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List of works by Mark P Molloy

A Protein Annotation Framework Empowered with Semantic Reasoning

scientific article published in proceedings of the iswc 2013 posters & demonstrations track

A longitudinal study of the protein components of marsupial milk from birth to weaning in the tammar wallaby (Macropus eugenii).

scientific article

A multiplexed, targeted mass spectrometry assay of the S100 protein family uncovers the isoform-specific expression in thyroid tumours

scientific article

A proteomics-based approach identifies secreted protein acidic and rich in cysteine as a prognostic biomarker in malignant pleural mesothelioma

scientific article published on 18 February 2016

Age-related neurodegenerative disease associated pathways identified in retinal and vitreous proteome from human glaucoma eyes.

scientific article published on 4 October 2017

Alternative assembly of respiratory complex II connects energy stress to metabolic checkpoints.

scientific article published on 7 June 2018

An iTRAQ proteomics screen reveals the effects of the MDM2 binding ligand Nutlin-3 on cellular proteostasis.

scientific article

Analysis of the outer membrane proteome of Caulobacter crescentus by two-dimensional electrophoresis and mass spectrometry

scientific article

Analytical performance of nano-LC-SRM using nondepleted human plasma over an 18-month period

scientific article

Angiotensin II-inducible platelet-derived growth factor-D transcription requires specific Ser/Thr residues in the second zinc finger region of Sp1

scientific article

CCNF mutations in amyotrophic lateral sclerosis and frontotemporal dementia

scientific article published on 15 April 2016

Casein kinase II phosphorylation of cyclin F at serine 621 regulates the Lys48-ubiquitylation E3 ligase activity of the SCF(cyclin F) complex.

scientific article

Changes in dietary fiber intake in mice reveal associations between colonic mucin O-glycosylation and specific gut bacteria

scientific article published on 01 November 2020

Changes in the in vitro activity of platinum drugs when administered in two aliquots.

scientific article

Characterisation of the immune compounds in koala milk using a combined transcriptomic and proteomic approach

scientific article published on 07 October 2016

Characterisation of wool intermediate filament proteins separated by micropreparative two-dimensional electrophoresis

scientific article published on 01 March 1997

Characterization of a beta-catenin nuclear localization defect in MCF-7 breast cancer cells

scientific article published on 01 February 2016

Characterization of the rat liver membrane proteome using peptide immobilized pH gradient isoelectric focusing.

scientific article published on 23 January 2008

Classification of cancer patients using pathway analysis and network clustering

scientific article published on 01 January 2011

Clinicopathological correlates and prognostic significance of glutathione S-transferase Pi expression in 468 patients after potentially curative resection of node-positive colonic cancer

scientific article published on December 2011

Clinicopathological correlates and prognostic significance of maspin expression in 450 patients after potentially curative resection of node-positive colonic cancer

scientific article published on 01 February 2010

Combining protein ratio p-values as a pragmatic approach to the analysis of multirun iTRAQ experiments

scientific article published on 13 January 2015

Comparing SILAC and two-dimensional gel electrophoresis image analysis for profiling urokinase plasminogen activator signaling in ovarian cancer cells.

scientific article

Complementing genomics with proteomics: the membrane subproteome of Pseudomonas aeruginosa PAO1.

scientific article published in November 2000

Comprehensive glycomics comparison between colon cancer cell cultures and tumours: implications for biomarker studies.

scientific article published on 17 May 2014

Coverage and consistency: bioinformatics aspects of the analysis of multirun iTRAQ experiments with wheat leaves.

scientific article published on 20 September 2013

Cytokine profiling of docetaxel-resistant castration-resistant prostate cancer.

scientific article

Development of a data independent acquisition mass spectrometry workflow to enable glycopeptide analysis without predefined glycan compositional knowledge.

scientific article

Development of mini-gel technology in two-dimensional electrophoresis for mass-screening of samples: application to tears.

scientific article published in May 1998

Differential expression of the skeletal muscle proteome in mdx mice at different ages.

scientific article published in August 2004

Differential proteome expression associated with urokinase plasminogen activator receptor (uPAR) suppression in malignant epithelial cancer.

scientific article published on 23 September 2008

Establishment of the human reflex tear two-dimensional polyacrylamide gel electrophoresis reference map: new proteins of potential diagnostic value.

