Citations

Published Papers

NEW Alfonso P, Dolado I, Swat A, Nunez A, Cuadrado A, Nebreda AR, Casal JI. Proteomic analysis of p38alpha mitogen-activated protein kinase-regulated changes in membrane fractions of RAS-transformed fibroblasts. Proteomics 6 Suppl 1, S262-71 (2006).

NEW Amme S, Matros A, Schlesier B, Mock HP. Proteome analysis of cold stress response in Arabidopsis thaliana using DIGE-technology. J Exp Bot 57, 1537-46 (2006).

NEW Bruggeman V, Van den Bergh G, Clerens S, Dumez L, Onagbesan O, Arckens L, Decuypere E. Effect of a single in ovo injection of 2,3,7,8-tetrachlorodibenzo-p-dioxin on protein expression in liver and ovary of the one-day-old chick analyzed by fluorescent two-dimensional difference gel electrophoresis and mass spectrometry. Proteomics 6, 2576-85 (2006).

NEW Canals F, Colome N, Ferrer C, Plaza-Calonge MD, Rodriguez-Manzaneque JC. Identification of substrates of the extracellular protease ADAMTS1 by DIGE proteomic analysis. Proteomics 6 Suppl 1, S28-35 (2006).

NEW Cantero L, Palacios JM, Ruiz-Argueso T, Imperial J. Proteomic analysis of quorum sensing in Rhizobium leguminosarum biovar viciae UPM791. Proteomics 6 Suppl 1, S97-S106 (2006).

NEW Chivasa S, Hamilton JM, Pringle RS, Ndimba BK, Simon WJ, Lindsey K, Slabas AR. Proteomic analysis of differentially expressed proteins in fungal elicitor-treated Arabidopsis cell cultures. J Exp Bot 57, 1553-62 (2006).

NEW Coiras M, Camafeita E, Urena T, Lopez JA, Caballero F, Fernandez B, Lopez-Huertas MR, Perez-Olmeda M, Alcami J. Modifications in the human T cell proteome induced by intracellular HIV-1 Tat protein expression. Proteomics 6 Suppl 1, S63-73 (2006).

NEW Eman MR, Regan-Klapisz E, Pinkse MW, Koop IM, Haverkamp J, Heck AJ, Verkleij AJ, Post JA. Protein expression dynamics during replicative senescence of endothelial cells studied by 2-D difference in-gel electrophoresis. Electrophoresis 27, 1669-82 (2006).

NEW Huang HL, Stasyk T, Morandell S, Dieplinger H, Falkensammer G, Griesmacher A, Mogg M, Schreiber M, Feuerstein I, Huck CW, Stecher G, Bonn GK, Huber LA. Biomarker discovery in breast cancer serum using 2-D differential gel electrophoresis/ MALDI-TOF/TOF and data validation by routine clinical assays. Electrophoresis 27, 1641-50 (2006).

NEW Lilley KS, Dupree P. Methods of quantitative proteomics and their application to plant organelle characterization. J Exp Bot 57, 1493-9 (2006).

NEW Shamseldin A, Nyalwidhe J, Werner D. A Proteomic Approach Towards the Analysis of Salt Tolerance in Rhizobium etli and Sinorhizobium meliloti Strains. Curr Microbiol 52, 333-9 (2006).

NEW Suzuki I, Simon WJ, Slabas AR. The heat shock response of Synechocystis sp. PCC 6803 analysed by transcriptomics and proteomics. J Exp Bot 57, 1573-8 (2006).

NEW Wan J, Sun W, Li X, Ying W, Dai J, Kuai X, Wei H, Gao X, Zhu Y, Jiang Y, Qian X, He F. Inflammation inhibitors were remarkably up-regulated in plasma of severe acute respiratory syndrome patients at progressive phase. Proteomics 6, 2886-2894 (2006).

NEW Watanabe T, Ohashi Y, Kosaka T, Arakawa S, Shibaya Y, Yamoto T, Manabe S, Takasaki W. Expression of the theta class GST isozyme, Yd(f)Yd(f), in low GST dogs. Arch Toxicol 80, 250-7 (2005).

NEW Weeks ME, Sinclair J, Butt A, Chung YL, Worthington JL, Wilkinson CR, Griffiths J, Jones N, Waterfield MD, Timms JF. A parallel proteomic and metabolomic analysis of the hydrogen peroxide- and Sty1p-dependent stress response in Schizosaccharomyces pombe. Proteomics 6, 2772-2796 (2006).

Alm H, Scholz B, Fischer C, Kultima K, Viberg H, Eriksson P, Dencker L, Stigson M. Proteomic evaluation of neonatal exposure to 2,2 ,4,4 ,5-pentabromodiphenyl ether. Environ Health Perspect 114, 254-9 (2006).

