Publications with FGCZ Coauthors

Publications since 2003

2010

Widmer, C. C., C. P. Pereira, P. Gehrig, F. Vallelian, G. Schoedon, P. W. Buehler and D. J. Schaer (2010)
"Hemoglobin can attenuate hydrogen peroxide-induced oxidative stress by acting as an antioxidative peroxidase".
Antioxid Redox Signal 12(2): 185-98.

2009

Abu-Ali, G. S., D. W. Lacher, L. M. Wick, W. Qi and T. S. Whittam (2009)
"Genomic diversity of pathogenic Escherichia coli of the EHEC 2 clonal complex".
BMC Genomics 10: 296.

Albinger-Hegyi, A., S. J. Stoeckli, S. Schmid, M. Storz, G. Iotzova, N. M. Probst-Hensch, H. Rehrauer, M. Tinguely, H. Moch and I. Hegyi (2009)
"Lysyl oxidase expression is an independent marker of prognosis and a predictor of lymph node metastasis in oral and oropharyngeal squamous cell carcinoma (OSCC)".
Int J Cancer.

Baumgartel, K., R. Y. Tweedie-Cullen, J. Grossmann, P. Gehrig, M. Livingstone-Zatchej and I. M. Mansuy (2009)
"Changes in the Proteome after Neuronal Zif268 Overexpression".
J Proteome Res.

Berthier, C. C., C. Pally, G. Weckbecker, F. Raulf, H. Rehrauer, U. Wagner, M. Le Hir and H. P. Marti (2009)
"Experimental heart transplantation: effect of cyclosporine on expression and activity of metzincins".
Swiss Med Wkly 139(15-16): 233-40.

Carranza, P., I. Hartmann, A. Lehner, R. Stephan, P. Gehrig, J. Grossmann, S. Barkow-Oesterreicher, B. Roschitzki, L. Eberl and K. Riedel (2009)
"Proteomic profiling of Cronobacter turicensis 3032, a food-borne opportunistic pathogen".
Proteomics 9(13): 3564-3579.

Delmotte, N., C. Knief, S. Chaffron, G. Innerebner, B. Roschitzki, R. Schlapbach, C. von Mering and J. A. Vorholt (2009)
"Community proteogenomics reveals insights into the physiology of phyllosphere bacteria".
Proc Natl Acad Sci U S A 106(38): 16428-33.

Djouder, N., R. D. Tuerk, M. Suter, P. Salvioni, R. F. Thali, R. Scholz, K. Vaahtomeri, Y. Auchli, H. Rechsteiner, R. A. Brunisholz, B. Viollet, T. P. Makela, T. Wallimann, D. Neumann and W. Krek (2009)
"PKA phosphorylates and inactivates AMPKalpha to promote efficient lipolysis".
Embo J.

Drissner, D., P. Gehrig, R. Marti, E. Hildbrand and F. Hesford (2009)
"Identification of a Red Wine Marker in Residues from a 13th Century Cellar".
Chimia 63(3): 169-169.

Duc, L., S. Neuenschwander, H. Rehrauer, U. Wagner, J. Sobek, R. Schlapbach and J. Zeyer (2009)
"Development and experimental validation of a nifH oligonucleotide microarray to study diazotrophic communities in a glacier forefield".
Environ Microbiol 11(8): 2179-89.

Endler, A., S. Reiland, B. Gerrits, U. G. Schmidt, S. Baginsky and E. Martinoia (2009)
"In vivo phosphorylation sites of barley tonoplast proteins identified by a phosphoproteomic approach".
Proteomics 9(2): 310-21.

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.

Feng, J., E. Lucchinetti, G. Enkavi, Y. Wang, P. Gehrig, B. Roschitzki, M. C. Schaub, E. Tajkhorshid, K. Zaugg and M. Zaugg (2009)
"Tyrosine phosphorylation by Src within the cavity of the adenine nucleotide translocase 1 regulates ADP/ATP exchange in mitochondria".
Am J Physiol Cell Physiol.

Gamper, M., V. Viereck, V. Geissbuhler, J. Eberhard, J. Binder, C. Moll, H. Rehrauer and R. Moser (2009)
"Gene expression profile of bladder tissue of patients with ulcerative interstitial cystitis".
BMC Genomics 10: 199.

Gehrig, P. M., B. Roschitzki, D. Rutishauser, S. Reiland and R. Schlapbach (2009)
"Phosphorylated serine and threonine residues promote site-specific fragmentation of singly charged, arginine-containing peptide ions".
Rapid Commun Mass Spectrom 23(10): 1435-45.

Goetze, S., E. Qeli, C. Mosimann, A. Staes, B. Gerrits, B. Roschitzki, S. Mohanty, E. M. Niederer, E. Laczko, E. Timmerman, V. Lange, E. Hafen, R. Aebersold, J. Vandekerckhove, K. Basler, C. H. Ahrens, K. Gevaert and E. Brunner (2009)
"Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster".
PLoS Biol 7(11): e1000236.

Grobei, M. A., E. Qeli, E. Brunner, H. Rehrauer, R. Zhang, B. Roschitzki, K. Basler, C. H. Ahrens and U. Grossniklaus (2009)
"Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function".
Genome Res.

Hecht, M. L., B. Rosental, T. Horlacher, O. Hershkovitz, J. L. De Paz, C. Noti, S. Schauer, A. Porgador and P. H. Seeberger (2009)
"Natural cytotoxicity receptors NKp30, NKp44 and NKp46 bind to different heparan sulfate/heparin sequences".
J Proteome Res 8(2): 712-20.

Hodel, E. M., S. D. Ley, W. Qi, F. Ariey, B. Genton and H. P. Beck (2009)
"A microarray-based system for the simultaneous analysis of single nucleotide polymorphisms in human genes involved in the metabolism of anti-malarial drugs".
Malar J 8: 285.

Huber, A., B. Bodenmiller, A. Uotila, M. Stahl, S. Wanka, B. Gerrits, R. Aebersold and R. Loewith (2009)
"Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis".
Genes &Development.

