans-Pacific and Regional Atmospheric Transport of PAHs in the Pacific Northwest, U.S.

scientific article

Release of severe acute respiratory syndrome coronavirus nuclear import block enhances host transcription in human lung cells

scientific article published on 30 January 2013

Retinoic acid-dependent regulation of miR-19 expression elicits vertebrate axis defects.

scientific article published on 23 August 2013

Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics

scientific article published on 22 April 2015

Sequential projection pursuit principal component analysis--dealing with missing data associated with new -omics technologies

scientific article

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

scientific article (publication date: 9 August 2016)

Silymarin Suppresses Cellular Inflammation By Inducing Reparative Stress Signaling

scientific article

Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice

scientific article

Statistically Driven Metabolite and Lipid Profiling of Patients from the Undiagnosed Diseases Network

scientific article published on 05 December 2019

Surface functionalities of gold nanoparticles impact embryonic gene expression responses.

scientific article

Systems virology identifies a mitochondrial fatty acid oxidation enzyme, dodecenoyl coenzyme A delta isomerase, required for hepatitis C virus replication and likely pathogenesis

scientific article

Temporal Proteome and Lipidome Profiles Reveal Hepatitis C Virus-Associated Reprogramming of Hepatocellular Metabolism and Bioenergetics

scientific article (publication date: 2010)

The Role of EGFR in Influenza Pathogenicity: Multiple Network-Based Approaches to Identify a Key Regulator of Non-lethal Infections

scientific article published on 20 September 2019

The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus

scientific article

The effects of low-dose irradiation on inflammatory response proteins in a 3D reconstituted human skin tissue model.

scientific article published on 3 October 2012

The landscape of viral proteomics and its potential to impact human health

scientific article published on 30 April 2016

The mammary epithelial cell secretome and its regulation by signal transduction pathways

scientific article published in January 2008

The multi-dimensional embryonic zebrafish platform predicts flame retardant bioactivity

scientific article published on 19 August 2020

Time-dependent behavioral data from zebrafish reveals novel signatures of chemical toxicity using point of departure analysis

scientific article published on 10 November 2018

Topological analysis of protein co-abundance networks identifies novel host targets important for HCV infection and pathogenesis

scientific article

Unified feature association networks through integration of transcriptomic and proteomic data

scientific article published on 17 September 2019

pmartR: Quality Control and Statistics for Mass Spectrometry-Based Biological Data

scientific article published on 28 January 2019

List of works by Katrina M. Waters

A Statistical Analysis of the Effects of Urease Pre-treatment on the Measurement of the Urinary Metabolome by Gas Chromatography-Mass Spectrometry ⬇️

A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments.

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

A comprehensive collection of systems biology data characterizing the host response to viral infection.

A network integration approach to predict conserved regulators related to pathogenicity of influenza and SARS-CoV respiratory viruses

A statistical selection strategy for normalization procedures in LC-MS proteomics experiments through dataset-dependent ranking of normalization scaling factors.

A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics.

AHR2 mutant reveals functional diversity of aryl hydrocarbon receptors in zebrafish

Accumulation of CD11b⁺Gr-1⁺ cells in the lung, blood and bone marrow of mice infected with highly pathogenic H5N1 and H1N1 influenza viruses

An approach for calculating a confidence interval from a single aquatic sample for monitoring hydrophobic organic contaminants ⬇️

Analytics challenge---High-throughput visual analytics biological sciences

Annexin A2 modulates radiation-sensitive transcriptional programming and cell fate

Association of carcinogenic polycyclic aromatic hydrocarbon emissions and smoking with lung cancer mortality rates on a global scale.

Atomic Force Microscopy and Infrared Nanospectroscopy of COVID-19 Spike Protein for the Quantification of Adhesion to Common Surfaces

Bayesian proteoform modeling improves protein quantification of global proteomic measurements.

Bone growth and turnover in progesterone receptor knockout mice

Cellular dichotomy between anchorage-independent growth responses to bFGF and TPA reflects molecular switch in commitment to carcinogenesis.

Combination Attenuation Offers Strategy for Live Attenuated Coronavirus Vaccines

Combination attenuation offers strategy for live-attenuated coronavirus vaccines

Combined statistical analyses of peptide intensities and peptide occurrences improves identification of significant peptides from MS-based proteomics data

Comparative developmental toxicity of environmentally relevant oxygenated PAHs.

Comparative iron oxide nanoparticle cellular dosimetry and response in mice by the inhalation and liquid cell culture exposure routes

Comparative proteomics and pulmonary toxicity of instilled single-walled carbon nanotubes, crocidolite asbestos, and ultrafine carbon black in mice

Completing the Link between Exposure Science and Toxicology for Improved Environmental Health Decision Making: The Aggregate Exposure Pathway Framework.

Conserved host response to highly pathogenic avian influenza virus infection in human cell culture, mouse and macaque model systems

Controlling the response: predictive modeling of a highly central, pathogen-targeted core response module in macrophage activation

Coupling Genome-wide Transcriptomics and Developmental Toxicity Profiles in Zebrafish to Characterize Polycyclic Aromatic Hydrocarbon (PAH) Hazard.