Alfonso P, Nunez A, Madoz-Gurpide J, Lombardia L, Sanchez L, Casal JI. Proteomic expression analysis of colorectal cancer by two-dimensional differential gel electrophoresis. Proteomics 5, 2602-11 (2005).

Anazawa Y, Nakagawa H, Furihara M, Ashida S, Tamura K, Yoshioka H, Shuin T, Fujioka T, Katagiri T, Nakamura Y. PCOTH, a novel gene overexpressed in prostate cancers, promotes prostate cancer cell growth through phosphorylation of oncoprotein TAF-Ibeta/SET. Cancer Res 65, 4578-86 (2005).

Blake CA. Physiological proteomics: cells, organs, biological fluids, and biomarkers. Exp Biol Med (Maywood) 230, 785-6 (2005).

Blake CA, Brown LM, Duncan MW, Hunsucker SW, Helmke SM. Estrogen regulation of the rat anterior pituitary gland proteome. Exp Biol Med (Maywood) 230, 800-7 (2005).

Blake CA, Helmke SM. Proteomics of the anterior pituitary gland as a model for studying the physiology of a heterogeneous organ. Exp Biol Med (Maywood) 230, 793-9 (2005).

Baldwin MA. Protein identification by Mass Spectrometry: Issues to be considered. Mol Cell Proteomics 3, 1-9 (2004).

Beckner ME, Chen X, An J, Day BW Pollack IF. Proteomic characterization of harvested pseudopodia with differential gel electrophoresis and specific antibodies. Lab Invest 85, 316-27 (2005).

Berendt FJ, Frohlich T, Schmidt SE, Reichenbach HD, Wolf E, Arnold GJ. Holistic differential analysis of embryo-induced alterations in the proteome of bovine endometrium in the preattachment period. Proteomics 5, 2551-60 (2005).

Beynon RJ, Pratt JM. Metabolic labelling of proteins for proteomics. Mol Cell Proteomics 4, 857-72 (2005).

Blonder J, Conrads TP, Veenstra TD. Characterization and quantitation of membrane proteomes using multidimensional MS-based proteomic technologies. Expert Rev Proteomics 1, 153-163 (2004).

Borner GH, Sherrier DJ, Weimar T, Michaelson LV, Hawkins ND, Macaskill A, Napier JA, Beale MH, Lilley KS, Dupree P. Analysis of detergent-resistant membranes in Arabidopsis. evidence for plasma membrane lipid rafts. Plant Physiol 137, 104-16 (2005).

Borner GH, Lilley KS, Stevens TJ, Dupree P. Identification of glycosylphosphatidylinositol-anchored proteins in Arabidopsis. A proteomic and genomic analysis. Plant Physiology 132, 568-577 (2003).

Bredemeyer AJ, Lewis RM, Malone JP, Davis AE, Gross J, Townsend RR, Ley TJ. A proteomic approach for the discovery of protease substrates. Proc Natl Acad Sci USA 101, 11785-11790 (2004).

Brzeski H, Katenhusen RA, Sullivan AG, Russell S, George A, Somiari RI, Shriver C. Albumin depletion method for improved plasma glycoprotein analysis by two-dimensional difference gel electrophoresis. Biotechniques 35, 1128-1132 (2003).

Baker MA, Witherdin R, Hetherington L, Cunningham-Smith K, Aitken RJ. Identification of post-translational modifications that occur during sperm maturation using difference in two-dimensional gel electrophoresis. Proteomics 5, 1003-1012 (2005).

Carlsohn E, Nystrom J, Bolin I, Nilsson CL, Svennerholm AM. HpaA is essential for Helicobacter pylori colonization in mice. Infect Immun 74, 920-6 (2006).

Chan CH, Ko CC, Chang JG, Chen SF, Wu MS, Lin JT, Chow LP. Sub-cellular and functional proteomic analysis of the cellular responses induced by helicobacter pylori. Mol Cell Proteomics 5, 702-13 (2006).

Chen WS, Chang HY, Li CP, Liu JM, Huang TS. Tumor beta-1,4-galactosyltransferase IV overexpression is closely associated with colorectal cancer metastasis and poor prognosis. Clin Cancer Res 11, 8615-22 (2005).

Chhabra SR, He Q, Huang KH, Gaucher SP, Alm EJ, He Z, Hadi MZ, Hazen TC, Wall JD, Zhou J, Arkin AP, Singh AK. Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough. J Bacteriol 188, 1817-28 (2006).

Candas M, Loseva O, Oppert B, Kosaraju P, Bulla LA Jr. Insect resistance to Bacillus thuringiensis: Alterations in the Indianmeal moth larval gut proteome. Molecular and Cellular Proteomics 2, 19-28 (2003).

