By Associate Professor Mark Raftery

Book Chapters

Ping P; Vondriska TM; Creighton CJ; Gandhi TKB; Yang Z; Menon R; Kwon MS; Cho SY; Drwal G; Kellmann M; Peri S; Suresh S; Gronborg M; Molina H; Chaerkady R; Rekha B; Shet AS; Gerszten RE; Wu H; Raftery M; Wasinger V; Schulz-Knappe P; Hanash SM; Paik YK; Hancock WS; States DJ; Omenn GS; Pandey A, 2006, 'A functional annotation of subproteomes in human plasma', in Exploring the Human Plasma Proteome, pp. 329 - 351, http://dx.doi.org/10.1002/9783527609482.ch16

Cavicchioli R; Goodchild A; Raftery M, 2005, 'Proteomics of Archaea', in Microbial Proteomics: Functional Biology of Whole Organisms, pp. 57 - 72, http://dx.doi.org/10.1002/0471973165.ch5

Raftery MJ, 2000, 'Methods in Molecular Biology', in Mass spectrometry of proteins and peptides, Humana Press, Totowa, USA, pp. 27 - 39

Journal articles

McIntyre KL; Waters SA; Zhong L; Hart-Smith G; Raftery M; Chew ZA; Patel HR; Graves JAM; Waters PD, 2024, 'Identification of the RSX interactome in a marsupial shows functional coherence with the Xist interactome during X inactivation', Genome Biology, 25, http://dx.doi.org/10.1186/s13059-024-03280-0

Mercier C; Thies D; Zhong L; Raftery MJ; Erdmann S, 2023, 'Characterization of an archaeal virus-host system reveals massive genomic rearrangements in a laboratory strain', Frontiers in Microbiology, 14, http://dx.doi.org/10.3389/fmicb.2023.1274068

Poljak A; Raftery M; Polly P, 2023, 'Evaluating Cellular Viability by iTRAQ Proteomic Profiling', , 2644, pp. 193 - 209, http://dx.doi.org/10.1007/978-1-0716-3052-5_12

Suyama H; Luu LDW; Zhong L; Raftery MJ; Lan R, 2023, 'Integrating proteomic data with metabolic modeling provides insight into key pathways of Bordetella pertussis biofilms', Frontiers in Microbiology, 14, http://dx.doi.org/10.3389/fmicb.2023.1169870

Bӧhm JW; Sia KCS; Jones C; Evans K; Mariana A; Pang I; Failes T; Zhong L; Mayoh C; Landman R; Collins R; Erickson SW; Arndt G; Raftery MJ; Wilkins MR; Norris MD; Haber M; Marshall GM; Lock RB, 2021, 'Combination efficacy of ruxolitinib with standard-of-care drugs in CRLF2-rearranged Ph-like acute lymphoblastic leukemia', Leukemia, 35, pp. 3101 - 3112, http://dx.doi.org/10.1038/s41375-021-01248-8

Santiago FS; Li Y; Zhong L; Raftery MJ; Lins L; Khachigian LM, 2021, 'Truncated YY1 interacts with BASP1 through a ³³⁹KLK³⁴¹motif in YY1 and suppresses vascular smooth muscle cell growth and intimal hyperplasia after vascular injury', Cardiovascular Research, 117, pp. 2395 - 2406, http://dx.doi.org/10.1093/cvr/cvab021

Luu LDW; Zhong L; Kaur S; Raftery MJ; Lan R, 2021, 'Comparative Phosphoproteomics of Classical Bordetellae Elucidates the Potential Role of Serine, Threonine and Tyrosine Phosphorylation in Bordetella Biology and Virulence', Frontiers in Cellular and Infection Microbiology, 11, http://dx.doi.org/10.3389/fcimb.2021.660280

Kaur G; Poljak A; Ali SA; Zhong L; Raftery MJ; Sachdev P, 2021, 'Extending the Depth of Human Plasma Proteome Coverage Using Simple Fractionation Techniques', Journal of Proteome Research, 20, pp. 1261 - 1279, http://dx.doi.org/10.1021/acs.jproteome.0c00670

