Publications

2017

Albrecht M, Stichel D, Müller B, Merkle R, Sticht C, Gretz N, Klingmüller, U, Breuhahn K & Matthäus F TTCA: an R package for the identification of differentially expressed genes in time course microarray data BMC Informatics 18: 33. Link to paper here.

Bosisio FM & van den Oord JJ Immunoplasticity in cutaneous melanoma: beyond pure morphology. Virchows Arch  DOI: 10.1007/s00428-016-2058-y. Link to paper here.

De Landtsheer S, Trairatphisan P, Lucarelli P & Sauter T FALCON: a toolbox for the fast contextualization of logical networks. Bioinformatics btx380. Link to paper here.

Hantusch A, Brunner T, Frickey T & Rehm M Bcl-2-Ome – A database and interactive web service for dissecting the Bcl-2 interactome. Cell Death Diff 24(1): 192. Link to paper here.

Moran B, Rahman A, Palonen K, Lanigan FT & Gallagher W Master transcriptional regulators in cancer: discovery via reverse engineering approaches and subsequent validation. Cancer Res. 77(9):2186-2190. Link to paper here.

Rufo N, Garg AD, Agostinis P The Unfolded Protein Response in Immunogenic Cell Death and Cancer Immunotherapy. Trends in Cancer DOI: 10.1016/j.trecan.2017.07.002. Link to paper here.

Vetma V, Rozanc J, Charles EM, Hellwig CT, Alexopoulos LG & Rehm M Examining the in vitro efficacy of the IAP antagonist Birinapant as a single-agent or in combination with dacarbazine to induce melanoma cell death. Oncology Research. Link to paper here.

2016

Albrecht M, Sciume G, Lucarelli P & Sauter T Thermodynamically constrained averaging theory for cancer growth modeling. IFAC-PapersOnLine 49(26): 289-294. Link to paper here.

Bosisio FM, Wilmot JS, Volders N, Mercier M, Wouters J, Stas M, Blokx WA, Massi D, Thompson JF, Scolyer RA, van Baren N &  van den Oord JJ Plasma cells in primary melanoma. Prognostic significance and possible role of IgA. Mod Pathol 29 (4): 347-358. Link to paper here.

Garg AD, Romano E, Rufo N & Agostinis P Immunogenic versus tolerogenic phagocytosis during anticancer therapy: mechanisms and clinical translation. Cell Death Diff. 23: 938-951. Link to paper here.

Hellwig CT, Ludwig-Galezowska AH & Rehm M FRET-based measurement of apoptotic caspase activities by high-throughput screening flow citometry. In Apoptosis Methods in Toxicology, Humana Press/Srpinger. Link to book here.

Jacob SF, Wurstle ML, Delgado ME & Rehm M (2016) An analysis of the truncated Bid- and ROS-dependent spatial propagation of mitochondrial permeabilization waves during apoptosis. J Biol Chem 291 (9): 4603-4613. Link to paper here.

Niessner H, Schmitz J, Tabatabai G, Schmid Am, Calaminus C, Sinnberg T, Weide B, Eigentler T, Garbe C, Schittek B, Quintanilla-Fend L, Bender B, Mai M, Praetorius C, Beissert S, Schackert G, Muders Mh, Meinhardt M, Baretton G, Dummer R, Flaherty K, Pichler Bj, Kulms D, Westphal D & Meier F  PI3K pathway inhibition achieves potent antitumor activity in melanoma brain metastases in vitro and in vivo. Clin Cancer Res 22(23): 5818-5828. Link to paper here.

Weyhenmeyer BC, Noonan J, Wurstle ML, Lincoln FA, Johnston G, Rehm M & Murphy BM Predicting the cell death responsiveness and sensitization of glioma cells to TRAIL and temozolomide. Oncotarget DOI: 10.18632/oncotarget.10973. Link to paper here.

