Lista de obras - Joshua N Adkins - Dominio Público Uruguay

A Comprehensive Subcellular Proteomic Survey of Salmonella Grown under Phagosome-Mimicking versus Standard Laboratory Conditions

artículo científico publicado en 2012

A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection

artículo científico publicado en 2013

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

artículo científico publicado en 2011

A computational strategy to analyze label-free temporal bottom-up proteomics data

artículo científico publicado en 2008

A method for investigating protein-protein interactions related to salmonella typhimurium pathogenesis

scientific article published on March 2009

A multi-omic systems approach to elucidating Yersinia virulence mechanisms.

artículo científico publicado en 2012

A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins

artículo científico publicado en 2010

A porcine ligated loop model reveals new insight into the host immune response against Campylobacter jejuni

artículo científico publicado en 2020

A proteomic study of the HUPO Plasma Proteome Project's pilot samples using an accurate mass and time tag strategy

artículo científico publicado en 2005

A semiautomated framework for integrating expert knowledge into disease marker identification

artículo científico publicado en 2013

A statistical framework for protein quantitation in bottom-up MS-based proteomics.

artículo científico publicado en 2009

A statistical method for assessing peptide identification confidence in accurate mass and time tag proteomics

artículo científico publicado en 2011

A systems biology approach to infectious disease research: innovating the pathogen-host research paradigm

artículo científico publicado en 2011

An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and specificity analysis

An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis

artículo científico publicado en 2005

An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92.

artículo científico publicado en 2011

Applying a targeted label-free approach using LC-MS AMT tags to evaluate changes in protein phosphorylation following phosphatase inhibition

artículo científico publicado en 2007

Assessment of the Utility of the Oral Fluid and Plasma Proteomes for Hydrocodone Exposure

artículo científico publicado en 2019

Biomarker candidate identification in Yersinia pestis using organism-wide semiquantitative proteomics

artículo científico publicado en 2006

Characterization of strategies for obtaining confident identifications in bottom-up proteomics measurements using hybrid FTMS instruments

artículo científico publicado en 2008

Characterization of the mouse bronchoalveolar lavage proteome by micro-capillary LC-FTICR mass spectrometry

artículo científico publicado en 2008

Comparative bacterial proteomics: analysis of the core genome concept

artículo científico publicado en 2008

Comparative omics-driven genome annotation refinement: application across Yersiniae

artículo científico publicado en 2012

Comparative proteomics of human monkeypox and vaccinia intracellular mature and extracellular enveloped virions

artículo científico publicado en 2008

Comprehensive computational design of ordered peptide macrocycles.

artículo científico publicado en 2017

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

artículo científico publicado en 2011

Cross-linking and mass spectrometry methodologies to facilitate structural biology: finding a path through the maze

artículo científico publicado en 2013

Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data

artículo científico publicado en 2009

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

artículo científico publicado en 2012

Discovery of novel secreted virulence factors from Salmonella enterica serovar Typhimurium by proteomic analysis of culture supernatants

artículo científico publicado en 2010

Distance restraints from crosslinking mass spectrometry: mining a molecular dynamics simulation database to evaluate lysine-lysine distances

artículo científico publicado en 2014

Distinct cerebrospinal fluid proteomes differentiate post-treatment lyme disease from chronic fatigue syndrome

artículo científico publicado en 2011

Diverse secreted effectors are required for Salmonella persistence in a mouse infection model

artículo científico publicado en 2013

Elimination of systematic mass measurement errors in liquid chromatography-mass spectrometry based proteomics using regression models and a priori partial knowledge of the sample content

artículo científico publicado en 2007

Evaluation of selected binding domains for the analysis of ubiquitinated proteomes

scientific article published on 07 May 2013

Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium

artículo científico publicado en 2011

Functional consequences of preorganized helical structure in the intrinsically disordered cell-cycle inhibitor p27(Kip1).

artículo científico publicado en 2002

Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: implications for virulence and global protein translation

artículo científico publicado en 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

High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labeling in a Nanodroplet Sample Preparation Platform

artículo científico publicado en 2019

High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip

artículo científico publicado en 2021

Identification of cross-linked peptides after click-based enrichment using sequential collision-induced dissociation and electron transfer dissociation tandem mass spectrometry

artículo científico publicado en 2009

Identification of shed proteins from Chinese hamster ovary cells: application of statistical confidence using human and mouse protein databases

artículo científico publicado en 2005

Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis

artículo científico publicado en 2013

Immunoassay and antibody microarray analysis of the HUPO Plasma Proteome Project reference specimens: systematic variation between sample types and calibration of mass spectrometry data

artículo científico publicado en 2005

Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information.

