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Biomolecular Frontiers Research Centre

Publications

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Journals

2012

  1. Jones, Alexandra M. E. ; Aebersold, Ruedi ; Ahrens, Christian H. ; Apweiler, Rolf ; Baerenfaller, Katja ; Baker, Mark ; Bendixen, Emoke ; Briggs, Steve ; Brownridge, Philip ; Brunner, Erich ; Daube, Michael ; Deutsch, Eric, W. ; Grossniklaus, Ueli ; Heazlewood, Joshua ; Hengartner, Michael O. ; Hermjakob, Henning ; Jovanovic, Marko ; Lawless, Craig ; Lochnit, Gunter ; Martens, Lennart ; Ravnsborg, Christian ; Schrimpf, Sabine P. ; Shim, Yhong-Hee ; Subasic, Deni ; Tholey, Andreas ; van Wijk, Klaas, J. ; von Mering, Christian ; Weiss, Manuel ; Zheng, Xue, The HUPO initiative on Model Organism Proteomes, iMOP, Proteomics, 2012, 12, 3, 340-345
  2. Kinsinger, Christopher R. ; Apffel, James ; Baker, Mark ; Bian, Xiaopeng ; Borchers, Christoph ; Bradshaw, R ; Brusniak, Mi-Youn ; Chan, Daniel ; Deutsch, Eric ; Domon, Bruno ; Gorman, Jeffrey ; Grimm, Rudolf ; Hancock, William ; Hermjakob, Henning ; Horn, David ; Hunter, Christie ; Kolar, Patrik ; Kraus, Hans-Joachim ; Langen, Hanno ; Linding, Rune ; Moritz, Robert ; Omenn, Gilbert ; Orlando, Ron ; Pandey, Akhilesh ; Ping, Peipei ; Rahbar, Amir ; Rivers, Robert ; Seymour, Sean L. ; Simpson, Richard ; Slotta, Douglas ; Smith, Richard ; Stein, Stephen ; Tabb, David L. ; Tagle, Danilo ; Yates, John ; Rodriguez, Henry, Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles), Proteomics, 2012, 12, 1, 11-20
  3. Kinsinger, Christopher R. ; Apffel, James ; Baker, Mark ; Bian, Xiaopeng ; Borchers, Christoph ; Bradshaw, R ; Brusniak, Mi-Youn ; Chan, Daniel ; Deutsch, Eric ; Domon, Bruno ; Gorman, Jeffrey ; Grimm, Rudolf ; Hancock, William ; Hermjakob, Henning ; Horn, David ; Hunter, Christie ; Kolar, Patrik ; Kraus, Hans-Joachim ; Langen, Hanno ; Linding, Rune ; Moritz, Robert ; Omenn, Gilbert ; Orlando, Ron ; Pandey, Akhilesh ; Ping, Peipei ; Rahbar, Amir ; Rivers, Robert ; Seymour, Sean L. ; Simpson, Richard ; Slotta, Douglas ; Smith, Richard ; Stein, Stephen ; Tabb, David L. ; Tagle, Danilo ; Yates, John ; Rodriguez, Henry, Recommendations for mass spectrometry data quality metrics for open access data (Corollary to the Amsterdam Principles), Journal Of Proteome Research, 2012, 11, 2, 1412-1419
  4. Paik, Young-Ki ; Omenn, Gilbert, S. ; Uhlen, Mathias ; Hanash, Samir, M. ; Marko-Varga, György ; Aebersold, Ruedi ; Bairoch, Amos ; Yamamoto, Tadashi ; Legrain, Pierre ; Lee, Hyoung-Joo ; Na, Keun ; Jeong, Seul-Ki ; He, Fuchu ; Binz, P ; Nishimura, Toshihide ; Keown, Paul ; Baker, Mark ; Yoo, Jong-Shin ; Garin, Jerome ; Archakov, Alexander ; Bergeron, John, J. M. ; Salekdeh, G ; Hancock, William, Standard guidelines for the chromosome-centric human proteome project, Journal Of Proteome Research, 2012, 11, 4, 2005-2013
  5. Tan, Sock, Hwee ; Mohamedali, Abidali ; Kapur, Amit ; Lukjanenko, Laura ; Baker, Mark, A Novel, cost-effective and efficient chicken egg IgY purification procedure, Journal Of Immunological Methods, 2012, 380, 1-2, 73-76
  6. Khan, Javed, Mohammed ; Kumar, Gaurav ; Ranganathan, Shoba, In silico prediction of immunogenic T cell epitopes for HLA-DQ8, Immunome Research, 2012, 8, 1, 1-9
  7. Packer, Joanne, Michelle ; Brouwer, Nynke ; Harrington, David, George ; Gaikwad, Jitendra, Ashok ; Heron, Ronald ; Yaegl, Community Elde ; Ranganathan, Shoba ; Vemulpad, Subramanyam ; Jamie, Joanne, Faith, An Ethnobotanical study of medicinal plants used by the Yaegl Aboriginal community in northern New South Wales, Australia, Journal Of Ethnopharmacology, 2012, 139, 1, 244-255
  8. Young, Neil, D. ; Jex, Aaron ; Li, Bo ; Liu, Shiping ; Yang, Linfeng ; Xiong, Zijun ; Li, Yingrui ; Cantacessi, Cinzia ; Hall, Ross, S ; Xu, Xun ; Chen, Fangyuan ; Wu, Xuan ; Zerlotini, Adhemar ; Oliveira, Guilherme ; Hofmann, Andreas ; Zhang, Guojie ; Fang, Xiaodong ; Kang, Yi ; Campbell, Bronwyn, E ; Loukas, Alex ; Ranganathan, Shoba ; Rollinson, David ; Rinaldi, Gabriel ; Brindley, Paul ; Yang, Huanming ; Wang, Jun ; Wang, Jian ; Gasser, Robin, B, Whole-genome sequence of Schistosoma haematobium, Nature Genetics, 2012, 44, 2, 221-225
  9. Cantacessi, Cinzia ; Campbell, Bronwyn, E ; Jex, Aaron ; Young, Neil, D. ; Hall, R, S ; Ranganathan, Shoba ; Gasser, Robin, Bioinformatics meets parasitology, Parasite Immunology, 2012, 34, 5, 265-275
  10. 0.     Say, Jana ; Bradac, Carlo ; Gaebel, Torsten, Henrik ; Rabeau, James ; Brown, Louise, Processing 15-nm nanodiamonds containing nitrogen-vacancy centres for single-molecule FRET, Australian Journal Of Chemistry, 2012, 65, 5, 496-503
  11. 1.     Gaebel, Torsten, Henrik ; Bradac, Carlo ; Chen, J ; Say, Jana ; Brown, Louise ; Hemmer, Philip ; Rabeau, James, Size-reduction of nanodiamonds via air oxidation, Diamond And Related Materials, 2012, 21, 28-32
  12. 2.     Allen, Lisa, Zeigler ; Allen, Eric, E. ; Badger, Jonathan ; McCrow, John, P. ; Paulsen, Ian ; Elbourne, Liam, Davin Hunt ; Thiagarajan, Mathangi ; Rusch, Doug ; Nealson, K, H ; Williamson, Shannon ; Venter, J., Craig ; Allen, Andrew, Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic, The ISME Journal, 2012, 6, 7, 1403-1414
  13. 3.     Ma, Yingfei ; Paulsen, Ian ; Palenik, Brian.  Analysis of two marine metagenomes reveals the diversity of plasmids in oceanic environments, Environmental Microbiology, 2012, 14, 2, 453-466
  14. 4.     Partridge, Sally R. ; Paulsen, Ian ; Iredell, Jonathan.  pJIE137 carrying blaCTX-M-62 is closely related to p271A carrying blaNDM-1, Antimicrobial Agents And Chemotherapy, 2012, 56, 4, 2166-2168
  15. 5.     Lim, Chee, Kent ; Hassan, Karl ; Tetu, Sasha, Gabrielle ; Loper, Joyce ; Paulsen, Ian. The Effect of iron limitation on the transcriptome and proteome of Pseudomonas fluorescens Pf-5. 2012 PLoS ONE7.
  16. 6.     Ballor, Nicholas ; Paulsen, Ian ; Leadbetter, William. Genomic analysis reveals multiple [FeFe] hydrogenases and hydrogen sensors encoded by treponemes from the H?-rich termite gut, Microbial Ecology, 2012, 63, 2, 282-294
  17. 7.     Couttas, Timothy A. ; Raftery, Mark, James ; Padula, Matthew, P. ; Herbert, Benjamin ; Wilkins, Marc, R, Methylation of translation-associated proteins in Saccharomyces cerevisiae : identification of methylated lysines and their methyltransferases, Proteomics, 2012, 12, 7, 960-972