Jecklin, M. C., S. Schauer, C. E. Dumelin and R. Zenobi (2009)
"Label-free determination of protein-ligand binding constants using mass spectrometry and validation using surface plasmon resonance and isothermal titration calorimetry".
J Mol Recognit 22(4): 319-29.

Kraljevic Pavelic, S., M. Sedic, K. Hock, S. Vucinic, D. Jurisic, P. Gehrig, M. Scott, R. Schlapbach, T. Cacev, S. Kapitanovic and K. Pavelic (2009)
"An integrated proteomics approach for studying the molecular pathogenesis of Dupuytren's disease".
J Pathol 217(4): 524-33.

Meier-Trummer, C. S., H. Rehrauer, M. Franchini, A. Patrignani, U. Wagner and M. Ackermann (2009)
"Malignant catarrhal fever of cattle is associated with low abundance of IL-2 transcript and a predominantly latent profile of ovine herpesvirus 2 gene expression".
PLoS One 4(7): e6265.

Montani, L., B. Gerrits, P. Gehrig, A. Kempf, L. Dimou, B. Wollscheid and M. E. Schwab (2009)
"Neuronal Nogo-A modulates growth cone motility via Rho-GTP/LIMK1/cofilin in the unlesioned adult nervous system".
J Biol Chem 284(16): 10793-807.

Pahlich, S., L. Quero, B. Roschitzki, R. P. Leemann-Zakaryan and H. Gehring (2009)
"Analysis of Ewing sarcoma (EWS)-binding proteins: interaction with hnRNP M, U, and RNA-helicases p68/72 within protein-RNA complexes".
J Proteome Res 8(10): 4455-65.

Pilop, C., F. Aregger, R. C. Gorman, R. Brunisholz, B. Gerrits, T. Schaffner, J. H. Gorman, 3rd, G. Matyas, T. Carrel and B. M. Frey (2009)
"Proteomic analysis in aortic media of patients with Marfan syndrome reveals increased activity of calpain 2 in aortic aneurysms".
Circulation 120(11): 983-91.

Pimenova, T., L. Meier, B. Roschitzki, G. Paraschiv, M. Przybylski and R. Zenobi (2009)
"Polystyrene beads as an alternative support material for epitope identification of a prion-antibody interaction using proteolytic excision-mass spectrometry".
Anal Bioanal Chem.

Qi, W., M. Kaser, K. Roltgen, D. Yeboah-Manu and G. Pluschke (2009)
"Genomic diversity and evolution of Mycobacterium ulcerans revealed by next-generation sequencing".
PLoS Pathog 5(9): e1000580.

Qi, W., G. Nong, J. F. Preston, F. Ben-Ami and D. Ebert (2009)
"Comparative metagenomics of Daphnia symbionts".
BMC Genomics 10: 172.

Raschle, T., D. Speziga, W. Kress, C. Moccand, P. Gehrig, N. Amrhein, E. Weber-Ban and T. B. Fitzpatrick (2009)
"Intersubunit cross-talk in pyridoxal 5'-phosphate synthase, coordinated by the C terminus of the synthase subunit".
J Biol Chem 284(12): 7706-18.

Reding, T., U. Wagner, A. B. Silva, L. K. Sun, M. Bain, S. Y. Kim, D. Bimmler and R. Graf (2009)
"Inflammation-dependent expression of SPARC during development of chronic pancreatitis in WBN/Kob rats and a microarray gene expression analysis".
Physiol Genomics 38(2): 196-204.

Rehrauer, H., C. Aquino, W. Gruissem, S. Henz, P. Hilson, S. Laubinger, N. Naouar, A. Patrignani, S. Rombauts, H. Shu, Y. Van de Peer, M. Vuylsteke, D. Weigel, G. Zeller and L. Hennig (2009)
"AGRONOMICS1 - A new resource for Arabidopsis transcriptome profiling".
Plant Physiol.

Reiland, S., G. Messerli, K. Baerenfaller, B. Gerrits, A. Endler, J. Grossmann, W. Gruissem and S. Baginsky (2009)
"Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks".
Plant Physiol 150(2): 889-903.

Rutishauser, D., K. D. Mertz, R. Moos, E. Brunner, T. Rulicke, A. M. Calella and A. Aguzzi (2009)
"The comprehensive native interactome of a fully functional tagged prion protein".
PLoS One 4(2): e4446.

Sayi, A., E. Kohler, I. Hitzler, I. Arnold, R. Schwendener, H. Rehrauer and A. Muller (2009)
"The CD4+ T cell-mediated IFN-gamma response to Helicobacter infection is essential for clearance and determines gastric cancer risk".
J Immunol 182(11): 7085-101.

Schneider, T., M. Schellenberg, S. Meyer, F. Keller, P. Gehrig, K. Riedel, Y. Lee, L. Eberl and E. Martinoia (2009)
"Quantitative detection of changes in the leaf-mesophyll tonoplast proteome in dependency of a cadmium exposure of barley (Hordeum vulgare L.) plants".
Proteomics 9(10): 2668-77.

Schonmann, S., A. Loy, C. Wimmersberger, J. Sobek, C. Aquino, P. Vandamme, B. Frey, H. Rehrauer and L. Eberl (2009)
"16S rRNA gene-based phylogenetic microarray for simultaneous identification of members of the genus Burkholderia".
Environ Microbiol 11(4): 779-800.

Schrimpf, S. P., M. Weiss, L. Reiter, C. H. Ahrens, M. Jovanovic, J. Malmstrom, E. Brunner, S. Mohanty, M. J. Lercher, P. E. Hunziker, R. Aebersold, C. von Mering and M. O. Hengartner (2009)
"Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes".
PLoS Biol 7(3): e48.

Tennant, S. M., M. Tauschek, K. Azzopardi, A. Bigham, V. Bennett-Wood, E. L. Hartland, W. Qi, T. S. Whittam and R. M. Robins-Browne (2009)
"Characterisation of atypical enteropathogenic E. coli strains of clinical origin".
BMC Microbiol 9: 117.

