Publications

Waanders, L. F. Hanke, S. Mann, M. (2007). Top-down quantitation and characterization of SILAC-labeled proteins. J Am Soc Mass Spectrom. 18:2058-64..
abstract
 [WP07]


Visser, A. Van Zeveren, A. M. Meyvis, Y. Peelaers, I. Van den Broeck, W. Gevaert, K. Vercruysse, J. Claerebout, E. Geldhof, P. (2007). Gender-enriched transcription of activation associated secreted proteins in Ostertagia ostertagi. Int J Parasitol. Sep.20..
abstract
 [WP02]


Saverwyns, H. Visser, A. Nisbet, A. J. Peelaers, I. Gevaert, K. Vercruysse, J. Claerebout, E. Geldhof, P. (2007). Identification and characterization of a novel specific secreted protein family for selected members of the subfamily Ostertagiinae (Nematoda). Parasitology. 135:63-70..
abstract
 [WP02]


Orchard, S. Salwinski, L. Kerrien, S. Montecchi-Palazzi, L. Oesterheld, M. Stumpflen, V. Ceol, A. Chatr-aryamontri, A. Armstrong, J. Woollard, P. Salama, J. J. Moore, S. Wojcik, J. Bader, G. D. Vidal, M. Cusick, M. E. Gerstein, M. Gavin, A. C. Superti-Furga, G. Greenblatt, J. Bader, J. Uetz, P. Tyers, M. Legrain, P. Fields, S. Mulder, N. Gilson, M. Niepmann, M. Burgoon, L. De Las Rivas, J. Prieto, C. Perreau, V. M. Hogue, C. Mewes, H. W. Apweiler, R. Xenarios, I. Eisenberg, D. Cesareni, G. Hermjakob, H. (2007). The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol. 25:894-8..
abstract
 [WP12]


Millington, M. Grindlay, G. J. Altenbach, K. Neely, R. K. Kolch, W. Bencina, M. Read, N. D. Jones, A. C. Dryden, D. T. Magennis, S. W. (2007). High-precision FLIM-FRET in fixed and living cells reveals heterogeneity in a simple CFP-YFP fusion protein. Biophys Chem. 149:239-45..
abstract
 [WP03]


Meyvis, Y. Geldhof, P. Gevaert, K. Timmerman, E. Vercruysse, J. Claerebout, E. (2007). Vaccination against Ostertagia ostertagi with subfractions of the protective ES-thiol fraction. Vet Parasitol. 149:239-245..
abstract
 [WP02]


Maeder, C. I. Hink, M. A. Kinkhabwala, A. Mayr, R. Bastiaens, P. I. Knop, M. (2007). Spatial regulation of Fus3 MAP kinase activity through a reaction-diffusion mechanism in yeast pheromone signalling. Nat Cell Biol. 9:1319-26..
abstract
 [WP03]


Macek, B. Gnad, F. Soufi, B. Kumar, C. Olsen, J. V. Mijakovic, I. Mann, M. (2007). Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation. Mol Cell Proteomics 2007 Oct.15..
abstract
 [WP05]


Konstantinidis, K. Tebbe, A. Klein, C. Scheffer, B. Aivaliotis, M. Bisle, B. Falb, M. Pfeiffer, F. Siedler, F. Oesterhelt, D. (2007). Genome-wide proteomics of Natronomonas pharaonis. J Proteome Res. 6:185-193..
abstract
 [WP02]


Juul, N. Timmerman, E. Gevaert, K. Christiansen, G. Birkelund, S. (2007). Proteolytic cleavage of the Chlamydia pneumoniae major outer membrane protein in the absence of Pmp10. Proteomics. 7:4477-87..
abstract
 [WP02]


Gnad, F. Ren, S. Cox, J. Olsen, J. V. Macek, B. Oroshi, M. Mann, M. (2007). PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. Genome Biol. 8: R250..
abstract
 [WP05]


Gloeckner, C. J. Boldt, K. Schumacher, A. Roepman, R. Ueffing, M. (2007). A novel tandem affinity purification strategy for the efficient isolation and characterisation of native protein complexes. Proteomics.7:4228-34..
abstract
 [WP11]


Ghesquiere, B. Buyl, L. Demol, H. Van Damme, J. Staes, A. Timmerman, E. Vandekerckhove, J. Gevaert, K. (2007). A new approach for mapping sialylated N-glycosites in serum proteomes. J Proteome Res. 6:4304-12..
abstract
 [WP02]