Capraro A; Wong S; Adhikari A; Allan K; Patel H; Zhong L; Raftery M; Jaffe A; Yeang M; Aggarwal A; Wu L; Pandzic E; Whan R; Turville S; Vittorio O; Bull R; Kaakoush N; Rawlinson W; Tedla N; Vafaee F; Waters S, 2021, 'Ageing impairs the airway epithelium defence response to SARS-CoV-2', , http://dx.doi.org/10.1101/2021.04.05.437453

Verma A; Meitei NS; Gajbhiye PU; Raftery MJ; Ambatipudi K, 2020, 'Comparative analysis of milk triglycerides profile between jaffarabadi buffalo and holstein friesian cow', Metabolites, 10, pp. 1 - 27, http://dx.doi.org/10.3390/metabo10120507

Sia KCS; Zhong L; Mayoh C; Norris MD; Haber M; Marshall GM; Raftery MJ; Lock RB, 2020, 'Targeting TSLP-induced tyrosine kinase signaling pathways in CRLF2-Rearranged Ph-like ALL', Molecular Cancer Research, 18, pp. 1767 - 1776, http://dx.doi.org/10.1158/1541-7786.MCR-19-1098

Li Y; Alhendi AMN; Yeh MC; Elahy M; Santiago FS; Deshpande NP; Wu B; Chan E; Inam S; Prado-Lourenco L; Marchand J; Joyce RD; Wilkinson-White LE; Raftery MJ; Zhu M; Adamson SJ; Barnat F; Viaud-Quentric K; Sockler J; Mackay JP; Chang A; Mitchell P; Marcuccio SM; Khachigian LM, 2020, 'Thermostable small-molecule inhibitor of angiogenesis and vascular permeability that suppresses a pERK-FosB/ΔFosB-VCAM-1 axis', Science Advances, 6, pp. eaaz7815, http://dx.doi.org/10.1126/sciadv.aaz7815

Luu LDW; Octavia S; Aitken C; Zhong L; Raftery MJ; Sintchenko V; Lan R, 2020, 'Surfaceome analysis of Australian epidemic Bordetella pertussis reveals potential vaccine antigens', Vaccine, 38, pp. 539 - 548, http://dx.doi.org/10.1016/j.vaccine.2019.10.062

Santiago FS; Sanchez-Guerrero E; Zhang G; Zhong L; Raftery MJ; Khachigian LM, 2019, 'Extracellular signal-regulated kinase-1 phosphorylates early growth response-1 at serine 26', Biochemical and Biophysical Research Communications, 510, pp. 345 - 351, http://dx.doi.org/10.1016/j.bbrc.2019.01.019

Williams TJ; Allen MA; Liao Y; Raftery MJ; Cavicchioli R, 2019, 'Sucrose metabolism in haloarchaea: Reassessment using genomics, proteomics, and metagenomics', Applied and Environmental Microbiology, 85, pp. e02935 - e02918, http://dx.doi.org/10.1128/AEM.02935-18

Hamm JN; Erdmann S; Eloe-Fadrosh EA; Angeloni A; Zhong L; Brownlee C; Williams TJ; Barton K; Carswell S; Smith MA; Brazendale S; Hancock AM; Allen MA; Raftery MJ; Cavicchioli R, 2019, 'Unexpected host dependency of Antarctic Nanohaloarchaeota', Proceedings of the National Academy of Sciences of the United States of America, 116, pp. 14661 - 14670, http://dx.doi.org/10.1073/pnas.1905179116

Wai Luu LD; Octavia S; Zhong L; Raftery MJ; Sintchenko V; Lan R, 2018, 'Comparison of the whole cell proteome and secretome of epidemic bordetella pertussis strains from the 2008–2012 Australian epidemic under sulfate-modulating conditions', Frontiers in Microbiology, 9, http://dx.doi.org/10.3389/fmicb.2018.02851