scientific article

Evaluating bioanalytical capabilities of paper spray ionization for abiraterone drug quantification in patient plasma

scientific article published on 01 October 2020

Evaluation of blood collection tubes using selected reaction monitoring MS: implications for proteomic biomarker studies

scientific article published on 01 May 2010

Evaluation of endogenous plasma peptide extraction methods for mass spectrometric biomarker discovery

scientific article

Exhaled breath condensate for lung cancer protein analysis: a review of methods and biomarkers.

scientific article

Exploring the proteome: reviving emphasis on quantitative protein profiling

scientific article published on 01 October 2003

Expression of ALS/FTD-linked mutant CCNF in zebrafish leads to increased cell death in the spinal cord and an aberrant motor phenotype

scientific article published on 01 February 2019

Extraction of Escherichia coli proteins with organic solvents prior to two-dimensional electrophoresis

scientific article published on 01 April 1999

Extraction of membrane proteins by differential solubilization for separation using two-dimensional gel electrophoresis

scientific article published in May 1998

Fetuin B Is a Secreted Hepatocyte Factor Linking Steatosis to Impaired Glucose Metabolism.

scientific article published on 22 October 2015

Fiber Supplements Derived From Sugarcane Stem, Wheat Dextrin and Psyllium Husk Have Different Effects on the Human Gut Microbiota

scientific article published on 20 July 2018

From mice to men: GEMMs as trial patients for new NSCLC therapies

scientific article published on March 2014

Genetically and Phenotypically Distinct Pseudomonas aeruginosa Cystic Fibrosis Isolates Share a Core Proteomic Signature

scientific article published on 2 October 2015

Genome Modularization Reveals Overlapped Gene Topology Is Necessary for Efficient Viral Reproduction

scientific article published on 12 October 2020

Glutathione S-transferase Pi expression predicts response to adjuvant chemotherapy for stage C colon cancer: a matched historical control study

scientific article

HSP22, a new member of the small heat shock protein superfamily, interacts with mimic of phosphorylated HSP27 ((3D)HSP27)

scientific article (publication date: 20 July 2001)

High-abundance protein depletion: comparison of methods for human plasma biomarker discovery

scientific article published on 01 January 2010

High-throughput mass spectrometric discovery of protein post-translational modifications.

scientific article

How specific is my SRM?: The issue of precursor and product ion redundancy

scientific article published on 01 March 2009

Identification of candidate biomarkers of therapeutic response to docetaxel by proteomic profiling.

scientific article published on 22 September 2009

Identification of distinctive protein expression patterns in colorectal adenoma.

scientific article

Identification of protein targets in cerebral endothelial cells for brain arteriovenous malformation (AVMs) molecular therapies

scientific article

Identification of wallaby milk whey proteins separated by two-dimensional electrophoresis, using amino acid analysis and sequence tagging

scientific article published on 01 June 1997

Improved protein solubility in two-dimensional electrophoresis using tributyl phosphine as reducing agent.

scientific article published in May 1998

Improving Protein Detection Confidence Using SWATH Mass Spectrometry with Large Peptide Reference Libraries

scientific article

Ionizing radiation reduces ADAM10 expression in brain microvascular endothelial cells undergoing stress-induced senescence

scientific article

Isolation of bacterial cell membranes proteins using carbonate extraction.

scientific article published on January 2008

Label-free selected reaction monitoring enables multiplexed quantitation of S100 protein isoforms in cancer cells.

scientific article published on 3 July 2013

Large-scale evaluation of quantitative reproducibility and proteome coverage using acid cleavable isotope coded affinity tag mass spectrometry for proteomic profiling.

scientific article published in April 2005

Membrane proteins and proteomics: un amour impossible?

scientific article

Metformin, Microbiome and Protection Against Colorectal Cancer

scientific article published on 12 June 2020

Multi-laboratory analysis of the variability of shipped samples for proteomics following non-cooled international transport

scientific article published on 25 February 2018

Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry

scientific article

Multidimensional fractionation is a requirement for quantitation of Golgi-resident glycosylation enzymes from cultured human cells.

scientific article

Multidimensional protein identification technology-selected reaction monitoring improving detection and quantification for protein biomarker studies.

