Division Signaling and Functional Genomics
Publications
2012
Sandmann, T., Boutros, M. (2012). Screens, maps & networks: from genome sequences to personalized medicine. Curr Opin Genet Dev. 22(1):36-44. » Link
Shamu, C.E., Wiemann, S., Boutros, M. (2012). On target: a public repository for large-scale RNAi experiments. Nat Cell Biol. 14(2):115.
Augustin, I., Goidts, V., Bongers, A., Kerr, G., Vollert, G., Radlwimmer, B., Hartmann, C., Herold-Mende, C., Reifenberger, G., von Deimling, A., Boutros, M. (2011). The Wnt secretion protein Evi/Gpr177 promotes glioma tumorigenesis. EMBO Molecular Medicine 4(1):38-51. doi: 10.1002/emmm.201100186.
2011
Gilbert, D.F., Erdmann, G., Zhang, X., Fritzsche, A., Demir, K., Jaedicke, A., Muehlenberg, K., Wanker, EE., Boutros, M. (2011). A Novel Multiplex Cell Viability Assay for High-Throughput RNAi Screening. PLoS One 6(12):e28338.
Horn, T., Boutros, M. (2011). Design of RNAi reagents for invertebrate model organisms and human disease vectors. Nature Precedings 10101/npre.2011.6665.1
Buechling, T., Chaudhary, V., Spirohn, K., Weiss, M., Boutros, M. (2011). p24 proteins are required for secretion of Wnt ligands. EMBO reports 12(12):1265-72.
Glinka, A., Dolde, C., Kirsch, N., Huang, Y.L., Kazanskaya, O., Ingelfinger, D., Boutros, M., Cruciat, C.-M., Niehrs, C. (2011). LGR4 and LGR5 are R-spondin receptors mediating Wnt/beta-catenin and Wnt/PCP signaling. EMBO reports 12(10):1055-61.
Zacharogianni, M., Kondylis, V., Tang, Y., Farhan, H., Xanthakis, D., Fuchs, F., Boutros, M., Rabouille, C. (2011). ERK7 is a negative regulator of protein secretion in response to amino acid starvation. EMBO Journal 30(18):3684-700.
Sandmann, T., Vogg, M.C., Owlarn, S., Boutros, M., Bartscherer, K. (2011). The head-regeneration transcriptome of the planarian Schmidtea mediterranea. Genome Biology 12(8):R76.
Axelsson, E., Sandmann, T., Horn, T., Boutros, M., Huber, W. Fischer, B. (2011). Extracting quantitative genetic interaction phenotypes from matrix combinatorial RNAi. BMC Bioinformatics 12:342.
Horn, T., Sandmann, T., Fischer, B., Axelsson, E., Huber, W., Boutros, M. (2011). Mapping of signaling networks through synthetic genetic interaction analysis by RNAi. Nat Methods 8(4):341-6. 10.1038/nmeth.1581
Ragab, A., Buechling, T., Gesellchen, V., Spirohn, K., Boettcher, AL., Boutros, M. (2011). Drosophila Ras/MAPK signalling regulates innate immune responses in immune and intestinal stem cells. EMBO J. 30(6):1123-36. 10.1038/emboj.2011.4
Metzig, M., Nickles, D., Boutros M. (2011). Large-scale RNAi screens to dissect TNF and NF-κB signaling pathways. Adv Exp Med Biol. 691:131-9.
Huhn, S., Ingelfinger, D., Bermejo, JL., Bevier, M., Pardini, B., Naccarati, A., Steinke, V., Rahner, N., Holinski-Feder, E., Morak, M., Schackert, HK., Görgens, H., Pox, CP., Goecke, T., Kloor, M., Loeffler, M., Büttner, R., Vodickova, L., Novotny, J., Demir, K., Cruciat, CM., Renneberg, R., Huber, W., Niehrs, C., Boutros, M., Propping, P., Vodièka, P., Hemminki, K., Försti, A. (2011). Polymorphisms in CTNNBL1 in relation to colorectal cancer with evolutionary implications. Int J Mol Epidemiol Genet. 2(1):36-50.