  18. 8.     Webster, Rebecca, Anne ; Blaber, Sinead, Pamela ; Herbert, Benjamin ; Wilkins, Marc, R ; Vesey, Graham, The Role of mesenchymal stem cells in veterinary therapeutics - a review, New Zealand Veterinary Journal, 2012, 60, 5, 265-272
  19. 9.     Packer, Joanne, Michelle ; Irish, Julie ; Herbert, Benjamin; Hill, Cameron, J. ; Padula, Matthew ; Blair, Shona E. ; Carter, Dee A. ; Harry, Elizabeth.  Specific non-peroxide antibacterial effect of manuka honey on the Staphylococcus aureus proteome, International Journal Of Antimicrobial Agents, 2012, 40, 1, 43-50
  20. 0.     Fanayan, Susan ; Hincapie, Maria ; Hancock, William, Using lectins to harvest the plasma/serum glycoproteome, Electrophoresis, 2012, 33, 12, 1746-1754
  21. 1.     Tian, Lu ; Dai, Zhichao ; Zhang, Lin ; Zhang, Ruoyu ; Ye, Zhiqiang ; Wu, Jing ; Jin, Dayong ; Yuan, Jinhong, Preparation and time-gated luminescence bioimaging applications of long wavelength-excited silica-encapsulated europium nanoparticles, Nanoscale, 2012, 4, 11, 3551-3557
  22. 2.     Calander, Nils, Pontus ; Jin, Dayong ; Goldys, Ewa, Taking plasmonic core-shell nanoparticles toward laser threshold, Journal of Physical Chemistry C, 2012, 116, 13, 7546-7551
  23. 3.     Zhang, Lin ; Wang, Yanjiao ; Ye, Zhiqiang ; Jin, Dayong ; Yuan, Jingli, New class of tetradentate ?-diketonate-europium complexes that can be covalently bound to proteins for time-gated fluorometric application, Bioconjugate Chemistry, 2012, 23, 6, 1244-1251
  24. 4.     Liu, Yujia ; Ding, Yichen ; Alonas, Eric ; Zhao, Wenli ; Santangelo, Philip J. ; Jin, Dayong ; Piper, James; Teng, Junlin ; Ren, Qiushi ; Xi, Peng.  Achieving ?/10 resolution CW STED nanoscopy with a Ti : Sapphire oscillator, PLoS ONE, 2012, 7, 6, 1-9
  25. 5.     Zhang, Run ; Ye, Zhiqiang ; Yin, Yuejiao ; Wang, Guilan ; Jin, Dayong ; Yuan, Jingli ; Piper, James.  Developing red-emissive ruthenium(II) complex-based luminescent probes for cellular imaging, Bioconjugate Chemistry, 2012, 23, 4, 725-733
  26. 6.     Zhang, Wenzhu ; Zhang, Run ; Zhang, Jingmei ; Ye, Zhiqiang ; Jin, Dayong ; Yuan, Jingli, Photoluminescent and electrochemiluminescent dual-signaling probe for bio-thiols based on a ruthenium(II) complex, Analytica Chimica Acta, 2012, 740, 1, 80-87
  27. 7.     Ding, Yichen ; Xie, Hao ; Peng, T. ; Lu, Yiqing ; Jin, Dayong ; Teng, Junlin ; Ren, Qiushi ; Xi, Peng, Laser oblique scanning optical microscopy (LOSOM) for phase relief imaging, Optics Express, 2012, 20, 13, 14100-14108
  28. 8.     Schartner, Erik, P. ; Jin, Dayong ; Ebendorff-Heidepriem, Heike ; Piper, James; Monro, Tanya, Lanthanide upconversion nanocrystals within microstructured optical fibres : a sensitive platform for biosensing and a new tool for nanocrystal characterisation, Third Asia Pacific Optical Sensors Conference : 31 January - 3 February 2012, Sydney, Australia, 2012, N/A, Vol. 8351, 83512Q-1-83512Q-4
  29. 9.     Peng, T. ; Xie, Hao ; Ding, Yichen ; Wang, Weichao ; Li, Zhiming ; Jin, Dayong ; Tang, Yuanhe ; Ren, Qiushi ; Xi, Peng, CRAFT: multimodality confocal skin imaging for early cancer diagnosis, Journal of Biophotonics, 2012, 5, 5-6, 469-476
  30. 0.     Leif, Robert ; Yang, Sean ; Lu, Yiqing ; Jin, Dayong ; Chambers, Stephen, A Cost-effective analog method to produce time-gated luminescence images, Imaging, manipulation, and analysis of biomolecules, cells, and tissues X : 21-23 January 2012, San Francisco, California, United States, 2012, N/A, Vol. 8225, 82250Z-1-82250Z-8
  31. 1.     Christiansen, Maja ; Packer, Nicolle ; Jørgensen, Christian ; Jensen, Ole, O-glycosylation affects function of fungal hydrolases, Journal Of Biotechnology, 2012, , , 1-1
  32. 2.     Kolarich, Daniel ; Jensen, Pia Honnerup ; Altmann, Fritz ; Packer, Nicolle, 1+1 = 3: Combining Glycan and Peptide Analysis for Glycopeptide Characterisation, Methods in Molecular Biology, 2012,  1-1
  33. 3.     Jensen, Pia, Honnerup ; Karlsson, Niclas, G. ; Kolarich, Daniel ; Packer, Nicolle, Structural analysis of N- and O-glycans released from glycoproteins, Nature Protocols, 2012, 7, 7, 1299-1310
  34. 4.     Kolarich, Daniel ; Jensen, Pia, Honnerup ; Altmann, Friedrich ; Packer, Nicolle, Determination of site-specific glycan heterogeneity on glycoproteins, Nature Protocols, 2012, 7, 7, 1285-1298
  35. 5.     He, Xu ; Galpin, Jason, D. ; Tropak, Michael, B. ; Mahuran, Don ; Haselhorst, Thomas ; von Itzstein, Mark ; Kolarich, Daniel, Konrad ; Packer, Nicolle ; Miao, Yansong ; Jiang, Liwen ; Grabowski, Greg ; Clarke, Lorne, A. ; Kermode, Allison, R., Production of active human glucocerebrosidase in seeds of Arabidopsis thaliana complex-glycan-deficient (cgl) plants, Glycobiology, 2012, 22, 4, 492-503
  36. 6.     He, Xu ; Haselhorst, Thomas ; von Itzstein, Mark ; Kolarich, Daniel ; Packer, Nicolle ; Kermode, Allison, R., Influence of an ER-retention signal on the N-glycosylation of recombinant human ?-L-iduronidase generated in seeds of Arabidopsis, Plant Molecular Biology, 2012, 79, 1-2, 157-169
  37. 7.     Wilkinson, Brendan, L. ; Stone, Robin, S. ; Capicciotti, Chantelle, J. ; Thaysen-Andersen, Morten ; Matthews, Jacqueline ; Packer, Nicolle ; Ben, Robert ; Payne, Richard. Total synthesis of homogeneous antifreeze glycopeptides and glycoproteins, Angewandte Chemie-International Edition, 2012, 51, 15, 3606-3610
  38. 8.     Mirzaei, Mehdi ; Pascovici, Dana ; Atwell, Brian ; Haynes, Paul.  Differential regulation of aquaporins, small GTPases and V-ATPases proteins in rice leaves subjected to drought stress and recovery, Proteomics, 2012, 12, 6, 864-877
  39. 9.     Duursma, Remko ; Falster, Daniel ; Valladares, Fernando ; Sterck, Frank ; Pearcy, R, W ; Lusk, Christopher, Harley ; Sendall, Kerrie ; Nordenstahl, Marisa ; Houter, N, C ; Atwell, Brian ; Kelly, N ; Kelly, Jeff ; Liberloo, M. ; Tissue, D, T ; Medlyn, Belinda, Elizabeth ; Ellsworth, David, S. Light interception efficiency explained by two simple variables : a test using a diversity of small- to medium-sized woody plants, New Phytologist, 2012, 193, 2, 397-408
  40. 0.     Scafaro, Andrew ; Yamori, Wataru ; Carmo-Silva, Elizabete ; Salvucci, Michael E. ; Von Caemmerer, Susanne ; Atwell, Brian, Rubisco activity is associated with photosynthetic thermotolerance in a wild rice (Oryza meridionalis), Physiologia Plantarum, 2012, 146, 1, 99-109