Cytochrome P450 1b1 in polycyclic aromatic hydrocarbon (PAH)-induced skin carcinogenesis: Tumorigenicity of individual PAHs and coal-tar extract, DNA adduction and expression of select genes in the Cyp1b1 knockout mouse

DNA microarray analysis reveals a role for lysophosphatidic acid in the regulation of anti-inflammatory genes in MC3T3-E1 cells.

Data merging for integrated microarray and proteomic analysis

Dibenzo[def,p]chrysene transplacental carcinogenesis in wild-type, Cyp1b1 knockout, and CYP1B1 humanized mice.

Diet-induced obesity reprograms the inflammatory response of the murine lung to inhaled endotoxin

Differential gene expression in response to methoxychlor and estradiol through ERalpha, ERbeta, and AR in reproductive tissues of female mice.

Discovery of common chemical exposures across three continents using silicone wristbands

Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics

ERK oscillation-dependent gene expression patterns and deregulation by stress response

Early life stage trimethyltin exposure induces ADP-ribosylation factor expression and perturbs the vascular system in zebrafish

Effect of Native American fish smoking methods on dietary exposure to polycyclic aromatic hydrocarbons and possible risks to human health.

Enabling high-throughput data management for systems biology: the Bioinformatics Resource Manager

Estrogen Regulation of a Transforming Growth Factor-β Inducible Early Gene That Inhibits Deoxyribonucleic Acid Synthesis in Human Osteoblasts* ⬇️

Estrogen regulation of human osteoblast function is determined by the stage of differentiation and the estrogen receptor isoform.

Expanding on Successful Concepts, Models, and Organization

Genetic and epigenetic changes in chromosomally stable and unstable progeny of irradiated cells

Host regulatory network response to infection with highly pathogenic H5N1 avian influenza virus

How Adverse Outcome Pathways Can Aid the Development and Use of Computational Prediction Models for Regulatory Toxicology

Impaired transcriptional response of the murine heart to cigarette smoke in the setting of high fat diet and obesity

Implications of Bioremediation of Polycyclic Aromatic Hydrocarbon-Contaminated Soils for Human Health and Cancer Risk.

Improved quality control processing of peptide-centric LC-MS proteomics data

Influenza-Omics and the Host Response: Recent Advances and Future Prospects

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

Integration of data systems and technology improves research and collaboration for a superfund research center.

Integrative transcriptomic and proteomic analysis of osteocytic cells exposed to fluid flow reveals novel mechano-sensitive signaling pathways

Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models

Ligand-Specific Transcriptional Mechanisms Underlie Aryl Hydrocarbon Receptor-Mediated Developmental Toxicity of Oxygenated PAHs.

Localization of a polyunsaturated fatty acid response region in stearoyl-CoA desaturase gene 1.

MERS-CoV Accessory ORFs Play Key Role for Infection and Pathogenesis

MERS-CoV NSP16 necessary for IFN resistance and viral pathogenesis

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

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

Macrophage responses to silica nanoparticles are highly conserved across particle sizes

Mechanism-Based Classification of PAH Mixtures to Predict Carcinogenic Potential

Mechanisms of severe acute respiratory syndrome coronavirus-induced acute lung injury

Middle East Respiratory Syndrome Coronavirus Nonstructural Protein 16 Is Necessary for Interferon Resistance and Viral Pathogenesis

Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis

Network analysis of epidermal growth factor signaling using integrated genomic, proteomic and phosphorylation data

P-Mart: Interactive Analysis of Ion Abundance Global Proteomics Data

Pathogenic influenza viruses and coronaviruses utilize similar and contrasting approaches to control interferon-stimulated gene responses.

Phenotypically anchored transcriptome profiling of developmental exposure to the antimicrobial agent, triclosan, reveals hepatotoxicity in embryonic zebrafish

Phosphoproteomics profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing radiation

Proteome and computational analyses reveal new insights into the mechanisms of hepatitis C virus-mediated liver disease posttransplantation

Proteomic analysis reveals down-regulation of surfactant protein B in murine type II pneumocytes infected with influenza A virus.

Quantitative phosphoproteome analysis of lysophosphatidic acid induced chemotaxis applying dual-step (18)O labeling coupled with immobilized metal-ion affinity chromatography.

Quantitative phosphoproteomics identifies filaggrin and other targets of ionizing radiation in a human skin model.

Quantitative proteomic analysis of mitochondrial proteins reveals prosurvival mechanisms in the perpetuation of radiation-induced genomic instability.

Regulation of gene expression and subcellular protein distribution in MLO-Y4 osteocytic cells by lysophosphatidic acid: Relevance to dendrite outgrowth

Regulation of hepatic stearoyl-CoA desaturase gene 1 by vitamin A

Relative Influence of Trans-Pacific and Regional Atmospheric Transport of PAHs in the Pacific Northwest, U.S.

Release of severe acute respiratory syndrome coronavirus nuclear import block enhances host transcription in human lung cells

Retinoic acid-dependent regulation of miR-19 expression elicits vertebrate axis defects.