MILES

Grossbach, J., L. Gillet, M. Clément-Ziza, C. L. Schmalohr, O. T. Schubert, M. Schütter, J. S. P. Mawer, C. A. Barnes, I. Bludau, M. Weith, P. Tessarz, M. Graef, R. Aebersold, and A. Beyer (2022). "The impact of genomic variation on protein phosphorylation states and regulatory networks." Mol Syst Biol 18(5): e10712. MILES  doi.org/10.15252/msb.202110712.

Rusyn, L., S. Reinartz, A. Nikiforov, N. Mikhael, A. vom Stein, V. Kohlhas, J. Bloehdorn, S. Stilgenbauer, P. Lohneis, R. Buettner, S. Robrecht, K. Fischer, C. Pallasch, M. Hallek, P. H. Nguyen, and T. Seeger-Nukpezah (2022). "The scaffold protein NEDD9 is necessary for leukemia-cell migration and disease progression in a mouse model of chronic lymphocytic leukemia." Leukemia. MILES  doi.org/10.1038/s41375-022-01586-1.

Dammert, M. A., Bragelmann, J., Olsen, R. R., Bohm, S., Monhasery, N., Whitney, C. P., Chalishazar, M. D., Tumbrink, H. L., Guthrie, M. R., Klein, S., Ireland, A. S., Ryan, J., Schmitt, A., Marx, A., Ozretic, L., Castiglione, R., Lorenz, C., Jachimowicz, R. D., Wolf, E., Thomas, R. K., Poirier, J. T., Buttner, R., Sen, T., Byers, L. A., Reinhardt, H. C., Letai, A., Oliver, T. G. and Sos, M. L. (2019). "MYC paralog-dependent apoptotic priming orchestrates a spectrum of vulnerabilities in small cell lung cancer." Nat Commun 10(1): 3485. www.ncbi.nlm.nih.gov/pubmed/31375684.

Jachimowicz, R. D., Beleggia, F., Isensee, J., Velpula, B. B., Goergens, J., Bustos, M. A., Doll, M. A., Shenoy, A., Checa-Rodriguez, C., Wiederstein, J. L., Baranes-Bachar, K., Bartenhagen, C., Hertwig, F., Teper, N., Nishi, T., Schmitt, A., Distelmaier, F., Lüdecke, H.-J., Albrecht, B., Krüger, M., Schumacher, B., Geiger, T., Hoon, D. S. B., Huertas, P., Fischer, M., Hucho, T., Peifer, M., Ziv, Y., Reinhardt, H. C., Wieczorek, D. and Shiloh, Y. (2019). "UBQLN4 Represses Homologous Recombination and Is Overexpressed in Aggressive Tumors." Cell. www.ncbi.nlm.nih.gov/pubmed/30612738.

Ackermann, S., Cartolano, M., Hero, B., Welte, A., Kahlert, Y., Roderwieser, A., Bartenhagen, C., Walter, E., Gecht, J., Kerschke, L., Volland, R., Menon, R., Heuckmann, J. M., Gartlgruber, M., Hartlieb, S., Henrich, K.-O., Okonechnikov, K., Altmüller, J., Nürnberg, P., Lefever, S., Wilde, B. d., Sand, F., Ikram, F., Rosswog, C., Fischer, J., Theissen, J., Hertwig, F., Singhi, A. D., Simon, T., Vogel, W., Perner, S., Krug, B., Schmidt, M., Rahmann, S., Achter, V., Lang, U., Vokuhl, C., Ortmann, M., Büttner, R., Eggert, A., Speleman, F., O’Sullivan, R. J., Thomas, R. K., Berthold, F., Vandesompele, J., Schramm, A., Westermann, F., Schulte, J. H., Peifer, M. and Fischer, M. (2018). "A mechanistic classification of clinical phenotypes in neuroblastoma." Science 362(6419): 1165-1170. www.ncbi.nlm.nih.gov/pubmed/30523111.

Cun, Y., Yang, T.-P., Achter, V., Lang, U. and Peifer, M. (2018). "Copy-number analysis and inference of subclonal populations in cancer genomes using Sclust." Nature Protocols 13(6): 1488-1501. www.ncbi.nlm.nih.gov/pubmed/29844525.