Konstantinidis K, Tebbe A, Klein C, Scheffer B, Aivaliotis M, Bisle B, Falb M, Pfeiffer F, Siedler F, Oesterhelt D (2007). Genome-wide proteomics of Natronomonas pharaonis. J Proteome Res. Jan;6(1):185-93.
abstract
 [WP02]


Olsen JV, Macek B, Lange O, Makarov A, Horning S, Mann M (2007). Higher-energy C-trap dissociation for peptide modification analysis. Nat Methods. Sep;4(9):709-12..
abstract
 [WP11]


Lakshmipathy SK, Tomic S, Kaiser CM, Chang HC, Genevaux P, Georgopoulos C, Barral JM, Johnson AE, Hartl FU, Etchells SA. (2007). Identification of nascent chain interaction sites on trigger factor. J Biol Chem. Apr 20;282(16):12186-93.
abstract
 [WP10]


Bernaschi M, Castiglione F, Ferranti A, Gavrila C, Tinti M, Cesareni G (2007). ProtNet: a tool for stochastic simulations of protein interaction networks dynamics. BMC Bioinformatics.Mar 8;8 Suppl 1:S4.
abstract
 [WP13]


Kiemer L, Costa S, Ueffing M, Cesareni G. (2007). WI-PHI: a weighted yeast interactome enriched for direct physical interactions. Proteomics. Mar;7(6):932-43.
abstract
 [WP13]


Chatr-aryamontri A, Ceol A, Palazzi LM, Nardelli G, Schneider MV, Castagnoli L, Cesareni G (2007). MINT: the Molecular INTeraction database. Nucleic Acids Res. Jan;35(Database issue):D572-4.
abstract
 [WP12]


Ceol A, Chatr-aryamontri A, Santonico E, Sacco R, Castagnoli L, Cesareni G. (2007). DOMINO: a database of domain-peptide interactions. Nucleic Acids Res. Jan;35(Database issue):D557-60.
abstract
 [WP12]


Matallanas D, Romano D, Yee K, Meissl K, Kucerova L, Piazzolla D, Baccarini M, Vass JK, Kolch W, O'neill E (2007). RASSF1A elicits apoptosis through an MST2 pathway directing proapoptotic transcription by the p73 tumor suppressor protein. Mol Cell. Sep 21;27(6): 962-75.
abstract
 [WP11]


Klein C, Aivaliotis M, Olsen JV, Falb M, Besir H, Scheffer B, Bisle B, Tebbe A, Konstantinidis K, Siedler F, Pfeiffer F, Mann M, Oesterhelt D. (2007). The low molecular weight proteome of Halobacterium salinarum.. J Proteome Res. Apr;6(4):1510-8.
abstract
 [WP11]


den Hollander AI, Koenekoop RK, Mohamed MD, Arts HH, Boldt K, Towns KV, Sedmak T, Beer M, Nagel-Wolfrum K, McKibbin M, Dharmaraj S, Lopez I, Ivings L, Williams GA, Springell K, Woods CG, Jafri H, Rashid Y, Strom TM, van der Zwaag B, Gosens I, Kersten FF, van Wijk E, Veltman JA, Zonneveld MN, van Beersum SE, Maumenee IH, Wolfrum U, Cheetham ME, Ueffing M, Cremers FP, Inglehearn CF, Roepman R (2007). Mutations in LCA5, encoding the ciliary protein lebercilin, cause Leber congenital amaurosis. Nat Genet. Jul;39(7):889-95.
abstract
 [WP11]


Kiemer, L. Cesareni, G. (2007). Comparative interactomics: comparing apples and pears?. Trends Biotechnol. 25:448-454..
abstract
 [WP06]


Kiel C, Serrano L. (2007). Prediction of Ras-effector interactions using position energy matrices. Bioinformatics. Sep 1;23(17):2226-30.
abstract
 [WP08]


Beltrao P, Kiel C, Serrano L (2007). Structures in systems biology. Curr Opin Struct Biol. Jun;17(3):378-84.
abstract
 [WP08]


Kiel C, Foglierini M, Kuemmerer N, Beltrao P, Serrano L (2007). A genome-wide Ras-effector interaction network. J Mol Biol. Jul 27;370(5):1020-32.
abstract
 [WP08]