Chan HL, Gharbi S, Gaffney PR, Cramer R, Waterfield MD, Timms JF. Proteomic analysis of redox- and ErbB2-dependent changes in mammary luminal epithelial cells using cysteine- and lysine-labelling two-dimensional difference gel electrophoresis. Proteomics 5, 2908-26 (2005).

Chen C, Boylan MT, Evans CA, Whetton AD, Wright EG. Application of two-dimensional difference gel electrophoresis to studying bone marrow macrophages and their in vivo responses to ionizing radiation. J Proteome Res 5, 1371-80 (2005).

Chromy BA, Gonzales AD, Perkins J, Choi MW, Corzett MH, Chang BC, Corzett CH, McCutchen-Maloney SL. Proteomic analysis of human serum by two-dimensional differential gel electrophoresis after depletion of high-abundant proteins. J Proteome Res 3, 1120-7 (2004).

Chu R, Lim H, Brumfield L, Liu H, Herring C, Ulintz P, Reddy JK, Davison M. Protein Profiling of Mouse Livers with Peroxisome Proliferator-Activated Receptor Activation. Mol Cell Biol 24, 6288-6297 (2004).

Corbett M, Virtue S, Bell K, Birch P, Burr T, Hyman L, Lilley K, Poock S, Toth I, Salmond G. Identification of a new quorum-sensing-controlled virulence factor in Erwinia carotovora subsp. atroseptica secreted via the type II targeting pathway. Mol Plant Microbe Interact 18, 334-42 (2005).

Cristea IM, Gaskell SJ, Whetton AD. Proteomics techniques and their application to haematology. Blood 103, 3624-3634 (2004).

Cutillas P, Burlingame A, Unwin R. Proteomic Strategies and Their Application in Studies of Renal Function. News Physiol Sci 19, 114-119 (2004).

Casati P, Zhang X, Burlingame AL, Walbot V. Analysis of leaf proteome after UV-B irradiation in maize lines differing in sensitivity. Mol Cell Proteomics 4, 1673-1685 (2005).

Chromy BA, Choi MW, Murphy GA, Gonzales AD, Corzett CH, Chang BC, Fitch JP, McCutchen-Maloney SL. Proteomic characterization of Yersinia pestis virulence. J Bacteriol 187, 8172-80 (2005).

Czupalla C, Mansukoski H, Pursche T, Krause E, Hoflack B. Comparative study of protein and mRNA expression during osteoclastogenesis. Proteomics 5, 3868-75 (2005).

Dirksen EH, Cloos J, Braakhuis BJ, Brakenhoff RH, Heck AJ, Slijper M. Human lymphoblastoid proteome analysis reveals a role for the inhibitor of acetyltransferases complex in DNA double-strand break response. Cancer Res 66, 1473-80 (2006).

Douette P, Gerkens P, Navet R, Leprince P, De Pauw E, Sluse FE. Uncoupling protein 1 affects the yeast mitoproteome and oxygen free radical production. Free Radic Biol Med 40, 303-15 (2006).

Dhingra V, Li Q, Allison AB, Stallknecht DE, Fu ZF. Proteomic profiling and neurodegeneration in west-nile-virus-infected neurons. J Biomed Biotechnol 2005, 271-9 (2005).

Douette P, Navet R, Gerkens P, de Pauw E, Leprince P, Sluse-Goffart C, Sluse FE. Steatosis-induced proteomic changes in liver mitochondria evidenced by two-dimensional differential in-gel electrophoresis. J Proteome Res 4, 2024-31 (2005).

Duncan MW, Hunsucker SW. Proteomics as a tool for clinically relevant biomarker discovery and validation. Exp Biol Med (Maywood) 230, 808-17 (2005).

Daikoku T, Tranguch S, Friedman DB, Das SK, Smith DF, Dey SK. Proteomic analysis identifies immunophilin FKBP52 as a downstream target of Hoxa10 in the periimplantation mouse uterus. Mol Endocrinol 19, 683-97 (2005).

de Graauw M, Tijdens I, Cramer R, Corless S, Timms JF, van de Water B. Heat shock protein 27 is the major differentially phosphorylated protein Involved in renal epithelial cellular stress response and controls focal adhesion organization and apoptosis. J Biol Chem 280, 29885-98 (2005).

Delcourt N, Jouin P, Poncet J, Demey E, Mauger E, Bockaert J, Marin P, Galeotti N. Difference in mass analysis using labeled lysines (DIMAL-K): A new efficient proteomic quantification method applied to the analysis of astrocytic secretomes. Mol Cell Proteomics 4, 1085-94 (2005).