2015

Garg AD, Galluzzi L, Apetoh L, Baert T, Birge RB, Bravo-San Pedro JM, Breckpot K, Brough D, Chaurio R, Cirone M, Coosemans A, Coulie PG, De Ruysscher D, Dini L, De Witte P, Dudek-Peric AM, Faggioni A, Fucikova J, Gaipl US, Golab J, Gougeon M-L, Hamblin MR, Hemminki A, Herrmann M, Hodge JW, Kepp O, Kroemer G, Krysko DV, Land WG, Madeo F, Manfredi AA, Mattarollo SR, Maueroder C, Merendino N, Multhoff G, Pabst T, Ricci J-E, Riganti C, Romano E, Rufo N, Smyth MJ, Sonnemann J, Spisek R, Stagg J, Vacchelli E, Vandenabeele P, Vandenberk L, van den Eynde BJ, van Gool S, Velotti F, Zitvogel L & Agostinis P Molecular and Translational Classifications of DAMPs in Immunogenic Cell Death. Frontiers Immunol. 6: 588. Link to paper here.

Geserick P; Wang J; Schilling R; Horn S; Harris PA; Bertin J; Gough PJ; Feoktistova M & Leverkus M. Absence of RIPK3 predicts necroptosis resistance in malignant melanoma. Cell Death Dis 6: e1884. Link to paper here.


 

Partners background publications:

2014

Agur, Z.; Elishmereni, M. & Kheifetz, Y. Personalizing oncology treatments by predicting drug efficacy, side-effects, and improved therapy: mathematics, statistics, and their integration. Wiley Interdiscip Rev Syst Biol Med 6(3): 239-253.

Fitzgerald, J. B.; Johnson, B. W.; Baum, J.; Adams, S.; Iadevaia, S.; Tang, J.; Rimkunas, V.; Xu, L.; Kohli, N.; Rennard, R.; Razlog, M.; Jiao, Y.; Harms, B. D.; Olivier, K. J., Jr.; Schoeberl, B.; Nielsen, U. B. & Lugovskoy, A. A. MM-141, an IGF-IR- and ErbB3-directed bispecific antibody, overcomes network adaptations that limit activity of IGF-IR inhibitors. Mol Cancer Ther 13(2): 410-425.

Flaherty, K. T.; Hennig, M.; Lee, S. J.; Ascierto, P. A.; Dummer, R.; Eggermont, A. M.; Hauschild, A.; Kefford, R.; Kirkwood, J. M.; Long, G. V.; Lorigan, P.; Mackensen, A.; McArthur, G.; O’Day, S.; Patel, P. M.; Robert, C. & Schadendorf, D. Surrogate endpoints for overall survival in metastatic melanoma: a meta-analysis of randomised controlled trials. Lancet Oncol 15(3): 297-304.

Galhardo, M.; Sinkkonen, L.; Berninger, P.; Lin, J.; Sauter, T. & Heinaniemi, M. Integrated analysis of transcript-level regulation of metabolism reveals disease-relevant nodes of the human metabolic network. Nucleic Acid Res 42(3): 1474-1496.

Garg, A. D.; Martin, S.; Golab, J. & Agostinis, P. Danger signalling during cancer cell death: origins, plasticity and regulation. Cell Death Differ 21(1): 26-38.

 Konrath, F.; Witt, J.; Sauter, T. & Kulms, D. Identification of new IkappaBalpha complexes by an iterative experimental and mathematical modeling approach. PLoS Comput Biol 10(3): e1003528.

Sullivan, R. J. & Flaherty, K. T. Major therapeutic developments and current challenges in advanced melanoma. Br J Dermatol 170(1): 36-44.

Trairatphisan, P.; Mizera, A.; Pang, J.; Tantar, A. A. & Sauter, T. optPBN: an optimisation toolbox for probabilistic Boolean networks. PLoS One 9(7): e98001.

Vlassis, N.; Pacheco, M. P. & Sauter, T. Fast reconstruction of compact context-specific metabolic network models. PLoS Comput Biol 10(1): e1003424.

Wurstle, M. L.; Zink, E.; Prehn, J. H. & Rehm, M. From computational modelling of the intrinsic apoptosis pathway to a systems-based analysis of chemotherapy resistance: achievements, perspectives and challenges in systems medicine. Cell Death Dis 5: e1258.

2013

Ascierto, P. A.; Schadendorf, D.; Berking, C.; Agarwala, S. S.; van Herpen, C. M.; Queirolo, P.; Blank, C. U.; Hauschild, A.; Beck, J. T.; St-Pierre, A.; Niazi, F.; Wandel, S.; Peters, M.; Zubel, A. & Dummer, R. MEK162 for patients with advanced melanoma harbouring NRAS or Val600 BRAF mutations: a non-randomised, open-label phase 2 study. Lancet Oncol 14(3): 249-256.