Thoma, R. S., J. S. Smith, W. Sandoval, J. W. Leone, P. Hunziker, B. Hampton, K. D. Linse and N. D. Denslow (2009)
"The ABRF Edman Sequencing Research Group 2008 Study: investigation into homopolymeric amino acid N-terminal sequence tags and their effects on automated Edman degradation".
J Biomol Tech 20(4): 216-25.

Tschumi, A., C. Nai, Y. Auchli, P. Hunziker, P. Gehrig, P. Keller, T. Grau and P. Sander (2009)
"Identification of apolipoprotein N-acyltransferase (Lnt) in mycobacteria".
J Biol Chem 284(40): 27146-56.

Tuerk, R. D., Y. Auchli, R. F. Thali, R. Scholz, T. Wallimann, R. A. Brunisholz and D. Neumann (2009)
"Tracking and quantification of 32P-labeled phosphopeptides in liquid chromatography matrix-assisted laser desorption/ionization mass spectrometry".
Anal Biochem 390(2): 141-8.

Türker, C., F. Akal, D. Joho and R. Schlapbach (2009).
"B-Fabric: an open source life sciences data management system".
21st. Int. Conf. on Scientific and Statistical Database Management, New Orleans, Louisiana, USA.

Türker, C., D. Joho, F. Akal, C. Panse, S. Barkow-Oesterreicher, H. Rehrauer and R. Schlapbach (2009)
"The B-Fabric Life Sciences Data Management System. In: Daten in den Lebenswissenschaften - Vom Paperüber Datenbanken zur integrierten Informationsquelle."
GI Jahrestagung 2009: ILW/GMDS/FGIR Workshop. Lübeck.

Türker, C., D. Joho, C. Panse, S. Barkow-Oesterreicher, F. Akal and R. Schlapbach (2009).
"Application coupling and data feeding in an integrative life sciences data management system".
Int. Conf. on Bioinformatics, Computational Biology, Genomics and Chemoinformatics, Orlando, FL, USA.

Zheng, L., R. Kanagaraj, B. Mihaljevic, S. Schwendener, A. A. Sartori, B. Gerrits, I. Shevelev and P. Janscak (2009)
"MRE11 complex links RECQ5 helicase to sites of DNA damage".
Nucleic Acids Res 37(8): 2645-57.

2008

Amantonico, A., J. Y. Oh, J. Sobek, M. Heinemann and R. Zenobi (2008)
"Mass spectrometric method for analyzing metabolites in yeast with single cell sensitivity".
Angew Chem Int Ed Engl 47(29): 5382-5.

Baerenfaller, K., J. Grossmann, M. A. Grobei, R. Hull, M. Hirsch-Hoffmann, S. Yalovsky, P. Zimmermann, U. Grossniklaus, W. Gruissem and S. Baginsky (2008)
"Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics".
Science 320(5878): 938-41.

Bitton, D. A., M. J. Okoniewski, Y. Connolly and C. J. Miller (2008)
"Exon level integration of proteomics and microarray data".
BMC Bioinformatics 9: 118.

Bodenmiller, B., D. Campbell, B. Gerrits, H. Lam, M. Jovanovic, P. Picotti, R. Schlapbach and R. Aebersold (2008)
"PhosphoPep--a database of protein phosphorylation sites in model organisms".
Nat Biotechnol 26(12): 1339-40.

Bovet, C., M. Ruff, A. Wortmann, S. Eiler, F. Granger, B. Gerrits, D. Moras and R. Zenobi (2008)
"Identification of Endocrine-Disrupting Compounds Using Nanoelectrospray Ionization Mass Spectrometry".
Chimia 62(5): 329–334.

Buerki, C., K. M. Rothgiesser, T. Valovka, H. R. Owen, H. Rehrauer, M. Fey, W. S. Lane and M. O. Hottiger (2008)
"Functional relevance of novel p300-mediated lysine 314 and 315 acetylation of RelA/p65".
Nucleic Acids Res 36(5): 1665-80.

Eng, J. K., B. Fischer, J. Grossmann and M. J. Maccoss (2008)
"A fast SEQUEST cross correlation algorithm".
J Proteome Res 7(10): 4598-602.

Feng, J., M. Zhu, M. C. Schaub, P. Gehrig, B. Roschitzki, E. Lucchinetti and M. Zaugg (2008)
"Phosphoproteome analysis of isoflurane-protected heart mitochondria: phosphorylation of adenine nucleotide translocator-1 on Tyr194 regulates mitochondrial function".
Cardiovasc Res.

Foerg, C., K. M. Weller, H. Rechsteiner, H. M. Nielsen, J. Fernandez-Carneado, R. Brunisholz, E. Giralt and H. P. Merkle (2008)
"Metabolic cleavage and translocation efficiency of selected cell penetrating peptides: a comparative study with epithelial cell cultures".
Aaps J 10(2): 349-59.

Kleinert, P., M. Schmid, K. Zurbriggen, O. Speer, M. Schmugge, B. Roschitzki, S. S. Durka, U. Leopold, T. Kuster, C. W. Heizmann, H. Frischknecht and H. Troxler (2008)
"Mass spectrometry: a tool for enhanced detection of hemoglobin variants".
Clin Chem 54(1): 69-76.

Kraljevic Pavelic, S., M. Sedic, K. Hock, S. Vucinic, D. Jurisic, P. Gehrig, M. Scott, R. Schlapbach, T. Cacev, S. Kapitanovic and K. Pavelic (2008)
"An integrated proteomics approach for studying the molecular pathogenesis of Dupuytren's disease".
J Pathol.

Nowik, M., M. R. Lecca, A. Velic, H. Rehrauer, A. W. Brandli and C. A. Wagner (2008)
"Genome-wide gene expression profiling reveals renal genes regulated during metabolic acidosis".
Physiol Genomics 32(3): 322-34.

Okoniewski, M. J. and C. J. Miller (2008)
"Comprehensive analysis of affymetrix exon arrays using BioConductor".
PLoS Comput Biol 4(2): e6.