Ecelbarger CA. Targeted proteomics using immunoblotting technique for studying dysregulation of ion transporters in renal disorders. Expert Rev Proteomics 1, 219-227 (2004).

Fujii K, Kondo T, Yokoo H, Okano T, Yamada M, Yamada T, Iwatsuki K, Hirohashi S. Database of two-dimensional polyacrylamide gel electrophoresis of proteins labeled with CyDye DIGE Fluor saturation dye. Proteomics 6, 1640-53 (2006).

Frazier MC, Jackson KM, Jankowska-Stephens E, Anderson MG, Harris WB. Proteomic analysis of proteins altered by dibenzoylmethane in human prostatic cancer LNCaP cells. Proteomics 4, 2814-21 (2004).

Freeman WM, Brebner K, Amara SG, Reed MS, Pohl J, Phillips AG. Distinct proteomic profiles of amphetamine self-administration transitional states. Pharmacogenomics J 5, 203-14 (2005).

Freeman WM, Hemby SE. Proteomics for protein expression profiling in neuroscience. Neurochem Res 29, 1065-81 (2004).

Friedman DB, Hill S, Keller JW, Merchant NB, Levy SE, Coffey RJ, Caprioli RM. Proteome analysis of human colon cancer by two-dimensional difference gel electrophoresis and mass spectrometry. Proteomics 4, 793-811 (2004).

Fujii K, Kondo T, Yokoo H, Yamada T, Iwatsuki K, Hirohashi S. Proteomic study of human hepatocellular carcinoma using two-dimensional difference gel electrophoresis with saturation cysteine dye. Proteomics 5, 1411-1422 (2005).

Fodor IK, Nelson DO, Alegria-Hartman M, Robbins K, Langlois RG, Turteltaub KW, Corzett TH, McCutchen-Maloney SL. Statistical challenges in the analysis of two-dimensional difference gel electrophoresis experiments using DeCyderTM. Bioinformatics 21, 3733-40 (2005).

Guest PC, Skynner HA, Salim K, Tattersall FD, Knowles MR, Atack JR. Detection of gender differences in rat lens proteins using 2-D-DIGE. Proteomics 6, 667-76 (2006).

Gade D, Gobom J, Rabus R. Proteomic analysis of carbohydrate catabolism and regulation in the marine bacterium Rhodopirellula baltica. Proteomics 5, 3672-83 (2005), in press.

Gade D, Stuhrmann T, Reinhardt R, Rabus R. Growth phase dependent regulation of protein composition in Rhodopirellula baltica. Environ Microbiol 7, 1074-84 (2005).

Gade D, Thiermann J, Markowsky D, Rabus R. Evaluation of Two-Dimensional Difference Gel Electrophoresis for Protein Profiling. Soluble Proteins of the Marine Bacterium PIRELLULA sp. Strain 1. J Mol Microbiol Biotechnol. 5, 240-251 (2003).

Gerbasi VR, Weaver CM, Hill S, Friedman DB, Link AJ. Yeast Asc1p and Mammalian RACK1 Are Functionally Orthologous Core 40S Ribosomal Proteins That Repress Gene Expression. Mol Cell Biol 24, 8276-8287 (2004).

Gharbi S, Gaffney P, Yang A, Zvelebil MJ, Cramer R, Waterfield MD, Timms JF. Evaluation of 2-D differential gel electrophoresis for proteomic expression analysis of a model breast cancer cell system. Molecular and Cellular Proteomics 1, 91-98 (2002).

Ghazalpour A, Doss S, Yang X, Aten J, Toomey EM, Van Nas A, Wang S, Drake TA, Lusis AJ. Toward a biological network for atherosclerosis. J Lipid Res 45, 1793-1805 (2004).

Girard M, Allaire PD, McPherson PS, Blondeau F. Non-stoichiometric relationship between clathrin heavy and light chains revealed by quantitative comparative proteomics of clathrin-coated vesicles from brain and liver. Mol Cell Proteomics 4, 1145-54 (2005).

Gong L, Puri M, Unlu M, Young M, Robertson K, Viswanathan S, Krishnaswamy A, Dowd SR, Minden JS. Drosophila ventral furrow morphogenesis: a proteomic analysis. Development 131, 643-56 (2004).

Graham DR, Elliott ST, Van Eyk JE. Broad-based proteomic strategies: a practical guide to proteomics and functional screening. J Physiol 563, 1-9 (2005).

Greengauz-Roberts O, Stoppler H, Nomura S, Yamaguchi H, Goldenring JR, Podolsky RH, Lee JR, Dynan WS. Saturation labeling with cysteine-reactive cyanine fluorescent dyes provides increased sensitivity for protein expression profiling of laser-microdissected clinical specimens. Proteomics 5, 1746-57 (2005).