Unnikrishnan A; Vo ANQ; Pickford R; Raftery MJ; Nunez AC; Verma A; Hesson LB; Pimanda JE, 2018, 'AZA-MS: A novel multiparameter mass spectrometry method to determine the intracellular dynamics of azacitidine therapy in vivo', Leukemia, 32, pp. 900 - 910, http://dx.doi.org/10.1038/leu.2017.340

Luu LDW; Octavia S; Zhong L; Raftery MJ; Sintchenko V; Lan R, 2018, 'Proteomic Adaptation of Australian Epidemic Bordetella pertussis', Proteomics, 18, http://dx.doi.org/10.1002/pmic.201700237

Erdmann S; Tschitschko B; Zhong L; Raftery MJ; Cavicchioli R, 2017, 'A plasmid from an Antarctic haloarchaeon uses specialized membrane vesicles to disseminate and infect plasmid-free cells', Nature Microbiology, 2, pp. 1446 - 1455, http://dx.doi.org/10.1038/s41564-017-0009-2

Strbenac D; Zhong L; Raftery MJ; Wang P; Wilson SR; Armstrong NJ; Yang JYH, 2017, 'Quantitative Performance Evaluator for Proteomics (QPEP): Web-based Application for Reproducible Evaluation of Proteomics Preprocessing Methods', Journal of Proteome Research, 16, pp. 2359 - 2369, http://dx.doi.org/10.1021/acs.jproteome.6b00882

Williams TJ; Liao Y; Ye J; Kuchel RP; Poljak A; Raftery MJ; Cavicchioli R, 2017, 'Cold adaptation of the Antarctic haloarchaea Halohasta litchfieldiae and Halorubrum lacusprofundi', Environmental Microbiology, 19, pp. 2210 - 2227, http://dx.doi.org/10.1111/1462-2920.13705

Luu LDW; Octavia S; Zhong L; Raftery M; Sintchenko V; Lan R, 2017, 'Characterisation of the Bordetella pertussis secretome under different media', Journal of Proteomics, 158, pp. 43 - 51, http://dx.doi.org/10.1016/j.jprot.2017.02.010

Unnikrishnan A; Guan YF; Huang Y; Beck D; Thoms JAI; Peirs S; Knezevic K; Ma S; De Walle IV; De Jong IDE; Ali Z; Zhong L; Raftery MJ; Taghon T; Larsson J; MacKenzie KL; Van Vlierberghe P; Wong JWH; Pimanda JE, 2016, 'A quantitative proteomics approach identifies ETV6 and IKZF1 as new regulators of an ERG-driven transcriptional network', Nucleic Acids Research, 44, pp. 10644 - 10661, http://dx.doi.org/10.1093/nar/gkw804

Liao Y; Williams TJ; Ye J; Charlesworth J; Burns BP; Poljak A; Raftery MJ; Cavicchioli R, 2016, 'Morphological and proteomic analysis of biofilms from the Antarctic archaeon, Halorubrum lacusprofundi', Scientific Reports, 6, pp. 37454, http://dx.doi.org/10.1038/srep37454

Jayasena T; Poljak A; Braidy N; Zhong L; Rowlands B; Muenchhoff J; Grant R; Smythe G; Teo C; Raftery M; Sachdev PS, 2016, 'Application of targeted mass spectrometry for the quantification of sirtuins in the central nervous system', Scientific Reports, 6, pp. 35391 - 35391, http://dx.doi.org/10.1038/srep35391

Park M; Raftery MJ; Thomas PS; Geczy CL; Bryant K; Tedla N, 2016, 'Leukocyte immunoglobulin-like receptor B4 regulates key signalling molecules involved in FcγRI-mediated clathrin-dependent endocytosis and phagocytosis', Scientific Reports, 6, pp. 35085, http://dx.doi.org/10.1038/srep35085