Cox J, Mann M (2007). Is proteomics the new genomics?. Cell. Aug 10;130(3):.
abstract
 [WP07]


Omerovic J, Santangelo L, Puggioni EM, Marrocco J, Dall'Armi C, Palumbo C, Belleudi F, Di Marcotullio L, Frati L, Torrisi MR, Cesareni G, Gulino A, Alimandi M. (2007). The E3 ligase Aip4/Itch ubiquitinates and targets ErbB-4 for degradation. FASEB J. Sep;21(11):2849-62.
abstract
 [WP06]


Kiemer L, Costa S, Ueffing M, Cesareni G (2007). WI-PHI: a weighted yeast interactome enriched for direct physical interactions. Proteomics. Mar;7(6):932-43.
abstract
 [WP06]


Miller ML, Hanke S, Hinsby AM, Friis C, Brunak S, Mann M, Blom N (2007). Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2. Mol Cell Proteomics. Oct 15.
abstract
 [WP05]


Ingrell CR, Miller ML, Jensen ON, Blom N (2007). NetPhosYeast: prediction of protein phosphorylation sites in yeast. Bioinformatics. Apr 1;23(7):895-7.
abstract
 [WP05]


Emanuelsson O, Brunak S, von Heijne G, Nielsen H (2007). Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc. 2(4):953-71.
abstract
 [WP05]


Sun N, Beck F, Knispel RW, Siedler F, Scheffer B, Nickell S, Baumeister W, Nagy I (2007). Proteomics analysis of Thermoplasma acidophilum with a focus on protein complexes. Mol Cell Proteomics. Mar;6(3):492-502.
abstract
 [WP04]


Santos SD, Verveer PJ, Bastiaens PI (2007). Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate. Nat Cell Biol. Mar;9(3):324-30.
abstract
 [WP03]


Yudushkin IA, Schleifenbaum A, Kinkhabwala A, Neel BG, Schultz C, Bastiaens PI (2007). Live-Cell Imaging of Enzyme-Substrate Interaction Reveals Spatial Regulation. Science 315, 115 .
abstract
 [WP03]


Flikka, K. Meukens, J. Helsens, K. Vandekerckhove, J. Eidhammer, I. Gevaert, K. Martens, L. (2007). Implementation and application of a versatile clustering tool for tandem mass spectrometry data. Proteomics, 7, 3245-58.
abstract
 [WP02]


del Rosario, R. C. Staudinger, W. F. Streif, S. Pfeiffer, F. Mendoza, E. Oesterhelt, D. (2007). Modelling the CheY(D10K,Yl00W) Halobacterium salinarum mutant: sensitivity analysis allows choice of parameter to be modified in the phototaxis model. IET Syst Biol, 1, 207-21.
abstract
 [WP13]


Gevaert K, Van Damme P, Ghesquière B, Impens F, Martens L, Helsens K, Vandekerckhove J. (2007). A la carte proteomics with an emphasis on gel-free techniques. Proteomics. Aug;7(16):2698-718.
abstract
 [WP02]


Staes A, Timmerman E, Van Damme J, Helsens K, Vandekerckhove J, Vollmer M, Gevaert K (2007). Assessing a novel microfluidic interface for shotgun proteome analyses. J Sep Sci. Jul;30(10):1468-76.
abstract
 [WP02]


Denecker G, Hoste E, Gilbert B, Hochepied T, Ovaere P, Lippens S, Van den Broecke C, Van Damme P, D'Herde K, Hachem JP, Borgonie G, Presland RB, Schoonjans L, Libert C, Vandekerckhove J, Gevaert K, Vandenabeele P, Declercq W (2007). Caspase-14 protects against epidermal UVB photodamage and water loss. Nat Cell Biol. Jun;9(6):666-74. Epub 2007 May 21.
abstract
 [WP02]


Aivaliotis M, Gevaert K, Falb M, Tebbe A, Konstantinidis K, Bisle B, Klein C, Martens L, Staes A, Timmerman E, Van Damme J, Siedler F, Pfeiffer F, Vandekerckhove J, Oesterhelt D (2007). Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis. J. Proteome Res. 6, 2195-2204.
abstract
 [WP02]


Sandra K, Verleysen K, Labeur C, Vanneste L, D’Hondt F, Thomas G, Kas K, Gevaert K, Vandekerckhove J, Sandra P (2007). Combination of COFRADIC and high temperature - extended column length conventional liquid chromatography: A very efficient way to tackle complex protein samples. J. Sep. Sci. 30, 658-668.
abstract
 [WP02]