Pani, E., M. Menigatti, S. Schubert, D. Hess, B. Gerrits, K. H. Klempnauer and S. Ferrari (2008)
"Pin1 interacts with c-Myb in a phosphorylation-dependent manner and regulates its transactivation activity".
Biochim Biophys Acta 1783(6): 1121-8.

Payeli, S. K., R. Latini, C. Gebhard, A. Patrignani, U. Wagner, T. F. Luscher and F. C. Tanner (2008)
"Prothrombotic gene expression profile in vascular smooth muscle cells of human saphenous vein, but not internal mammary artery".
Arterioscler Thromb Vasc Biol 28(4): 705-10.

Pflieger, D., M. A. Junger, M. Muller, O. Rinner, H. Lee, P. M. Gehrig, M. Gstaiger and R. Aebersold (2008)
"Quantitative proteomic analysis of protein complexes: concurrent identification of interactors and their state of phosphorylation".
Mol Cell Proteomics 7(2): 326-46.

Pierce, A., R. D. Unwin, C. A. Evans, S. Griffiths, L. Carney, L. Zhang, E. Jaworska, C. F. Lee, D. Blinco, M. J. Okoniewski, C. J. Miller, D. A. Bitton, E. Spooncer and A. D. Whetton (2008)
"Eight-channel iTRAQ enables comparison of the activity of six leukemogenic tyrosine kinases".
Mol Cell Proteomics 7(5): 853-63.

Pimenova, T., A. Nazabal, B. Roschitzki, J. Seebacher, O. Rinner and R. Zenobi (2008)
"Epitope mapping on bovine prion protein using chemical cross-linking and mass spectrometry".
J Mass Spectrom 43(2): 185-95.

Polymenidou, M., R. Moos, M. Scott, C. Sigurdson, Y. Z. Shi, B. Yajima, I. Hafner-Bratkovic, R. Jerala, S. Hornemann, K. Wuthrich, A. Bellon, M. Vey, G. Garen, M. N. James, N. Kav and A. Aguzzi (2008)
"The POM monoclonals: a comprehensive set of antibodies to non-overlapping prion protein epitopes".
PLoS One 3(12): e3872.

Raschle, T., D. Speziga, W. Kress, C. Moccand, P. Gehrig, N. Amrhein, E. Weber-Ban and T. B. Fitzpatrick (2008)
"Intersubunit crosstalk in pyridoxal 5'-phosphate synthase, co-ordinated by the C-terminus of the synthase subunit".
J Biol Chem.

Rehrauer, H., S. Schonmann, L. Eberl and R. Schlapbach (2008)
"PhyloDetect: a likelihood-based strategy for detecting microorganisms with diagnostic microarrays".
Bioinformatics 24(16): i83-9.

Rohde, B., J. Hans, S. Martens, A. Baumert, P. Hunziker and U. Matern (2008)
"Anthranilate N-methyltransferase, a branch-point enzyme of acridone biosynthesis".
Plant J 53(3): 541-53.

Scheuermann, J., C. E. Dumelin, S. Melkko, Y. Zhang, L. Mannocci, M. Jaggi, J. Sobek and D. Neri (2008)
"DNA-encoded chemical libraries for the discovery of MMP-3 inhibitors".
Bioconjug Chem 19(3): 778-85.

Schönmann, S., A. Loy, C. Wimmersberger, J. Sobek, C. Aquino, P. Vandamme, B. Frey, H. Rehrauer and L. Eberl (2008)
"16S rRNA gene-based phylogenetic microarray for simultaneous identification of members of the genus Burkholderia".
Environmental Microbiology 10.1111/j.1462-2920.2008.01800.x.

Sedic, M., M. Poznic, P. Gehrig, M. Scott, R. Schlapbach, M. Hranjec, G. Karminski-Zamola, K. Pavelic and S. K. Pavelic (2008)
"Differential antiproliferative mechanisms of novel derivative of benzimidazo[1,2-{alpha}]quinoline in colon cancer cells depending on their p53 status".
Mol Cancer Ther 7(7): 2121-32.

Sims, A. H., G. J. Smethurst, Y. Hey, M. J. Okoniewski, S. D. Pepper, A. Howell, C. J. Miller and R. B. Clarke (2008)
"The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets - improving meta-analysis and prediction of prognosis".
BMC Med Genomics 1: 42.

Wimmer, U., E. Ferrari, P. Hunziker and U. Hubscher (2008)
"Control of DNA polymerase lambda stability by phosphorylation and ubiquitination during the cell cycle".
EMBO Rep 9(10): 1027-33.

Yates, T., M. J. Okoniewski and C. J. Miller (2008)
"X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis".
Nucleic Acids Res 36(Database issue): D780-6.

2007

Ahrens, C. H., U. Wagner, H. K. Rehrauer, C. Türker and R. Schlapbach (2007)
"Current challenges and approaches for the synergistic use of systems biology data in the scientific community".
Plant Systems Biology S. Baginsky and F. R. Alisdair. Berlin, Springer Verlag (Birkhäuser). 97: 357.

Baginsky, S., J. Grossmann and W. Gruissem (2007)
"Proteome analysis of chloroplast mRNA processing and degradation".
J Proteome Res 6(2): 809-20.

Bergmuller, E., P. M. Gehrig and W. Gruissem (2007)
"Characterization of Post-Translational Modifications of Histone H2B-Variants Isolated from Arabidopsis thaliana".
J Proteome Res 6(9): 3655-68.

Berthier, C. C., P. R. Wahl, M. Le Hir, H. P. Marti, U. Wagner, H. Rehrauer, R. P. Wuthrich and A. L. Serra (2007)
"Sirolimus Ameliorates the Enhanced Expression of Metalloproteinases in a Rat Model of Autosomal Dominant Polycystic Kidney Disease".
Nephrol Dial Transplant.

Bich, C., M. Scott, A. Panagiotidis, R. J. Wenzel, A. Nazabal and R. Zenobi (2007)
"Characterization of antibody-antigen interactions: Comparison between surface plasmon resonance measurements and high-mass matrix-assisted laser desorption/ionization mass spectrometry".
Anal Biochem.