Guadagnoli JA, Braun AM, Roberts SP, Reiber CL. Environmental hypoxia influences hemoglobin subunit composition in the branchiopod crustacean Triops longicaudatus. Journal of Experimental Biology 208, 3543-3551 (2005).

Guest PC, Knowles MR, Molon-Noblot S, Salim K, Smith D, Murray F, Laroque P, Hunt SP, De Felipe C, Rupniak NM, McAllister G. Mechanisms of action of the antidepressants fluoxetine and the substance P antagonist L-000760735 are associated with altered neurofilaments and synaptic remodelling. Brain Research 1002, 1-10 (2004).

Guldberg Klenø T, Ronnedal Leonardsen L, Ørsted Kjeldal H, Møller Laursen S, Nørregaard Jensen O, Baunsgaard D. Mechanisms of hydrazine toxicity in rat liver investigated by proteomics and multivariate data analysis. Proteomics 4, 868-880 (2004).

Hjerno K, Alm R, Canback B, Matthiesen R, Trajkovski K, Bjork L, Roepstorff P, Emanuelsson C. Down-regulation of the strawberry Bet v 1-homologous allergen in concert with the flavonoid biosynthesis pathway in colorless strawberry mutant. Proteomics 6, 1574-87 (2006).

Hu Y, Malone JP, Fagan AM, Townsend RR, Holtzman DM. Comparative proteomics analysis of intra- and inter-individual variation in human cerebrospinal fluid. Mol Cell Proteomics 4, 2000-9 (2005).

Hoorn EJ, Hoffert JD, Knepper MA. Combined Proteomics and Pathways Analysis of Collecting Duct Reveals a Protein Regulatory Network Activated in Vasopressin Escape. J Am Soc Nephrol 16, 2852-63 (2005).

Hamdan M, Righetti PG. Modern strategies for protein quantification in proteome analysis: Advantages and limitations. Mass Spectrometry Reviews 21, 287-302 (2002).

Heinemann FS, Korza G, Ozols JA. Plasminogen-like Protein Selectively Degrades Stearoyl-CoA Desaturase in Liver Microsomes. J. Biol Chem 278, 42966 - 42975 (2003).

Henkel C, Roderfeld M, Weiskirchen R, Scheibe B, Matern S, Roeb E. Identification of fibrosis-relevant proteins using DIGE (difference in gel electrophoresis) in different models of hepatic fibrosis. Z Gastroenterol 43, 23-29 (2005).

Hewitt SM, Dear J, Star RA. Discovery of Protein Biomarkers for Renal Diseases. J Am Soc Nephrol 15, 1677-1689 (2004).

Hirsch J, Hansen KC, Burlingame AL, Matthay MA. Proteomics: current techniques and potential applications to lung disease. Am J Physiol Lung Cell Mol Physiol 287, L1-L23 (2004).

Hoffert JD, Van Balkom BW, Chou CL, Knepper MA. Application of Difference Gel Electrophoresis (DIGE) to the Identification of Inner Medullary Collecting Duct Proteins. Am J Physiol Renal Physiol. 286, F170-9 (2003).

Hu X, Friedman D, Hill S, Caprioli R, Nicholson W, Powers AC, Hunter L, Limbird LE. Proteomic exploration of pancreatic islets in mice null for the alpha2A adrenergic receptor. J Mol Endocrinol 35, 73-88 (2005).

Hu Y, Huang X, Chen GY, Yao SQ. Recent advances in gel-based proteome profiling techniques. Mol Biotechnol 28, 63-76 (2004).

Ibuki Y, Naitou H, Ohashi N, Goto R. Proteome Analysis of UVB-Induced Anti-Apoptotic Regulatory Factors. Photochem Photobiol 81, 823-9 (2005).

Jiang XS, Tang LY, Dai J, Zhou H, Li SJ, Xia QC, Wu JR, Zeng R. Quantitative analysis of SARS-coronavirus infected cells using proteomic approaches: Implications for cellular responses to virus infection. Mol Cell Proteomics 4, 902-13 (2005).

Jiang XS, Dai J, Sheng QH, Zhang L, Xia QC, Wu JR, Zeng R. A comparative proteomic strategy for subcellular proteome research: icat approach coupled with bioinformatics prediction to ascertain rat liver mitochondrial proteins and indication of mitochondrial localization for catalase. Mol Cell Proteomics 4, 12-34 (2005).

Jin K, Mao XO, Cottrell B, Schilling B, Xie L, Row RH, Sun Y, Peel A, Childs J, Gendeh G, Gibson BW, Greenberg DA. Proteomic and immunochemical characterization of a role for stathmin in adult neurogenesis. FASEB J 18, 287-299 (2004).