Hosking CR, Ulloa F, Hogan C, Ferber E, Figueroa A, Gevaert K, Birchmeier W, Briscoe J, Fujita Y (2007). The transcriptional repressor Glis2 is a novel binding partner for p120 catenin. Mol. Biol. Cell 18, 1918-1927.
abstract
 [WP02]


Stucke VM, Timmerman E, Vandekerckhove J, Gevaert K, Hall A (2007). Stucke VM, Timmerman E, Vandekerckhove J, Gevaert K, Hall A. Mol. Biol. Cell 18, 1744-1755.
abstract
 [WP02]


Vande Walle L, Van Damme P, Lamkanfi M, Parthoens E, Saelens X, Vandekerckhove J, Gevaert K, Vandenabeele P (2007). Proteome-wide identification of HtrA2/Omi substrates. J. Proteome Res. 6, 1006-1015.
abstract
 [WP02]


Lavens D, Ulrichts P, Catteeuw D, Gevaert K, Vandekerckhove J, Peelman F, Eyckerman S, Tavernier J (2007). The C-terminus of CIS defines its interaction pattern. Biochem. J. 401, 257-26.
abstract
 [WP02]


Beltrao, P. Kiel, C. Serrano, L. (2007). Structures in systems biology. Curr Opin Struct Biol, 17, 378-84.
abstract
 [WP08]


Kiel, C., and Serrano, L. (2006). The ubiquitin domain superfold: structure-based sequence alignments and characterization of binding epitopes. J Mol Biol 355, 821-844..
abstract
 [WP08]


Vercauteren, I., De Maere, V., Vercruysse, J., Stevens, M., Gevaert, K., and Claerebout, E. (2006). A small heat shock protein of Ostertagia ostertagi: stage-specific expression, heat inducibility, and protection trial. J Parasitol 92, 1244-1250..
abstract
 [WP02]


Rushworth, L. K., Hindley, A. D., O'Neill, E., and Kolch, W. (2006). Regulation and role of Raf-1/B-Raf heterodimerization.. Mol Cell Biol 26, 2262-2272..
abstract
 [WP11]


von Kriegsheim, A., Pitt, A., Grindlay, G. J., Kolch, W., and Dhillon, A. S. (2006). Regulation of the Raf-MEK-ERK pathway by protein phosphatase. 5. Nat Cell Biol 8, 1011-1016..
abstract
 [WP]


Kaiser, C. M., Chang, H. C., Agashe, V. R., Lakshmipathy, S. K., Etchells, S. A., Hayer-Hartl, M., Hartl, F. U., and Barral, J. M. (2006). Real-time observation of trigger factor function on translating ribosomes.. Nature 444, 455-460..
abstract
 [WP10]


Ghesquiere, B., Van Damme, J., Martens, L., Vandekerckhove, J., and Gevaert, K. (2006). Proteome-wide characterization of N-glycosylation events by diagonal chromatography.. J Proteome Res 5, 2438-2447..
abstract
 [WP02]


Gevaert, K., Van Damme, P., Ghesquiere, B., and Vandekerckhove, J. (2006). Protein processing and other modifications analyzed by diagonal peptide chromatography. Biochim Biophys Acta 1764, 1801-1810..
abstract
 [WP02]


Jones, P., Cote, R. G., Martens, L., Quinn, A. F., Taylor, C. F., Derache, W., Hermjakob, H., and Apweiler, R. (2006). PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res 34, D659-663.
abstract
 [WP02]


Fernandez-Ballester, G., and Serrano, L. (2006). Prediction of protein-protein interaction based on structure. Methods Mol Biol 340, 207-234..
abstract
 [WP08]


Reidegeld, K. A., Muller, M., Stephan, C., Bluggel, M., Hamacher, M., Martens, L., Korting, G., Chamrad, D. C., Parkinson, D., Apweiler, R., et al. (2006). The power of cooperative investigation: summary and comparison of the HUPO Brain Proteome Project pilot study results. Proteomics 6, 4997-5014..
abstract
 [WP02]


Gloeckner, C. J., Kinkl, N., Schumacher, A., Braun, R. J., O'Neill, E., Meitinger, T., Kolch, W., Prokisch, H., and Ueffing, M. (2006). The Parkinson disease causing LRRK2 mutation I2020T is associated with increased kinase activity.. Hum Mol Genet 15, 223-232..
abstract
 [WP11]