Drapkin, B. J., George, J., Christensen, C. L., Mino-Kenudson, M., Dries, R., Sundaresan, T., Phat, S., Myers, D. T., Zhong, J., Igo, P., Hazar-Rethinam, M. H., Licausi, J. A., Gomez-Caraballo, M., Kem, M., Jani, K. N., Azimi, R., Abedpour, N., Menon, R., Lakis, S., Heist, R. S., Büttner, R., Haas, S., Sequist, L. V., Shaw, A. T., Wong, K.-K., Hata, A. N., Toner, M., Maheswaran, S., Haber, D. A., Peifer, M., Dyson, N., Thomas, R. K. and Farago, A. F. (2018). "Genomic and Functional Fidelity of Small Cell Lung Cancer Patient-Derived Xenografts." Cancer Discovery 8(5): 600-615. www.ncbi.nlm.nih.gov/pubmed/29483136.

Fassunke, J., Müller, F., Keul, M., Michels, S., Dammert, M. A., Schmitt, A., Plenker, D., Lategahn, J., Heydt, C., Brägelmann, J., Tumbrink, H. L., Alber, Y., Klein, S., Heimsoeth, A., Dahmen, I., Fischer, R. N., Scheffler, M., Ihle, M. A., Priesner, V., Scheel, A. H., Wagener, S., Kron, A., Frank, K., Garbert, K., Persigehl, T., Püsken, M., Haneder, S., Schaaf, B., Rodermann, E., Engel-Riedel, W., Felip, E., Smit, E. F., Merkelbach-Bruse, S., Reinhardt, H. C., Kast, S. M., Wolf, J., Rauh, D., Büttner, R. and Sos, M. L. (2018). "Overcoming EGFRG724S-mediated osimertinib resistance through unique binding characteristics of second-generation EGFR inhibitors." Nature Communications 9(1): 4655. www.ncbi.nlm.nih.gov/pubmed/30405134.

Gao, F., Thiebes, S. and Sunyaev, A. (2018). "Rethinking the Meaning of Cloud Computing for Health Care: A Taxonomic Perspective and Future Research Directions." Journal of Medical Internet Research 20(7): e10041. www.ncbi.nlm.nih.gov/pubmed/29997108.

George, J., Walter, V., Peifer, M., Alexandrov, L. B., Seidel, D., Leenders, F., Maas, L., Müller, C., Dahmen, I., Delhomme, T. M., Ardin, M., Leblay, N., Byrnes, G., Sun, R., De Reynies, A., McLeer-Florin, A., Bosco, G., Malchers, F., Menon, R., Altmüller, J., Becker, C., Nürnberg, P., Achter, V., Lang, U., Schneider, P. M., Bogus, M., Soloway, M. G., Wilkerson, M. D., Cun, Y., McKay, J. D., Moro-Sibilot, D., Brambilla, C. G., Lantuejoul, S., Lemaitre, N., Soltermann, A., Weder, W., Tischler, V., Brustugun, O. T., Lund-Iversen, M., Helland, Å., Solberg, S., Ansén, S., Wright, G., Solomon, B., Roz, L., Pastorino, U., Petersen, I., Clement, J. H., Sänger, J., Wolf, J., Vingron, M., Zander, T., Perner, S., Travis, W. D., Haas, S. A., Olivier, M., Foll, M., Büttner, R., Hayes, D. N., Brambilla, E., Fernandez-Cuesta, L. and Thomas, R. K. (2018). "Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct subtypes of high-grade neuroendocrine lung tumors." Nature Communications 9(1): 1048. www.ncbi.nlm.nih.gov/pubmed/29535388.

Herling, C. D., Abedpour, N., Weiss, J., Schmitt, A., Jachimowicz, R. D., Merkel, O., Cartolano, M., Oberbeck, S., Mayer, P., Berg, V., Thomalla, D., Kutsch, N., Stiefelhagen, M., Cramer, P., Wendtner, C.-M., Persigehl, T., Saleh, A., Altmüller, J., Nürnberg, P., Pallasch, C., Achter, V., Lang, U., Eichhorst, B., Castiglione, R., Schäfer, S. C., Büttner, R., Kreuzer, K.-A., Reinhardt, H. C., Hallek, M., Frenzel, L. P. and Peifer, M. (2018). "Clonal dynamics towards the development of venetoclax resistance in chronic lymphocytic leukemia." Nature Communications 9(1): 727. www.ncbi.nlm.nih.gov/pubmed/29463802.

