Publications

Publications

Journals

2015

As at 31 May 2015

Professor NH Packer

Moh ES, Thaysen-Andersen M, Packer NH. Relative versus absolute quantitation in disease glycomics. Proteomics Clin Appl. 2015 Apr;9(3-4):368-82. doi:10.1002/prca.201400184. Epub 2015 Mar 24. PubMed PMID: 25684231.

Thaysen-Andersen M, Venkatakrishnan V, Loke I, Laurini C, Diestel S, Parker BL, Packer NH. Human neutrophils secrete bioactive paucimannosidic proteins from azurophilic granules into pathogen-infected sputum. J Biol Chem. 2015 Apr 3;290(14):8789-802. doi: 10.1074/jbc.M114.631622. Epub 2015 Feb 2. PubMed PMID:25645918; PubMed Central PMCID: PMC4423670.

Lin CH, Chik JH, Packer NH, Molloy MP. Multidimensional fractionation is a requirement for quantitation of Golgi-resident glycosylation enzymes from cultured human cells. J Proteome Res. 2015 Feb 6;14(2):747-55. doi:10.1021/pr500785f. Epub 2014 Dec 24. PubMed PMID: 25495351.

Gustafsson OJ, Briggs MT, Condina MR, Winderbaum LJ, Pelzing M, McColl SR, Everest-Dass AV, Packer NH, Hoffmann P. MALDI imaging mass spectrometry of N-linked glycans on formalin-fixed paraffin-embedded murine kidney. Anal Bioanal Chem. 2015 Mar;407(8):2127-39. doi: 10.1007/s00216-014-8293-7. Epub 2014 Dec 2.PubMed PMID: 25434632; PubMed Central PMCID: PMC4357650.

Nguyen-Khuong T, Everest-Dass AV, Kautto L, Zhao Z, Willcox MD, Packer NH. Glycomic characterization of basal tears and changes with diabetes and diabetic retinopathy. Glycobiology. 2015 Mar;25(3):269-83. doi: 10.1093/glycob/cwu108. Epub 2014 Oct 9. PubMed PMID: 25303961.

Venkatakrishnan V, Thaysen-Andersen M, Chen SC, Nevalainen H, Packer NH. Cystic fibrosis and bacterial colonization define the sputum N-glycosylation phenotype. Glycobiology. 2015 Jan;25(1):88-100. doi: 10.1093/glycob/cwu092. Epub 2014 Sep 4. PubMed PMID: 25190359.

 Professor IT Paulsen

Hassan KA, Elbourne LD, Li L, Gamage HK, Liu Q, Jackson SM, Sharples D, Kolstø AB, Henderson PJ, Paulsen IT. An ace up their sleeve: a transcriptomic approach exposes the AceI efflux protein of Acinetobacter baumannii and reveals the drug efflux potential hidden in many microbial pathogens. Front Microbiol. 2015 Apr 22;6:333. doi: 10.3389/fmicb.2015.00333. eCollection 2015. PubMed PMID: 25954261; PubMed Central PMCID: PMC4406071.

Farrugia DN, Elbourne LD, Mabbutt BC, Paulsen IT. A novel family of integrases associated with prophages and genomic islands integrated within the tRNA-dihydrouridine synthase A (dusA) gene. Nucleic Acids Res. 2015 May 19;43(9):4547-57. doi: 10.1093/nar/gkv337. Epub 2015 Apr 16. PubMed PMID: 25883135.

Dexter C, Murray GL, Paulsen IT, Peleg AY. Community-acquired Acinetobacter baumannii: clinical characteristics, epidemiology and pathogenesis. Expert Rev Anti Infect Ther. 2015 May;13(5):567-73. doi: 10.1586/14787210.2015.1025055. PubMed PMID: 25850806.

Penesyan A, Gillings M, Paulsen IT. Antibiotic discovery: combating bacterial resistance in cells and in biofilm communities. Molecules. 2015 Mar 24;20(4):5286-98. doi: 10.3390/molecules20045286. Review. PubMed PMID: 25812150.

Kaur J, Duan SY, Vaas LA, Penesyan A, Meyer W, Paulsen IT, Nevalainen H. Phenotypic profiling of Scedosporium aurantiacum, an opportunistic pathogen colonizing human lungs. PLoS One. 2015 Mar 26;10(3):e0122354. doi: 10.1371/journal.pone.0122354. eCollection 2015. PubMed PMID: 25811884; PubMed Central PMCID: PMC4374879.

Ioannidis A, Magana M, Bologa CG, Oprea TI, Paulsen IT, Tegos GP. Defining the microbial effluxome in the content of the host-microbiome interaction. Front Pharmacol. 2015 Feb 19;6:31. doi: 10.3389/fphar.2015.00031. eCollection 2015. PubMed PMID: 25745401; PubMed Central PMCID: PMC4333769.