Dublanche, Y., Michalodimitrakis, K., Kummerer, N., Foglierini, M., and Serrano, L. (2006). Noise in transcription negative feedback loops: simulation and experimental analysis.. Mol Syst Biol 2, 41..
abstract
 [WP13]


Hanoulle, X., Van Damme, J., Staes, A., Martens, L., Goethals, M., Vandekerckhove, J., and Gevaert, K. (2006). A new functional, chemical proteomics technology to identify purine nucleotide binding sites in complex proteomes.. J Proteome Res 5, 3438-3445..
abstract
 [WP02]


Yudushkin, I. A., Schleifenbaum, A., Kinkhabwala, A., Neel, B. G., Schultz, C., and Bastiaens, P. I. (2007). Live-cell imaging of enzyme-substrate interaction reveals spatial regulation of PTP1B.. Science 315, 115-119..
abstract
 [WP03]


Ghesquiere, B., Goethals, M., Van Damme, J., Staes, A., Timmerman, E., Vandekerckhove, J., and Gevaert, K. (2006). Improved tandem mass spectrometric characterization of 3-nitrotyrosine sites in peptides. Rapid Commun Mass Spectrom 20, 2885-2893..
abstract
 [WP02]


Svenstrup, H. F., Jensen, J. S., Gevaert, K., Birkelund, S., and Christiansen, G. (2006). Identification and characterization of immunogenic proteins of mycoplasma genitalium.. Clin Vaccine Immunol 13, 913-922..
abstract
 [WP02]


Hamacher, M., Stephan, C., Bluggel, M., Chamrad, D., Korting, G., Martens, L., Muller, M., Hermjakob, H., Parkinson, D., Dowsey, A., et al. (2006). The HUPO Brain Proteome Project jamboree: centralised summary of the pilot studies.. Proteomics 6, 1719-1721..
abstract
 [WP02]


Gevaert, K. Impens, F. Van Damme, P. Ghesquiere, B. Hanoulle, X. Vandekerckhove, J. (2007). Applications of diagonal chromatography for proteome-wide characterization of protein modifications and activity-based analyses. Febs J 274:6277-6289..
abstract
 [WP02]


Olsen, J. V., Blagoev, B., Gnad, F., Macek, B., Kumar, C., Mortensen, P., and Mann, M. (2006). Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.. Cell 127, 635-648..
abstract
 [WP07]


Hauck, S. M., Kinkl, N., Deeg, C. A., Swiatek-de Lange, M., Schoffmann, S., and Ueffing, M. (2006). GDNF family ligands trigger indirect neuroprotective signaling in retinal glial cells. Mol Cell Biol 26, 2746-2757..
abstract
 [WP11]


Mueller, M., Martens, L., Reidegeld, K. A., Hamacher, M., Stephan, C., Bluggel, M., Korting, G., Chamrad, D., Scheer, C., Marcus, K., et al. (2006). Functional annotation of proteins identified in human brain during the HUPO Brain Proteome Project pilot study.. Proteomics 6, 5059-5075..
abstract
 [WP02]


Ceol, A., Chatr-aryamontri, A., Santonico, E., Sacco, R., Castagnoli, L., and Cesareni, G. (2007). DOMINO: a database of domain-peptide interactions.. Nucleic Acids Res 35, D557-560..
abstract
 [WP09]


Zischka, H., Braun, R. J., Marantidis, E. P., Buringer, D., Bornhovd, C., Hauck, S. M., Demmer, O., Gloeckner, C. J., Reichert, A. S., Madeo, F., and Ueffing, M. (2006). Differential analysis of Saccharomyces cerevisiae mitochondria by free flow electrophoresis. Mol Cell Proteomics 5, 2185-2200..
abstract
 [WP02]


Braun, R. J., Zischka, H., Madeo, F., Eisenberg, T., Wissing, S., Buttner, S., Engelhardt, S. M., Buringer, D., and Ueffing, M. (2006). Crucial mitochondrial impairment upon CDC48 mutation in apoptotic yeast. J Biol Chem 281, 25757-25767..
abstract
 [WP02]