Bodenmiller, B., J. Malmstrom, B. Gerrits, D. Campbell, H. Lam, A. Schmidt, O. Rinner, L. N. Mueller, P. T. Shannon, P. G. Pedrioli, C. Panse, H. K. Lee, R. Schlapbach and R. Aebersold (2007)
"PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells".
Mol Syst Biol 3: 139.

Bovet, C., A. Wortmann, S. Eiler, F. Granger, M. Ruff, B. Gerrits, D. Moras and R. Zenobi (2007)
"Estrogen receptor-ligand complexes measured by chip-based nanoelectrospray mass spectrometry: an approach for the screening of endocrine disruptors".
Protein Sci 16(5): 938-46.

Braun, O., M. Knipp, S. Chesnov and M. Vasak (2007)
"Specific reactions of S-nitrosothiols with cysteine hydrolases: A comparative study between dimethylargininase-1 and CTP synthetase".
Protein Sci 16(8): 1522-34.

Brunner, E., B. Gerrits, M. Scott, B. Roschitzki and S. Baginsky (2007)
"Differential display and protein quantification".
Plant Systems Biology S. Baginsky and F. R. Alisdair. Berlin, Springer Verlag (Birkhäuser). 97: 357.

Cannavo, E., B. Gerrits, G. Marra, R. Schlapbach and J. Jiricny (2007)
"Characterization of the interactome of the human MutL homologues MLH1, PMS1, and PMS2".
J Biol Chem 282(5): 2976-86.

Drissner, D., G. Kunze, N. Callewaert, P. Gehrig, M. Tamasloukht, T. Boller, G. Felix, N. Amrhein and M. Bucher (2007)
"Lyso-phosphatidylcholine is a signal in the arbuscular mycorrhizal symbiosis".
Science 318(5848): 265-8.

Eckhardt, K., J. Troger, J. Reissmann, D. M. Katschinski, K. F. Wagner, P. Stengel, U. Paasch, P. Hunziker, E. Borter, S. Barth, P. Schlafli, P. Spielmann, D. P. Stiehl, G. Camenisch and R. H. Wenger (2007)
"Male germ cell expression of the PAS domain kinase PASKIN and its novel target eukaryotic translation elongation factor eEF1A1".
Cell Physiol Biochem 20(1-4): 227-40.

El-Andaloussi, N., T. Valovka, M. Toueille, P. O. Hassa, P. Gehrig, M. Covic, U. Hubscher and M. O. Hottiger (2007)
"Methylation of DNA polymerase beta by protein arginine methyltransferase 1 regulates its binding to proliferating cell nuclear antigen".
Faseb J 21(1): 26-34.

Fakitsas, P., G. Adam, D. Daidie, M. X. van Bemmelen, F. Fouladkou, A. Patrignani, U. Wagner, R. Warth, S. M. Camargo, O. Staub and F. Verrey (2007)
"Early Aldosterone-Induced Gene Product Regulates the Epithelial Sodium Channel by Deubiquitylation".
J Am Soc Nephrol.

Grossmann, J., B. Fischer, K. Baerenfaller, J. Owiti, J. M. Buhmann, W. Gruissem and S. Baginsky (2007)
"A workflow to increase the detection rate of proteins from unsequenced organisms in high-throughput proteomics experiments".
Proteomics 7(23): 4245-54.

Gyenesei, A., U. Wagner, S. Barkow-Oesterreicher, E. Stolte and R. Schlapbach (2007)
"Mining co-regulated gene profiles for the detection of functional associations in gene expression data".
Bioinformatics 23(15): 1927-35.

Julius, C., G. Hutter, U. Wagner, H. Seeger, V. Kana, J. Kranich, P. Klohn, C. Weissmann, G. Miele and A. Aguzzi (2007)
"Transcriptional Stability of Cultured Cells upon Prion Infection".
J Mol Biol.

Kleffmann, T., A. von Zychlinski, D. Russenberger, M. Hirsch-Hoffmann, P. Gehrig, W. Gruissem and S. Baginsky (2007)
"Proteome Dynamics during Plastid Differentiation in Rice".
Plant Physiol 143(2): 912-23.

Knipp, M., A. V. Karotki, S. Chesnov, G. Natile, P. J. Sadler, V. Brabec and M. Vasak (2007)
"Reaction of Zn7metallothionein with cis- and trans-[Pt(N-donor)2Cl2] anticancer complexes: trans-Pt(II) complexes retain their N-donor ligands".
J Med Chem 50(17): 4075-86.

König-Ries, B., F. Lehner, R. Malaka and C. Türker, Eds. (2007)
"MMS 2007 - Mobilität und mobile Informationssysteme".
Lecture Notes in Informatics. Bonn, Gesellschaft für Informatik.

Maillet, I., P. Berndt, C. Malo, S. Rodriguez, R. A. Brunisholz, Z. Pragai, S. Arnold, H. Langen and M. Wyss (2007)
"From the genome sequence to the proteome and back: evaluation of E. coli genome annotation with a 2-D gel-based proteomics approach".
Proteomics 7(7): 1097-106.

Mathur, S., M. Badertscher, M. Scott and R. Zenobi (2007)
"Critical evaluation of mass spectrometric measurement of dissociation constants: accuracy and cross-validation against surface plasmon resonance and circular dichroism for the calmodulin-melittin system".
Phys Chem Chem Phys 9(47): 6187-98.

Matyas, G., S. Alonso, A. Patrignani, M. Marti, E. Arnold, I. Magyar, C. Henggeler, T. Carrel, B. Steinmann and W. Berger (2007)
"Large genomic fibrillin-1 (FBN1) gene deletions provide evidence for true haploinsufficiency in Marfan syndrome".
Hum Genet 122(1): 23-32.

Mayer, D., K. Molawi, L. Martinez-Sobrido, A. Ghanem, S. Thomas, S. Baginsky, J. Grossmann, A. Garcia-Sastre and M. Schwemmle (2007)
"Identification of cellular interaction partners of the influenza virus ribonucleoprotein complex and polymerase complex using proteomic-based approaches".
J Proteome Res 6(2): 672-82.