Pérez-Bercoff Å, Papanicolaou A, Ramsperger M, Kaur J, Patel HR, Harun A, Duan SY, Elbourne L, Bouchara JP, Paulsen IT, Nevalainen H, Meyer W, Huttley GA. Draft Genome of Australian Environmental Strain WM 09.24 of the Opportunistic Human Pathogen Scedosporium aurantiacum. Genome Announc. 2015 Feb 12;3(1). pii: e01526-14. doi: 10.1128/genomeA.01526-14. PubMed PMID: 25676755; PubMed Central PMCID: PMC4333655.

Hassan KA, Liu Q, Henderson PJ, Paulsen IT. Homologs of the Acinetobacter baumannii AceI transporter represent a new family of bacterial multidrug efflux systems. MBio. 2015 Feb 10;6(1). pii: e01982-14. doi: 10.1128/mBio.01982-14. PubMed PMID: 25670776; PubMed Central PMCID: PMC4337561.

Song C, van der Voort M, van de Mortel J, Hassan KA, Elbourne LD, Paulsen IT, Loper JE, Raaijmakers JM. The Rsm regulon of plant growth-promoting Pseudomonas fluorescens SS101: role of small RNAs in regulation of lipopeptide biosynthesis. Microb Biotechnol. 2015 Mar;8(2):296-310. doi: 10.1111/1751-7915.12190. Epub 2014 Dec 9. PubMed PMID: 25488342; PubMed Central PMCID: PMC4353343.

Hassan KA, Elbourne LD, Tetu SG, Melville SB, Rood JI, Paulsen IT. Genomic analyses of Clostridium perfringens isolates from five toxinotypes. Res Microbiol. 2015 May;166(4):255-63. doi: 10.1016/j.resmic.2014.10.003. Epub 2014 Oct 16. PubMed PMID: 25445567.

Kamath KS, Kumar SS, Kaur J, Venkatakrishnan V, Paulsen IT, Nevalainen H, Molloy MP. Proteomics of hosts and pathogens in cystic fibrosis. Proteomics Clin Appl. 2015 Feb;9(1-2):134-46. doi: 10.1002/prca.201400122. Epub 2015 Jan 19.PubMed PMID: 25418359.

Professor H Nevalainen

Kaur J, Duan SY, Vaas LA, Penesyan A, Meyer W, Paulsen IT, Nevalainen H. Phenotypic profiling of Scedosporium aurantiacum, an opportunistic pathogen colonizing human lungs. PLoS One. 2015 Mar 26;10(3):e0122354. doi: 10.1371/journal.pone.0122354. eCollection 2015. PubMed PMID: 25811884; PubMed Central PMCID: PMC4374879.

Pérez-Bercoff Å, Papanicolaou A, Ramsperger M, Kaur J, Patel HR, Harun A, Duan SY, Elbourne L, Bouchara JP, Paulsen IT, Nevalainen H, Meyer W, Huttley GA. Draft Genome of Australian Environmental Strain WM 09.24 of the Opportunistic Human Pathogen Scedosporium aurantiacum. Genome Announc. 2015 Feb 12;3(1). pii: e01526-14. doi: 10.1128/genomeA.01526-14. PubMed PMID: 25676755; PubMed Central PMCID: PMC4333655.

Kamath KS, Kumar SS, Kaur J, Venkatakrishnan V, Paulsen IT, Nevalainen H, Molloy MP. Proteomics of hosts and pathogens in cystic fibrosis. Proteomics Clin Appl. 2015 Feb;9(1-2):134-46. doi: 0.1002/prca.201400122. Epub 2015 Jan 19. PubMed PMID: 25418359.

Venkatakrishnan V, Thaysen-Andersen M, Chen SC, Nevalainen H, Packer NH. Cystic fibrosis and bacterial colonization define the sputum N-glycosylation phenotype. Glycobiology. 2015 Jan;25(1):88-100. doi: 10.1093/glycob/cwu092. Epub 2014 Sep 4. PubMed PMID: 25190359.

Associate Professor MP Molloy

Martínez-Aguilar J, Clifton-Bligh R, Molloy MP. A multiplexed, targeted mass spectrometry assay of the S100 protein family uncovers the isoform-specific expression in thyroid tumours. BMC Cancer. 2015 Mar 29;15:199. doi: 10.1186/s12885-015-1217-x. PubMed PMID: 25880590; PubMed Central PMCID: PMC4391164.

Krisp C, Yang H, van Soest R, Molloy MP. Online peptide fractionation using a multiphasic microfluidic LC chip improves reproducibility and detection limits for quantitation in discovery and targeted proteomics. Mol Cell Proteomics. 2015 Apr 7. pii: mcp.M114.046425. [Epub ahead of print] PubMed PMID: 25850434.

Jankova L, Dent OF, Molloy MP, Chan C, Chapuis PH, Howell VM, Clarke SJ. Reporting in studies of protein biomarkers of prognosis in colorectal cancer in relation to the REMARK guidelines. Proteomics Clin Appl. 2015 Mar 9. doi:10.1002/prca.201400177. [Epub ahead of print] PubMed PMID: 25755195.

