Biomolecular Frontiers Research Centre
Publications
Journals | Books | Conference papers
Journals
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)
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.
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.
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).
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.
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
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.
Conference papers
N. H. Packer, C-W. von der Lieth, K.F. Aoki-Kinoshita, C.B. Lebrilla, J.C. Paulson, R. Raman, P. Rudd, R. Sasisekharan, N. Taniguchi and W. S. York (2008). 'Frontiers in Glycomics: bioinformatics and biomarkers in disease.' An NIH white paper prepared from discussions by the focus groups at a workshop on the NIH campus, Bethesda MD (September 11-13, 2006). Proteomics. 8:8-20.