Plenker, D., Bertrand, M., de Langen, A. J., Riedel, R., Lorenz, C., Scheel, A. H., Müller, J., Brägelmann, J., Daßler-Plenker, J., Kobe, C., Persigehl, T., Kluge, A., Wurdinger, T., Schellen, P., Hartmann, G., Zacherle, T., Menon, R., Thunnissen, E., Büttner, R., Griesinger, F., Wolf, J., Heukamp, L., Sos, M. L. and Heuckmann, J. M. (2018). "Structural Alterations of MET Trigger Response to MET Kinase Inhibition in Lung Adenocarcinoma Patients." Clinical Cancer Research: An Official Journal of the American Association for Cancer Research 24(6): 1337-1343. www.ncbi.nlm.nih.gov/pubmed/29284707.

Brägelmann, J., Böhm, S., Guthrie, M.R., Mollaoglu, G., Oliver, T.G., Sos, M.L., 2017a. Family matters: How MYC family oncogenes impact small cell lung cancer. Cell Cycle 16, 1489–1498. doi.org/10.1080/15384101.2017.1339849

Brägelmann, J., Dammert, M.A., Dietlein, F., Heuckmann, J.M., Choidas, A., Böhm, S., Richters, A., Basu, D., Tischler, V., Lorenz, C., Habenberger, P., Fang, Z., Ortiz-Cuaran, S., Leenders, F., Eickhoff, J., Koch, U., Getlik, M., Termathe, M., Sallouh, M., Greff, Z., Varga, Z., Balke-Want, H., French, C.A., Peifer, M., Reinhardt, H.C., Örfi, L., Kéri, G., Ansén, S., Heukamp, L.C., Büttner, R., Rauh, D., Klebl, B.M., Thomas, R.K., Sos, M.L., 2017b. Systematic Kinase Inhibitor Profiling Identifies CDK9 as a Synthetic Lethal Target in NUT Midline Carcinoma. Cell Reports 20, 2833–2845. doi.org/10.1016/j.celrep.2017.08.082

Büttner, R., Wolf, J., Thomas, R.K., Sos, M.L., 2017. Resistance Mechanisms to AZD9291 and Rociletinib-Response. Clin. Cancer Res. 23, 3967–3968. doi.org/10.1158/1078-0432.CCR-17-0948

Knittel, G., Rehkämper, T., Korovkina, D., Liedgens, P., Fritz, C., Torgovnick, A., Al-Baldawi, Y., Al-Maarri, M., Cun, Y., Fedorchenko, O., Riabinska, A., Beleggia, F., Nguyen, P.-H., Wunderlich, F.T., Ortmann, M., Montesinos-Rongen, M., Tausch, E., Stilgenbauer, S., P Frenzel, L., Herling, M., Herling, C., Bahlo, J., Hallek, M., Peifer, M., Buettner, R., Persigehl, T., Reinhardt, H.C., 2017. Two mouse models reveal an actionable PARP1 dependence in aggressive chronic lymphocytic leukemia. Nat Commun 8, 153. doi.org/10.1038/s41467-017-00210-6

Malchers, F., Ercanoglu, M.S., Schütte, D., Castiglione, R., Tischler, V., Michels, S., Dahmen, I., Brägelmann, J., Menon, R., Heuckmann, J.M., George, J., Ansén, S., Sos, M.L., Soltermann, A., Peifer, M., Wolf, J., Büttner, R., Thomas, R.K., 2017. Mechanisms of primary drug resistance in FGFR1 amplified lung cancer. Clin. Cancer Res. doi.org/10.1158/1078-0432.CCR-17-0478

Mollaoglu, G., Guthrie, M.R., Böhm, S., Brägelmann, J., Can, I., Ballieu, P.M., Marx, A., George, J., Heinen, C., Chalishazar, M.D., Cheng, H., Ireland, A.S., Denning, K.E., Mukhopadhyay, A., Vahrenkamp, J.M., Berrett, K.C., Mosbruger, T.L., Wang, J., Kohan, J.L., Salama, M.E., Witt, B.L., Peifer, M., Thomas, R.K., Gertz, J., Johnson, J.E., Gazdar, A.F., Wechsler-Reya, R.J., Sos, M.L., Oliver, T.G., 2017. MYC Drives Progression of Small Cell Lung Cancer to a Variant Neuroendocrine Subtype with Vulnerability to Aurora Kinase Inhibition. Cancer Cell. doi.org/10.1016/j.ccell.2016.12.005