Lin CH, Chik JH, Packer NH, Molloy MP. Multidimensional fractionation is a requirement for quantitation of Golgi-resident glycosylation enzymes from cultured human cells. J Proteome Res. 2015 Feb 6;14(2):747-55. doi: 10.1021/pr500785f. Epub 2014 Dec 24. PubMed PMID: 25495351.

Pascovici D, Song X, Solomon PS, Winterberg B, Mirzaei M, Goodchild A, Stanley WC, Liu J, Molloy MP. Combining protein ratio p-values as a pragmatic approach to the analysis of multirun iTRAQ experiments. J Proteome Res. 2015 Feb 6;14(2):738-46. doi: 10.1021/pr501091e. Epub 2015 Jan 13. PubMed PMID: 25495031.

Kamath KS, Kumar SS, Kaur J, Venkatakrishnan V, Paulsen IT, Nevalainen H, Molloy MP. Proteomics of hosts and pathogens in cystic fibrosis. Proteomics Clin Appl. 2015 Feb;9(1-2):134-46. doi: 10.1002/prca.201400122. Epub 2015 Jan 19. PubMed PMID: 25418359.

Professor PA Haynes

George IS, Pascovici D, Mirzaei M, Haynes PA. Quantitative proteomic analysis of cabernet sauvignon grape cells exposed to thermal stresses reveals alterations in sugar and phenylpropanoid metabolism. Proteomics. 2015 May 9. doi: 10.1002/pmic.201400541. [Epub ahead of print] PubMed PMID: 25959233.

George IS, Fennell AY, Haynes PA. Protein identification and quantification from riverbank grape, vitis riparia: Comparing sds-page and fasp-gpf techniques for shotgun proteomic analysis. Proteomics. 2015 May 1. doi: 10.1002/pmic.201500085. [Epub ahead of print] PubMed PMID: 25929842.

Halden RU, Hartmann EM, Denslow ND, Haynes PA, LaBaer J. Recent advances in proteomics applied to elucidate the role of environmental impacts on human health and organismal function. J Proteome Res. 2015 Jan 2;14(1):1-4. doi: 10.1021/pr501224f. PubMed PMID: 25751307.

Emery SJ, Lacey E, Haynes PA. Quantitative proteomic analysis of Giardia duodenalis assemblage A: A baseline for host, assemblage, and isolate variation. Proteomics. 2015 Feb 27. doi: 10.1002/pmic.201400434. [Epub ahead of print] PubMed PMID: 25728068.

Wearne TA, Mirzaei M, Franklin JL, Goodchild AK, Haynes PA, Cornish JL. Methamphetamine-induced sensitization is associated with alterations to the proteome of the prefrontal cortex: implications for the maintenance of psychotic disorders. J Proteome Res. 2015 Jan 2;14(1):397-410. doi: 10.1021/pr500719f. Epub 2014 Oct 17. PubMed PMID: 25245100.

Professor DA Raftos

Allam B, Raftos D. Immune responses to infectious diseases in bivalves. J Invertebr Pathol. 2015 May 20. pii: S0022-2011(15)00089-0. doi: 10.1016/j.jip.2015.05.005. [Epub ahead of print] Review. PubMed PMID: 26003824.

Anderson K, Taylor DA, Thompson EL, Melwani AR, Nair SV, Raftos DA. Meta-analysis of studies using suppression subtractive hybridization and microarrays to investigate the effects of environmental stress on gene transcription in oysters. PLoS One. 2015 Mar 13;10(3):e0118839. doi: 10.1371/journal.pone.0118839. eCollection 2015. PubMed PMID: 25768438; PubMed Central PMCID: PMC4358831.

Associate Professor BJ Atwell

Dani KG, Jamie IM, Prentice IC, Atwell BJ. Species-specific photorespiratory rate, drought tolerance and isoprene emission rate in plants. Plant Signal Behav. 2015;10(3):e990830. doi: 10.4161/15592324.2014.990830. PubMed PMID: 25734586.

Narsai R, Edwards JM, Roberts TH, Whelan J, Joss GH, Atwell BJ. Mechanisms of growth and patterns of gene expression in oxygen-deprived rice coleoptiles. Plant J. 2015 Apr;82(1):25-40. doi: 10.1111/tpj.12786. PubMed PMID: 25650041.

Atwell BJ, Greenway H, Colmer TD. Efficient use of energy in anoxia-tolerant plants with focus on germinating rice seedlings. New Phytol. 2015 Apr;206(1):36-56. doi: 10.1111/nph.13173. Epub 2014 Dec 4. PubMed PMID: 25472708.

Associate Professor B Mabbutt

 Farrugia DN, Elbourne LD, Mabbutt BC, Paulsen IT. A novel family of integrases associated with prophages and genomic islands integrated within the tRNA-dihydrouridine synthase A (dusA) gene. Nucleic Acids Res. 2015 May 19;43(9):4547-57. doi: 10.1093/nar/gkv337. Epub 2015 Apr 16. PubMed PMID: 25883135.

