Publications with FGCZ Contributions

Publications with or without acknowledged contributions of FGCZ members since its foundation

2010

Hulsmeier, A. J., P. Deplazes, S. Naem, N. Nonaka, T. Hennet and P. Kohler (2010)
"An Echinococcus multilocularis coproantigen is a surface glycoprotein with unique O-gycosylation".
Glycobiology 20(1): 127-35.

2009

Buehler, P. W., B. Abraham, F. Vallelian, C. Linnemayr, C. P. Pereira, J. F. Cipollo, Y. Jia, M. Mikolajczyk, F. S. Boretti, G. Schoedon, A. I. Alayash and D. J. Schaer (2009)
"Haptoglobin preserves the CD163 hemoglobin scavenger pathway by shielding hemoglobin from peroxidative modification".
Blood 113(11): 2578-86.

Dip, R., S. Lenz, H. Gmuender and H. Naegeli (2009)
"Pleiotropic combinatorial transcriptomes of human breast cancer cells exposed to mixtures of dietary phytoestrogens".
Food Chem Toxicol 47(4): 787-95.

Falk, N., M. Kaestli, W. Qi, M. Ott, K. Baea, A. Cortes and H. P. Beck (2009)
"Analysis of Plasmodium falciparum var Genes Expressed in Children from Papua New Guinea".
J Infect Dis 200(3): 347-56.

Fischer, B., V. Roth and J. M. Buhmann (2009)
"Adaptive bandwidth selection for biomarker discovery in mass spectrometry".
Artif Intell Med 45(2-3): 207-14.

Gourion, B., S. Sulser, J. Frunzke, A. Francez-Charlot, P. Stiefel, G. Pessi, J. A. Vorholt and H. M. Fischer (2009)
"The PhyR-sigma(EcfG) signalling cascade is involved in stress response and symbiotic efficiency in Bradyrhizobium japonicum".
Mol Microbiol 73(2): 291-305.

Izquierdo, L., B. L. Schulz, J. A. Rodrigues, M. L. Guther, J. B. Procter, G. J. Barton, M. Aebi and M. A. Ferguson (2009)
"Distinct donor and acceptor specificities of Trypanosoma brucei oligosaccharyltransferases".
Embo J 28(17): 2650-61.

Jaric, J., S. Bilokapic, S. Lesjak, A. Crnkovic, N. Ban and I. Weygand-Durasevic (2009)
"Identification of amino acids in the N-terminal domain of atypical methanogenic-type Seryl-tRNA synthetase critical for tRNA recognition".
J Biol Chem 284(44): 30643-51.

Kamada, H., T. Fugmann, D. Neri and C. Roesli (2009)
"Improved protein sequence coverage by on resin deglycosylation and cysteine modification for biomarker discovery".
Proteomics 9(3): 783-7.

Mugasa, J. P., M. Rottman, W. Qi, H. Mshinda and H. P. Beck (2009)
"Analysis of Plasmodium falciparum var Gene Repertoire Expressed in Childrenwith Severe Malaria from Tanzania".
Infection Genetics and Evolution 9(3): 378-378.

Nazabal, A., S. Hornemann, A. Aguzzi and R. Zenobi (2009)
"Hydrogen/deuterium exchange mass spectrometry identifies two highly protected regions in recombinant full-length prion protein amyloid fibrils".
J Mass Spectrom 44(6): 965-77.

Reiter, L., M. Claassen, S. P. Schrimpf, M. Jovanovic, A. Schmidt, J. M. Buhmann, M. O. Hengartner and R. Aebersold (2009)
"Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry".
Mol Cell Proteomics 8(11): 2405-17.

Roba, M., M. Naka, E. Gautier, N. D. Spencer and R. Crockett (2009)
"The adsorption and lubrication behavior of synovial fluid proteins and glycoproteins on the bearing-surface materials of hip replacements".
Biomaterials 30(11): 2072-8.

Roesli, C., B. Borgia, C. Schliemann, M. Gunthert, H. Wunderli-Allenspach, R. Giavazzi and D. Neri (2009)
"Comparative analysis of the membrane proteome of closely related metastatic and nonmetastatic tumor cells".
Cancer Res 69(13): 5406-14.

San Paolo, S., S. Vanacova, L. Schenk, T. Scherrer, D. Blank, W. Keller and A. P. Gerber (2009)
"Distinct roles of non-canonical poly(A) polymerases in RNA metabolism".
PLoS Genet 5(7): e1000555.

Schafer, N. F., U. F. Luhmann, S. Feil and W. Berger (2009)
"Differential gene expression in Ndph-knockout mice in retinal development".
Invest Ophthalmol Vis Sci 50(2): 906-16.

Schegg, B., A. J. Hulsmeier, C. Rutschmann, C. Maag and T. Hennet (2009)
"Core glycosylation of collagen is initiated by two beta(1-O)galactosyltransferases".
Mol Cell Biol 29(4): 943-52.