  41. 1.     Mirzaei, Mehdi ; Soltani, Neda ; Sarhadi, Elham ; Pascovici, Dana ; Keighley, Timothy ; Salekdeh, G ; Haynes, Paul ; Atwell, Brian. Shotgun proteomic analysis of long-distance drought signaling in rice roots, Journal Of Proteome Research, 2012, 11, 1, 348-358
  42. 2.     Dheilly, Nolwenn, Marie ; Haynes, Paul ; Raftos, David ; Nair, Sham, Time course proteomic profiling of cellular responses to immunological challenge in the sea urchin, Heliocidaris erythrogramma, Developmental And Comparative Immunology, 2012, 37, 2, 243-256
  43. 3.     Komatsu, Setsuko ; Haynes, Paul ; Salekdeh, G, Editorial : Promoting agriculture proteome research activities in the asia and oceania region (Journal of proteome research), Journal Of Proteome Research, 2012, 11, 3, 1461
  44. 4.     Thompson, Emma ; Taylor, Daisy ; Nair, Sham ; Birch, Gavin ; Haynes, Paul ; Raftos, David, Proteomic discovery of biomarkers of metal contamination in Sydney Rock oysters (Saccostrea glomerata), Aquatic Toxicology, 2012, 109, 202-212
  45. 5.     Pascovici, Dana ; Keighley, Timothy ; Mirzaei, Mehdi ; Haynes, Paul ; Cooke, Brett.  PloGO : plotting gene ontology annotation and abundance in multi-condition proteomics experiments, Proteomics, 2012, 12, 3, 406-410
  46. 6.     Kuchel,RP;  Nair, SV; Raftos, DA. Changes in the transcriptional expression of oxidative stress response genes in Akoya pearl oysters (Pinctada fucata) exposed to air and mechanical agitation. Aquaculture, 2012, 362/363: 33-38. JIF: 2.696.
  47. 7.     Thompson, EL; Taylor, DA; Nair SV; Birch, G; Coleman, R; Raftos, DA. Optimal acclimation periods for oysters in laboratory-based experiments. Journal of Molluscan Studies, 2012, 78 (3): 304-307. JIF: 1.227.
  48. 8.     Muralidharan, Sridevi ; Thompson, Emma ; Raftos, David ; Birch, Gavin ; Haynes, Paul, Quantitative proteomics of heavy metal stress responses in Sydney rock oysters, Proteomics, 2012, 12, 6, 906-921
  49. 9.     Marangon, M; Van Sluyter, S;  Robinson, E; Muhlack, R; Holt, H; Haynes, P; Godden, P; Smith, P; Waters E. Degradation of white wine haze proteins by Aspergillopepsin I and II during juice flash pasteurization. Food Chemistry,  2012 1;135(3):1157-65. Epub 2012 May 17.
  50. 0.     Thompson, Emma ; Taylor, Daisy ; Nair, Sham ; Birch, Gavin ; Hose, Grant, Christopher ; Raftos, David, Proteomic analysis of Sydney Rock oysters (Saccostrea glomerata) exposed to metal contamination in the field, Environmental Pollution, 2012, 170, 102-112
  51. 1.     Karuso, Peter, Quasicrystals or Quasiscience? : 2011 Nobel prize in chemistry I, Chemistry in Australia, 2012, 79, 2, 18-21
  52. 2.     Karuso, Peter, Quasicrystals or quasiscience? : 2011 Nobel prize in chemistry II, Chemistry in Australia, 2012, 79, 2, 16-21
  53. 3.     McRae, Christopher ; Karuso, Peter ; Liu, Fei.  ChemVoyage : a web-based, simulated learning environment with scaffolding and linking visualization to conceptualization, Journal Of Chemical Education, 2012, 89, 7, 878-883
  54. 4.     van Es, Theodorus ; Staskun, Benjamin ; Karuso, Peter, The Transposing of isomer yields in the methanolyses of N-substituted quinolinimides by triethylamine, South African Journal Of Chemistry, 2012, 65 , 53-61
  55. 5.     Sobhan, Mushtaq Ahmed ; Sreenivasan, Varun, Kumaraswamy Annayya ; Withford, Michael ; Goldys, Ewa, Non-specific internalization of laser ablated pure gold nanoparticles in pancreatic tumor cell, Colloids And Surfaces B-Biointerfaces, 2012, 92, 190-195
  56. 6.     Butterworth, Philip, Alan ; Moraes, Henrique, Thadeu Baltar de Medeiros Cabr ; Kratzmeier, Martin ; Goldys, Ewa, Detection of specific strains of viable bacterial pathogens by using RNA bead assays and flow cytometry with 2100 Bioanalyzer, Methods in Molecular Biology, 2012, 875, 253-262
  57. 7.     Lung, Mandy ; Pilowsky, Paul, Martin ; Goldys, Ewa. Activation of the mammalian cells by using light-sensitive ion channels, Methods in Molecular Biology, 2012, 875, 241-251
  58. 8.     Nevalainen, Kaisu ; Bradner, John ; Wadud, Sania ; Mohammed, Suja ; McRae, Christopher ; Te'o, Valentino, Enzyme activities and biotechnological applications of cold-active microfungi, Extremophiles : Microbiology and Biotechnology, 2012,  89-108
  59. 9.     Peterson, Robyn; Nevalainen, Helena. Trichoderma reesei RUT-C30- 30 years of strain improvement. Microbiology, 2012,  158: 59-68
  60. 0.     Kautto, Liisa;  Grinyer, Jasmine;  Paulsen, Ian;  Tetu, Sasha; Pillai, Aneesh;  Pardiwalla, Swapneel; Sezerman, Ugur ; Akcapinar,  Gunseli ; Bergquist, Peter; Te'o, Junior; Nevalainen, Helena, Cellular effects caused by expression of a mutant cellobiohydrolase I in Trichoderma reesei and effects of proteasome inhibition on stress response. New Biotechnology, 2012,  http://dx.doi.org/10.1016/j.nbt.2012.07.005
  61. 1.     Everest-Dass, Arun ; Jin, Dayong ; Thaysen-Andersen, Morten;  Nevalainen, Helena; Kolarich, Daniel;  Packer, Nicolle.  Comparative structural analysis of the glycosylation of salivary and buccal cell proteins: innate protection against infection by C. albicans. Glycobiology, 2012, doi: 10.1093/glycob/cws112
  62. 2.     Krisp, Christoph ; Randall, Sarah ; McKay, Matthew ; Molloy, Mark, Towards clinical applications of selected reaction monitoring for plasma protein biomarker studies, Proteomics Clinical Applications, 2012, 6, 1-2, 42-59
  63. 3.     Krisp, Christoph ; McKay, Matthew ; Wolters, Dirk ; Molloy, Mark,  Multidimensional protein identification technology-selected reaction monitoring improving detection and quantification for protein biomarker studies, Analytical Chemistry, 2012, 84, 3, 1592-1600
  64. 4.     Sherman, Jamie ; Molloy, Mark ; Burlingame, Alma, S., Why complexity and entropy matter : information, posttranslational modifications, and assay fidelity, Proteomics, 2012, 12, 8, 1147-1150
  65. 5.     Sigglekow, Nicholas, D. ; Pangon, Laurent ; Brummer, Tilman ; Molloy, Mark ; Hawkins, Nicholas, J. ; Ward, Robyn ; Musgrove, Elizabeth, A. ; Kohonen - Corish, Maija. Mutated in colorectal cancer protein modulates the NF?B pathway, Anticancer Research, 2012, 32, 1, 73-79
  66. 6.     Sharma, Manisha ; Jamieson, Cara ; Johnson, Michael ; Molloy, Mark ; Henderson, Beric, Specific Armadillo repeat sequences facilitate ?-catenin nuclear transport in live cells via direct binding to nucleoporins Nup62, Nup153, and RanBP2/Nup358, Journal Of Biological Chemistry, 2012, 287, 2, 819-831