Dr LJ Brown

Al Khamici H, Brown LJ, Hossain KR, Hudson AL, Sinclair-Burton AA, Ng JP, Daniel EL, Hare JE, Cornell BA, Curmi PM, Davey MW, Valenzuela SM. Members of the chloride intracellular ion channel protein family demonstrate glutaredoxin-like enzymatic activity. PLoS One. 2015 Jan 12;10(1):e115699. doi: 10.1371/journal.pone.0115699. eCollection 2015. PMCID: PMC4291220 PMID: 25581026 [PubMed – in process]

 Professor P Bergquist and Dr A Sunna

Care A Bergquist PL, Sunna A. Solid-binding peptides: smart tools for nanobiotechnology. Trends Biotechnol. 2015 May;33(5):259-268. doi: 10.1016/j.tibtech.2015.02.005. Epub 2015 Mar 19. PMID: 25796487 [PubMed – as supplied by publisher]

Professor S Ranganathan

Mahboob S, Ahn SB, Cheruku HR, Cantor D, Rennel E, Fredriksson S, Edfeldt G, Breen EJ, Khan A, Mohamedali A, Muktadir MG, Ranganathan S, Tan SH, Nice E, Baker MS. A novel multiplexed immunoassay identifies CEA, IL-8 and prolactin as prospective markers for Dukes’ stages A-D colorectal cancers. Clin Proteomics. 2015 Apr 8;12(1):10. doi: 10.1186/s12014-015-9081-x. eCollection 2015. PMCID: PMC4435647 PMID: 25987887 [PubMed]

Associate Professor IJ Wright

Zanne AE, Tank DC, Cornwell WK, Eastman JM, Smith SA, FitzJohn RG, McGlinn DJ, O’Meara BC, Moles AT, Reich PB, Royer DL, Soltis DE, Stevens PF, Westoby M, Wright IJ, Aarssen L, Bertin RI, Calaminus A, Govaerts R, Hemmings F, Leishman MR, Oleksyn J, Soltis PS, Swenson NG, Warman L, Beaulieu JM. Zanne et al. reply. Nature. 2015 May 21;521(7552):E6-7. doi: 10.1038/nature14394. PubMed PMID: 25993971.

Zanne AE, Tank DC, Cornwell WK, Eastman JM, Smith SA, FitzJohn RG, McGlinn DJ, O’Meara BC, Moles AT, Reich PB, Royer DL, Soltis DE, Stevens PF, Westoby M, Wright IJ, Aarssen L, Bertin RI, Calaminus A, Govaerts R, Hemmings F, Leishman MR, Oleksyn J, Soltis PS, Swenson NG, Warman L, Beaulieu JM. Corrigendum: Three keys to the radiation of angiosperms into freezing environments. Nature. 2015 May 21;521(7552):380. doi: 10.1038/nature14371. PubMed PMID: 25993966.

Ziemińska K, Westoby M, Wright IJ. Broad Anatomical Variation within a Narrow Wood Density Range-A Study of Twig Wood across 69 Australian Angiosperms. PLoS One. 2015 Apr 23;10(4):e0124892. doi: 10.1371/journal.pone.0124892. eCollection 2015. PubMed PMID: 25906320; PubMed Central PMCID: PMC4408027.

Atkin OK, Bloomfield KJ, Reich PB, Tjoelker MG, Asner GP, Bonal D, Bönisch G, Bradford MG, Cernusak LA, Cosio EG, Creek D, Crous KY, Domingues TF, Dukes JS, Egerton JJ, Evans JR, Farquhar GD, Fyllas NM, Gauthier PP, Gloor E, Gimeno TE, Griffin KL, Guerrieri R, Heskel MA, Huntingford C, Ishida FY, Kattge J, Lambers H, Liddell MJ, Lloyd J, Lusk CH, Martin RE, Maksimov AP, Maximov TC, Malhi Y, Medlyn BE, Meir P, Mercado LM, Mirotchnick N, Ng D, Niinemets Ü, O’Sullivan OS, Phillips OL, Poorter L, Poot P, Prentice IC, Salinas N, Rowland LM, Ryan MG, Sitch S, Slot M, Smith NG, Turnbull MH, VanderWel MC, Valladares F, Veneklaas EJ, Weerasinghe LK, Wirth C, Wright IJ, Wythers KR, Xiang J, Xiang S, Zaragoza-Castells J. Global variability in leaf respiration in relation to climate, plant functional types and leaf traits. New Phytol. 2015 Apr;206(2):614-36. doi: 10.1111/nph.13253. Epub 2015 Jan 8. PubMed PMID: 25581061.

2014

Dani KG, Jamie IM, Prentice IC, Atwell BJ. Evolution of isoprene emission capacity in plants. Trends Plant Sci. 2014 Jul;19(7):439-446. doi:10.1016/j.tplants.2014.01.009. Epub 2014 Feb 26. Review. PubMed PMID: 24582468.