scientific article

Mutated in colorectal cancer protein modulates the NFκB pathway.

scientific article published in January 2012

Online Peptide fractionation using a multiphasic microfluidic liquid chromatography chip improves reproducibility and detection limits for quantitation in discovery and targeted proteomics.

scientific article published on 7 April 2015

Overcoming technical variation and biological variation in quantitative proteomics

scientific article published on October 2003

Overexpression of protein S100A4 is independently associated with overall survival in stage C colonic cancer but only in cytoplasm at the advancing tumour front.

scientific article published on 09 May 2012

Pathogenic mutation in the ALS/FTD gene, CCNF, causes elevated Lys48-linked ubiquitylation and defective autophagy

scientific article published on 29 August 2017

Pharmacological Inhibition of Casein Kinase 2 Enhances the Effectiveness of PI3K Inhibition in Colon Cancer Cells

scientific article published on 01 November 2018

Phosphopeptide derivatization signatures to identify serine and threonine phosphorylated peptides by mass spectrometry

scientific article

Phosphoproteomic Analysis of Cell-Based Resistance to BRAF Inhibitor Therapy in Melanoma

scientific article published on 15 May 2015

Phosphoproteomics of MAPK inhibition in BRAF-mutated cells and a role for the lethal synergism of dual BRAF and CK2 inhibition.

scientific article published on 13 May 2014

Plasma biomarker proteins for detection of human growth hormone administration in athletes

scientific article published on 30 August 2017

Polyomic profiling reveals significant hepatic metabolic alterations in glucagon-receptor (GCGR) knockout mice: implications on anti-glucagon therapies for diabetes.

scientific article

Polyphenol extracts from dried sugarcane inhibit inflammatory mediators in an in vitro colon cancer model.

scientific article published on 9 February 2018

Prefractionation of protein samples prior to two-dimensional electrophoresis

scientific article published on 01 March 1997

Priming Adipose-Derived Mesenchymal Stem Cells with Hyaluronan Alters Growth Kinetics and Increases Attachment to Articular Cartilage.

scientific article

Profiling the alkaline membrane proteome of Caulobacter crescentus with two-dimensional electrophoresis and mass spectrometry

scientific article

Protein Paucimannosylation Is an Enriched N-Glycosylation Signature of Human Cancers

scientific article published on 16 October 2019

Proteome analysis reveals antiangiogenic environments in chronic wounds of diabetes mellitus type 2 patients

scientific article published on 30 July 2013

Proteome profiling of Pseudomonas aeruginosa PAO1 identifies novel responders to copper stress

scientific article published on 01 April 2019

Proteomic analysis of early lactation milk of the tammar wallaby (Macropus eugenii)

article

Proteomic analysis of mdx skeletal muscle: Great reduction of adenylate kinase 1 expression and enzymatic activity

scientific article

Proteomic analysis of the Escherichia coli outer membrane.

scientific article

Proteomic comparison of colorectal tumours and non-neoplastic mucosa from paired patient samples using iTRAQ mass spectrometry.

scientific article published on 02 August 2011

Proteomic identification of lynchpin urokinase plasminogen activator receptor protein interactions associated with epithelial cancer malignancy.

scientific article published on March 2007

Proteomic phenotyping of metastatic melanoma reveals putative signatures of MEK inhibitor response and prognosis

scientific article published on 17 August 2018

Proteomic profile of sex-sorted bull sperm evaluated by SWATH-MS analysis

scientific article published on 22 September 2018

Proteomics identification of radiation-induced changes of membrane proteins in the rat model of arteriovenous malformation in pursuit of targets for brain AVM molecular therapy

scholarly article by Margaret Simonian et al published 2018 in Clinical Proteomics

Proteomics of Smad4 regulated transforming growth factor-beta signalling in colon cancer cells.

scientific article published on 22 September 2010

Proteomics of hosts and pathogens in cystic fibrosis

scientific article

Proteomics of thyroid tumours provides new insights into their molecular composition and changes associated with malignancy.