Schliemann, C., C. Roesli, H. Kamada, B. Borgia, T. Fugmann, W. Klapper and D. Neri (2009)
"In vivo biotinylation of the vasculature in B cell lymphomaidentifies BST-2 as a target for antibody-based therapy".
Blood.

Schulz, B. L. and M. Aebi (2009)
"Analysis of glycosylation site occupancy reveals a role for Ost3p and Ost6p in site-specific N-glycosylation efficiency".
Mol Cell Proteomics 8(2): 357-64.

Schulz, B. L., C. U. Stirnimann, J. P. Grimshaw, M. S. Brozzo, F. Fritsch, E. Mohorko, G. Capitani, R. Glockshuber, M. G. Grutter and M. Aebi (2009)
"Oxidoreductase activity of oligosaccharyltransferase subunits Ost3p and Ost6p defines site-specific glycosylation efficiency".
Proc Natl Acad Sci U S A 106(27): 11061-6.

Seeger, M. A., C. von Ballmoos, F. Verrey and K. M. Pos (2009)
"Crucial role of Asp408 in the proton translocation pathway of multidrug transporter AcrB: evidence from site-directed mutagenesis and carbodiimide labeling".
Biochemistry 48(25): 5801-12.

Stewart-Jones, G., A. Wadle, A. Hombach, E. Shenderov, G. Held, E. Fischer, S. Kleber, N. Nuber, F. Stenner-Liewen, S. Bauer, A. McMichael, A. Knuth, H. Abken, A. A. Hombach, V. Cerundolo, E. Y. Jones and C. Renner (2009)
"Rational development of high-affinity T-cell receptor-like antibodies".
Proc Natl Acad Sci U S A 106(14): 5784-8.

Striebel, F., F. Imkamp, M. Sutter, M. Steiner, A. Mamedov and E. Weber-Ban (2009)
"Bacterial ubiquitin-like modifier Pup is deamidated and conjugated to substrates by distinct but homologous enzymes".
Nat Struct Mol Biol.

Titz, A., A. Butschi, B. Henrissat, Y. Y. Fan, T. Hennet, E. Razzazi-Fazeli, M. O. Hengartner, I. B. Wilson, M. Kunzler and M. Aebi (2009)
"Molecular basis for galactosylation of core fucose residues in invertebrates: identification of caenorhabditis elegans N-glycan core alpha1,6-fucoside beta1,4-galactosyltransferase GALT-1 as a member of a novel glycosyltransferase family".
J Biol Chem 284(52): 36223-33.

Tweedie-Cullen, R. Y., J. M. Reck and I. M. Mansuy (2009)
"Comprehensive mapping of post-translational modifications on synaptic, nuclear, and histone proteins in the adult mouse brain".
J Proteome Res 8(11): 4966-82.

2008

Baumgartel, K., D. Genoux, H. Welzl, R. Y. Tweedie-Cullen, K. Koshibu, M. Livingstone-Zatchej, C. Mamie and I. M. Mansuy (2008)
"Control of the establishment of aversive memory by calcineurin and Zif268".
Nat Neurosci 11(5): 572-8.

Beyer, T. A., W. Xu, D. Teupser, U. auf dem Keller, P. Bugnon, E. Hildt, J. Thiery, Y. W. Kan and S. Werner (2008)
"Impaired liver regeneration in Nrf2 knockout mice: role of ROS-mediated insulin/IGF-1 resistance".
Embo J 27(1): 212-23.

Biellmann, F., A. J. Hulsmeier, D. Zhou, P. Cinelli and T. Hennet (2008)
"The Lc3-synthase gene B3gnt5 is essential to pre-implantation development of the murine embryo".
BMC Dev Biol 8: 109.

Bovet, C. and R. Zenobi (2008)
"Determination of active enzyme concentration using activity-based probes and direct mass spectrometric readout".
Anal Biochem 373(2): 380-2.

Buehler, P. W., F. Vallelian, M. G. Mikolajczyk, G. Schoedon, T. Schweizer, A. I. Alayash and D. J. Schaer (2008)
"Structural stabilization in tetrameric or polymeric hemoglobin determines its interaction with endogenous antioxidant scavenger pathways".
Antioxid Redox Signal 10(8): 1449-62.

Conrotto, P., C. Roesli, J. Rybak, P. Kischel, D. Waltregny, D. Neri and V. Castronovo (2008)
"Identification of new accessible tumor antigens in human colon cancer by ex vivo protein biotinylation and comparative mass spectrometry analysis".
Int J Cancer 123(12): 2856-64.

Dip, R., S. Lenz, J. P. Antignac, B. Le Bizec, H. Gmuender and H. Naegeli (2008)
"Global gene expression profiles induced by phytoestrogens in human breast cancer cells".
Endocr Relat Cancer 15(1): 161-73.