artículo científico publicado en 2006

In silico method for modelling metabolism and gene product expression at genome scale

artículo científico publicado en 2012

Integrated post-experiment monoisotopic mass refinement: an integrated approach to accurately assign monoisotopic precursor masses to tandem mass spectrometric data

artículo científico publicado en 2010

Intrinsic structural disorder and sequence features of the cell cycle inhibitor p57Kip2

scientific journal article

Linear discriminant analysis-based estimation of the false discovery rate for phosphopeptide identifications

artículo científico publicado en 2008

MASIC: a software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features

artículo científico publicado en 2008

Mass measurement accuracy in analyses of highly complex mixtures based upon multidimensional recalibration

artículo científico publicado en 2006

Mixed-isotope labeling with LC-IMS-MS for characterization of protein-protein interactions by chemical cross-linking.

artículo científico publicado en 2013

Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation

artículo científico publicado en 2012

Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics

artículo científico publicado en 2006

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

artículo científico publicado en 2010

Omics.pnl.gov: A Portal for the Distribution and Sharing of Multi-Disciplinary Pan-Omics Information

artículo científico publicado en 2010

Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

artículo científico publicado en 2005

Performing comparative peptidomics analyses of Salmonella from different growth conditions

artículo científico publicado en 2010

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

artículo científico publicado en 2006

Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags

artículo científico publicado en 2008

Proteomic analysis of Salmonella enterica serovar typhimurium isolated from RAW 264.7 macrophages: identification of a novel protein that contributes to the replication of serovar typhimurium inside macrophages

artículo científico publicado en 2006

Proteomic biomarkers in plasma that differentiate rapid and slow decline in lung function in adult cigarette smokers with chronic obstructive pulmonary disease (COPD).

artículo científico publicado en 2010

Proteomic investigation of the time course responses of RAW 264.7 macrophages to infection with Salmonella enterica

artículo científico publicado en 2009

Proteomics analysis of the causative agent of typhoid fever

artículo científico publicado en 2008

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

artículo científico publicado en 2008

RNA type III secretion signals that require Hfq

artículo científico publicado en 2013

Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate mass and time tag data analysis pipeline

artículo científico publicado en 2006

Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes ⬇️

artículo científico publicado en 2013

Simple protein complex purification and identification method for high-throughput mapping of protein interaction networks

scientific article published on 01 March 2005

Stoichiometry of cyclin A-cyclin-dependent kinase 2 inhibition by p21Cip1/Waf1.

artículo científico publicado en 2000

Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling

artículo científico publicado en 2013

Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella

artículo científico publicado en 2011

THE CHALLENGE OF PROTEOMIC DATA, FROM MOLECULAR SIGNALS TO BIOLOGICAL NETWORKS AND DISEASE: SESSION INTRODUCTION

Targeted protein degradation by Salmonella under phagosome-mimicking culture conditions investigated using comparative peptidomics.

artículo científico publicado en 2007

Technologies and approaches to elucidate and model the virulence program of salmonella

artículo científico publicado en 2011

The Campylobacter jejuni CiaD effector co-opts the host cell protein IQGAP1 to promote cell entry

artículo científico publicado en 2021

The food-borne pathogen Campylobacter jejuni responds to the bile salt deoxycholate with countermeasures to reactive oxygen species.

artículo científico publicado en 2017

The genome organization of Thermotoga maritima reflects its lifestyle

artículo científico publicado en 2013

The influence of sample preparation and replicate analyses on HeLa Cell phosphoproteome coverage

artículo científico publicado en 2008

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

artículo científico publicado en 2016

The proteome of dissimilatory metal-reducing microorganism Geobacter sulfurreducens under various growth conditions

artículo científico publicado en 2006

The utility of accurate mass and LC elution time information in the analysis of complex proteomes

artículo científico publicado en 2005

Transcriptional activity of the TFIIA four-helix bundle in vivo

artículo científico publicado en 2001

Unified feature association networks through integration of transcriptomic and proteomic data

scientific article published on 17 September 2019

Use of high-throughput mass spectrometry to elucidate host-pathogen interactions in Salmonella

scientific article published on December 2008

Utilizing human blood plasma for proteomic biomarker discovery

artículo científico publicado en 2005

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data

artículo científico publicado en 2012

Viral afterlife: SARS-CoV-2 as a reservoir of immunomimetic peptides that reassemble into proinflammatory supramolecular complexes

artículo científico publicado en 2024

Xlink-identifier: an automated data analysis platform for confident identifications of chemically cross-linked peptides using tandem mass spectrometry

artículo científico publicado en 2011

Lista de obras de Joshua N Adkins

A Comprehensive Subcellular Proteomic Survey of Salmonella Grown under Phagosome-Mimicking versus Standard Laboratory Conditions

A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

A computational strategy to analyze label-free temporal bottom-up proteomics data

A method for investigating protein-protein interactions related to salmonella typhimurium pathogenesis

A multi-omic systems approach to elucidating Yersinia virulence mechanisms.