Munton, R. P., R. Tweedie-Cullen, M. Livingstone-Zatchej, F. Weinandy, M. Waidelich, D. Longo, P. Gehrig, F. Potthast, D. Rutishauser, B. Gerrits, C. Panse, R. Schlapbach and I. M. Mansuy (2007)
"Qualitative and Quantitative Analyses of Protein Phosphorylation in Naive and Stimulated Mouse Synaptosomal Preparations".
Mol Cell Proteomics 6(2): 283-293.

Pessi, G., C. H. Ahrens, H. Rehrauer, A. Lindemann, F. Hauser, H. M. Fischer and H. Hennecke (2007)
"Genome-wide transcript analysis of Bradyrhizobium japonicum bacteroids in soybean root nodules".
Mol Plant Microbe Interact 20(11): 1353-63.

Pflieger, D., M. Junger, M. Muller, O. Rinner, H. Lee, P. Gehrig, M. Gstaiger and R. Aebersold (2007)
"Quantitative proteomic analysis of protein complexes: Concurrent identification of interactors and their state of phosphorylation".
Mol Cell Proteomics.

Pogoryelov, D., C. Reichen, A. L. Klyszejko, R. Brunisholz, D. J. Muller, P. Dimroth and T. Meier (2007)
"The oligomeric state of c rings from cyanobacterial F-ATP synthases varies from 13 to 15".
J Bacteriol 189(16): 5895-902.

Potthast, F., B. Gerrits, J. Hakkinen, D. Rutishauser, C. H. Ahrens, B. Roschitzki, K. Baerenfaller, R. P. Munton, P. Walther, P. Gehrig, P. Seif, P. H. Seeberger and R. Schlapbach (2007)
"The Mass Distance Fingerprint: a statistical framework for de novo detection of predominant modifications using high-accuracy mass spectrometry".
J Chromatogr B Analyt Technol Biomed Life Sci 854(1-2): 173-82.

Raschle, T., D. Arigoni, R. Brunisholz, H. Rechsteiner, N. Amrhein and T. B. Fitzpatrick (2007)
"Reaction mechanism of pyridoxal 5'-phosphate synthase. Detection of an enzyme-bound chromophoric intermediate".
J Biol Chem 282(9): 6098-105.

Rehrauer, H., S. Zoller and R. Schlapbach (2007)
"MAGMA: analysis of two-channel microarrays made easy".
Nucleic Acids Res 35(Web Server issue): W86-90.

Reinhardt, A., C. Emmenegger, B. Gerrits, C. Panse, J. Dommen, U. Baltensperger, R. Zenobi and M. Kalberer (2007)
"Ultrahigh mass resolution and accurate mass measurements as a tool to characterize oligomers in secondary organic aerosols".
Anal Chem 79(11): 4074-82.

Roos, F. F., R. Jacob, J. Grossmann, B. Fischer, J. M. Buhmann, W. Gruissem, S. Baginsky and P. Widmayer (2007)
"PepSplice: cache-efficient search algorithms for comprehensive identification of tandem mass spectra".
Bioinformatics 23(22): 3016-23.

Sabates-Bellver, J., L. G. Van der Flier, M. de Palo, E. Cattaneo, C. Maake, H. Rehrauer, E. Laczko, M. A. Kurowski, J. M. Bujnicki, M. Menigatti, J. Luz, T. V. Ranalli, V. Gomes, A. Pastorelli, R. Faggiani, M. Anti, J. Jiricny, H. Clevers and G. Marra (2007)
"Transcriptome profile of human colorectal adenomas".
Mol Cancer Res 5(12): 1263-75.

Schlosser, E., C. Otero, C. Wuensch, B. Kessler, M. Edelmann, R. Brunisholz, I. Drexler, D. F. Legler and M. Groettrup (2007)
"A novel cytosolic class I antigen-processing pathway for endoplasmic-reticulum-targeted proteins".
EMBO Rep 8(10): 945-51.

Sobek, J., C. Aquino and R. Schlapbach (2007)
"Optimization workflow for the processing of high quality glass-based microarrays. Application in DNA, peptide, antibody, and carbohydrate microarraying".
Microarrays. J. B. Rampal. Totowa, N.J., Humana. 2.

Sobek, J., C. Aquino and R. Schlapbach (2007)
"Quality considerations and selection of surface chemistry for glass-based DNA, peptide, antibody, carbohydrate, and small molecule microarrays".
Microarrays. J. B. Rampal. Totowa, N.J., Humana. 2.

Sobek, J., C. Aquino and R. Schlapbach (2007)
"Processing protocols for high qualiity glass.based microarrays. Application in DNA, peptide, antibody, and carbohydrate microarraying".
Microarrays. J. B. Rampal. Totowa, N.J., Humana. 2.

Tuerk, R. D., R. F. Thali, Y. Auchli, H. Rechsteiner, R. A. Brunisholz, U. Schlattner, T. Wallimann and D. Neumann (2007)
"New candidate targets of AMP-activated protein kinase in murine brain revealed by a novel multidimensional substrate-screen for protein kinases".
J Proteome Res 6(8): 3266-77.

Türker, C. (2007)
"Objektrelationale Datenbanken".
Taschenbuch Datenbanken. T. Kudrass. Leipzig, Hanser: 338-360.

Türker, C. (2007)
"Die Datenbanksprache SQL".
Taschenbuch Datenbanken. T. Kudrass. Leipzig, Hanser: 106-152.

2006

Bernasconi, M., C. Berger, J. A. Sigrist, A. Bonanomi, J. Sobek, F. K. Niggli and D. Nadal (2006)
"Quantitative profiling of housekeeping and Epstein-Barr virus gene transcription in Burkitt lymphoma cell lines using an oligonucleotide microarray".
Virol J 3: 43.

Cai, H., P. Gehrig, T. M. Scott, R. Zimmermann, R. Schlapbach and A. H. Zisch (2006)
"MnSOD marks cord blood late outgrowth endothelial cells and accompanies robust resistance to oxidative stress".
Biochem Biophys Res Commun 350(2): 364-9.