scientific article published on 30 March 2016

Proteomics: technologies and applications

scientific article

Pseudomonas aeruginosa Cell Membrane Protein Expression from Phenotypically Diverse Cystic Fibrosis Isolates Demonstrates Host-Specific Adaptations

scientific article published in June 2016

Pseudomonas aeruginosa Proteome under Hypoxic Stress Conditions Mimicking the Cystic Fibrosis Lung.

scientific article

Purification and characterization of a serine protease and chitinases from Paecilomyces lilacinus and detection of chitinase activity on 2D gels.

scientific article

Quantitation of the anticancer drug abiraterone and its metabolite Δ(4)-abiraterone in human plasma using high-resolution mass spectrometry

scientific article published on 06 March 2018

Quantitative Age-specific Variability of Plasma Proteins in Healthy Neonates, Children and Adults

scientific article

Quantitative chemical proteomics in small-scale culture of phorbol ester stimulated basal breast cancer cells

scientific article published on 31 May 2011

Quantitative mass spectrometry for colorectal cancer proteomics

scientific article published on January 2013

Quantitative phosphoproteomics of transforming growth factor-β signaling in colon cancer cells.

scientific article published on August 2011

Radiosurgery Alters the Endothelial Surface Proteome: Externalized Intracellular Molecules as Potential Vascular Targets in Irradiated Brain Arteriovenous Malformations

scientific article published on 5 January 2017

Recent progress in selected reaction monitoring MS-driven plasma protein biomarker analysis

scientific article published on July 2009

Remarkable temporal stability of high-abundance human plasma proteins assessed by targeted mass spectrometry.

scientific article published on 8 November 2012

Reporting in studies of protein biomarkers of prognosis in colorectal cancer in relation to the REMARK guidelines.

scientific article published on 7 May 2015

SWATH Mass Spectrometry Performance Using Extended Peptide MS/MS Assay Libraries

scientific article published on 09 May 2016

SWATH Mass Spectrometry for Proteomics of Non-Depleted Plasma

scientific article

SecDF as part of the Sec-translocase facilitates efficient secretion of Bacillus cereus toxins and cell wall-associated proteins

scientific article published in August 2014

Serotype classification and characterisation of the rotavirus SA11 VP6 protein using mass spectrometry and two-dimensional gel electrophoresis

scientific article published on 01 May 2000

Stoichiometry of Saccharomyces cerevisiae lysine methylation: insights into non-histone protein lysine methyltransferase activity

scientific article

TMT One-Stop Shop: From Reliable Sample Preparation to Computational Analysis Platform

2017 scientific article

Tandem ion exchange fractionation of chicken egg white reveals the presence of proliferative bioactivity

scientific article published on 19 April 2013

The Australian Proteome Analysis Facility (APAF): assembling large scale proteomics through integration and automation

scientific article

The challenge of industrializing proteomics

scientific article published on 01 June 2003

The development of multiple reaction monitoring assays for liver-derived plasma proteins

scientific article published on 16 November 2007

The mannose-6-phosphate analogue, PXS64, inhibits fibrosis via TGF-β1 pathway in human lung fibroblasts.

scientific article published on 27 April 2015

The necrotrophic effector protein SnTox3 re-programs metabolism and elicits a strong defence response in susceptible wheat leaves

scientific article

Towards clinical applications of selected reaction monitoring for plasma protein biomarker studies

scientific article published on 27 December 2011

Two-dimensional electrophoresis and peptide mass fingerprinting of bacterial outer membrane proteins

scientific article published in May 2001

Two-dimensional electrophoresis of membrane proteins using immobilized pH gradients.

scientific article

Two-stepping to increase peptide spectra matches in large databases.

scientific article published in April 2013

Unique ion signature mass spectrometry, a deterministic method to assign peptide identity.

scientific article published on 25 June 2009

Unravelling the role of protein kinase CK2 in metal toxicity using gene deletion mutants

scientific article published on 14 February 2017

Using proteomics to identify ubiquitin ligase-substrate pairs: how novel methods may unveil therapeutic targets for neurodegenerative diseases

scientific article published on 27 March 2019

Why complexity and entropy matter: information, posttranslational modifications, and assay fidelity.

scientific article published in April 2012

iSwathX: an interactive web-based application for extension of DIA peptide reference libraries

scientific article published on 01 February 2019

iTRAQ experimental design for plasma biomarker discovery

scientific article published on 13 June 2008

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