A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins

A porcine ligated loop model reveals new insight into the host immune response against Campylobacter jejuni

A proteomic study of the HUPO Plasma Proteome Project's pilot samples using an accurate mass and time tag strategy

A semiautomated framework for integrating expert knowledge into disease marker identification

A statistical framework for protein quantitation in bottom-up MS-based proteomics.

A statistical method for assessing peptide identification confidence in accurate mass and time tag proteomics

A systems biology approach to infectious disease research: innovating the pathogen-host research paradigm

An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and specificity analysis

An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis

An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92.

Applying a targeted label-free approach using LC-MS AMT tags to evaluate changes in protein phosphorylation following phosphatase inhibition

Assessment of the Utility of the Oral Fluid and Plasma Proteomes for Hydrocodone Exposure

Biomarker candidate identification in Yersinia pestis using organism-wide semiquantitative proteomics

Characterization of strategies for obtaining confident identifications in bottom-up proteomics measurements using hybrid FTMS instruments

Characterization of the mouse bronchoalveolar lavage proteome by micro-capillary LC-FTICR mass spectrometry

Comparative bacterial proteomics: analysis of the core genome concept

Comparative omics-driven genome annotation refinement: application across Yersiniae

Comparative proteomics of human monkeypox and vaccinia intracellular mature and extracellular enveloped virions

Comprehensive computational design of ordered peptide macrocycles.

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

Cross-linking and mass spectrometry methodologies to facilitate structural biology: finding a path through the maze

Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data

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

Discovery of novel secreted virulence factors from Salmonella enterica serovar Typhimurium by proteomic analysis of culture supernatants

Distance restraints from crosslinking mass spectrometry: mining a molecular dynamics simulation database to evaluate lysine-lysine distances

Distinct cerebrospinal fluid proteomes differentiate post-treatment lyme disease from chronic fatigue syndrome

Diverse secreted effectors are required for Salmonella persistence in a mouse infection model

Elimination of systematic mass measurement errors in liquid chromatography-mass spectrometry based proteomics using regression models and a priori partial knowledge of the sample content

Evaluation of selected binding domains for the analysis of ubiquitinated proteomes

Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium

Functional consequences of preorganized helical structure in the intrinsically disordered cell-cycle inhibitor p27(Kip1).

Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: implications for virulence and global protein translation

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

High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labeling in a Nanodroplet Sample Preparation Platform

High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip

Identification of cross-linked peptides after click-based enrichment using sequential collision-induced dissociation and electron transfer dissociation tandem mass spectrometry

Identification of shed proteins from Chinese hamster ovary cells: application of statistical confidence using human and mouse protein databases

Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis

Immunoassay and antibody microarray analysis of the HUPO Plasma Proteome Project reference specimens: systematic variation between sample types and calibration of mass spectrometry data

Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information.

In silico method for modelling metabolism and gene product expression at genome scale

Integrated post-experiment monoisotopic mass refinement: an integrated approach to accurately assign monoisotopic precursor masses to tandem mass spectrometric data

Intrinsic structural disorder and sequence features of the cell cycle inhibitor p57Kip2

Linear discriminant analysis-based estimation of the false discovery rate for phosphopeptide identifications

MASIC: a software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features

Mass measurement accuracy in analyses of highly complex mixtures based upon multidimensional recalibration

Mixed-isotope labeling with LC-IMS-MS for characterization of protein-protein interactions by chemical cross-linking.

Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation

Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

Omics.pnl.gov: A Portal for the Distribution and Sharing of Multi-Disciplinary Pan-Omics Information

Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

Performing comparative peptidomics analyses of Salmonella from different growth conditions

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

Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags

Proteomic analysis of Salmonella enterica serovar typhimurium isolated from RAW 264.7 macrophages: identification of a novel protein that contributes to the replication of serovar typhimurium inside macrophages

Proteomic biomarkers in plasma that differentiate rapid and slow decline in lung function in adult cigarette smokers with chronic obstructive pulmonary disease (COPD).

Proteomic investigation of the time course responses of RAW 264.7 macrophages to infection with Salmonella enterica

Proteomics analysis of the causative agent of typhoid fever

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

RNA type III secretion signals that require Hfq

Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate mass and time tag data analysis pipeline

Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes ⬇️

Simple protein complex purification and identification method for high-throughput mapping of protein interaction networks

Stoichiometry of cyclin A-cyclin-dependent kinase 2 inhibition by p21Cip1/Waf1.

Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling

Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella

THE CHALLENGE OF PROTEOMIC DATA, FROM MOLECULAR SIGNALS TO BIOLOGICAL NETWORKS AND DISEASE: SESSION INTRODUCTION

Targeted protein degradation by Salmonella under phagosome-mimicking culture conditions investigated using comparative peptidomics.

Technologies and approaches to elucidate and model the virulence program of salmonella

The Campylobacter jejuni CiaD effector co-opts the host cell protein IQGAP1 to promote cell entry

The food-borne pathogen Campylobacter jejuni responds to the bile salt deoxycholate with countermeasures to reactive oxygen species.