Plenker, D., Riedel, M., Brägelmann, J., Dammert, M.A., Chauhan, R., Knowles, P.P., Lorenz, C., Keul, M., Bührmann, M., Pagel, O., Tischler, V., Scheel, A.H., Schütte, D., Song, Y., Stark, J., Mrugalla, F., Alber, Y., Richters, A., Engel, J., Leenders, F., Heuckmann, J.M., Wolf, J., Diebold, J., Pall, G., Peifer, M., Aerts, M., Gevaert, K., Zahedi, R.P., Buettner, R., Shokat, K.M., McDonald, N.Q., Kast, S.M., Gautschi, O., Thomas, R.K., Sos, M.L., 2017. Drugging the catalytically inactive state of RET kinase in RET-rearranged tumors. Sci Transl Med 9. doi.org/10.1126/scitranslmed.aah6144

Schmitt, A., Knittel, G., Welcker, D., Yang, T.-P., George, J., Nowak, M., Leeser, U., Büttner, R., Perner, S., Peifer, M., Reinhardt, H.C., 2017. ATM Deficiency Is Associated with Sensitivity to PARP1- and ATR Inhibitors in Lung Adenocarcinoma. Cancer Res. doi.org/10.1158/0008-5472.CAN-16-3398

Weischenfeldt, J., Dubash, T., Drainas, A.P., Mardin, B.R., Chen, Y., Stütz, A.M., Waszak, S.M., Bosco, G., Halvorsen, A.R., Raeder, B., Efthymiopoulos, T., Erkek, S., Siegl, C., Brenner, H., Brustugun, O.T., Dieter, S.M., Northcott, P.A., Petersen, I., Pfister, S.M., Schneider, M., Solberg, S.K., Thunissen, E., Weichert, W., Zichner, T., Thomas, R., Peifer, M., Helland, A., Ball, C.R., Jechlinger, M., Sotillo, R., Glimm, H., Korbel, J.O., 2017. Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking. Nat. Genet. 49, 65–74. doi.org/10.1038/ng.3722

Ortiz-Cuaran, S., Scheffler, M., Plenker, D., Dahmen, L., Scheel, A.H., Fernandez-Cuesta, L., Meder, L., Lovly, C.M., Persigehl, T., Merkelbach-Bruse, S., Bos, M., Michels, S., Fischer, R., Albus, K., König, K., Schildhaus, H.-U., Fassunke, J., Ihle, M.A., Pasternack, H., Heydt, C., Becker, C., Altmüller, J., Ji, H., Müller, C., Florin, A., Heuckmann, J.M., Nuernberg, P., Ansén, S., Heukamp, L.C., Berg, J., Pao, W., Peifer, M., Buettner, R., Wolf, J., Thomas, R.K., Sos, M.L., 2016. Heterogeneous Mechanisms of Primary and Acquired Resistance to Third-Generation EGFR Inhibitors. Clin. Cancer Res. 22, 4837–4847. doi.org/10.1158/1078-0432.CCR-15-1915

Rehimi, R., Nikolic, M., Cruz-Molina, S., Tebartz, C., Frommolt, P., Mahabir, E., Clément-Ziza, M., Rada-Iglesias, A., 2016. Epigenomics-Based Identification of Major Cell Identity Regulators within Heterogeneous Cell Populations. Cell Rep 17, 3062–3076. doi.org/10.1016/j.celrep.2016.11.046

Thiebes, S., Dehling, T., Sunyaev, A., 2016. One Size Does Not Fit All: Information Security and Information Privacy for Genomic Cloud Services (SSRN Scholarly Paper No. ID 2770946). Social Science Research Network, Rochester, NY.