  67. 7.     Mousavi, Seyed Mohammad ; Raftos, David, In vitro antifungal activity of a new combination of essential oils against some filamentous fungi, Middle-East journal of scientific research, 2012, 11, 2, 156-161
  68. 8.     Amaral, Valter, Luis Morgado ; Thompson, Emma ; Bishop, Melanie, Jane ; Raftos, David, The Proteomes of Sydney rock oysters vary spatially according to exposure to acid sulfate runoff, Marine And Freshwater Research, 2012, 63, 4, 361-369
  69. 9.     Parker, Laura ; Ross, Pauline ; O'Connor, Wayne, A ; Borysko, Larissa ; Raftos, David ; Portner, Hans, Adult exposure influences offspring response to ocean acidification in oysters, Global Change Biology, 2012, 18, 1, 82-92
  70. 0.     Gillings, Michael, How evolution generates complexity without design : language as an instructional metaphor, Evolution, 2012, 66, 3, 617-622
  71. 1.     Gillings, Michael ; Stokes, Harold, William, Are humans increasing bacterial evolvability?, Trends In Ecology and Evolution, 2012, 27, 6, 346-352
  72. 2.     Stelting, Scott ; Burns, Richard ; Sunna, Anwar ; Visnovsky, Gabriel ; Bunt, Craig, Immobilization of Pseudomonas sp. strain ADP : a stable inoculant for the bioremediation of atrazine, Applied Clay Science, 2012, 64, 90-93
  73. 3.     Li, Yaqiong ; Scales, Nicholas ; Blankenship, Robert ; Willows, Robert ; Chen, Min, Extinction coefficient for red-shifted chlorophylls : chlorophyll d and chlorophyll f, Biochimica Et Biophysica Acta-Bioenergetics, 2012, 1817, 8, 1292-1298
  74. 4.     Smith, Jason, Ross ; Evans, Krystal, J. ; Wright, Adam ; Willows, Robert ; Jamie, Joanne, Faith ; Griffith, Renate, Novel indoleamine 2,3-dioxygenase-1 inhibitors from a multistep in silico screen, Bioorganic and Medicinal Chemistry, 2012, 20, 3, 1354-1363
  75. 5.     Zhou, S; Sawicki A; Willows R. C-terminal residues of Oryza sativa GUN4 are required for the activation of the ChlH subunit of magnesium chelatase in chlorophyll synthesis. 2012  FEBS Letters 586, 205-210
  76. 6.     Chen, M; Li Y; Birch D; Willows R.  A cyanobacterium that contains chlorophyll f - a red-absorbing photopigment. FEBS Letters, 586 (19), 3249-3254
  77. 7.     Lee LY, Hincapie M, Packer Nicolle, Baker Mark, Fanayan Susan, Hancock William. Optimization of native multi-lectin affinity chromatography for enrichment of glycoproteins from MCF 7 total protein lysate, Journal of Separation Science. 2012 Sep;35(18):2445-52. doi: 10.1002/jssc.201200049
  78. 8.     Tousi, F; Bones, J; Iliopoulos, O; Hancock, W; Hincapie, M. Multidimensional liquid chromatography platform for profiling alterations of clusterin N-glycosylation in the plasma of patients with renal cell carcinoma,  Journal of Chromatography A, 2012 Sep 21;1256:121-8. doi: 10.1016/j.chroma.2012.07.066. Epub 2012 Jul 28. PMID: 22885037
  79. 9.     Tep, S;  Hincapi,e M;  Hancock, W. The characterization and quantitation of glycomic changes in CHO cells during a bioreactor campaign. Biotechnology and Bioengineering, 2012, 2. doi: 10.1002/bit.24590. [Epub ahead of print] PMID: 22752974
  80. 0.     Vickers D; Kulik, M; Hincapie, M; Hancock, W; Dalton, S; Murthy, S. Lectin-functionalized microchannels for characterizing pluripotent cells and early differentiation, Biomicrofluidics, 2012, 2012 Jun;6(2):24122-2412210. Epub 2012 May 22. PMID: 22712033
  81. 1.     Carlage, T; Kshirsagar, R; Zang, L; Janakiraman, V; Hincapie, M; Lyubarskaya, Y; Weiskopf, A; Hancock W. Analysis of dynamic changes in the proteome of a Bcl-XL overexpressing Chinese hamster ovary cell culture during exponential and stationary phases, Biotechnology Progress, 2012 May;28(3):814-23. doi: 10.1002/btpr.1534. Epub 2012 May 2. PMID: 22556165
  82. 2.     Paik, Y; Jeong, S; Omenn, G; Uhlen, M; Hanash, S; Cho, S; Lee, H; Na, K; Choi, E; Yan, F; Zhang, F; Zhang, Y; Snyder, M; Cheng, Y; Chen, R; Marko-Varga, G; Deutsch, E; Kim, H; Kwon, J; Aebersold, R; Bairoch, A; Taylor, A; Kim, K; Lee, E; Hochstrasser, D; Legrain, P; Hancock, W. The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nature Biotechnology, . 2012 Mar 7;30(3):221-3. doi: 10.1038/nbt.2152.  PMID: 22398612
  83. 3.     Lu, Q; Padler-Karavani, V; Yu, H; Chen, X; Wu, S; Varki, A; Hancock, W. LC-MS analysis of polyclonal human anti-Neu5Gc xeno-autoantibodies immunoglobulin G Subclass and partial sequence using multistep intravenous immunoglobulin affinity purification and multienzymatic digestion. Analytical Chemistry,  2012 Mar 20;84(6):2761-8. Epub 2012 Feb 28. PMID: 22390546
  84. 4.     Tep, S; Hincapie, M; Hancock, W. A general approach for the purification and quantitative glycomic analysis of human plasma. Analytical and  Bioanalytical Chemistry,  2012 Mar;402(9):2687-700. Epub 2012 Jan 26.
  85. 5.     PMID: 22274286
  86. 6.     Tep, S; Hincapie, M; Hancock, W. A MALDI-TOF MS method for the simultaneous and quantitative analysis of neutral and sialylated glycans of CHO-expressed glycoproteins. Carbohydrate Researc, 2012 Jan 10;347(1):121-9. Epub 2011 Oct 20. PMID: 22138464
  87. 7.     Rafalko, A; Dai, S; Hancock, W; Karger, B; Hincapie, M.  Development of a Chip/Chip/SRM platform using digital chip isoelectric focusing and LC-Chip mass spectrometry for enrichment and quantitation of low abundance protein biomarkers in human plasma. Journal of Proteome Research, 2012 Feb 3;11(2):808-17
  88. 8.     Tan, S-W;  Kapur, A; Baker, MS. Chicken Immune Responses to Variations in Human Plasma Protein Ratios [A Rationale for Polyclonal IgY Ultraimmunodepletion].  J Proteome Res., in press - accepted Oct. 18th 2012. Manuscript ID: pr-2012-00717b.R1 [IF=6.9].
  89. 9.     Tan, S-W; Kapur A, Abidali, ;  Baker, MS. A Novel Human Plasma Ultradepletion Strategy. J Proteome Res. in press - accepted Oct. 22nd 2012. Manuscript ID: pr-2012-007182.R1. [IF=6.9].
  90. 0.     Raftos DA, Nair SV, Crockford M, Jones B.  Aquatic Animal Health Subprogram: Development of a DNA microarray to identify markers of disease in pearl oysters (Pinctada maxima) and to assess overall oyster health. 2012,  Final Report FRDC Project No.2008/030. Fisheries Research Report No. 230. Department of Fisheries, Western Australia. ISBN: 978-1-921845-40-6.