Jogie-Brahim S, Min H-K, Oh Y. Potential of proteomics towards the investigation of the IGF-independent actions of IGFBP-3. Expert Rev Proteomics 2, 71-86 (2005).

Kasamatsu A, Uzawa K, Nakashima D, Kouzu Y, Endo Y, Koike H, Yokoe H, Harada K, Sato M, Tanzawa H. A proteomics approach to characterizing human submandibular gland cell lines by fluorescent two-dimensional differential in-gel electrophoresis. Int J Mol Med 17, 253-60 (2006).

Komatsu S, Zang X, Tanaka N. Comparison of two proteomics techniques used to identify proteins regulated by gibberellin in rice. J Proteome Res 5, 270-6 (2006).

Karp NA, Lilley KS. Maximising sensitivity for detecting changes in protein expression: experimental design using minimal CyDyes. Proteomics 5, 3105-15 (2005).

Karp NA, Griffin JL, Lilley KS. Application of partial least squares discriminant analysis to two-dimensional difference gel studies in expression proteomics. Proteomics 22;5, 81-90 (2005).

Karp NA, Kreil DP, Lilley KS. Determining a significant change in protein expression with DeCyder during a pair-wise comparison using two-dimensional difference gel electrophoresis. Proteomics 4, 1421-32 (2004).

Knowles MR, Cervino S, Skynner HA, Hunt SP, De Felipe C, Salim K, Meneses-Lorente G, McAllister G, Guest PC. Multiplex proteomic analysis by two-dimensional differential in-gel electrophoresis. Proteomics 3, 1162-1171 (2003).

Koeck T, Fu X, Hazen SL, Crabb JW, Stuehr DJ, Aulak KS. Rapid and selective oxygen regulated protein tyrosine "denitration" and nitration in mitochondria. J Biol Chem 279, 27257-27262 (2004).

Koike H, Uzawa K, Nakashima D, Shimada K, Kato Y, Higo M, Kouzu Y, Endo Y, Kasamatsu A, Tanzawa H. Identification of differentially expressed proteins in oral squamous cell carcinoma using a global proteomic approach. Int J Oncol 27, 59-67 (2005).

Kolkman A, Dirksen EH, Slijper M, Heck AJ. Double standards in quantitative proteomics: Direct comparative assessment of difference in Gel electrophoresis (DiGE) and metabolic stable isotope labeling. Mol Cell Proteomics 4, 255-66 (2005).

Kondo T, Seike M, Mori Y, Fujii K, Yamada T, Hirohashi S. Application of sensitive fluorescent dyes in linkage of laser microdissection and two-dimensional gel electrophoresis as a cancer proteomic study tool. Proteomics 3, 1758-1766 (2003).

Kreil DP, Karp NA, Lilley KS. DNA microarray normalization methods can remove bias from differential protein expression analysis of 2-D difference gel electrophoresis results. Bioinformatics 20, 2026-2034 (2004).

Krishnan HB, Bennett JO, Kim WS, Krishnan AH, Mawhinney TP. Nitrogen lowers the sulfur amino acid content of soybean (Glycine max [L.] Merr.) by regulating the accumulation of Bowman-Birk protease inhibitor. J Agric Food Chem 53, 6347-54 (2005).

Kubis S, Baldwin A, Patel R, Razzaq A, Dupree P, Lilley K, Kurth J, Leister D, Jarvis P. The Arabidopsis ppi1 Mutant Is Specifically Defective in the Expression, Chloroplast Import, and Accumulation of Photosynthetic Proteins. Plant Cell 15, 1859 - 1871 (2003).

Kubota K, Kosaka T, Ichikawa K. Combination of two-dimensional electrophoresis and shotgun peptide sequencing in comparative proteomics. J Chromatogr B 815, 3-9 (2005).

Kuhner S, Wohlbrand L, Fritz I, Wruck W, Hultschig C, Hufnagel P, Kube M, Reinhardt R, Rabus R. Substrate-dependent regulation of anaerobic degradation pathways for toluene and ethylbenzene in a denitrifying bacterium, strain EbN1. (Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359 Bremen, Germany). J Bacteriol 187, 1493-503 (2005).

Kakhniashvili DG, Griko NB, Bulla LA Jr, Goodman SR. The Proteomics of Sickle Cell Disease: Profiling of Erythrocyte Membrane Proteins by 2D-DIGE and Tandem Mass Spectrometry. Exp Biol Med (Maywood) 230, 787-92 (2005).

Karp NA, Spencer M, Lindsay H, O'dell K, Lilley KS. Impact of Replicate Types on Proteomic Expression Analysis. J Proteome Res 4, 1867-1871 (2005).