Liang, J., Fu, Y., Cruciat, CM., Jia, S., Wang, Y., Tong, Z., Tao, Q., Ingelfinger, D., Boutros, M., Meng, A., Niehrs, C., Wu, W. (2011). Transmembrane Protein 198 Promotes LRP6 Phosphorylation and Wnt Signaling Activation. Mol Cell Biol. 31(13):2577-90.
Kondylis, V., Tang, Y., Fuchs, F., Boutros, M., Rabouille, C. (2011). Identification of ER Proteins involved in the Functional Organisation of the Early Secretory Pathway in Drosophila Cells by a Targeted RNAi Screen. PLOS One 6(2):e17173.
2010
Gilboa, L., Boutros, M. (2010). Celebrating 100 years of Drosophila research. EMBO reports 11(10):724-6. link
Müller, H., Schmidt, D., Steinbrink, S., Mirgorodskaya, E., Lehmann, V., Habermann, K., Dreher, F., Gustavsson, N., Kessler, T., Lehrach, H., Herwig, R., Gobom, J., Ploubidou, A., Boutros, M., Lange, B.M. (2010). Proteomic and functional analysis of the mitotic Drosophila centrosome. EMBO Journal 29(19):3344-57. link
Niehrs, C., Boutros, M. (2010). Trafficking, Acidification, and Growth Factors Signaling. Science Signaling 3(134):pe26. link
Buechling, T., Bartscherer, K., Ohkawara, B., Chaudhary, V., Spirohn, K., Niehrs, C., Boutros., M. (2010). Wnt/Frizzled signaling requires dPRR, the Drosophila homolog of the prorenin receptor. Current Biology 20(14):1263-1268. link
Horn, T., Sandmann, T., Boutros., M. (2010). Design and evaluation of genome-wide libraries for RNAi screens. Genome Biology 11(6):R61. link companion website
Fuchs, F., Pau, G., Kranz, D., Sklyar, O., Budjan, C., Steinbrink, S., Horn, T., Pedal, A., Huber, W., Boutros, M. (2010). Clustering phenotype populations by genome-wide RNAi and multiparametric imaging. Molecular Systems Biology 6:370. link companion website
Leber, B., Maier, B., Fuchs, F., Chi, J., Riffel, P., Anderhub, S., Wagner, L., Ho, A.D., Salisbury, J.L., Boutros, M., Krämer, A. (2010). Proteins required for centrosome clustering in cancer cells. Science Translational Medicine 2(33):33ra38. link
Saj, A., Arziman, Z., Stempfle, D., van Belle, W., Sauder, U., Horn, T., Dürrenberger, M., Paro, R., Boutros, M., Merdes, G. (2010). A combined ex vivo and in vivo RNAi screen for notch regulators in Drosophila reveals an extensive notch interaction network. Developmental Cell 18(5):862-76.
Horn, T., Boutros, M. (2010). E-RNAi: a web application for the multi-species design of RNAi reagents - 2010 update. Nucleic Acids Research 38:W332-339. link tool
Pelz, O., Gilsdorf, M., Boutros, M. (2010). web cellHTS: A web application for the analysis of high-throughput screening data. BMC Bioinformatics 11:185. link tool source
Gobert, V., Osman, D., Bras, S., Auge, B., Boube, M., Bourbon, H.M., Horn, T., Boutros, M., Haenlin, M., Waltzer, L. (2010). A genome-wide RNA interference screen identifies a differential role of the Mediator CDK8 module subunits for GATA/RUNX-activated transcription in Drosophila. Mol Cell Biol. 30(11):2837-48. link
Falschlehner, C., Steinbrink, S., Erdmann, G., Boutros, M. (2010). High-throughput RNAi screening to dissect cellular pathways: a how-to guide. Biotechnology J. 5(4):368-76. link
Pau, G., Fuchs, F., Sklyar, O., Boutros, M., Huber, W. (2010). EBImage - an R package for image processing with applications to cellular phenotypes. Bioinformatics 26(7):979-81. link
Cruciat, C.M., Ohkawara, B., Acebron, S.P., Karaulanov, E., Reinhard, C., Ingelfinger, D., Boutros, M., Niehrs, C. (2010). Requirement of prorenin receptor an vacuolar H+-ATPase-mediated acidification for Wnt signaling. Science 327(5964):459-63.