  91. 1.     Zeynep Sumer-Bayraktara, Roxana Jayo, Yaseen Fatani, Terry Nguyen-Khuong, David D.Y. Chen, Sinan Ali, Nicolle H. Packer, Morten Thaysen-Andersen Detailed Characterisation of N- and O-linked Glycosylation of Serum-Derived Human Sex Hormone-Binding Globulin. Accepted Electrophoresis. (2012)  August.
  92. 2.     Katherine Wongtrakul-Kish, Daniel Kolarich, Dana Pascovici, Janice L. Joss, Elizabeth Deane, Nicolle H. Packer.(2012) Characterization of N- and O-linked glycosylation changes in milk of the tammar wallaby (Macropus eugenii) over lactation. Accepted Glycoconjugate Journal.  September 10.
  93. 3.     Xu He, Thomas Haselhorst, Mark von Itzstein, Daniel Kolarich, Nicolle H. Packer, Tracey M. Gloster, David J. Vocadlo, Lorne A. Clarke, Yi Qian, Allison R. KermodeProduction of α-L-iduronidase in maize for the potential treatment of a human lysosomal storage disease. . (2012)  Accepted Nature Communications August 16.
  94. 4.     Kolarich,D. & Packer  N.H. Mass spectrometry for glycomics analysis of N- and O-linked glycoproteins, Chapter 8 in Structural Glycobiology,(eds. P.R Ramsland & E Yuriev] 2012. CRC Press, Taylor & Francis Group (ISBN: 9781439854600) pp141-162.
  95. 5.     F Lisacek, M. P. Campbell andN. H. Packer (2012) Expanding Knowledge on the Biological Context of Glycan Structures in Proceedings of the International Beistein Symposium on Glyco-Bioinformatics: Cracking the Sugar Code by Navigating the Glycospace (Eds: Martin G Hicks and Carsten Kettner). Deutsche nationalbibliothek FrankFurt, Germany. pp197 -208.
  96. 6.     M.P. Campbell, F. Lisacek, M.R. Wilkins, P.M. Rudd, Daniel Kolarich, C.A. Hayes, N.G. Karlsson, N. H. Packer Linking Glycomics Repositories with Data Capture. 2012.  in Proceedings of the International Beistein Symposium on Glyco-Bioinformatics: Cracking the Sugar Code by Navigating the Glycospace (Eds: Martin G Hicks and Carsten Kettner). Deutsche nationalbibliothek FrankFurt, Germany. Pp.165-178.
  97. 7.     Sureshan, Deshpande, Boucher, Koenig, MCSG, Stokes, Harrop, Curmie, B. Mabbutt. Integron gene cassettes: a repository of novel protein folds with distinct interaction sites. PLoS ONE. Accepted 2012.
  98. 8.     Nevalainen, Helena; Kautto, Liisa; Te'o, Junior. Methods for Isolation and Cultivation of Filamentous Fungi.  In: Methods in Molecular Biology, Environmental Microbiology. Walker J (ed) 2nd Ed, Humana Press, a part of Springer Science + Business Media. In press.
  99. 9.     Jankova, L., Robertson, G., Chan, C., Tan, K. L., Kohonen-Corish, M., Fung, C. L.-S., Clarke, C., Lin, B. P. C., Molloy, M., Chapuis, P. H., Bokey, L., Dent, O. F., Clarke, S. J. Glutathione S-transferase Pi Expression Predicts Response to Adjuvant Chemotherapy for Stage C Colon Cancer: a Matched Historical Control Study. BMC Cancer 2012 12:196.
  100. 00.  Kho, P.S.S., Jankova, L., Fung, C. L-S., Chan, C., Clarke, C., Lin, B. P. C., Robertson G., Molloy, M., Chapuis, P. H., Bokey, E. L., Dent, O. F., Clarke, S. Overexpression of protein S100A4 is independently associated with overall survival in stage C colonic cancer but only in cytoplasm at the advancing tumor front. Int. J. Colorectal Dis. 2012, DOI 10.1007/s00384-012-1469-8.
  101. 01.  Randall, S. A., McKay, M. J., Pascovici, D., Mahon, K., Horvath, L., Clarke, S.J., Molloy, M. P. Remarkable temporal stability of high abundance human plasma proteins assessed by targeted mass spectrometry. Proteomics Clin. Appls. 2012. Accepted 14/8/2012.
  102. 02.  Keseler IM, Mackie A, Peralta-Gil M, Santos-Zavaleta A, Gama-Castro S, Bonavides-Martínez C, Fulcher C, Huerta AM, Kothari A, Krummenacker M, Latendresse M, Muñiz-Rascado L, Ong Q, Paley S, Schröder I, Shearer AG, Subhraveti P, Travers M, Weerasinghe D, Weiss V, Collado-Vides J, Gunsalus RP, Paulsen I, Karp PD. 2012. EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Research. Nov 9. [Epub ahead of print]
  103. 03.  Lu J, Martin J, Lu Y, Zhao J, Yuan J, Ostrowski M, Paulsen I, Piper JA, Jin D. 2012. Resolving Low-Expression Cell Surface Antigens by Time-Gated Orthogonal Scanning Automated Microscopy. Analitical Chemistry. Nov 2. [Epub ahead of print]
  104. 04.  Dupont CL, Johnson DA, Phillippy K, Paulsen IT, Brahamsha B, Palenik B. 2012. Genetic Identification of a High-Affinity Ni Transporter and the Transcriptional Response to Ni Deprivation in Synechococcus sp. Strain WH8102. Appl Environ Microbiol. Nov;78(22):7822-32. doi: 10.1128/AEM.01739-12. Epub 2012 Aug 17.
  105. 05.  Humphreys W, Tetu S, Elbourne L, Gillings M, Seymour J, Mitchell J, Paulsen I. 2012. Geochemical and microbial diversity of bundera sinkhole, an anchialine system in the eastern Indian ocean. Natura Croatica 21:59-63.
  106. 06.  Lim CK, Hassan KA, Penesyan A, Loper JE, Paulsen IT. 2012. The effect of zinc limitation on the transcriptome of Pseudomonas protegens Pf-5. Environmental Microbiology. DOI: 10.1111/j.1462-2920.2012.02849.
  107. 07.  Loper JE, Hassan KA, Mavrodi DV, Davis Ii EW, Lim CK, Shaffer BT, Elbourne LDH, Stockwell VO, Hartney SL, Breakwell K, Henkels MD, Tetu SG, Rangel LI, Kidarsa TA, Wilson NL, van de Mortel JE, Song C, Blumhagen R, Radune D, Hostetler JB, Brinkac LM, Durkin AS, Kluepfel DA, Wechter WP, Anderson AJ, Kim YC, Pierson Iii LS, Pierson EA, Lindow SE, Kobayashi DY, Raaijmakers JM, Weller DM, Thomashow LS, Allen AE, Paulsen IT. 2012. Comparative genomics of plant-associated Pseudomonas spp.: Insights into diversity and inheritance of traits involved in multitrophic interactions. PLoS Genetics 8.
  108. 08.  Partridge SR, Ginn AN, Paulsen IT, Iredell JR. 2012. pEl1573 carrying bla IMP-4, from Sydney, Australia, is closely related to other IncL/M plasmids. Antimicrobial Agents and Chemotherapy 56:6029-6032.
  109. 09.  Francis SE, Ersoy RA, Ahn J-W, Atwell BJ and Roberts TH (2012) Serpins in rice: protein sequence analysis, phylogeny and gene expression during development. BMC Genomics 13: 449.
  110. 10.  Edwards JM, TH Roberts and BJ Atwell (2012) Quantifying ATP turnover in anoxic coleoptiles of rice (Oryza sativa) demonstrates preferential allocation of energy to protein synthesis Journal of Experimental Botany 63: 4389-4402.
  111. 11.  Harrison SP, Morfopoulos C, Srikanta Dani KG, Prentice IC, Arneth A, Atwell BJ, Barkley MP, Leishman MR, Loreto F, Medlyn BE, Niinemets Ü, Possell M, Peñuelas J and Wright IJ (2012) Volatile isoprenoid emissions from plastid to planet. New Phytologist (in press).