Dumelin, C. E., S. Trussel, F. Buller, E. Trachsel, F. Bootz, Y. Zhang, L. Mannocci, S. C. Beck, M. Drumea-Mirancea, M. W. Seeliger, C. Baltes, T. Muggler, F. Kranz, M. Rudin, S. Melkko, J. Scheuermann and D. Neri (2008)
"A portable albumin binder from a DNA-encoded chemical library".
Angew Chem Int Ed Engl 47(17): 3196-201.

Hoek, K. S., N. C. Schlegel, O. M. Eichhoff, D. S. Widmer, C. Praetorius, S. O. Einarsson, S. Valgeirsdottir, K. Bergsteinsdottir, A. Schepsky, R. Dummer and E. Steingrimsson (2008)
"Novel MITF targets identified using a two-step DNA microarray strategy".
Pigment Cell Melanoma Res 21(6): 665-76.

Keller, M., A. Ruegg, S. Werner and H. D. Beer (2008)
"Active caspase-1 is a regulator of unconventional protein secretion".
Cell 132(5): 818-31.

Lang, K., A. Lindemann, F. Hauser and M. Gottfert (2008)
"The genistein stimulon of Bradyrhizobium japonicum".
Mol Genet Genomics 279(3): 203-11.

Malojcic, G., R. L. Owen, J. P. Grimshaw, M. S. Brozzo, H. Dreher-Teo and R. Glockshuber (2008)
"A structural and biochemical basis for PAPS-independent sulfuryl transfer by aryl sulfotransferase from uropathogenic Escherichia coli".
Proc Natl Acad Sci U S A 105(49): 19217-22.

Mesa, S., F. Hauser, M. Friberg, E. Malaguti, H. M. Fischer and H. Hennecke (2008)
"Comprehensive assessment of the regulons controlled by the FixLJ-FixK2-FixK1 cascade in Bradyrhizobium japonicum".
J Bacteriol 190(20): 6568-79.

Nasab, F. P., B. L. Schulz, F. Gamarro, A. J. Parodi and M. Aebi (2008)
"All in one: Leishmania major STT3 proteins substitute for the whole oligosaccharyltransferase complex in Saccharomyces cerevisiae".
Mol Biol Cell 19(9): 3758-68.

Pahlich, S., R. P. Zakaryan and H. Gehring (2008)
"Identification of proteins interacting with protein arginine methyltransferase 8: The Ewing sarcoma (EWS) protein binds independent of its methylation state".
Proteins 72(4): 1125-1137.

Pereira, C., D. J. Schaer, E. B. Bachli, M. O. Kurrer and G. Schoedon (2008)
"Wnt5A/CaMKII signaling contributes to the inflammatory response of macrophages and is a target for the antiinflammatory action of activated protein C and interleukin-10".
Arterioscler Thromb Vasc Biol 28(3): 504-10.

Peroza, E. A. and E. Freisinger (2008)
"Tris is a non-innocent buffer during intein-mediated protein cleavage".
Protein Expr Purif 57(2): 217-25.

Roesli, C., V. Mumprecht, D. Neri and M. Detmar (2008)
"Identification of the surface-accessible, lineage-specific vascular proteome by two-dimensional peptide mapping".
Faseb J 22(6): 1933-44.

Rosli, C., J. N. Rybak, D. Neri and G. Elia (2008)
"Quantitative recovery of biotinylated proteins from streptavidin-based affinity chromatography resins".
Methods Mol Biol 418: 89-100.

Schegg, B., A. J. Hulsmeier, C. Rutschmann, C. Maag and T. Hennet (2008)
"Core glycosylation of collagen is initiated by two {beta}(1-O)galactosyltransferases".
Mol Cell Biol.

Schenker, P., P. Alfarano, P. Kolb, A. Caflisch and A. Baici (2008)
"A double-headed cathepsin B inhibitor devoid of warhead".
Protein Sci 17(12): 2145-55.

Schulz, B. L. and M. Aebi (2008)
"Analysis of glycosylation site occupancy reveals a role for Ost3p and Ost6p in site-specific N-glycosylation efficiency".
Mol Cell Proteomics.

Seeger, M. A., C. von Ballmoos, T. Eicher, L. Brandstatter, F. Verrey, K. Diederichs and K. M. Pos (2008)
"Engineered disulfide bonds support the functional rotation mechanism of multidrug efflux pump AcrB".
Nat Struct Mol Biol 15(2): 199-205.

Spirig, T., A. Tiaden, P. Kiefer, C. Buchrieser, J. A. Vorholt and H. Hilbi (2008)
"The Legionella autoinducer synthase LqsA produces an alpha-hydroxyketone signaling molecule".
J Biol Chem 283(26): 18113-23.

Stallmach, R. and S. M. Gloor (2008)
"Neurobin/TMPRSS11C, a novel type II transmembrane serine protease which cleaves fibroblast growth factor-2 in vitro".
Biochem J.