Atwell BJ, Wang H, Scafaro AP. Could abiotic stress tolerance in wild relatives of rice be used to improve Oryza sativa? Plant Sci. 2014 Feb;215-216:48-58. doi: 10.1016/j.plantsci.2013.10.007. Epub 2013 Oct 21. PubMed PMID: 24388514.

Mirzaei M, Soltani N, Sarhadi E, George IS, Neilson KA, Pascovici D, Shahbazian S, Haynes PA, Atwell BJ, Salekdeh GH. Manipulating root water supply elicits major shifts in the shoot proteome. J Proteome Res. 2014 Feb 7;13(2):517-26. doi: 10.1021/pr400696u. Epub 2013 Dec 3. PubMed PMID: 24266738.

Ahn SB, Mohamedali A, Chan C, Fletcher J, Kwun SY, Clarke C, Dent OF, Chapuis PH, Nice E, Baker MS. Correlations between integrin ανβ6 expression and clinico-pathological features in stage B and stage C rectal cancer. PLoS One. 2014 May 12;9(5):e97248. doi: 10.1371/journal.pone.0097248. eCollection 2014. PubMed PMID: 24821188; PubMed Central PMCID: PMC4018280.

Sowmya G, Khan JM, Anand S, Ahn SB, Baker MS, Ranganathan S. A site for direct integrin αvβ6-uPAR interaction from structural modelling and docking. J Struct Biol. 2014 Mar;185(3):327-35. doi: 10.1016/j.jsb.2014.01.001. Epub 2014 Jan 11.PubMed PMID: 24423664.

Islam MT, Garg G, Hancock WS, Risk BA, Baker MS, Ranganathan S. Protannotator:a semiautomated pipeline for chromosome-wise functional annotation of the”missing” human proteome. J Proteome Res. 2014 Jan 3;13(1):76-83. doi:10.1021/pr400794x. Epub 2013 Dec 13. PubMed PMID: 24313344.

Sethi MK, Thaysen-Andersen M, Smith JT, Baker MS, Packer NH, Hancock WS, Fanayan S. Comparative N-glycan profiling of colorectal cancer cell lines reveals unique bisecting GlcNAc and α-2,3-linked sialic acid determinants are associated with membrane proteins of the more metastatic/aggressive cell lines. J Proteome Res. 2014 Jan 3;13(1):277-88. doi: 10.1021/pr400861m. Epub 2013 Dec 2. PubMed PMID: 24295106.

Gillings MR. Integrons: past, present, and future. Microbiol Mol Biol Rev. 2014 Jun;78(2):257-77. doi: 10.1128/MMBR.00056-13. PubMed PMID: 24847022; PubMed Central PMCID: PMC4054258.

Gillings MR. Rapid extraction of PCR-competent DNA from recalcitrant environmental samples. Methods Mol Biol. 2014;1096:17-23. doi:10.1007/978-1-62703-712-9_2. PubMed PMID: 24515357.

Gillings MR, Westoby M. DNA technology and evolution of the Central Dogma. Trends Ecol Evol. 2014 Jan;29(1):1-2. doi: 10.1016/j.tree.2013.10.001. Epub 2013 Oct 19. PubMed PMID: 24148293.

Hsu WL, Inglis DW, Startsev MA, Goldys EM, Davidson MR, Harvie DJ. Isoelectric Focusing in a Silica Nanofluidic Channel: Effects of Electromigration and Electroosmosis. Anal Chem. 2014 Aug 6. [Epub ahead of print] PubMed PMID:25098739.

Hsu WL, Harvie DJ, Davidson MR, Jeong H, Goldys EM, Inglis DW. Concentration gradient focusing and separation in a silica nanofluidic channel with a non-uniform electroosmotic flow. Lab Chip. 2014 Sep 21;14(18):3539-49. doi: 10.1039/c4lc00504j. Epub 2014 Jul 16. PubMed PMID: 25027204.

Lu Y, Lu J, Zhao J, Cusido J, Raymo FM, Yuan J, Yang S, Leif RC, Huo Y, Piper JA, Paul Robinson J, Goldys EM, Jin D. On-the-fly decoding luminescence lifetimes in the microsecond region for lanthanide-encoded suspension arrays. Nat Commun. 2014 May 6;5:3741. doi: 10.1038/ncomms4741. PubMed PMID: 24796249; PubMed Central PMCID: PMC4024748.

Ye Z, Zhang R, Song B, Dai Z, Jin D, Goldys EM, Yuan J. Development of a functional ruthenium(II) complex for probing hypochlorous acid in living cells. Dalton Trans. 2014 Jun 14;43(22):8414-20. doi: 10.1039/c4dt00179f. PubMed PMID: 24740358.

Hsu WL, Inglis DW, Jeong H, Dunstan DE, Davidson MR, Goldys EM, Harvie DJ. Stationary chemical gradients for concentration gradient-based separation and focusing in nanofluidic channels. Langmuir. 2014 May 13;30(18):5337-48. doi: 10.1021/la500206b. Epub 2014 Apr 29. PubMed PMID: 24725102.