 

Prior papers

Randall, S.R., McKay, M.J., Molloy, M.P.  Evaluation of blood collection tubes using selected reaction monitoring mass spectrometry: implications for proteomic biomarker studies.  Proteomics. 2010 May;10(10):2050-6.

Sherman, J., McKay, M. J., Ashman, K., Molloy, M. P., Unique ion signature Mass Spectrometry: a deterministic method to assign peptide identity. Mol. Cell. Proteomics 2009, 8, 2051-2062.

Liaw T.Y., Salam N.K., McKay M.J., Cunningham A.M., Hibbs D.E., Kavallaris M., Class I beta-tubulin mutations in 2-methoxyestradiol-resistant acute lymphoblastic leukemia cells: implications for drug-target interactions. Mol. Cancer Ther. 2008; 7(10):3150-9.

McKay, M. J.; Sherman, J.; Laver, M. T.; Baker, M. S.; Clarke, S. J.; Molloy, M. P. The development of multiple reaction monitoring assays for liver-derived plasma proteins Peoteomics Clin. Appl. 2007, 1 ( 12) 1570- 1581.

M. D. Gibbs, R. A Reeves, P. R. Choudhary and P. L. Bergquist. Alteration of the pH optimum of a family 11 xylanase, XynB6 of Dictyoglomus thermophilum. New Biotechnol. 27: 803-809, 2010.

M. D. Gibbs, R. A. Reeves, P. R. Choudhary, R. M. Daniel and P. L. Bergquist. The activity of family 11 xylanases at alkaline pH. New Biotechnol. 27: 795-802, 2010.

Y. Wada, P. Azadi, C. E. Costello, A.Dell, R. Geyer, K. Kakehi, K. Kato, N. Kawasaki, K.-H.Khoo, S. Kim, A.Kondo, K. Nakamura, H. Narimatsu, M.V Novotny, N. H. Packer, H.Perreault, J. Peter-Katalinic, V. N. Reinhold, P. M. Rudd, A.Suzuki and N. Taniguchi (2007): Mass Spectrometry of Glycoprotein Glycans: HUPO/HGPI (Human Proteome Organisation Human Disease Glycomics/Proteome Initiative) Multi-institutional Study: Glycobiology, 17, 411-422.

B.L. Schulz, A.J. Sloane, L.J. Robinson, S.S. Prasad, R. A. Lindner, M.Robinson, P.T. Bye, D.W. Nielson, J.L. Harry, N. H. Packer, N.G. Karlsson (2007). Glycosylation of sputum mucins is altered in cystic fibrosis patients. Glycobiology, 17, 698-712.