Stephan, A., J. M. Mateos, S. V. Kozlov, P. Cinelli, A. D. Kistler, S. Hettwer, T. Rulicke, P. Streit, B. Kunz and P. Sonderegger (2008)
"Neurotrypsin cleaves agrin locally at the synapse".
Faseb J 22(6): 1861-73.

Tiaden, A., T. Spirig, P. Carranza, H. Bruggemann, K. Riedel, L. Eberl, C. Buchrieser and H. Hilbi (2008)
"Synergistic contribution of the Legionella pneumophila lqs genes to pathogen-host interactions".
J Bacteriol 190(22): 7532-47.

2007

Clement, F. C., R. Dip and H. Naegeli (2007)
"Expression profile of human cells in culture exposed to glycidamide, a reactive metabolite of the heat-induced food carcinogen acrylamide".
Toxicology 240(1-2): 111-24.

Domanitskaya, E. V., H. Liu, S. Chen and E. Kubli (2007)
"The hydroxyproline motif of male sex peptide elicits the innate immune response in Drosophila females".
Febs J 274(21): 5659-68.

Ebauer, M., M. Wachtel, F. K. Niggli and B. W. Schafer (2007)
"Comparative expression profiling identifies an in vivo target gene signature with TFAP2B as a mediator of the survival function of PAX3/FKHR".
Oncogene 26(51): 7267-81.

Fischer, B., V. Roth and J. M. Buhmann (2007)
"Time-series alignment by non-negative multiple generalized canonical correlation analysis".
BMC Bioinformatics 8 Suppl 10: S4.

Galliciotti, G., M. Glatzel, J. Kinter, S. V. Kozlov, P. Cinelli, T. Rulicke and P. Sonderegger (2007)
"Accumulation of mutant neuroserpin precedes development of clinical symptoms in familial encephalopathy with neuroserpin inclusion bodies".
Am J Pathol 170(4): 1305-13.

Hauser, F., G. Pessi, M. Friberg, C. Weber, N. Rusca, A. Lindemann, H. M. Fischer and H. Hennecke (2007)
"Dissection of the Bradyrhizobium japonicum NifA+sigma54 regulon, and identification of a ferredoxin gene (fdxN) for symbiotic nitrogen fixation".
Mol Genet Genomics 278(3): 255-71.

Hulsmeier, A. J., P. Paesold-Burda and T. Hennet (2007)
"N-glycosylation site occupancy in serum glycoproteins using multiple reaction monitoring liquid chromatography-mass spectrometry".
Mol Cell Proteomics 6(12): 2132-8.

Johnston, A. J., P. Meier, J. Gheyselinck, S. E. Wuest, M. Federer, E. Schlagenhauf, J. D. Becker and U. Grossniklaus (2007)
"Genetic subtraction profiling identifies genes essential for Arabidopsis reproduction and reveals interaction between the female gametophyte and the maternal sporophyte".
Genome Biol 8(10): R204.

Kreymborg, K., R. Etzensperger, L. Dumoutier, S. Haak, A. Rebollo, T. Buch, F. L. Heppner, J. C. Renauld and B. Becher (2007)
"IL-22 Is Expressed by Th17 Cells in an IL-23-Dependent Fashion, but Not Required for the Development of Autoimmune Encephalomyelitis".
J Immunol 179(12): 8098-104.

Kuenzle, S., H. C. von Budingen, M. Meier, M. D. Harrer, E. Urich, B. Becher and N. Goebels (2007)
"Pathogen specificity and autoimmunity are distinct features of antigen-driven immune responses in neuroborreliosis".
Infect Immun 75(8): 3842-7.

Laloi, C., M. Stachowiak, E. Pers-Kamczyc, E. Warzych, I. Murgia and K. Apel (2007)
"Cross-talk between singlet oxygen- and hydrogen peroxide-dependent signaling of stress responses in Arabidopsis thaliana".
Proc Natl Acad Sci U S A 104(2): 672-7.

Lindemann, A., A. Moser, G. Pessi, F. Hauser, M. Friberg, H. Hennecke and H. M. Fischer (2007)
"New target genes controlled by the Bradyrhizobium japonicum two-component regulatory system RegSR".
J Bacteriol 189(24): 8928-43.

Lovato, V., C. Roesli, J. Ahlskog, J. Scheuermann and D. Neri (2007)
"A monoclonal antibody prevents aggregation of the NBD1 domain of the cystic fibrosis transmembrane conductance regulator".
Protein Eng Des Sel 20(12): 607-14.

Lucchinetti, E., J. Aguirre, J. Feng, M. Zhu, M. Suter, D. R. Spahn, L. Harter and M. Zaugg (2007)
"Molecular evidence of late preconditioning after sevoflurane inhalation in healthy volunteers".
Anesth Analg 105(3): 629-40.