Cannavo, E., B. Gerrits, G. Marra, R. Schlapbach and J. Jiricny (2006)
"Characterisation of the interactome of the human MUTL homologues MLH1, PMS1 and PMS2".
J Biol Chem.

David, D. C., L. M. Ittner, P. Gehrig, D. Nergenau, C. Shepherd, G. Halliday and J. Gotz (2006)
"Beta-amyloid treatment of two complementary P301L tau-expressing Alzheimer's disease models reveals similar deregulated cellular processes".
Proteomics 6(24): 6566-77.

Devi, V. S., C. B. Sprecher, P. Hunziker, P. R. Mittl, H. R. Bosshard and I. Jelesarov (2006)
"Disulfide formation and stability of a cysteine-rich repeat protein from Helicobacter pylori".
Biochemistry 45(6): 1599-607.

Diet, A., B. Link, G. J. Seifert, B. Schellenberg, U. Wagner, M. Pauly, W. D. Reiter and C. Ringli (2006)
"The Arabidopsis root hair cell wall formation mutant lrx1 is suppressed by mutations in the RHM1 gene encoding a UDP-L-rhamnose synthase".
Plant Cell 18(7): 1630-41.

Eggenschwiler, J., A. Patrignani, U. Wagner, H. Rehrauer, R. Schlapbach, L. Rist, M. H. Ramos and A. Viviani (2006)
"Gene expression profiles of different breast cancer cells compared with their responsiveness to fermented mistletoe (Viscum album L.) extracts Iscador from oak (Quercus), pine (Pinus), white fir (Abies) and apple tree (Malus) in vitro".
Arzneimittelforschung 56(6A): 483-96.

El-Andaloussi, N., T. Valovka, M. Toueille, R. Steinacher, F. Focke, P. Gehrig, M. Covic, P. O. Hassa, P. Schar, U. Hubscher and M. O. Hottiger (2006)
"Arginine methylation regulates DNA polymerase beta".
Mol Cell 22(1): 51-62.

Fischer, B., J. Grossmann, V. Roth, W. Gruissem, S. Baginsky and J. M. Buhmann (2006)
"Semi-supervised LC/MS alignment for differential proteomics".
Bioinformatics 22(14): e132-40.

Gyenesei, A., R. Schlapbach, E. Stolte and U. Wagner (2006)
"Frequent pattern discovery without binarization: Mining attribute profiles".
Knowledge Discovery in Databases: Pkdd 2006, Proceedings 4213: 528-535.

Hauser, F., A. Lindemann, S. Vuilleumier, A. Patrignani, R. Schlapbach, H. M. Fischer and H. Hennecke (2006)
"Design and validation of a partial-genome microarray for transcriptional profiling of the Bradyrhizobium japonicum symbiotic gene region".
Mol Genet Genomics 275(1): 55-67.

Hoerstrup, S. P., I. Cummings Mrcs, M. Lachat, F. J. Schoen, R. Jenni, S. Leschka, S. Neuenschwander, D. Schmidt, A. Mol, C. Gunter, M. Gossi, M. Genoni and G. Zund (2006)
"Functional growth in tissue-engineered living, vascular grafts: follow-up at 100 weeks in a large animal model".
Circulation 114(1 Suppl): I159-66.

Kraljevic, S., M. Sedic, M. Scott, P. Gehrig, R. Schlapbach and K. Pavelic (2006)
"Casting light on molecular events underlying anti-cancer drug treatment: What can be seen from the proteomics point of view?"
Cancer Treat Rev.

Laczko, E. (2006)
"Method for predicting biological, biochemical, biophysical, or pharmacological characteristics of a substance". 23912 EP, F. Hoffmann-La Roche Ltd., Basel, Switzerland.

Murtaza, I., G. Marra, R. Schlapbach, A. Patrignani, M. Kunzli, U. Wagner, J. Sabates and A. Dutt (2006)
"A preliminary investigation demonstrating the effect of quercetin on the expression of genes related to cell-cycle arrest, apoptosis and xenobiotic metabolism in human CO115 colon-adenocarcinoma cells using DNA microarray".
Biotechnol Appl Biochem 45(Pt 1): 29-36.

Nesvizhskii, A. I., F. F. Roos, J. Grossmann, M. Vogelzang, J. S. Eddes, W. Gruissem, S. Baginsky and R. Aebersold (2006)
"Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides".
Mol Cell Proteomics 5(4): 652-70.

Ramadan, T., S. M. Camargo, V. Summa, P. Hunziker, S. Chesnov, K. M. Pos and F. Verrey (2006)
"Basolateral aromatic amino acid transporter TAT1 (Slc16a10) functions as an efflux pathway".
Journal of Cellular Physiology 206(3): 771-9.

Riedel, K., P. Carranza, P. Gehrig, F. Potthast and L. Eberl (2006)
"Towards the proteome of Burkholderia cenocepacia H111: setting up a 2-DE reference map".
Proteomics 6(1): 207-16.

Schmidt, D., A. Mol, C. Breymann, J. Achermann, B. Odermatt, M. Gossi, S. Neuenschwander, R. Pretre, M. Genoni, G. Zund and S. P. Hoerstrup (2006)
"Living autologous heart valves engineered from human prenatally harvested progenitors".
Circulation 114(1 Suppl): I125-31.

Schmidt, D., A. Mol, B. Odermatt, S. Neuenschwander, C. Breymann, M. Gossi, M. Genoni, G. Zund and S. P. Hoerstrup (2006)
"Engineering of Biologically Active Living Heart Valve Leaflets Using Human Umbilical Cord-Derived Progenitor Cells".
Tissue Eng.

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.

Sobek, J., K. Bartscherer, A. Jacob, J. D. Hoheisel and P. Angenendt (2006)
"Microarray technology as a universal tool for high-throughput analysis of biological systems".
Comb Chem High Throughput Screen 9(5): 365-80.