Martens, L., Muller, M., Stephan, C., Hamacher, M., Reidegeld, K. A., Meyer, H. E., Bluggel, M., Vandekerckhove, J., Gevaert, K., and Apweiler, R. (2006). A comparison of the HUPO Brain Proteome Project pilot with other proteomics studies.. Proteomics 6, 5076-5086..
abstract
 [WP02]


Behrends, C., Langer, C. A., Boteva, R., Bottcher, U. M., Stemp, M. J., Schaffar, G., Rao, B. V., Giese, A., Kretzschmar, H., Siegers, K., and Hartl, F. U. (2006). Chaperonin TRiC promotes the assembly of polyQ expansion proteins into nontoxic oligomers. Mol Cell 23, 887-897..
abstract
 [WP02]


Martens, L., Monsieur, G., Ampe, C., Gevaert, K., and Vandekerckhove, J. (2006). Cell_motility: a cross-platform, open source application for the study of cell motion paths.. BMC Bioinformatics 7, 289. .
abstract
 [WP02]


Falb, M., Aivaliotis, M., Garcia-Rizo, C., Bisle, B., Tebbe, A., Klein, C., Konstantinidis, K., Siedler, F., Pfeiffer, F., and Oesterhelt, D. (2006). Archaeal N-terminal protein maturation commonly involves N-terminal acetylation: a large-scale proteomics survey. J Mol Biol 362, 915-924..
abstract
 [WP02]


von Kriegsheim A, Pitt A, Grindlay GJ, Kolch W, Dhillon AS (2006). Regulation of the Raf-MEK-ERK pathway by protein phosphatase 5. Nat Cell Biol. 8(9):1011-6.
abstract
 [WP11]


Hauck SM, Kinkl N, Deeg CA, Swiatek-de Lange M, Schoffmann S, Ueffing M (2006). GDNF family ligands trigger indirect neuroprotective signaling in retinal glial cells. Mol Cell Biol. 26(7):2746-57.
abstract
 [WP11]


Rushworth LK, Hindley AD, O'Neill E, Kolch W (2006). Regulation and role of Raf-1/B-Raf heterodimerization. Mol Cell Biol. 26(6):2262-72.
abstract
 [WP11]


Gloeckner CJ, Kinkl N, Schumacher A, Braun RJ, O'Neill E, Meitinger T, Kolch W, Prokisch H, Ueffing M (2006). The Parkinson disease causing LRRK2 mutation I2020T is associated with increased kinase activity. Hum Mol Genet. 15(2):223-32.
abstract
 [WP11]


Kiel C, Serrano L. (2006). The ubiquitin domain superfold: structure-based sequence alignments and characterization of binding epitopes. J Mol Biol. 355(4):821-44..
abstract
 [WP08]


Roeben A, Kofler C, Nagy I, Nickell S, Hartl FU, Bracher A (2006). Crystal structure of an archaeal actin homolog. J Mol Biol. 358(1):145-56.
abstract
 [WP04]


Hamacher M, Stephan C, Bluggel M, Chamrad D, Korting G, Martens L, Muller M, Hermjakob H, Parkinson D, Dowsey A, Reidegeld KA, Marcus K, Dunn MJ, Meyer HE, Apweiler R. (2006). The HUPO Brain Proteome Project jamboree: centralised summary of the pilot studies. Proteomics.6(6):1719-21.
abstract
 [WP02]


Lavens D, Montoye T, Piessevaux J, Zabeau L, Vandekerckhove J, Gevaert K, Becker W, Eyckerman S, Tavernier J (2006). A complex interaction pattern of CIS and SOCS2 with the leptin receptor. J Cell Sci.119(Pt 11):2214-24. Epub 2006 May 9.
abstract
 [WP02]


Jones P, Cote RG, Martens L, Quinn AF, Taylor CF, Derache W, Hermjakob H, Apweiler R (2006). PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res. 34(Database issue):D659-63.
abstract
 [WP02]


Flikka K, Martens L, Vandekerckhove J, Gevaert K, Eidhammer I (2006). Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering. Proteomics 6(7):2086-94..
abstract
 [WP02]


Martens L, Monsieur G, Ampe C, Gevaert K, Vandekerckhove J (2006). Cell_motility: a cross-platform, open source application for the study of cell motion paths. BMC Bioinformatics. 7:289.
abstract
 [WP02]


Kolch W, Calder M, Gilbert D (2005). When kinases meet mathematics: the systems biology of MAPK signalling. FEBS Lett. 579(8):1891-5.
abstract
 [WP13]