Baumuratova, T.; Dobre, S.; Bastogne, T. &  Sauter, T. Switch of sensitivity dynamics revealed with DyGloSA toolbox for dynamical global sensitivity analysis as an early warning for system’s critical transition. PLoS One 8(12): e82973.

Eisenberg, G.; Uzana, R.; Pato, A.; Frankenburg, S.; Merims, S.; Yefenof, E.; Ferrone, S.; Peretz, T.; Machlenkin, A. & Lotem, M. Imprinting of lymphocytes with melanoma antigens acquired by trogocytosis facilitates identification of tumor-reactive T cells J Immunol 190(11): 5856-5865.

Garg, A. D.; Dudek, A. M.; Ferreira, G. B.; Verfaillie, T.; Vandenabeele, P.; Krysko, D. V.; Mathieu, C. & Agostinis, P. ROS-induced autophagy in cancer cells assists in evasion from determinants of immunogenic cell death. Autophagy 9(9): 1292-1307.

Johannessen, C. M.; Johnson, L. A.; Piccioni, F.; Townes, A.; Frederick, D. T.; Donahue, M. K.; Narayan, R.; Flaherty, K. T.; Wargo, J. A.; Root, D. E. & Garraway, L. A. A melanocyte lineage program confers resistance to MAP kinase pathway inhibition. Nature 504(7478): 138-142.

Kogan, Y.; Agur, Z. & Elishmereni, M. A mathematical model for the immunotherapeutic control of the Th1/Th2 imbalance in melanoma. Discrete and Continuous Dynamics – Series B 18(4): 1017-1030.

Liu, H.; He, Z.; von Rutte, T.; Yousefi, S.; Hunger, R. E. & Simon, H. U. Down-regulation of autophagy-related protein 5 (ATG5) contributes to the pathogenesis of early-stage cutaneous melanoma. Sci Transl Med 5(202): 202ra123.

Maskey, D.; Yousefi, S.; Schmid, I.; Zlobec, I.; Perren, A.; Friis, R. & Simon, H. U. ATG5 is induced by DNA-damaging agents and promotes mitotic catastrophe independent of autophagy. Nat Commun 4: 2130.

Merlo, P. & Cecconi, F. XIAP: inhibitor of two worlds. EMBO J 32(16): 2187-2188.

Mitchem, J. B.; Brennan, D. J.; Knolhoff, B. L.; Belt, B. A.; Zhu, Y.; Sanford, D. E.; Belaygorod, L.; Carpenter, D.; Collins, L.; Piwnica-Worms, D.; Hewitt, S.; Udupi, G. M.; Gallagher, W. M.; Wegner, C.; West, B. L.; Wang-Gillam, A.; Goedegebuure, P.; Linehan, D. C. & DeNardo, D. G. Targeting tumor-infiltrating macrophages decreases tumor-initiating cells, relieves immunosuppression, and improves chemotherapeutic responses. Cancer Res 73(3): 1128-1141.

Morris, M. K.; Chi, A.; Melas, I. N. & Alexopoulos, L. G. Phosphoproteomics in drug discovery. Drug Discov Today 19(4): 425-432.

Nazio, F.; Strappazzon, F.; Antonioli, M.; Bielli, P.; Cianfanelli, V.; Bordi, M.; Gretzmeier, C.; Dengjel, J.; Piacentini, M.; Fimia, G. M. & Cecconi, F. mTOR inhibits autophagy by controlling ULK1 ubiquitylation, self-association and function through AMBRA1 and TRAF6. Nat Cell Biol 15(4): 406-416.

Panayotova-Dimitrova, D.; Feoktistova, M.; Ploesser, M.; Kellert, B.; Hupe, M.; Horn, S.; Makarov, R.; Jensen, F.; Porubsky, S.; Schmieder, A.; Zenclussen, A. C.; Marx, A.; Kerstan, A.; Geserick, P.; He, Y. W. & Leverkus, M. cFLIP regulates skin homeostasis and protects against TNF-induced keratinocyte apoptosis. Cell Rep 5(2): 397-408.

Passante, E.; Wurstle, M. L.; Hellwig, C. T.; Leverkus, M. & Rehm, M. Systems analysis of apoptosis protein expression allows the case-specific prediction of cell death responsiveness of melanoma cells. Cell Death Differ 20(11): 1521-1531.