Zimmermann, P., B. Schildknecht, D. Craigon, M. Garcia-Hernandez, W. Gruissem, S. May, G. Mukherjee, H. Parkinson, S. Rhee, U. Wagner and L. Hennig (2006)
"MIAME/Plant - adding value to plant microarrray experiments".
Plant Methods 2: 1.

2005

Dallinger, R., M. Chabicovsky, E. Hodl, C. Prem, P. Hunziker and C. Manzl (2005)
"Copper in Helix pomatia (Gastropoda) is regulated by one single cell type: differently responsive metal pools in rhogocytes".
American Journal of Physiology - Regulatory Integrative & Comparative Physiology 289(4): R1185-95.

Fischer, B., V. Roth, F. Roos, J. Grossmann, S. Baginsky, P. Widmayer, W. Gruissem and J. M. Buhmann (2005)
"NovoHMM: a hidden Markov model for de novo peptide sequencing".
Anal Chem 77(22): 7265-73.

Gressmann, H., B. Linz, R. Ghai, K. P. Pleissner, R. Schlapbach, Y. Yamaoka, C. Kraft, S. Suerbaum, T. F. Meyer and M. Achtman (2005)
"Gain and loss of multiple genes during the evolution of Helicobacter pylori".
PLoS Genet 1(4): e43.

Grossmann, J., F. F. Roos, M. Cieliebak, Z. Liptak, L. K. Mathis, M. Muller, W. Gruissem and S. Baginsky (2005)
"AUDENS: a tool for automated peptide de novo sequencing".
J Proteome Res 4(5): 1768-74.

Lecca, M. R., U. Wagner, A. Patrignani, E. G. Berger and T. Hennet (2005)
"Genome-wide analysis of the unfolded protein response in fibroblasts from congenital disorders of glycosylation type-I patients".
Faseb J 19(2): 240-2.

Lourdel, S., J. Loffing, G. Favre, M. Paulais, A. Nissant, P. Fakitsas, C. Creminon, E. Feraille, F. Verrey, J. Teulon, A. Doucet and G. Deschenes (2005)
"Hyperaldosteronemia and activation of the epithelial sodium channel are not required for sodium retention in puromycin-induced nephrosis".
J Am Soc Nephrol 16(12): 3642-50.

Melkko, S., J. Sobek, G. Guarda, J. Scheuermann, C. E. Dumelin and D. Neri (2005)
"Encoded self-assembling chemical libraries".
Chimia 59(11): 798-802.

Mittag, D., S. Vieths, L. Vogel, D. Wagner-Loew, A. Starke, P. Hunziker, W. M. Becker and B. K. Ballmer-Weber (2005)
"Birch pollen-related food allergy to legumes: identification and characterization of the Bet v 1 homologue in mungbean (Vigna radiata), Vig r 1".
Clinical & Experimental Allergy 35(8): 1049-55.

Potthast, F., J. Ocenasek, D. Rutishauser, M. Pelikan and R. Schlapbach (2005)
"Database independent detection of isotopically labeled MS/MS spectrum peptide pairs".
J Chromatogr B Analyt Technol Biomed Life Sci 817(2): 225-30.

Scheurer, S. B., J. N. Rybak, C. Roesli, R. A. Brunisholz, F. Potthast, R. Schlapbach, D. Neri and G. Elia (2005)
"Identification and relative quantification of membrane proteins by surface biotinylation and two-dimensional peptide mapping".
Proteomics 5(11): 2718-28.

Schrimpf, S. P., V. Meskenaite, E. Brunner, D. Rutishauser, P. Walther, J. Eng, R. Aebersold and P. Sonderegger (2005)
"Proteomic analysis of synaptosomes using isotope-coded affinity tags and mass spectrometry".
Proteomics 5(10): 2531-41.

2004

Benke, D., P. Fakitsas, C. Roggenmoser, C. Michel, U. Rudolph and H. Mohler (2004)
"Analysis of the presence and abundance of GABAA receptors containing two different types of alpha subunits in murine brain using point-mutated alpha subunits".
J Biol Chem 279(42): 43654-60.

Gehrig, P. M., P. E. Hunziker, S. Zahariev and S. Pongor (2004)
"Fragmentation pathways of N(G)-methylated and unmodified arginine residues in peptides studied by ESI-MS/MS and MALDI-MS".
J Am Soc Mass Spectrom 15(2): 142-9.

Niehus, E., H. Gressmann, F. Ye, R. Schlapbach, M. Dehio, C. Dehio, A. Stack, T. F. Meyer, S. Suerbaum and C. Josenhans (2004)
"Genome-wide analysis of transcriptional hierarchy and feedback regulation in the flagellar system of Helicobacter pylori".
Mol Microbiol 52(4): 947-61.

Pellegrini, A., A. J. Hulsmeier, P. Hunziker and U. Thomas (2004)
"Proteolytic fragments of ovalbumin display antimicrobial activity".
Biochimica Et Biophysica Acta-General Subjects 1672(2): 76-85.

Rozhkova, A., C. U. Stirnimann, P. Frei, U. Grauschopf, R. Brunisholz, M. G. Grutter, G. Capitani and R. Glockshuber (2004)
"Structural basis and kinetics of inter- and intramolecular disulfide exchange in the redox catalyst DsbD".
Embo J 23(8): 1709-19.

Sartori, A. A., G. M. Lingaraju, P. Hunziker, F. K. Winkler and J. Jiricny (2004)
"Pa-AGOG, the founding member of a new family of archaeal 8-oxoguanine DNA-glycosylases".
Nucleic Acids Research 32(22): 6531-9.

2003

Angenendt, P., J. Glokler, J. Sobek, H. Lehrach and D. J. Cahill (2003)
"Next generation of protein microarray support materials: evaluation for protein and antibody microarray applications".
J Chromatogr A 1009(1-2): 97-104.

Paglinawan, R., U. Malipiero, R. Schlapbach, K. Frei, W. Reith and A. Fontana (2003)
"TGFbeta directs gene expression of activated microglia to an anti-inflammatory phenotype strongly focusing on chemokine genes and cell migratory genes".
Glia 44(3): 219-31.