(2005). Computational modelling of the receptor-tyrosine-kinase-activated MAPK pathway. Orton RJ, Sturm OE, Vyshemirsky V, Calder M, Gilbert DR, Kolch W.
abstract
 [WP13]


Persico M, Ceol A, Gavrila C, Hoffmann R, Florio A, Cesareni G (2005). HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. BMC Bioinformatics. 6 Suppl 4:S21.
abstract
 [WP12]


Kolch W, Mischak H, Pitt AR (). The molecular make-up of a tumour: proteomics in cancer research. Clin Sci (Lond). ;108(5):369-83.
abstract
 [WP10]


Kolch W. (2005). Coordinating ERK/MAPK signalling through scaffolds and inhibitors. Nat Rev Mol Cell Biol. 6(11):827-37.
abstract
 [WP11]


O'Neill EE, Matallanas D, Kolch W. (2005). Mammalian sterile 20-like kinases in tumor suppression: an emerging pathway. Cancer Res. 65(13):5485-7.
abstract
 [WP11]


Nickell S, Forster F, Linaroudis A, Net WD, Beck F, Hegerl R, Baumeister W, Plitzko JM (2005). TOM software toolbox: acquisition and analysis for electron tomography. J Struct Biol.149(3):227-34..
abstract
 [WP04]


Martens L, Vandekerckhove J, Gevaert K (2005). DBToolkit: processing protein databases for peptide-centric proteomics. Bioinformatics 21(17):3584-5.
abstract
 [WP02]


Olsen JV, de Godoy LM, Li G, Macek B, Mortensen P, Pesch R, Makarov A, Lange O, Horning S, Mann M. (2005). Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol Cell Proteomics 4(12):2010-21.
abstract
 [WP01]


Olsen JV, de Godoy LM, Li G, Macek B, Mortensen P, Pesch R, Makarov A, Lange O, Horning S, Mann M (2005). Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol Cell Proteomics. 4(12):2010-21.
abstract
 [WP01]


Nutsch T, Oesterhelt D, Gilles ED, Marwan W. (2005). A quantitative model of the switch cycle of an archaeal flagellar motor and its sensory control. Biophys J. 89:2307-23.
abstract
 [WP12]


Kerner MJ, Naylor DJ, Ishihama Y, Maier T, Chang HC, Stines AP, Georgopoulos C, Frishman D, Hayer-Hartl M, Mann M, Hartl FU. (2005). Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli. Cell. 122:209-20.
abstract
 [WP10]


Wohlgemuth S, Kiel C, Kramer A, Serrano L, Wittinghofer F, Herrmann C. (2005). Recognizing and defining true Ras binding domains I: biochemical analysis. J Mol Biol. 348: 741-58.
abstract
 [WP08]


Kiel C, Wohlgemuth S, Rousseau F, Schymkowitz J, Ferkinghoff-Borg J, Wittinghofer F, Serrano L. (2005). Recognizing and defining true Ras binding domains II: In silico prediction based on homology modelling and energy calculations. J Mol Biol. 348:759-75.
abstract
 [WP08]


Stephan C, Hamacher M, Bluggel M, Korting G, Chamrad D, Scheer C, Marcus K, Reidegeld KA, Lohaus C, Schafer H, Martens L, Jones P, Muller M, Auyeung K, Taylor C, Binz PA, Thiele H, Parkinson D, Meyer HE, Apweiler R. (2005). 5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame. Proteomics 5:3560-2.
abstract
 [WP02]


Adamski M, Blackwell T, Menon R, Martens L, Hermjakob H, Taylor C, Omenn GS and States DJ. (2005). Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project. Proteomics 5:3246-61.
abstract
 [WP02]


Van Damme P, Martens L, Van Damme J, Hugelier K, Staes A, Vandekerckhove J and Gevaert K. (2005). Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis. Nat Methods 2:771-7.
abstract
 [WP02]


Gevaert K, Damme PV, Martens L and Vandekerckhove J. (2005). Diagonal reverse-phase chromatography applications in peptide-centric proteomics: Ahead of catalogue-omics?. Anal Biochem. 345:18-29.
abstract
 [WP02]


Kratchmarova I, Blagoev B, Haack-Sorensen M, Kassem M, and Mann M. (2005). Mechanism of divergent growth factor effects in mesenchymal stem cell differentiation. Science 308(5727):1472-7.
abstract
 [WP11]