Muenchhoff J; Poljak A; Thalamuthu A; Gupta VB; Chatterjee P; Raftery M; Masters CL; Morris JC; Bateman RJ; Fagan AM; Martins RN; Sachdev PS, 2016, 'Changes in the plasma proteome at asymptomatic and symptomatic stages of autosomal dominant Alzheimer's disease', Scientific Reports, 6, pp. 29078 - 29078, http://dx.doi.org/10.1038/srep29078

Dolai S; Sia KCS; Robbins AK; Zhong L; Heatley SL; Vincent TL; Hochgräfe F; Sutton R; Kurmasheva RT; Revesz T; White DL; Houghton PJ; Smith MA; Teachey DT; Daly RJ; Raftery MJ; Lock RB, 2016, 'Quantitative phosphotyrosine profiling of patient-derived xenografts identifies therapeutic targets in pediatric leukemia', Cancer Research, 76, pp. 2766 - 2777, http://dx.doi.org/10.1158/0008-5472.CAN-15-2786

Richards SL; Cawley AT; Cavicchioli R; Suann CJ; Pickford R; Raftery MJ, 2016, 'Aptamer based peptide enrichment for quantitative analysis of gonadotropin-releasing hormone by LC-MS/MS', Talanta, 150, pp. 671 - 680, http://dx.doi.org/10.1016/j.talanta.2016.01.006

Tschitschko B; Williams TJ; Allen MA; Zhong L; Raftery MJ; Cavicchioli R, 2016, 'Ecophysiological distinctions of haloarchaea from a hypersaline Antarctic lake determined using metaproteomics.', Appl Environ Microbiol, 82, pp. 3165 - 3173, http://dx.doi.org/10.1128/AEM.00473-16

Lyons B; Friedrich M; Raftery M; Truscott R, 2016, 'Amyloid Plaque in the Human Brain Can Decompose from Aβ(1-40/1-42) by Spontaneous Nonenzymatic Processes', Analytical Chemistry, 88, pp. 2675 - 2684, http://dx.doi.org/10.1021/acs.analchem.5b03891

Alexova R; Dang TC; Fujii M; Raftery MJ; Waite TD; Ferrari BC; Neilan BA, 2016, 'Specific global responses to N and Fe nutrition in toxic and non-toxic Microcystis aeruginosa', Environmental Microbiology, 18, pp. 401 - 413, http://dx.doi.org/10.1111/1462-2920.12958

Friedrich MG; Hancock SE; Raftery MJ; Truscott RJW, 2016, 'Isoaspartic acid is present at specific sites in myelin basic protein from multiple sclerosis patients: Could this represent a trigger for disease onset?', Acta Neuropathologica Communications, 4, http://dx.doi.org/10.1186/s40478-016-0348-x

Percy AJ; Tamura-Wells J; Albar JP; Aloria K; Amirkhani A; Araujo GDT; Arizmendi JM; Blanco FJ; Canals F; Cho JY; Colomé-Calls N; Corrales FJ; Domont G; Espadas G; Fernandez-Puente P; Gil C; Haynes PA; Hernáez ML; Kim JY; Kopylov A; Marcilla M; McKay MJ; Mirzaei M; Molloy MP; Ohlund LB; Paik YK; Paradela A; Raftery M; Sabidó E; Sleno L; Wilffert D; Wolters JC; Yoo JS; Zgoda V; Parker CE; Borchers CH, 2015, 'Inter-laboratory evaluation of instrument platforms and experimental workflows for quantitative accuracy and reproducibility assessment', EuPA Open Proteomics, 8, pp. 6 - 15, http://dx.doi.org/10.1016/j.euprot.2015.06.001

Tschitschko B; Williams TJ; Allen MA; Páez-Espino D; Kyrpides N; Zhong L; Raftery MJ; Cavicchioli R, 2015, 'Antarctic archaea–virus interactions: metaproteome-led analysis of invasion, evasion and adaptation', The ISME Journal, 9, pp. 2094 - 2107, http://dx.doi.org/10.1038/ismej.2015.110