Leonard JF, Courcol M, Mariet C, Charbonnier A, Boitier E, Duchesne M, Parker F, Genet B, Supatto F, Roberts R, Gautier JC. Proteomic characterization of the effects of clofibrate on protein expression in rat liver. Proteomics 6, 1915-33 (2006).

Lee IN, Chen CH, Sheu JC, Lee HS, Huang GT, Yu CY, Lu FJ, Chow LP. Identification of Human Hepatocellular Carcinoma-Related Biomarkers by Two-Dimensional Difference Gel Electrophoresis and Mass Spectrometry. J Proteome Res 4, 2062-2069 (2005).

Lee JR, Baxter TM, Yamaguchi H, Wang TC, Goldenring JR, Anderson MG. Differential Protein Analysis of Spasomolytic Polypeptide Expressing Metaplasia Using Laser Capture Microdissection and Two-dimensional Difference Gel Electrophoresis. Applied Immunohistochemistry and Molecular Morphology 11, 188-193 (2003).

Lehr S, Kotzka J, Avci H, Knebel B, Muller S, Hanisch FG, Jacob S, Haak C, Susanto F, Muller-Wieland D. Effect of Sterol Regulatory Element Binding Protein-1a on the Mitochondrial Protein Pattern in Human Liver Cells Detected by 2D-DIGE. Biochemistry 44, 5117-5128 (2005).

Liang CR, Leow CK, Neo JC, Tan GS, Lo SL, Lim JW, Seow TK, Lai PB, Chung MC. Proteome analysis of human hepatocellular carcinoma tissues by two-dimensional difference gel electrophoresis and mass spectrometry. Proteomics 5, 2258-71 (2005).

Lilley KS, Friedman DB. All about DIGE: quantification technology for differential-display 2D-gel proteomics. Expert Rev Proteomics 1, 401-409 (2004).

Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ. Localization, annotation and comparison of the Escherichia coli K-12 proteome under two states of growth. Mol Cell Proteomics 4, 1205-1209 (2005).

Lu ZH, Books JT, Ley TJ. YB-1 is important for late-stage embryonic development, optimal cellular stress responses, and the prevention of premature senescence. Mol Cell Biol 25, 4625-37 (2005).

Luppens SB, ten Cate JM. Effect of biofilm model, mode of growth, and strain on streptococcusmutans protein expression as determined by two-dimensional difference gel electrophoresis. J Proteome Res 4, 232-7 (2005).

Mathy G, Navet R, Gerkens P, Leprince P, De Pauw E, Sluse-Goffart CM, Sluse FE, Douette P. Saccharomyces cerevisiae mitoproteome plasticity in response to recombinant alternative ubiquinol oxidase. J Proteome Res 5, 339-48 (2006).

Mayrhofer C, Krieger S, Allmaier G, Kerjaschki D. DIGE compatible labelling of surface proteins on vital cells in vitro and in vivo. Proteomics 6, 579-85 (2006).

Metzner C, Salmons B, Gunzburg WH, Gemeiner M, Miller I, Gesslbauer B, Kungl A, Dangerfield JA. MMTV accessory factor Naf affects cellular gene expression. Virology 346, 139-50 (2006).

Maeda K, Finnie C, Svensson B. Cy5 maleimide-labelling for sensitive detection of free thiols in native protein extracts: Identification of seed proteins targeted by barley thioredoxin h isoforms. Biochem J 378, 497-507 (2004).

Macdonald N, Chevalier S, Tonge R, Davison M, Rowlinson R, Young J, Rayner S, Roberts R. Quantitative proteomic analysis of mouse liver response to the peroxisome proliferator diethylhexylphthalate (DEHP). Arch Toxicol 75, 415-424 (2001).

Meneses-Lorente G, Guest PC, Lawrence J, Muniappa N, Knowles MR, Skynner HA, Salim K, Cristea I, Mortishire-Smith R, Gaskell SJ, Watt A. A proteomic investigation of drug-induced steatosis in rat liver. Chem Res Toxicol 17, 605-12 (2004).

Matis M, Zakelj-Mavric M, Peter-Katalinic J. Global Analysis of the Hortaea werneckii Proteome: Studying Steroid Response in Yeast. J Proteome Res 4, 2043-2051 (2005).

Moumen A, Masterson P, O'connor MJ, Jackson SP. hnRNP K: An HDM2 Target and Transcriptional Coactivator of p53 in Response to DNA Damage. Cell 123, 1065-78 (2005).

Murphy ME. Regulation of cell death in oncogenesis. Cancer Res 65, 8069-71 (2005).

Nishimori T, Tomonaga T, Matsushita K, Oh-Ishi M, Kodera Y, Maeda T, Nomura F, Matsubara H, Shimada H, Ochiai T. Proteomic analysis of primary esophageal squamous cell carcinoma reveals downregulation of a cell adhesion protein, periplakin. Proteomics 6, 1011-8 (2006).