Neilson KA, George IS, Emery SJ, Muralidharan S, Mirzaei M, Haynes PA. Analysis of rice proteins using SDS-PAGE shotgun proteomics. Methods Mol Biol. 2014;1072:289-302. doi: 10.1007/978-1-62703-631-3_21. PubMed PMID: 24136530.

Xu X, Li J, Han X, Shi C, Jin D, Lou W. Clinical characteristics and prognostic factors of patients with gastric neuroendocrine carcinoma treated with radical surgery. Chin Med J (Engl). 2014 Jul;127(13):2419-22. PubMed PMID: 24985576.

Xie H, Jin D, Yu J, Peng T, Ding Y, Zhou C, Xi P. Schlieren confocal microscopy for phase-relief imaging. Opt Lett. 2014 Mar 1;39(5):1238-41. doi: 10.1364/OL.39.001238. PubMed PMID: 24690716.

Han X, Xu X, Jin D, Wang D, Ji Y, Lou W. Clinicopathological characteristics and prognosis-related factors of resectable pancreatic neuroendocrine tumours: a retrospective study of 104 cases in a single Chinese center. Pancreas. 2014 May;43(4):526-31. doi: 10.1097/MPA.0000000000000065. PubMed PMID: 24658317.

Zhang Y, Zhang L, Deng R, Tian J, Zong Y, Jin D, Liu X. Multicolor barcoding in a single upconversion crystal. J Am Chem Soc. 2014 Apr 2;136(13):4893-6. doi: 10.1021/ja5013646. Epub 2014 Mar 24. PubMed PMID: 24645923.

Wu W, Yao X, Lin C, Jin D, Wang D, Lou W, Qin X. Should Steroid Therapy Be Necessarily Needed for Autoimmune Pancreatitis Patients with Lesion Resected due to Misdiagnosed or Suspected Malignancy? Gastroenterol Res Pract.2014;2014:253471. doi: 10.1155/2014/253471. Epub 2014 Jan 22. PubMed PMID:24578705; PubMed Central PMCID: PMC3918699.

Jin D, Lu Y, Leif RC, Yang S, Rajendran M, Miller LW. How to build a time-gated luminescence microscope. Curr Protoc Cytom. 2014 Jan 2;67:Unit 2.22.. doi: 10.1002/0471142956.cy0222s67. PubMed PMID: 24510771.

Vörös A, Simm R, Slamti L, McKay MJ, Hegna IK, Nielsen-LeRoux C, Hassan KA, Paulsen IT, Lereclus D, Okstad OA, Molloy MP, Kolstø AB. SecDF as Part of the Sec-Translocase Facilitates Efficient Secretion of Bacillus cereus Toxins and Cell Wall-Associated Proteins. PLoS One. 2014 Aug 1;9(8):e103326. doi: 10.1371/journal.pone.0103326. eCollection 2014. PubMed PMID: 25083861; PubMed Central PMCID: PMC4118872.

Chik JH, Zhou J, Moh ES, Christopherson R, Clarke SJ, Molloy MP, Packer NH. Comprehensive glycomics comparison between colon cancer cell cultures and tumours: Implications for biomarker studies. J Proteomics. 2014 Aug 28;108:146-62. doi: 10.1016/j.jprot.2014.05.002. Epub 2014 May 17. PubMed PMID:24840470.

Parker R, Clifton-Bligh R, Molloy MP. Phosphoproteomics of MAPK Inhibition in BRAF-Mutated Cells and a Role for the Lethal Synergism of Dual BRAF and CK2 Inhibition. Mol Cancer Ther. 2014 Jul;13(7):1894-906. doi: 10.1158/1535-7163.MCT-13-0938. Epub 2014 May 13. PubMed PMID: 24825855.

Hayes SA, Hudson AL, Clarke SJ, Molloy MP, Howell VM. From mice to men: GEMMs as trial patients for new NSCLC therapies. Semin Cell Dev Biol. 2014 Mar;27:118-27. doi: 10.1016/j.semcdb.2014.04.002. Epub 2014 Apr 6. PubMed PMID: 24718320.

Hart-Smith G, Chia SZ, Low JK, McKay MJ, Molloy MP, Wilkins MR. Stoichiometry of Saccharomyces cerevisiae lysine methylation: insights into non-histone protein lysine methyltransferase activity. J Proteome Res. 2014 Mar 7;13(3):1744-56. doi: 10.1021/pr401251k. Epub 2014 Feb 21. PubMed PMID: 24517342.

Care A, Nevalainen H, Bergquist PL, Sunna A. Effect of Trichoderma reesei Proteinases on the Affinity of an Inorganic-Binding Peptide. Appl Biochem Biotechnol. 2014 Jun 27. [Epub ahead of print] PubMed PMID: 24970048.

Nevalainen H, Peterson R. Making recombinant proteins in filamentous fungi-are we expecting too much? Front Microbiol. 2014 Feb 27;5:75. doi:10.3389/fmicb.2014.00075. eCollection 2014. Review. PubMed PMID: 24578701; PubMed Central PMCID: PMC3936196.