Jayasena T; Poljak A; Braidy N; Smythe G; Raftery M; Hill M; Brodaty H; Trollor J; Kochan N; Sachdev P, 2015, 'Upregulation of glycolytic enzymes, mitochondrial dysfunction and increased cytotoxicity in glial cells treated with Alzheimer's disease plasma', PLoS ONE, 10, pp. e0116092, http://dx.doi.org/10.1371/journal.pone.0116092

Alexova R; Dang TC; Fujii M; Raftery MJ; Waite TD; Ferrari BC; Neilan BA, 2015, 'Specific global responses to N and Fe nutrition in toxic and non-toxic Microcystis aeruginosa', Environmental Microbiology, http://dx.doi.org/10.1111/1462-2920.12958

Kaakoush NO; Deshpande NP; Man SM; Burgos-Portugal JA; Khattak FA; Raftery MJ; Wilkins MR; Mitchell HM, 2015, 'Transcriptomic and proteomic analyses reveal key innate immune signatures in the host response to the gastrointestinal pathogen Campylobacter concisus', Infection and Immunity, 83, pp. 832 - 845, http://dx.doi.org/10.1128/IAI.03012-14

Gardiner M; Fernandes ND; Nowakowski D; Raftery M; Kjelleberg S; Zhong L; Thomas T; Egan S, 2015, 'VarR controls colonization and virulence in the marine macroalgal pathogen Nautella italica R11', Frontiers in Microbiology, 6, http://dx.doi.org/10.3389/fmicb.2015.01130

Muenchhoff J; Poljak A; Song F; Raftery M; Brodaty H; Duncan M; McEvoy M; Attia J; Schofield PW; Sachdev PS; Smythe G, 2015, 'Plasma protein profiling of mild cognitive impairment and Alzheimer's disease across two independent cohorts', Journal of Alzheimer's Disease, 43, pp. 1355 - 1373, http://dx.doi.org/10.3233/JAD-141266

Hou X; McMillan M; Coumans JVF; Poljak A; Raftery MJ; Pereg L, 2014, 'Cellular responses during morphological transformation in Azospirillum brasilense and its flcA knockout mutant', PLoS ONE, 9, http://dx.doi.org/10.1371/journal.pone.0114435

Liao BM; Raddatz K; Zhong L; Parker BL; Raftery MJ; Schmitz-Peiffer C, 2014, 'Proteomic analysis of livers from fat-fed mice deficient in either PKCδ or PKCε identifies Htatip2 as a regulator of lipid metabolism', Proteomics, 14, pp. 2578 - 2587, http://dx.doi.org/10.1002/pmic.201400202

Song F; Poljak A; Kochan N; Raftery M; Brodaty H; Smythe GA; Sachdev PS, 2014, 'Plasma protein profiling of Mild Cognitive Impairment and Alzheimer’s disease using iTRAQ quantitative proteomics', Proteome Science, 12, pp. 5, http://dx.doi.org/10.1186/1477-5956-12-5

Masoudi S; Zhong L; Raftery MJ; Stapleton FJ; Willcox MD, 2014, 'Method development for quantification of five tear proteins using selected reaction monitoring (SRM) mass spectrometry', Investigative Ophthalmology and Visual Science, 55, pp. 767 - 775, http://dx.doi.org/10.1167/iovs.13-12777

Raftery MJ, 2014, 'Determination of oxidative protein modifications using mass spectrometry', Redox Report, 19, pp. 140 - 147, http://dx.doi.org/10.1179/1351000214y.0000000089

Lee H; Ma R; Grimm MC; Riordan SM; Lan R; Zhong L; Raftery M; Zhang L, 2014, 'Examination of the anaerobic growth of Campylobacter concisus strains', International Journal of Microbiology, 2014, http://dx.doi.org/10.1155/2014/476047

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