R.P. Estrella, J.M. Whitelock, N. H. Packer and N.G. Karlsson (2007) Graphitized Carbon LC-MS Characterization of the Chondroitin Sulfate Oligosaccharides ofAggrecan Anal Chem.79, 3597-606.

N.G. Karlsson and N. H. Packer (2008) Glycomic mass spectrometric analysis and data interpretation tools in Bioinformatics for Glycomics (Ed. W. von der Lieth)(In press)

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N.L. Wilson, L.J. Robinson, N. H. Packer, and N.G. Karlsson (2008) Glycoproteomics of Milk: Differences in sugar epitopes on human and bovine milk fat globule membranes J. Proteome Res. 7(9), 3687-3696

N. Deshpande, M.R. Wilkins, N. H. Packer, H. Nevalainen (2008) Protein glycosylation pathways in filamentous fungi. Glycobiology 18, 626-637

Patrikis MI, Bryan EJ, Thomas NA, Rice GE, Quinn MA, Baker MS, Campbell IG. Mutation analysis of CDP, TP53, and KRAS in uterine leiomyomas. Mol. Carcinog. 2003, 37(2):61-4. 

Murthi P, Barker G, Nowell CJ, Rice GE, Baker MS, Kalionis B, Quinn MA. Plasminogen fragmentation and increased production of extracellular matrix-degrading proteinases are associated with serous epithelial ovarian cancer progression. Gynecol Oncol. 2004, 92(1):80-8.

Aristoteli LP, Molloy MP, Baker MS. Evaluation of Endogenous Plasma Peptide Extraction Methods for Mass Spectrometric Biomarker Discovery. J. Proteome Res., 6(2):571-81, 2007 [IF= 6.9].

Saldanha RG, Molloy MP, Bdeir K, Cines DB, Song X, Uitto PM, Weinreb PH, Violette SM, Baker MS. Proteomic Identification of Lynchpin Urokinase Plasminogen Activator Receptor Protein Interactions Associated with Epithelial Cancer Malignancy.  J. Proteome Res. 2007 6(3): 1016-1028.[IF=6.9]

Khan A, Baker MS. Non-specific binding of monoclonal human erythropoietin antibody AE7A5 to Escherichia coli and Saccharomyces cerevisiae proteins.  Clin. Chim. Acta. 379, 173-5, 2007. [IF=2.15]

Heinrich S, Cordwell SJ, Crossett B, Baker MS, Christopherson RI. The nuclear proteome and DNA-binding protein fraction of human Raji lymphoma cells.  Biochim. Biophys. Acta (Proteins & Proteomics), 1774:413-32, 2007. [IF: 2.98]

Chick JM, Haynes PA, Molloy MP, Bjellqvist B, Baker MS, Len ACL.Characterization of rat liver membrane proteome using peptide immobilized pH gradient isoelectric focusing (peptide IPG-IEF). J. Proteome Res. 2008, 7(3):1036-45 [IF= 6.9].

Xie F,Goldys E, Baker MS. Amplified protein sensing using Deep Purple fluorophores on homogeneous Au substrates. Biofactors. 2007;30(4):249-53.

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Gibson F, Anderson L, Babnigg G, Baker MS, Berth M, Binz P-A, Borthwick A, Cash P, Day BW, Friedman DB, Garland D, Gutstein HB, Hoogland C, Jones NA, Khan A, Klose J, Lamond AI, Lemkin PF, Lilley KS, Minden J, Morris NJ, Paton NW, Pisano MR,  Prime JE, Rabilloud T, Stead DA, Taylor CF, Voshol H, Wipat A, Jones AR. Guidelines for reporting the use of gel electrophoresis in proteomics Nature Biotech 2008. [IF= 22.8].

Chick JM, Haynes PA Bjellqvist B & Baker MS. Narrow Range Immobilised pH Gradients Improve Membrane Proteomics. J Proteome Res., 2008. [IF= 6.9].

Saldanha , Xu N, Molloy M, Veal D, Baker MS. Differential proteome expression associated with urokinase plasminogen activator receptor (uPAR) suppression in malignant epithelial cancer. J Proteome Res., 2008. [IF= 6.9].

M. D. Gibbs, R. A Reeves, P. R. Choudhary and P. L. Bergquist.. Alteration of the pH optimum of a family 11 xylanase, XynB6 of Dictyoglomus thermophilum. New Biotechnol. In press, July 2010.

M. D. Gibbs, R. A. Reeves, P. R. Choudhary, R. M. Daniel and P. L. Bergquist. The activity of family 11 xylanases at alkaline pH. New Biotechnol. In press, June 2010.

R. Ibanez-Peral, B. Ferrari and P. Bergquist.  Detection of environmental microorganisms with a bead-based assay and quantum dots. Internat. Jour. Of Biomedical Nanoscience and Nanotechnology. In press, 2010. 

E. Hardiman, M. Gibbs, R. Reeves and P. Bergquist.  Directed Evolution of a thermophilic ß-glucosidase for cellulosic bioethanol production.  Appl. Biochem. Biotech. 161: 301-312, 2010.

A. Alagappan, P. L. Bergquist and B. C. Ferrari. Species level identification of human infectious Cryptosporidium through development of a two-color fluorescence in situ hybridization technique. Appl. Environ. Microbiol. 75: 5996-5998, 2009 

R. A. Reeves, M. D. Gibbs, D. Mandelman, Q. Mi, J. Lee and P. L. Bergquist. Molecular diversity and catalytic activity of Thermus DNA polymerases. Extremophiles 13: 817-826, 2009. 

L.B. Pinheiro, M. D Gibbs, G. Vesey, J. Smith and P. L. Bergquist. Fluorescent reference strains of bacteria by chromosomal integration of a modified Green Fluorescent Protein Gene. Appl. Microbiol. Biotech. 77: 1287-1295, 2008.

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P. L. Bergquist, E. M. Hardiman, B. C. Ferrari and T. Winsley.  Applications of Flow Cytometry in Environmental Microbiology and Biotechnology. Extremophiles 13: 389-401, 2009.

R. Ibáñez-Peral, P. L. Bergquist, M. R. Walter, M. Gibbs, E. M. Goldys and B. Ferrari. Potential Use of Quantum Dots in Flow Cytometry. International Journal of Molecular Sciences 9: 2622-2683, 2008.

Nandan Deshpande, Marc R. Wilkins, Nicolle Packer and Helena Nevalainen (2008). Protein glycosylation pathways in filamentous fungi. Glycobiology 2008 18: 626-637.

Jasmine Grinyer, Liisa Kautto, Mathew Traini, Junior Te'o, Peter Bergquist and Helena Nevalainen (2007). Proteome mapping of the Trichoderma reesei 20S proteasome. Curr. Genet. 51(2):79-88.

Myers, G. S, Parker, D., Al-Hasani, K., Kennan, R. M., Seemann, T., Ren, Q., Badger, J. H., Selengut, J. D., Deboy, R. T., Tettelin, H., Boyce, J. D., McCarl, V. P., Han, X., Nelson, W. C., Madupu, R., Mohamoud, Y., Holley, T., Fedorova, N., Khouri, H., Bottomley, S. P., Whittington, R. J., Adler, B., Songer, J. G., Rood, J. I, and Paulsen, I. T. (2007) Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus. Nature Biotechnology 25:569-575.