Romano, D.; Maccario, H.; Doherty, C.; Quinn, N. P.; Kolch, W. & Matallanas, D. The differential effects of wild-type and mutated K-Ras on MST2 signaling are determined by K-Ras activation kinetics. Mol Cell Biol 33(9): 1859-1868.

Trairatphisan, P.; Mizera, A.; Pang, J.; Tantar, A. A.; Schneider, J. & Sauter, T. Recent development and biomedical applications of probabilistic Boolean networks. Cell Commun Signal 11: 46.

Vandamme, D.; Fitzmaurice, W.; Kholodenko, B. & Kolch, W. Systems medicine: helping us understand the complexity of disease. QJM 106(10): 891-895.

Vorsmann, H.; Groeber, F.; Walles, H.; Busch, S.; Beissert, S.; Walczak, H. & Kulms, D. Development of a human three-dimensional organotypic skin-melanoma spheroid model for in vitro drug testing. Cell Death Dis 4: e719.

2012

Barretina, J.; Caponigro, G.; Stransky, N.; Venkatesan, K.; Margolin, A. A.; Kim, S.; Wilson, C. J.; Lehar, J.; Kryukov, G. V.; Sonkin, D.; Reddy, A.; Liu, M.; Murray, L.; Berger, M. F.; Monahan, J. E.; Morais, P.; Meltzer, J.; Korejwa, A.; Jane-Valbuena, J.; Mapa, F. A.; Thibault, J.; Bric-Furlong, E.; Raman, P.; Shipway, A.; Engels, I. H.; Cheng, J.; Yu, G. K.; Yu, J.; Aspesi, P., Jr.; de Silva, M.; Jagtap, K.; Jones, M. D.; Wang, L.; Hatton, C.; Palescandolo, E.; Gupta, S.; Mahan, S.; Sougnez, C.; Onofrio, R. C.; Liefeld, T.; MacConaill, L.; Winckler, W.; Reich, M.; Li, N.; Mesirov, J. P.; Gabriel, S. B.; Getz, G.; Ardlie, K.; Chan, V.; Myer, V. E.; Weber, B. L.; Porter, J.; Warmuth, M.; Finan, P.; Harris, J. L.; Meyerson, M.; Golub, T. R.; Morrissey, M. P.; Sellers, W. R.; Schlegel, R. & Garraway, L. A. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483(7391): 603-607.

Flaherty, K. T.; Infante, J. R.; Daud, A.; Gonzalez, R.; Kefford, R. F.; Sosman, J.; Hamid, O.; Schuchter, L.; Cebon, J.; Ibrahim, N.; Kudchadkar, R.; Burris, H. A., 3rd; Falchook, G.; Algazi, A.; Lewis, K.; Long, G. V.; Puzanov, I.; Lebowitz, P.; Singh, A.; Little, S.; Sun, P.; Allred, A.; Ouellet, D.; Kim, K. B.; Patel, K. & Weber, J. Combined BRAF and MEK inhibition in melanoma with BRAF V600 mutations. N Engl J Med 367(18): 1694-1703.

Garg, A. D.; Krysko, D. V.; Verfaillie, T.; Kaczmarek, A.; Ferreira, G. B.; Marysael, T.; Rubio, N.; Firczuk, M.; Mathieu, C.; Roebroek, A. J.; Annaert, W.; Golab, J.; de Witte, P.; Vandenabeele, P. & Agostinis, P. A novel pathway combining calreticulin exposure and ATP secretion in immunogenic cancer cell death. EMBO J 31(5): 1062-1079.

Gomez de Aguero, M.; Vocanson, M.; Hacini-Rachinel, F.; Taillardet, M.; Sparwasser, T.; Kissenpfennig, A.; Malissen, B.; Kaiserlian, D. & Dubois, B. Langerhans cells protect from allergic contact dermatitis in mice by tolerizing CD8(+) T cells and activating Foxp3(+) regulatory T cells. J Clin Invest 122(5): 1700-1711.

Joyce, C. W.; Murphy, I. G.; Rafferty, M.; Ryan, D.; McDermott, E. W. & Gallagher, W. M. Tumor profiling using protein biomarker panels in malignant melanoma: application of tissue microarrays and beyond. Expert Rev Proteomics 9(4): 415-423.

Kogan, Y.; Halevi-Tobias, K.; Elishmereni, M.; Vuk-Pavlovic, S. & Agur, Z. Reconsidering the paradigm of cancer immunotherapy by computationally aided real-time personalization. Cancer Res 72(9): 2218-2227.