Lucchinetti, E., C. Hofer, L. Bestmann, M. Hersberger, J. Feng, M. Zhu, L. Furrer, M. C. Schaub, R. Tavakoli, M. Genoni, A. Zollinger and M. Zaugg (2007)
"Gene regulatory control of myocardial energy metabolism predicts postoperative cardiac function in patients undergoing off-pump coronary artery bypass graft surgery: inhalational versus intravenous anesthetics".
Anesthesiology 106(3): 444-57.

Meloni, G., P. Faller and M. Vasak (2007)
"Redox silencing of copper in metal-linked neurodegenerative disorders: reaction of Zn7metallothionein-3 with Cu2+ ions".
J Biol Chem 282(22): 16068-78.

Nagy, I., A. Caelers, A. Monge, S. Bonabi, A. M. Huber and D. Bodmer (2007)
"NF-kappaB-dependent apoptotic hair cell death in the auditory system".
Audiol Neurootol 12(4): 209-20.

Peroza, E. A. and E. Freisinger (2007)
"Metal ion binding properties of Triticum [corrected] aestivum Ec-1 metallothionein: evidence supporting two separate metal thiolate clusters".
J Biol Inorg Chem 12(3): 377-91.

Reif, R., S. Sales, S. Hettwer, B. Dreier, C. Gisler, J. Wolfel, D. Luscher, A. Zurlinden, A. Stephan, S. Ahmed, A. Baici, B. Ledermann, B. Kunz and P. Sonderegger (2007)
"Specific cleavage of agrin by neurotrypsin, a synaptic protease linked to mental retardation".
Faseb J 21(13): 3468-78.

Riedel, K. and A. Lehner (2007)
"Identification of proteins involved in osmotic stress response in Enterobacter sakazakii by proteomics".
Proteomics 7(8): 1217-31.

Rybak, J. N., C. Roesli, M. Kaspar, A. Villa and D. Neri (2007)
"The extra-domain A of fibronectin is a vascular marker of solid tumors and metastases".
Cancer Res 67(22): 10948-57.

von Ballmoos, C. and P. Dimroth (2007)
"Two distinct proton binding sites in the ATP synthase family".
Biochemistry 46(42): 11800-9.

2006

Auweter, S. D., R. Fasan, L. Reymond, J. G. Underwood, D. L. Black, S. Pitsch and F. H. Allain (2006)
"Molecular basis of RNA recognition by the human alternative splicing factor Fox-1".
Embo J 25(1): 163-73.

Baginsky, S. and W. Gruissem (2006)
"Arabidopsis thaliana proteomics: from proteome to genome".
J Exp Bot 57(7): 1485-91.

Barman, H., M. Walch, S. Latinovic-Golic, C. Dumrese, M. Dolder, P. Groscurth and U. Ziegler (2006)
"Cholesterol in negatively charged lipid bilayers modulates the effect of the antimicrobial protein granulysin".
J Membr Biol 212(1): 29-39.

Bouveret, R., N. Schonrock, W. Gruissem and L. Hennig (2006)
"Regulation of flowering time by Arabidopsis MSI1".
Development 133(9): 1693-702.

Brun, M. A., M. D. Disney and P. H. Seeberger (2006)
"Miniaturization of microwave-assisted carbohydrate functionalization to create oligosaccharide microarrays".
Chembiochem 7(3): 421-4.

Buterin, T., C. Koch and H. Naegeli (2006)
"Convergent transcriptional profiles induced by endogenous estrogen and distinct xenoestrogens in breast cancer cells".
Carcinogenesis 27(8): 1567-78.

Castronovo, V., D. Waltregny, P. Kischel, C. Roesli, G. Elia, J. N. Rybak and D. Neri (2006)
"A chemical proteomics approach for the identification of accessible antigens expressed in human kidney cancer".
Mol Cell Proteomics 5(11): 2083-91.

de Paz, J. L., C. Noti and P. H. Seeberger (2006)
"Microarrays of synthetic heparin oligosaccharides".
J Am Chem Soc 128(9): 2766-7.

Dias, R. L., R. Fasan, K. Moehle, A. Renard, D. Obrecht and J. A. Robinson (2006)
"Protein ligand design: from phage display to synthetic protein epitope mimetics in human antibody Fc-binding peptidomimetics".
J Am Chem Soc 128(8): 2726-32.

Dimou, L., L. Schnell, L. Montani, C. Duncan, M. Simonen, R. Schneider, T. Liebscher, M. Gullo and M. E. Schwab (2006)
"Nogo-A-deficient mice reveal strain-dependent differences in axonal regeneration".
J Neurosci 26(21): 5591-603.

Dumelin, C. E., J. Scheuermann, S. Melkko and D. Neri (2006)
"Selection of streptavidin binders from a DNA-encoded chemical library".
Bioconjug Chem 17(2): 366-70.