Cesareni G, Ceol A, Gavrila C, Palazzi LM, Persico M, and Schneider MV. (2005). Comparative interactomics. FEBS Lett.579(8):1828-33.
abstract
 [WP12]


Kiel C, Wohlgemuth S, Rousseau F, Schymkowitz J, Ferkinghoff-Borg J, Wittinghofer F, and Serrano L. (2005). Recognizing and defining true Ras binding domains II: in silico prediction based on homology modelling and energy calculations. J Mol Biol. 348(3):759-75.
abstract
 [WP08]


Wohlgemuth S, Kiel C, Kramer A, Serrano L, Wittinghofer F, and Herrmann C. (2005). Recognizing and defining true ras binding domains I: biochemical analysis. J Mol Biol. 348(3):741-58.
abstract
 [WP08]


Schulze W.X., Deng, L, and Mann, M. (2005). Phosphotyrosine interactome of the ErbB-receptor kinase family. Molecular Systems Biology, doi:10.1038/msb4100012 Published online: 25 May 2005 .
abstract
 [WP07]


Wolkenhauer O., Ullah M., Kolch W., and Cho K.H. (2004). Modeling and simulation of intracellular dynamics: choosing an appropriate framework. IEEE Trans. Nanobioscience 3, 200-207.
abstract
 [WP11]


O'Neill E., Rushworth L., Baccarini M., and Kolch W. (2004). Role of the kinase MST2 in suppression of apoptosis by the proto-oncogene product Raf-1. Science 306, 2267-2270.
abstract
 [WP11]


Neuhoff N., Kaiser T., Wittke S., Krebs R., Pitt A., Burchard A., Sundmacher A., Schlegelberger B., Kolch W., and Mischak H. (2004). Mass spectrometry for the detection of differentially expressed proteins: a comparison of surface-enhanced laser desorption/ionization and capillary electrophoresis/mass spectrometry. Rapid Commun. Mass Spectrom. 18, 149-156.
abstract
 [WP11]


Bisle, B., Schmidt, A., Scheibe, B., Klein, C., Tebbe, A., Kellermann, J., Siedler, F., Pfeiffer, F., Lottspeich, F., and Oesterhelt, D. (2006). Quantitative profiling of the membrane proteome in a halophilic archaeon.. Mol Cell Proteomics 5, 1543-1558..
abstract
 [WP02]


Dhillon, A.S., and Kolch, W. (2004). Oncogenic B-Raf mutations; Crystal clear at last. Cancer Cell 5, 303-304.
abstract
 [WP11]


Prokisch H., Scharfe C., Camp D.G. 2nd, Xiao W., David L., Andreoli C., Monroe M.E., Moore R.J., Gritsenko M.A., Kozany C., Hixson K.K., Mottaz H.M., Zischka H., Ueffing M., Herman Z.S., Davis R.W., Meitinger T., Oefner P.J., Smith R.D., and Steinmetz L.M. (2004). Integrative analysis of the mitochondrial proteome in yeast. PLoS Biol. 2, 795-804.
abstract
 [WP02]


Blagoev, M., Ong, S.-E., Kratchmarova, I., and Mann, M. (2004). Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nature Biotechnology, 22, 1139-1145.
abstract
 [WP07]


Staes, A., Demol, H., Van Damme, J., Martens, L., Vandekerckhove, J., and Gevaert, K. (2004). Global differential non-gel proteomics by quantitative and stable labeling of tryptic peptides with oxygen-18. J Proteome Res. 3, 786-791.
abstract
 [WP02]


Gevaert, K., Ghesquière, B., Staes, A., Martens, L., Van Damme, J., Thomas GR., and Vandekerckhove, J. (2004). Reversible labeling of cysteine containing peptides allows their chromatographic isolation for non-gel proteome studies. Proteomics 4, 897-908.
abstract
 [WP02]


Olsen, J.V. and Mann, M. (2004). Improved peptide identification in proteomics by two consecutive stages of mass spectromectric fragmentation. Proc Natl Acad Sci USA 101, 13417-22.
abstract
 [WP01]


Olsen, J.V., Ong, S.E., and Mann, M. (2004). Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol Cell Proteomics 3, 608-614.
abstract
 [WP01]


Schulze, W. X., and Mann, M. (2004). A novel proteomic screen for Peptide-protein interactions. J Biol Chem 279, 10756-10764.
abstract
 [WP07]





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