Nevalainen H, Kautto L, Te’o J. Methods for isolation and cultivation of filamentous fungi. Methods Mol Biol. 2014;1096:3-16. doi:10.1007/978-1-62703-712-9_1. PubMed PMID: 24515356.

Scott NE, Marzook NB, Cain JA, Solis N, Thaysen-Andersen M, Djordjevic SP, Packer NH, Larsen MR, Cordwell SJ. Comparative proteomics and glycoproteomics reveal increased N-linked glycosylation and relaxed sequon specificity in Campylobacter jejuni NCTC11168 O. J Proteome Res. 2014 Aug 5. [Epub ahead of print] PubMed PMID: 25093254.

Gotz L, Abrahams JL, Mariethoz J, Rudd PM, Karlsson NG, Packer NH, Campbell MP, Lisacek F. GlycoDigest: a tool for the targeted use of exoglycosidase digestions in glycan structure determination. Bioinformatics. 2014 Jul 10. pii:btu425. [Epub ahead of print] PubMed PMID: 25015990.

Anugraham M, Jacob F, Nixdorf S, Everest-Dass AV, Heinzelmann-Schwarz V,Packer NH. Specific glycosylation of membrane proteins in epithelial ovarian cancer cell lines: glycan structures reflect gene expression and DNA methylation status. Mol Cell Proteomics. 2014 May 22. pii: mcp.M113.037085. [Epub ahead ofprint] PubMed PMID: 24855066.

Thaysen-Andersen M, Packer NH. Advances in LC-MS/MS-based glycoproteomics: Getting closer to system-wide site-specific mapping of the N- and O-glycoproteome. Biochim Biophys Acta. 2014 Sep;1844(9):1437-1452. doi:10.1016/j.bbapap.2014.05.002. Epub 2014 May 12. Review. PubMed PMID: 24830338.

Williams KL, Gooley AA, Wilkins MR, Packer NH. A Sydney proteome story. J Proteomics. 2014 Jul 31;107C:13-23. doi: 10.1016/j.jprot.2014.04.006. Epub 2014 Apr 13. Review. PubMed PMID: 24735915.

York WS, Agravat S, Aoki-Kinoshita KF, McBride R, Campbell MP, Costello CE, Dell A, Feizi T, Haslam SM, Karlsson N, Khoo KH, Kolarich D, Liu Y, Novotny M, Packer NH, Paulson JC, Rapp E, Ranzinger R, Rudd PM, Smith DF, Struwe WB,Tiemeyer M, Wells L, Zaia J, Kettner C. MIRAGE: the minimum information required for a glycomics experiment. Glycobiology. 2014 May;24(5):402-6. doi:10.1093/glycob/cwu018. Epub 2014 Mar 20. PubMed PMID: 24653214; PubMed Central PMCID: PMC3976285.

Campbell MP, Ranzinger R, Lütteke T, Mariethoz J, Hayes CA, Zhang J, Akune Y, Aoki-Kinoshita KF, Damerell D, Carta G, York WS, Haslam SM, Narimatsu H, Rudd PM, Karlsson NG, Packer NH, Lisacek F. Toolboxes for a standardised and systematic study of glycans. BMC Bioinformatics. 2014;15 Suppl 1:S9. doi: 10.1186/1471-2105-15-S1-S9. Epub 2014 Jan 10. PubMed PMID: 24564482; PubMed Central PMCID: PMC4016020.

Christiansen MN, Chik J, Lee L, Anugraham M, Abrahams JL, Packer NH. Cell surface protein glycosylation in cancer. Proteomics. 2014 Mar;14(4-5):525-46.doi: 10.1002/pmic.201300387. PubMed PMID: 24339177.

Campbell MP, Peterson R, Mariethoz J, Gasteiger E, Akune Y, Aoki-Kinoshita KF, Lisacek F, Packer NH. UniCarbKB: building a knowledge platform for glycoproteomics. Nucleic Acids Res. 2014 Jan;42(Database issue):D215-21. doi: 10.1093/nar/gkt1128. Epub 2013 Nov 13. PubMed PMID: 24234447; PubMed Central PMCID: PMC3964942.

Campbell MP, Nguyen-Khuong T, Hayes CA, Flowers SA, Alagesan K, Kolarich D,Packer NH, Karlsson NG. Validation of the curation pipeline of UniCarb-DB: building a global glycan reference MS/MS repository. Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):108-16. doi: 10.1016/j.bbapap.2013.04.018. Epub 2013 Apr 25. PubMed PMID: 23624262.

Weaver DS, Keseler IM, Mackie A, Paulsen IT, Karp PD. A genome-scale metabolic flux model of Escherichia coli K-12 derived from the EcoCyc database. BMC Syst Biol. 2014 Jun 30;8:79. doi: 10.1186/1752-0509-8-79. PubMed PMID: 24974895; PubMed Central PMCID: PMC4086706.