Ren, Q., Chen, K., and Paulsen, I. T. (2007) TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. Nucleic Acids Research 35: D274-279.

Observation and control of blinking nitrogen vacancy centres in discrete nanodiamonds. C. Bradac, T. Gaebel, N. Naidoo, M..J. Sellars, J. Twamley, L.J. Brown, A.S. Barnard, T. Plakhotnik, A.V. Zvyagin, and J. R. Rabeau, Nature Nanotechnology (accepted March 1, 2010 doi: 10.1038/NNANO.2010.56)

Prediction and measurement of the size dependent stability of fluorescence in diamond over the entire nanoscale.  C. Bradac, T. Gaebel, N. Naidoo, J. R. Rabeau, A.S. Barnard. Nano Letters 9, 3555 (2009).

Lighting up 5-nm monocrystalline nanodiamond with luminescent nitrogen-vacancy defect centers. B.R. Smith, D. Inglis, B. Sandnes, J. R. Rabeau, A.V. Zvyagin, D. Gruber, C. Noble, R. Vogel, E. Osawa, T. Plakhotnik. Small 5, 1649 (2009).

Single photon emission from diamond nanocrystals in an opal photonic crystal. L.A. Stewart, Y. Zhai, J.M. Dawes, M.J. Steel, J. R. Rabeau, M.J. Withford.  Optics Express 17, 18044 (2009).

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Scanning kelvin-probe study of the hydrogen-terminated diamond surface in ultrahigh vacuum. C.I. Pakes, D. Hoxley, J. R. Rabeau, M.T. Edmonds, R. Kalish, S. Prawer  Applied Physics Letters 95, 123108 (2009)

CVD-diamond external cavity Raman laser at 573 nm. R.Mildren, J.E. Butler, J. R. Rabeau. Optics Express 16, 18950-55 (2008

Nonclassical photon statistics in a single nickel-nitrogen diamond color centre photoluminescence at room temperature.  E. Wu, J. R. Rabeau, F. Treussart, H. Zeng, P. Grangier, S. Prawer, J.-F. Roch.Journal of Modern Optics 55, 2893-2901 (2008).

Triggered single-photon source based on photoluminescence of single nickel-related colour centres in CVD-grown nanodiamonds.  C. Zhou, E. Wu, V. Jaques, J. R. Rabeau, F. Treussart, H. Zeng, S. Prawer, P. Grangier, J.-F. Roch. Annales de Physique 32, 159-161 (2007).

Room temperature triggered single-photon source in the near infrared. E. Wu, J. R. Rabeau, G. Roger, F. Treussart, H. Zeng, P. Grangier, S. Prawer, J.-F. Roch. New Journal of Physics 9, 434-444 (2007).

Single nitrogen vacancy centers in chemical vapor deposited diamond nanocrystals. J. R. Rabeau, A. Rabeau, A. Stacey, F. Jelezko, M. Khan, J. Wrachtrup, S. Prawer. NanoLetters 7, 3433 (2007).

Work function of hydrogenated diamond surfaces under ion impact.  C. I. Pakes, D. Hoxley, J. R. Rabeau, S. M. Hearne, D. N. Jamieson, S. Prawer, R. Kalish. Surface Science 601, 5732-5735 (2007).

Air-Clad Optical Fibre Filament for Generating Broadband Radiation. John Canning, Brant C. Gibson, James R. Rabeau, Adrian P. Mancuso, Mattias Aslund, Shane T. Huntington. Optics Communications (2007).

Optical manipulation of single spins in diamond C. Santori, Ph. Tamarat, P. Neumann, J. Wrachtrup, D. Fattal, R. G. Beausoleil, J. R. Rabeau, P. Olivero, A.D. Greentree, S. Prawer, F. Jelezko, P. Hemmer.  Proc. SPIE 6482, 648207 (2007).

Sherman, J., McKay, M. J., Ashman, K., Molloy, M. P. How specific is my SRM? The issue of precursor and product ion redundancy. Proteomics, 2009, 9, 1120-1123.

Song, X., Bandow, J., Sherman, J., Baker, J. D., Brown, P. T., McDowell, M. T., Molloy, M. P. iTRAQ experimental design for plasma biomarker discovery. J. Proteome Res. 2008, 7 (7), 2952-2958.

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Saldanha, R. G., Molloy, M. P., Bdeir, K, Cines, D. B., Song, X., Uitto, P. M., Weinreb, P. H., Voilette, S. M., Baker, M. S. Proteomic Identification of Lynchpin Urokinase Plasminogen Activator Receptor Protein Interactions Associated with Epithelial Cancer Malignancy. J. Proteome Res. 2007, 6, 1016-1028.

Lampl N, Budai-Hadrian O, Davydov O, Joss TV, Harrop SJ, Curmi PMG, Roberts TH and Fluhr R (2010). Arabidopsis AtSerpin1: crystal structure and in vivo interaction with its target protease RESPONSIVE TO DESICCATION-21 (RD21). Journal of Biological Chemistry 285, 13550-60

Jerkovic A, Kriegel AM, Bradner JR, Atwell BJ, Roberts TH and Willows RD (2010). Strategic distribution of protective proteins within bran layers of wheat (Triticum aestivum L.) protects the nutrient-rich endosperm. Plant Physiology 152, 1459-70

Ahn J-W, Atwell BJ and Roberts TH (2009). Serpin genes AtSRP2 and AtSRP3 are required for normal growth sensitivity to a DNA alkylating agent in Arabidopsis. BMC Plant Biology 9, Art 52 (11 pp)

Mak Y, Willows RD, Roberts TH, Wrigley CW, Sharp PJ and Copeland L (2009). Germination of wheat: a functional proteomics analysis of the embryo. Cereal Chemistry 86, 281-9

Peterson RA, Bradner JR, Roberts TH and Nevelainen KMH (2009). Fungi from koala (Phascolartos cinerus) faeces produce enzymes with activities against a range of recalcitrant substrates. Letters in Applied Microbiology 48, 218-25

Roberts TH and Hejgaard J (2008). Serpins in plants and green algae. Functional & Integrative Genomics 8, 1-27

Haynes PA and Roberts TH (2007). Subcellular shotgun proteomics in plants: looking beyond the usual suspects. Proteomics 7, 2963-75

Hejgaard J and Roberts TH (2007). Plant Serpins. Chapter 12 in Silverman GA & Lomas DA (eds). Molecular and Cellular Aspects of the Serpinopathies and Disorders in Serpin Activity. World Scientific. ISBN 981-256-963-4

Mak Y, Willows RD, Roberts TH, Wrigley CW, Sharp PJ and Copeland L (2006). Black Point is associated with reduced levels of stress-, disease- and defense-related proteins in wheat grain. Molecular Plant Pathology 7, 177-89

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Books

N. H. Packer, A. A. Gooley and M. R. Wilkins (2007) One gene: many proteins. In Proteome Research: Concepts, Technology and Application (Second Edition).  Wilkins, M.R., Appel, R.D., Williams, K.L., Hochstrasser, D.F. (Eds), Ch. 5, pp. 95-121. Springer-Verlag, Berlin Heidelberg.

N. H. Packer and N. G. Karlsson (2009) (Eds.) Glycomics: Methods and Protocols, Methods in Molecular Biology series. Humana Press.

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