Nakashima D, Uzawa K, Kasamatsu A, Koike H, Endo Y, Saito K, Hashitani S, Numata T, Urade M, Tanzawa H. Protein expression profiling identifies maspin and stathmin as potential biomarkers of adenoid cystic carcinoma of the salivary glands. Int J Cancer, 118, 704-13 (2005).

Nabetani T, Tabuse Y, Tsugita A, Shoda J. Proteomic analysis of livers of patients with primary hepatolithiasis. Proteomics 5, 1043-61 (2005).

Nakahara K, Kim K, Sciulli C, Dowd SR, Minden JS, Carthew RW. Targets of microRNA regulation in the Drosophila oocyte proteome. Proc Natl Acad Sci U S A 102, 12023-8 (2005).

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Sekhar KR, Crooks PA, Sonar VN, Friedman DB, Chan JY, Meredith MJ, Starnes JH, Kelton KR, Summar SR, Sasi S, Freeman ML. NADPH Oxidase Activity Is Essential for Keap1/Nrf2-mediated Induction of GCLC in Response to 2-Indol-3-yl-methylenequinuclidin-3-ols. Cancer Res. 63, 5636 - 5645 (2003).

Sharma K, Lee S, Han S, Lee S, Francos B, McCue P, Wassell R, Shaw MA, RamachandraRao S. Two-dimensional fluorescence difference gel electrophoresis analysis of the urine proteome in human diabetic nephropathy. Proteomics 5, 2648-55 (2005).

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Somiari RI, Somiari S, Russell S, Shriver CD. Proteomics of breast carcinoma. J Chromatogr B Analyt Technol Biomed Life Sci 815, 215-25 (2005).

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Steinacker P, Schwarz P, Reim K, Brechlin P, Jahn O, Kratzin H, Aitken A, Wiltfang J, Aguzzi A, Bahn E, Baxter HC, Brose N, Otto M. Unchanged Survival Rates of 14-3-3 Knockout Mice after Inoculation with Pathological Prion Protein. Mol Cell Biol 25, 1339-46 (2005).

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Papers in press

Abul-Husn NS, Devi LA. Neuroproteomics of the Synapse and Drug Addiction. J Pharmacol Exp Ther (2006), in press.

Apraiz I, Mi J, Cristobal S. Identification of proteomics signatures of exposure to marine pollutants in mussels (Mytilus edulis). Mol Cell Proteomics (2006), in press.

Bi X, Lin Q, Foo TW, Joshi S, You T, Shen HM, Ong CN, Cheah PY, Eu KW, Hew CL. Proteomics analysis of colorectal cancer reveals alterations in metabolic pathways - mechanism of tumorigenesis. Mol Cell Proteomics (2006), in press.

Hedman E, Widen C, Asadi A, Dinnetz I, Schroder WP, Gustafsson JA, Wikstrom A. Proteomic identification of glucocorticoid receptor interacting proteins. Proteomics (2006), in press.

Link V, Carvalho L, Castanon I, Stockinger P, Shevchenko A, Heisenberg CP. Identification of regulators of germ layer morphogenesis using proteomics in zebrafish. J Biol Chem (2006), in press.

Ryu OH, Atkinson JC, Hoehn GT, Illei GG, Hart TC. Identification of parotid salivary biomarkers in Sjogren's syndrome by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry and two-dimensional difference gel electrophoresis. Rheumatology (Oxford) (2006), in press.

Sizova D, Charbaut E, Delalande F, Poirier F, High AA, Parker F, Van Dorsselaer A, Duchesne M, Diu-Hercend A. Proteomic analysis of brain tissue from an Alzheimer's disease mouse model by two-dimensional difference gel electrophoresis. Neurobiol Aging (2006), in press.

Tannu N, Hemby SE. Quantitation in two-dimensional fluorescence difference gel electrophoresis: Effect of protein fixation. Electrophoresis (2006), in press.

Terhzaz S, Southall TD, Lilley KS, Kean L, Allan AK, Davies SA, Dow JAT. Differential gel electrophoresis and transgenic mitochondrial calcium reporters demonstrate spatiotemporal filtering in calcium control of mitochondria. J Biol Chem (2006), in press.

Vipond C, Suker J, Jones C, Tang C, Feavers IM, Wheeler JX. Proteomic analysis of a meningococcal outer membrane vesicle vaccine prepared from the group B strain NZ98/254. Proteomics (2006), in press.

Zheng QY, Rozanas CR, Isolde T, Mark CR, Kumar AN. Inner ear proteomics of mouse models for deafness, a discovery strategy. Brain Res J (2006), in press.


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