Hassan KA, Elbourne LD, Tetu SG, Johnson EA, Paulsen IT. Genome Sequence of the Neurotoxigenic Clostridium butyricum Strain 5521. Genome Announc. 2014 Jun 26;2(3). pii: e00632-14. doi: 10.1128/genomeA.00632-14. PubMed PMID: 24970833; PubMed Central PMCID: PMC4073117.

Mackie AM, Hassan KA, Paulsen IT, Tetu SG. Biolog Phenotype Microarrays for phenotypic characterization of microbial cells. Methods Mol Biol. 2014;1096:123-30. doi: 10.1007/978-1-62703-712-9_10. PubMed PMID: 24515365.

Mackie A, Paley S, Keseler IM, Shearer A, Paulsen IT, Karp PD. Addition of Escherichia coli K-12 growth observation and gene essentiality data to the EcoCyc database. J Bacteriol. 2014 Mar;196(5):982-8. doi: 10.1128/JB.01209-13. Epub 2013 Dec 20. PubMed PMID: 24363340; PubMed Central PMCID: PMC3957686.

Raftos DA, Kuchel R, Aladaileh S, Butt D. Infectious microbial diseases and host defence responses in Sydney rock oysters. Front Microbiol. 2014 Apr 23;5:135. doi: 10.3389/fmicb.2014.00135. eCollection 2014. Review. PubMed PMID: 24795701; PubMed Central PMCID: PMC4005933.

Taylor DA, Nair SV, Thompson EL, Raftos DA. Dose-dependent effects of metals on gene expression in the Sydney rock oyster, Saccostrea glomerata. Environ Toxicol. 2014 Feb 26. doi: 10.1002/tox.21972. [Epub ahead of print] PubMed PMID: 24615909.

Dheilly NM, Adema C, Raftos DA, Gourbal B, Grunau C, Du Pasquier L. No more non-model species: the promise of next generation sequencing for comparative immunology. Dev Comp Immunol. 2014 Jul;45(1):56-66. doi:10.1016/j.dci.2014.01.022. Epub 2014 Feb 6. PubMed PMID: 24508980; PubMed Central PMCID: PMC4096995.

Krajaejun T, Lerksuthirat T, Garg G, Lowhnoo T, Yingyong W, Khositnithikul R, Tangphatsornruang S, Suriyaphol P, Ranganathan S, Sullivan TD. Transcriptome analysis reveals pathogenicity and evolutionary history of the pathogenic oomycete Pythium insidiosum. Fungal Biol. 2014 Jul;118(7):640-53. doi: 10.1016/j.funbio.2014.01.009. Epub 2014 Feb 6. PubMed PMID: 25088078.

Tong JC, Tan TW, Ranganathan S. Structure-based clustering of major histocompatibility complex (MHC) proteins for broad-based T-cell vaccine design. Methods Mol Biol. 2014;1184:503-11. doi: 10.1007/978-1-4939-1115-8_27. PubMed PMID: 25048142.

Tang YT, Gao X, Rosa BA, Abubucker S, Hallsworth-Pepin K, Martin J, Tyagi R, Heizer E, Zhang X, Bhonagiri-Palsikar V, Minx P, Warren WC, Wang Q, Zhan B, Hotez PJ, Sternberg PW, Dougall A, Gaze ST, Mulvenna J, Sotillo J, Ranganathan S, Rabelo EM, Wilson RK, Felgner PL, Bethony J, Hawdon JM, Gasser RB, Loukas A, Mitreva M. Genome of the human hookworm Necator americanus. Nat Genet. 2014 Mar;46(3):261-9. doi: 10.1038/ng.2875. Epub 2014 Jan 19. PubMed PMID: 24441737; PubMed Central PMCID: PMC3978129.

Sowmya G, Ranganathan S. Protein-protein interactions and prediction: a comprehensive overview. Protein Pept Lett. 2014;21(8):779-89. PubMed PMID: 23855658.

Müller AH, Sawicki A, Zhou S, Tabrizi ST, Luo M, Hansson M, Willows RD. Inducing the oxidative stress response in Escherichia coli improves the quality of a recombinant protein: Magnesium chelatase ChlH.  Biochim Biophys Acta. 2014 Feb;1838(2):643-57. doi: 10.1016/j.bbamem.2013.05.025. Protein Expr Purif. 2014 Jun 12;101C:61-67. doi: 10.1016/j.pep.2014.06.004. [Epub ahead of print] PMID: 24931499

Jiang L, Phang JM, Yu J, Harrop SJ, Sokolova AV, Duff AP, Wilk KE, Alkhamici H, Breit SN, Valenzuela SM, Brown LJ, Curmi PM. CLIC proteins, ezrin, radixin, moesin and the coupling of membranes to the actin cytoskeleton: a smoking gun? Protein Expr Purif. 2014 Jun 12;101C:61-67. doi: 10.1016/j.pep.2014.06.004. [Epub ahead of print]  PMID: 23732235

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