Kogan, Y.; Halevi-Tobias, K. E.; Hochman, G.; Baczmanska, A. K.; Leyns, L. & Agur, Z. A new validated mathematical model of the Wnt signalling pathway predicts effective combinational therapy by sFRP and Dkk. Biochem J 444(1): 115-125.

Krysko, D. V.; Garg, A. D.; Kaczmarek, A.; Krysko, O.; Agostinis, P. & Vandenabeele, P. Immunogenic cell death and DAMPs in cancer therapy. Nat Rev Cancer 12(12): 860-875.

Lazar, I.; Perlman, R.; Lotem, M.; Peretz, T.; Ben-Yehuda, D. & Kadouri, L. The clinical effect of the inhibitor of apopotosis protein livin in melanoma Oncology 82(4): 197-204.

McDonagh, C. F.; Huhalov, A.; Harms, B. D.; Adams, S.; Paragas, V.; Oyama, S.; Zhang, B.; Luus, L.; Overland, R.; Nguyen, S.; Gu, J.; Kohli, N.; Wallace, M.; Feldhaus, M. J.; Kudla, A. J.; Schoeberl, B. & Nielsen, U. B. Antitumor activity of a novel bispecific antibody that targets the ErbB2/ErbB3 oncogenic unit and inhibits heregulin-induced activation of ErbB3. Mol Cancer Ther 11(3): 582-593.

Melas, I. N.; Mitsos, A.; Messinis, D. E.; Weiss, T. S.; Rodriguez, J. S. & Alexopoulos, L. G. Construction of large signaling pathways using an adaptive perturbation approach with phosphoproteomic data. Mol Biosyst 8(5): 1571-1584.

Rodriguez, B.; Prioult, G.; Hacini-Rachinel, F.; Moine, D.; Bruttin, A.; Ngom-Bru, C.; Labellie, C.; Nicolis, I.; Berger, B.; Mercenier, A.; Butel, M.-J. & Waligora-Dupriet, A.-J. Infant gut microbiota is protective against cow’s milk allergy in mice despite immature ileal T-cell response FEMS Microbiol Ecol 79(1): 192-202.

Salemi, S.; Yousefi, S.; Constantinescu, M. A.; Fey, M. F. & Simon, H. U. Autophagy is required for self-renewal and differentiation of adult human stem cells. Cell Res 22(2): 432-435.

Santra, T.; Kholodenko, B. & Kolch, W. An integrated Bayesian framework for identifying phosphorylation networks in stimulated cells. Adv Exp Med Biol 736: 59-80.

Vainas, O.; Ariad, S.; Amir, O.; Mermershtain, W.; Vainstein, V.; Kleiman, M.; Inbar, O.; Ben-Av, R.; Mukherjee, A.; Chan, S. & Agur, Z. Personalising docetaxel and G-CSF schedules in cancer patients by a clinically validated computational model. Br J Cancer 107(5): 814-822.

Verfaillie, T.; Rubio, N.; Garg, A. D.; Bultynck, G.; Rizzuto, R.; Decuypere, J. P.; Piette, J.; Linehan, C.; Gupta, S.; Samali, A. & Agostinis, P. PERK is required at the ER-mitochondrial contact sites to convey apoptosis after ROS-based ER stress. Cell Death Differ 19(11): 1880-1891.

Witt, J.; Konrath, F.; Sawodny, O.; Ederer, M.; Kulms, D. & Sauter, T. Analysing the role of UVB-induced translational inhibition and PP2Ac deactivation in NF-kappaB signalling using a minimal mathematical model. PLoS One 7(7): e40274.

2011

D’Amelio, M.; Cavallucci, V.; Middei, S.; Marchetti, C.; Pacioni, S.; Ferri, A.; Diamantini, A.; De Zio, D.; Carrara, P.; Battistini, L.; Moreno, S.; Bacci, A.; Ammassari-Teule, M.; Marie, H. & Cecconi, F. Caspase-3 triggers early synaptic dysfunction in a mouse model of Alzheimer’s disease. Nat Neurosci 14(1): 69-76.