Dehling, T., Gao, F., Schneider, S., Sunyaev, A., 2015. Exploring the Far Side of Mobile Health: Information Security and Privacy of Mobile Health Apps on iOS and Android. JMIR mHealth and uHealth 3, e8. doi.org/10.2196/mhealth.3672

Engel, J., Richters, A., Getlik, M., Tomassi, S., Keul, M., Termathe, M., Lategahn, J., Becker, C., Mayer-Wrangowski, S., Grütter, C., Uhlenbrock, N., Krüll, J., Schaumann, N., Eppmann, S., Kibies, P., Hoffgaard, F., Heil, J., Menninger, S., Ortiz-Cuaran, S., Heuckmann, J.M., Tinnefeld, V., Zahedi, R.P., Sos, M.L., Schultz-Fademrecht, C., Thomas, R.K., Kast, S.M., Rauh, D., 2015. Targeting Drug Resistance in EGFR with Covalent Inhibitors: A Structure-Based Design Approach. J. Med. Chem. 58, 6844–6863. doi.org/10.1021/acs.jmedchem.5b01082

Gandara, D.R., Hammerman, P.S., Sos, M.L., Lara, P.N., Hirsch, F.R., 2015. Squamous cell lung cancer: from tumor genomics to cancer therapeutics. Clin. Cancer Res. 21, 2236–2243. doi.org/10.1158/1078-0432.CCR-14-3039

George, J., Lim, J.S., Jang, S.J., Cun, Y., Ozretić, L., Kong, G., Leenders, F., Lu, X., Fernández-Cuesta, L., Bosco, G., Müller, C., Dahmen, I., Jahchan, N.S., Park, K.-S., Yang, D., Karnezis, A.N., Vaka, D., Torres, A., Wang, M.S., Korbel, J.O., Menon, R., Chun, S.-M., Kim, D., Wilkerson, M., Hayes, N., Engelmann, D., Pützer, B., Bos, M., Michels, S., Vlasic, I., Seidel, D., Pinther, B., Schaub, P., Becker, C., Altmüller, J., Yokota, J., Kohno, T., Iwakawa, R., Tsuta, K., Noguchi, M., Muley, T., Hoffmann, H., Schnabel, P.A., Petersen, I., Chen, Y., Soltermann, A., Tischler, V., Choi, C., Kim, Y.-H., Massion, P.P., Zou, Y., Jovanovic, D., Kontic, M., Wright, G.M., Russell, P.A., Solomon, B., Koch, I., Lindner, M., Muscarella, L.A., la Torre, A., Field, J.K., Jakopovic, M., Knezevic, J., Castaños-Vélez, E., Roz, L., Pastorino, U., Brustugun, O.-T., Lund-Iversen, M., Thunnissen, E., Köhler, J., Schuler, M., Botling, J., Sandelin, M., Sanchez-Cespedes, M., Salvesen, H.B., Achter, V., Lang, U., Bogus, M., Schneider, P.M., Zander, T., Ansén, S., Hallek, M., Wolf, J., Vingron, M., Yatabe, Y., Travis, W.D., Nürnberg, P., Reinhardt, C., Perner, S., Heukamp, L., Büttner, R., Haas, S.A., Brambilla, E., Peifer, M., Sage, J., Thomas, R.K., 2015. Comprehensive genomic profiles of small cell lung cancer. Nature 524, 47–53. doi.org/10.1038/nature14664

Peifer, M., Hertwig, F., Roels, F., Dreidax, D., Gartlgruber, M., Menon, R., Krämer, A., Roncaioli, J.L., Sand, F., Heuckmann, J.M., Ikram, F., Schmidt, R., Ackermann, S., Engesser, A., Kahlert, Y., Vogel, W., Altmüller, J., Nürnberg, P., Thierry-Mieg, J., Thierry-Mieg, D., Mariappan, A., Heynck, S., Mariotti, E., Henrich, K.-O., Gloeckner, C., Bosco, G., Leuschner, I., Schweiger, M.R., Savelyeva, L., Watkins, S.C., Shao, C., Bell, E., Höfer, T., Achter, V., Lang, U., Theissen, J., Volland, R., Saadati, M., Eggert, A., de Wilde, B., Berthold, F., Peng, Z., Zhao, C., Shi, L., Ortmann, M., Büttner, R., Perner, S., Hero, B., Schramm, A., Schulte, J.H., Herrmann, C., O’Sullivan, R.J., Westermann, F., Thomas, R.K., Fischer, M., 2015. Telomerase activation by genomic rearrangements in high-risk neuroblastoma. Nature 526, 700–704. http://doi.org/10.1038/nature14980