Endler, A., S. Meyer, S. Schelbert, T. Schneider, W. Weschke, S. W. Peters, F. Keller, S. Baginsky, E. Martinoia and U. G. Schmidt (2006)
"Identification of a vacuolar sucrose transporter in barley and Arabidopsis mesophyll cells by a tonoplast proteomic approach".
Plant Physiol 141(1): 196-207.

Ettorre, A., C. Rosli, M. Silacci, S. Brack, G. McCombie, R. Knochenmuss, G. Elia and D. Neri (2006)
"Recombinant antibodies for the depletion of abundant proteins from human serum".
Proteomics 6(16): 4496-505.

Hoek, K. S., N. C. Schlegel, P. Brafford, A. Sucker, S. Ugurel, R. Kumar, B. L. Weber, K. L. Nathanson, D. J. Phillips, M. Herlyn, D. Schadendorf and R. Dummer (2006)
"Metastatic potential of melanomas defined by specific gene expression profiles with no BRAF signature".
Pigment Cell Res 19(4): 290-302.

Kleffmann, T., M. Hirsch-Hoffmann, W. Gruissem and S. Baginsky (2006)
"plprot: a comprehensive proteome database for different plastid types".
Plant Cell Physiol 47(3): 432-6.

Kowarik, M., S. Numao, M. F. Feldman, B. L. Schulz, N. Callewaert, E. Kiermaier, I. Catrein and M. Aebi (2006)
"N-linked glycosylation of folded proteins by the bacterial oligosaccharyltransferase".
Science 314(5802): 1148-50.

Kowarik, M., N. M. Young, S. Numao, B. L. Schulz, I. Hug, N. Callewaert, D. C. Mills, D. C. Watson, M. Hernandez, J. F. Kelly, M. Wacker and M. Aebi (2006)
"Definition of the bacterial N-glycosylation site consensus sequence".
Embo J 25(9): 1957-66.

Lucchinetti, E., J. Feng, R. Silva, G. V. Tolstonog, M. C. Schaub, G. G. Schumann and M. Zaugg (2006)
"Inhibition of LINE-1 expression in the heart decreases ischemic damage by activation of Akt/PKB signaling".
Physiol Genomics 25(2): 314-24.

Melkko, S., C. E. Dumelin, J. Scheuermann and D. Neri (2006)
"On the magnitude of the chelate effect for the recognition of proteins by pharmacophores scaffolded by self-assembling oligonucleotides".
Chem Biol 13(2): 225-31.

Michel, K., O. Abderhalden, R. Bruggmann and R. Dudler (2006)
"Transcriptional changes in powdery mildew infected wheat and Arabidopsis leaves undergoing syringolin-triggered hypersensitive cell death at infection sites".
Plant Mol Biol 62(4-5): 561-78.

Pahlich, S., R. P. Zakaryan and H. Gehring (2006)
"Protein arginine methylation: Cellular functions and methods of analysis".
Biochim Biophys Acta 1764(12): 1890-903.

Pankow, S., C. Bamberger, A. Klippel and S. Werner (2006)
"Regulation of epidermal homeostasis and repair by phosphoinositide 3-kinase".
J Cell Sci 119(Pt 19): 4033-46.

Pieren, M., A. E. Prota, C. Ruch, D. Kostrewa, A. Wagner, K. Biedermann, F. K. Winkler and K. Ballmer-Hofer (2006)
"Crystal structure of the Orf virus NZ2 variant of vascular endothelial growth factor-E. Implications for receptor specificity".
J Biol Chem 281(28): 19578-87.

Roesli, C., G. Elia and D. Neri (2006)
"Two-dimensional mass spectrometric mapping".
Curr Opin Chem Biol 10(1): 35-41.

Roesli, C., D. Neri and J. N. Rybak (2006)
"In vivo protein biotinylation and sample preparation for the proteomic identification of organ- and disease-specific antigens accessible from the vasculature".
Nat Protoc 1(1): 192-9.

Rudolph, G., G. Semini, F. Hauser, A. Lindemann, M. Friberg, H. Hennecke and H. M. Fischer (2006)
"The Iron control element, acting in positive and negative control of iron-regulated Bradyrhizobium japonicum genes, is a target for the Irr protein".
J Bacteriol 188(2): 733-44.

Schaer, C. A., G. Schoedon, A. Imhof, M. O. Kurrer and D. J. Schaer (2006)
"Constitutive endocytosis of CD163 mediates hemoglobin-heme uptake and determines the noninflammatory and protective transcriptional response of macrophages to hemoglobin".
Circ Res 99(9): 943-50.

Schonrock, N., R. Bouveret, O. Leroy, L. Borghi, C. Kohler, W. Gruissem and L. Hennig (2006)
"Polycomb-group proteins repress the floral activator AGL19 in the FLC-independent vernalization pathway".
Genes Dev 20(12): 1667-78.

Schonrock, N., V. Exner, A. Probst, W. Gruissem and L. Hennig (2006)
"Functional genomic analysis of CAF-1 mutants in Arabidopsis thaliana".
J Biol Chem 281(14): 9560-8.