Feoktistova, M.; Geserick, P.; Kellert, B.; Dimitrova, D. P.; Langlais, C.; Hupe, M.; Cain, K.; MacFarlane, M.; Hacker, G. & Leverkus, M.  cIAPs block Ripoptosome formation, a RIP1/caspase-8 containing intracellular cell death complex differentially regulated by cFLIP isoforms. Mol. Cell. 43(3): 449-463.

Ferraro, E.; Pesaresi, M. G.; De Zio, D.; Cencioni, M. T.; Gortat, A.; Cozzolino, M.; Berghella, L.; Salvatore, A. M.; Oettinghaus, B.; Scorrano, L.; Perez-Paya, E. & Cecconi, F. Apaf1 plays a pro-survival role by regulating centrosome morphology and function. J Cell Sci 124(pt20): 3450-3463.

Gremel, G.; Ryan, D.; Rafferty, M.; Lanigan, F.; Hegarty, S.; Lavelle, M.; Murphy, I.; Unwin, L.; Joyce, C.; Faller, W.; McDermott, E. W.; Sheahan, K.; Ponten, F. & Gallagher, W. M. Functional and prognostic relevance of the homeobox protein MSX2 in malignant melanoma. Br J Cancer 105(4): 565-574.

Hornle, M.; Peters, N.; Thayaparasingham, B.; Vorsmann, H.; Kashkar, H. & Kulms, D. Caspase-3 cleaves XIAP in a positive feedback loop to sensitize melanoma cells to TRAIL-induced apoptosis. Oncogene 30(5): 575-587

Laussmann, M. A.; Passante, E.; Dussmann, H.; Rauen, J. A.; Wurstle, M. L.; Delgado, M. E.; Devocelle, M.; Prehn, J. H. & Rehm, M. Proteasome inhibition can induce an autophagy-dependent apical activation of caspase-8. Cell Death Differ 18(10): 1584-1597.

Lindsay, C. R.; Lawn, S.; Campbell, A. D.; Faller, W. J.; Rambow, F.; Mort, R. L.; Timpson, P.; Li, A.; Cammareri, P.; Ridgway, R. A.; Morton, J. P.; Doyle, B.; Hegarty, S.; Rafferty, M.; Murphy, I. G.; McDermott, E. W.; Sheahan, K.; Pedone, K.; Finn, A. J.; Groben, P. A.; Thomas, N. E.; Hao, H.; Carson, C.; Norman, J. C.; Machesky, L. M.; Gallagher, W. M.; Jackson, I. J.; Van Kempen, L.; Beermann, F.; Der, C.; Larue, L.; Welch, H. C.; Ozanne, B. W. & Sansom, O. J. P-Rex1 is required for efficient melanoblast migration and melanoma metastasis. Nat Commun 2: 555.

Matallanas, D.; Romano, D.; Al-Mulla, F.; O’Neill, E.; Al-Ali, W.; Crespo, P.; Doyle, B.; Nixon, C.; Sansom, O.; Drosten, M.; Barbacid, M. & Kolch, W. Mutant K-Ras activation of the proapoptotic MST2 pathway is antagonized by wild-type K-Ras. Mol Cell 44(6): 893-906.

Melas, I. N.; Mitsos, A.; Messinis, D. E.; Weiss, T. S. & Alexopoulos, L. G. Combined logical and data-driven models for linking signalling pathways to cellular response. BMC Syst Biol 5: 107.

Meyer, P.; Alexopoulos, L. G.; Bonk, T.; Califano, A.; Cho, C. R.; de la Fuente, A.; de Graaf, D.; Hartemink, A. J.; Hoeng, J.; Ivanov, N. V.; Koeppl, H.; Linding, R.; Marbach, D.; Norel, R.; Peitsch, M. C.; Rice, J. J.; Royyuru, A.; Schacherer, F.; Sprengel, J.; Stolle, K.; Vitkup, D. & Stolovitzky, G. Verification of systems biology research in the age of collaborative competition. Nat Biotechnol 29(9): 811-815.

Robert, C.; Thomas, L.; Bondarenko, I.; O’Day, S.; Weber, J.; Garbe, C.; Lebbe, C.; Baurain, J. F.; Testori, A.; Grob, J. J.; Davidson, N.; Richards, J.; Maio, M.; Hauschild, A.; Miller, W. H., Jr.; Gascon, P.; Lotem, M.; Harmankaya, K.; Ibrahim, R.; Francis, S.; Chen, T. T.; Humphrey, R.; Hoos, A. & Wolchok, J. D. Ipilimumab plus dacarbazine for previously untreated metastatic melanoma N Engl J Med 364(26): 2517-2526.