Siddique, M. A., J. Grossmann, W. Gruissem and S. Baginsky (2006)
"Proteome analysis of bell pepper (Capsicum annuum L.) chromoplasts".
Plant Cell Physiol 47(12): 1663-73.

Vgenopoulou, I., A. C. Gemperli and J. Steuber (2006)
"Specific modification of a Na+ binding site in NADH:quinone oxidoreductase from Klebsiella pneumoniae with dicyclohexylcarbodiimide".
J Bacteriol 188(9): 3264-72.

Wacker, M., M. F. Feldman, N. Callewaert, M. Kowarik, B. R. Clarke, N. L. Pohl, M. Hernandez, E. D. Vines, M. A. Valvano, C. Whitfield and M. Aebi (2006)
"Substrate specificity of bacterial oligosaccharyltransferase suggests a common transfer mechanism for the bacterial and eukaryotic systems".
Proc Natl Acad Sci U S A 103(18): 7088-93.

Yang, J., I. Sangwan, A. Lindemann, F. Hauser, H. Hennecke, H. M. Fischer and M. R. O'Brian (2006)
"Bradyrhizobium japonicum senses iron through the status of haem to regulate iron homeostasis and metabolism".
Mol Microbiol 60(2): 427-37.

Yepiskoposyan, H., D. Egli, T. Fergestad, A. Selvaraj, C. Treiber, G. Multhaup, O. Georgiev and W. Schaffner (2006)
"Transcriptome response to heavy metal stress in Drosophila reveals a new zinc transporter that confers resistance to zinc".
Nucleic Acids Res 34(17): 4866-77.

2005

Baginsky, S., T. Kleffmann, A. von Zychlinski and W. Gruissem (2005)
"Analysis of shotgun proteomics and RNA profiling data from Arabidopsis thaliana chloroplasts".
J Proteome Res 4(2): 637-40.

David, D. C., S. Hauptmann, I. Scherping, K. Schuessel, U. Keil, P. Rizzu, R. Ravid, S. Drose, U. Brandt, W. E. Muller, A. Eckert and J. Gotz (2005)
"Proteomic and functional analyses reveal a mitochondrial dysfunction in P301L tau transgenic mice".
J Biol Chem 280(25): 23802-14.

David, D. C., F. Hoerndli and J. Gotz (2005)
"Functional Genomics meets neurodegenerative disorders Part I: transcriptomic and proteomic technology".
Prog Neurobiol 76(3): 153-68.

di Pietro, M., J. S. Bellver, M. Menigatti, F. Bannwart, A. Schnider, A. Russell, K. Truninger, J. Jiricny and G. Marra (2005)
"Defective DNA Mismatch Repair Determines a Characteristic Transcriptional Profile in Proximal Colon Cancers".
Gastroenterology 129(3): 1047-1059.

Hoerndli, F., D. C. David and J. Gotz (2005)
"Functional Genomics meets neurodegenerative disorders. Part II: application and data integration".
Prog Neurobiol 76(3): 169-88.

Huber, C., C. Thielen, H. Seeger, P. Schwarz, F. Montrasio, M. R. Wilson, E. Heinen, Y. X. Fu, G. Miele and A. Aguzzi (2005)
"Lymphotoxin-beta receptor-dependent genes in lymph node and follicular dendritic cell transcriptomes".
J Immunol 174(9): 5526-36.

Lerch, M., H. Kamimori, G. Folkers, M. I. Aguilar, A. G. Beck-Sickinger and O. Zerbe (2005)
"Strongly altered receptor binding properties in PP and NPY chimeras are accompanied by changes in structure and membrane binding".
Biochemistry 44(25): 9255-64.

Pahlich, S., K. Bschir, C. Chiavi, L. Belyanskaya and H. Gehring (2005)
"Different methylation characteristics of protein arginine methyltransferase 1 and 3 toward the Ewing Sarcoma protein and a peptide".
Proteins 61(1): 164-75.

Polymenidou, M., K. Stoeck, M. Glatzel, M. Vey, A. Bellon and A. Aguzzi (2005)
"Coexistence of multiple PrPSc types in individuals with Creutzfeldt-Jakob disease".
Lancet Neurol 4(12): 805-14.

Raschle, T., N. Amrhein and T. B. Fitzpatrick (2005)
"On the two components of pyridoxal 5'-phosphate synthase from Bacillus subtilis".
J Biol Chem 280(37): 32291-300.

Rybak, J. N., A. Ettorre, B. Kaissling, R. Giavazzi, D. Neri and G. Elia (2005)
"In vivo protein biotinylation for identification of organ-specific antigens accessible from the vasculature".
Nat Methods 2(4): 291-8.