Saez-Rodriguez, J.; Alexopoulos, L. G.; Zhang, M.; Morris, M. K.; Lauffenburger, D. A. & Sorger, P. K. Comparing signaling networks between normal and transformed hepatocytes using discrete logical models. Cancer Res 71(16): 5400-5411.

Strappazzon, F.; Vietri-Rudan, M.; Campello, S.; Nazio, F.; Florenzano, F.; Fimia, G. M.; Piacentini, M.; Levine, B. & Cecconi, F. Mitochondrial BCL-2 inhibits AMBRA1-induced autophagy. EMBO J 30(7): 1195-1208.

2010

Alexopoulos, L. G.; Saez-Rodriguez, J.; Cosgrove, B. D.; Lauffenburger, D. A. & Sorger, P. K. Networks inferred from biochemical data reveal profound differences in toll-like receptor and inflammatory signaling between normal and transformed hepatocytes. Mol Cell Proteomics 9(9): 1849-1865.

Brennan, D. J.; O’Connor, D. P.; Rexhepaj, E.; Ponten, F. & Gallagher, W. M. Antibody-based proteomics: fast-tracking molecular diagnostics in oncology. Nat Rev Cancer 10(9): 605-617.

Romano, D.; Matallanas, D.; Weitsman, G.; Preisinger, C.; Ng, T. & Kolch, W. Proapoptotic kinase MST2 coordinates signaling crosstalk between RASSF1A, Raf-1, and Akt. Cancer Res 70(3): 1195-1203.

Sturm, O. E.; Orton, R.; Grindlay, J.; Birtwistle, M.; Vyshemirsky, V.; Gilbert, D.; Calder, M.; Pitt, A.; Kholodenko, B. & Kolch, W. The mammalian MAPK/ERK pathway exhibits properties of a negative feedback amplifier. Sci Signal 3(153): ra90.

2009

Geserick, P.; Hupe, M.; Moulin, M.; Wong, W. W.; Feoktistova, M.; Kellert, B.; Gollnick, H.; Silke, J. & Leverkus, M. Cellular IAPs inhibit a cryptic CD95-induced cell death by limiting RIP1 kinase recruitment. J Cell Biol 187(7): 1037-1054.

Hacini-Rachinel, F.; Nancey, S.; Boschetti, G.; Sardi, F.; Doucet-Ladeveze, R.; Durand, P. Y.; Flourie, B. & Kaiserlian, D. CD4+ T cells and Lactobacillus casei control relapsing colitis mediated by CD8+ T cells J Immunol 183(9): 5477-5486.

Mitsos, A.; Melas, I. N.; Siminelakis, P.; Chairakaki, A. D.; Saez-Rodriguez, J. & Alexopoulos, L. G. Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data. PLoS Comput Biol 5(12): e.1000591.

Schilling, M.; Maiwald, T.; Hengl, S.; Winter, D.; Kreutz, C.; Kolch, W.; Lehmann, W. D.; Timmer, J. & Klingmuller, U. Theoretical and experimental analysis links isoform-specific ERK signalling to cell fate decisions. Mol Syst Biol 5: 334.

Schlatter, R.; Schmich, K.; Avalos Vizcarra, I.; Scheurich, P.; Sauter, T.; Borner, C.; Ederer, M.; Merfort, I. & Sawodny, O. ON/OFF and beyond–a boolean model of apoptosis. PLoS Comput Biol 5(12): e1000595.

Schoeberl, B.; Pace, E. A.; Fitzgerald, J. B.; Harms, B. D.; Xu, L.; Nie, L.; Linggi, B.; Kalra, A.; Paragas, V.; Bukhalid, R.; Grantcharova, V.; Kohli, N.; West, K. A.; Leszczyniecka, M.; Feldhaus, M. J.; Kudla, A. J. & Nielsen, U. B. Therapeutically targeting ErbB3: a key node in ligand-induced activation of the ErbB receptor-PI3K axis. Sci Signal 2(77): ra31.

Thayaparasingham, B.; Kunz, A.; Peters, N. & Kulms, D. Sensitization of melanoma cells to TRAIL by UVB-induced and NF-kappaB-mediated downregulation of xIAP. Oncogene 28(3): 345-362.