Scheurer, S. B., C. Roesli, D. Neri and G. Elia (2005)
"A comparison of different biotinylation reagents, tryptic digestion procedures, and mass spectrometric techniques for 2-D peptide mapping of membrane proteins".
Proteomics 5(12): 3035-9.

Urosevic, M., R. Dummer, C. Conrad, M. Beyeler, E. Laine, G. Burg and M. Gilliet (2005)
"Disease-independent skin recruitment and activation of plasmacytoid predendritic cells following imiquimod treatment".
J Natl Cancer Inst 97(15): 1143-53.

Vandepoele, K., K. Vlieghe, K. Florquin, L. Hennig, G. T. Beemster, W. Gruissem, Y. Van de Peer, D. Inze and L. De Veylder (2005)
"Genome-wide identification of potential plant E2F target genes".
Plant Physiol 139(1): 316-28.

von Zychlinski, A., T. Kleffmann, N. Krishnamurthy, K. Sjolander, S. Baginsky and W. Gruissem (2005)
"Proteome analysis of the rice etioplast: metabolic and regulatory networks and novel protein functions".
Mol Cell Proteomics 4(8): 1072-84.

Wimmer, U., Y. Wang, O. Georgiev and W. Schaffner (2005)
"Two major branches of anti-cadmium defense in the mouse: MTF-1/metallothioneins and glutathione".
Nucleic Acids Res 33(18): 5715-27.

Zimmermann, P., L. Hennig and W. Gruissem (2005)
"Gene-expression analysis and network discovery using Genevestigator".
Trends Plant Sci 10(9): 407-9.

2004

Baginsky, S. and W. Gruissem (2004)
"Chloroplast proteomics: potentials and challenges".
J Exp Bot 55(400): 1213-20.

da Silva, R., E. Lucchinetti, T. Pasch, M. C. Schaub and M. Zaugg (2004)
"Ischemic but not pharmacological preconditioning elicits a gene expression profile similar to unprotected myocardium".
Physiol Genomics 20(1): 117-30.

Disney, M. D. and P. H. Seeberger (2004)
"The use of carbohydrate microarrays to study carbohydrate-cell interactions and to detect pathogens".
Chem Biol 11(12): 1701-7.

Franscini, N., E. B. Bachli, N. Blau, M. S. Leikauf, A. Schaffner and G. Schoedon (2004)
"Gene expression profiling of inflamed human endothelial cells and influence of activated protein C".
Circulation 110(18): 2903-9.

Hennig, L., W. Gruissem, U. Grossniklaus and C. Kohler (2004)
"Transcriptional programs of early reproductive stages in Arabidopsis".
Plant Physiol 135(3): 1765-75.

Kleffmann, T., D. Russenberger, A. von Zychlinski, W. Christopher, K. Sjolander, W. Gruissem and S. Baginsky (2004)
"The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions".
Curr Biol 14(5): 354-62.

Melkko, S., J. Scheuermann, C. E. Dumelin and D. Neri (2004)
"Encoded self-assembling chemical libraries".
Nat Biotechnol 22(5): 568-74.

Nagy, I., M. Bodmer, D. Brors and D. Bodmer (2004)
"Early gene expression in the organ of Corti exposed to gentamicin".
Hear Res 195(1-2): 1-8.

Rybak, J. N., S. B. Scheurer, D. Neri and G. Elia (2004)
"Purification of biotinylated proteins on streptavidin resin: a protocol for quantitative elution".
Proteomics 4(8): 2296-9.

Sergeev, P., R. da Silva, E. Lucchinetti, K. Zaugg, T. Pasch, M. C. Schaub and M. Zaugg (2004)
"Trigger-dependent gene expression profiles in cardiac preconditioning: evidence for distinct genetic programs in ischemic and anesthetic preconditioning".
Anesthesiology 100(3): 474-88.

Wille, A., P. Zimmermann, E. Vranova, A. Furholz, O. Laule, S. Bleuler, L. Hennig, A. Prelic, P. von Rohr, L. Thiele, E. Zitzler, W. Gruissem and P. Buhlmann (2004)
"Sparse graphical Gaussian modeling of the isoprenoid gene network in Arabidopsis thaliana".
Genome Biol 5(11): R92.

Zimmermann, P., M. Hirsch-Hoffmann, L. Hennig and W. Gruissem (2004)
"GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox".
Plant Physiol 136(1): 2621-32.

2003

Hennig, L., M. Menges, J. A. Murray and W. Gruissem (2003)
"Arabidopsis transcript profiling on Affymetrix GeneChip arrays".
Plant Mol Biol 53(4): 457-65.

Menges, M., L. Hennig, W. Gruissem and J. A. Murray (2003)
"Genome-wide gene expression in an Arabidopsis cell suspension".
Plant Mol Biol 53(4): 423-42.

2002

Menges, M., L. Hennig, W. Gruissem and J. A. Murray (2002)
"Cell cycle-regulated gene expression in Arabidopsis".
J Biol Chem 277(44): 41987-2002.