Witt, J.; Barisic, S.; Schumann, E.; Allgower, F.; Sawodny, O.; Sauter, T. & Kulms, D. Mechanism of PP2A-mediated IKK beta dephosphorylation: a systems biological approach. BMC Syst Biol 3: 71.

2008

Diessenbacher, P.; Hupe, M.; Sprick, M. R.; Kerstan, A.; Geserick, P.; Haas, T. L.; Wachter, T.; Neumann, M.; Walczak, H.; Silke, J. & Leverkus, M. NF-kappaB inhibition reveals differential mechanisms of TNF versus TRAIL-induced apoptosis upstream or at the level of caspase-8 activation independent of cIAP2. J Invest Dermatol 128(5): 1134-1147.

Geserick, P.; Drewniok, C.; Hupe, M.; Haas, T. L.; Diessenbacher, P.; Sprick, M. R.; Schon, M. P.; Henkler, F.; Gollnick, H.; Walczak, H. & Leverkus, M. Suppression of cFLIP is sufficient to sensitize human melanoma cells to TRAIL- and CD95L-mediated apoptosis. Oncogene 27(22): 3211-3220.

Yousefi, S.; Gold, J. A.; Andina, N.; Lee, J. J.; Kelly, A. M.; Kozlowski, E.; Schmid, I.; Straumann, A.; Reichenbach, J.; Gleich, G. J. & Simon, H. U. Catapult-like release of mitochondrial DNA by eosinophils contributes to antibacterial defense. Nat Med 14(9): 949-953.

2002-2007

Fimia, G. M.; Stoykova, A.; Romagnoli, A.; Giunta, L.; Di Bartolomeo, S.; Nardacci, R.; Corazzari, M.; Fuoco, C.; Ucar, A.; Schwartz, P.; Gruss, P.; Piacentini, M.; Chowdhury, K. & Cecconi, F. Ambra1 regulates autophagy and development of the nervous system. Nature 447(7148): 1121-1125.

Spatz, A., Gimotty, P.A., Cook, M.G., van den oord, J.J., Desai, N., Eggermont, A.M., Keilholz, U., Ruiter, D.J. & Mihm, M.C. Protective effect of a brisk tumor infiltrating lymphocyte infiltrate in melanoma: an EORTC melanoma group study. J Clin Oncol 25(18S): 8519.

Rehm, M.; Huber, H. J.; Dussmann, H. & Prehn, J. H. Systems analysis of effector caspase activation and its control by X-linked inhibitor of apoptosis protein. EMBO J 25(18): 4338-4349.

Yousefi, S.; Perozzo, R.; Schmid, I.; Ziemiecki, A.; Schaffner, T.; Scapozza, L.; Brunner, T. & Simon, H. U. Calpain-mediated cleavage of Atg5 switches autophagy to apoptosis. Nat Cell Biol 8(10): 1124-1132.

 O’Neill, E.; Rushworth, L.; Baccarini, M. & Kolch, W. Role of the kinase MST2 in suppression of apoptosis by the proto-oncogene product Raf-1. Science 306(5705): 2267-2270.

Serra, C.; Federici, M.; Buongiorno, A.; Senni, M. I.; Morelli, S.; Segratella, E.; Pascuccio, M.; Tiveron, C.; Mattei, E.; Tatangelo, L.; Lauro, R.; Molinaro, M.; Giaccari, A. & Bouche, M. Transgenic mice with dominant negative PKC-theta in skeletal muscle: a new model of insulin resistance and obesity. J Cell Physiol 196(1): 89-97.

D’Adamo, P.; Welzl, H.; Papadimitriou, S.; Raffaele di Barletta, M.; Tiveron, C.; Tatangelo, L.; Pozzi, L.; Chapman, P. F.; Knevett, S. G.; Ramsay, M. F.; Valtorta, F.; Leoni, C.; Menegon, A.; Wolfer, D. P.; Lipp, H. P. & Toniolo, D. Deletion of the mental retardation gene Gdi1 impairs associative memory and alters social behavior in mice. Hum Mol Genet 11(21): 2567-2580.

Odorisio, T.; Schietroma, C.; Zaccaria, M. L.; Cianfarani, F.; Tiveron, C.; Tatangelo, L.; Failla, C. M. & Zambruno, G. Mice overexpressing placenta growth factor exhibit increased vascularization and vessel permeability. J Cell Sci 115(Pt12): 2559-2567.

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