Gilsdorf, M., Horn, T., Arziman, Z., Pelz, O., Kiner E., Boutros, M. (2010). GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 Update. Nucleic Acids Research 38:D448-52. link database
Kuttenkeuler, D., Pelte, N., Ragab, A., Gesellchen, V., Schneider, L., Blass, C., Axelsson, E., Huber, W., Boutros, M. (2010). A Large-Scale RNAi Screen Identifies Deaf1 as a Regulator of Innate Immune Responses in Drosophila. Journal of Innate Immunity 2(2):181-194. link
2009
Davidson, G., Shen, J., Huang, Y.L., Su, Y., Karaulanov, E., Bartscherer, K., Hassler, C., Stannek, P., Boutros, M., Niehrs, C. (2009). Cell cycle control of Wnt receptor activation. Developmental Cell 17:788-99.
Mleczko-Sanecka, K., Casanovas, G., Ragab, A., Breitkopf, K., Muller, A., Boutros, M., Dooley, S., Hentze, M.W., Muckenthaler, M.U. (2009). SMAD7 controls iron metabolism as a potent inhibitor of hepcidin expression. Blood Epub ahead of print
Farfsing, A., Engel, F., Seiffert, M., Hartmann, E., Ott, G., Rosenwald, A., Stilgenbauer, S., Döhner, H., Boutros, M., Lichter, P., Pscherer, A. (2009). Gene knockdown studies revealed CCDC50 as a candidate gene in mantle cell lymphoma and chronic lymphocytic leukemia. Leukemia 11:2018-26.
Simons, M., Gault, W.J., Gotthardt, D., Rohatgi, R., Klein, T.J., Shao, Y., Lee, H.J., Wu, A.L., Fang, Y., Satlin, L.M., Dow, J.T., Chen, J., Zheng, J., Boutros, M., Mlodzik, M. (2009). Electrochemical cues regulate assembly of the Frizzled/Dishevelled complex at the plasma membrane during planar epithelial polarization. Nat Cell Biol., 11:286-94.
Gauhar, Z., Sun, L.V., Hua, S., Mason, C.E., Fuchs, F., Li, T.R., Boutros, M., White, K.P. (2009). Genomic mapping of binding regions for the ecdysone receptor protein complex. Genome Research 19:1006-1013.
Adell, T., Salo, E., Boutros, M., Bartscherer, K. (2009). Smed-Evi/Wntless is required for b-catenin-dependent and –independent processes during planarian regeneration. Development 136:905-910.
2008
Bartscherer, K., Boutros, M. (2008). Regulation of Wnt protein secretion and its role in gradient formation. EMBO Reports 9:977-982.
Steinbrink, S., Boutros, M. (2008). RNAi screening in cultured Drosophila cells. Methods Mol. Biol. 420:139-1353. link
Mueller, P., Boutros, M., Zeidler, M. (2008). Identification of JAK/STAT pathway regulators-Insights from RNAi screens. Seminar Cell Dev. Biol. 19:360-369. Link
Boutros, M., Ahringer, J. (2008). The art and design of genetic screens: RNA interference. Nature Reviews Genetics 9:554-566. link
Stielow, B., Sapetschig, A., Krueger, I., Kunert, N., Brehm, A., Boutros, M., Suske, G. (2008). Identification of SUMO-dependent chromatin-associated transcriptional repression components by a genome-wide RNAi screen. Molecular Cell 29:742-754. link
Goto, A., Matsushita, K., Gesellchen, V., El Chamy L., Kuttenkeuler, D., Takeuchi, O., Hoffmann, J.A., Akira, S., Boutros, M., Reichhart, J.M. (2008). Akirins are highly conserved nuclear proteins required for NF-kappaB-dependent gene expression in Drosophila and mice. Nature Immunology 9:97-10. link
2007
Eulalio, A., Rehwinkel, J., Stricker, M., Huntzinger, E., Yang, S.F., Doerks, T., Dorner, S., Bork, P., Boutros, M. and Izaurralde, E. (2007). Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing. Genes Development 21:2558-2570. Link
Horn, T., Arziman, Z., Berger, J., Boutros, M. (2007). GenomeRNAi: a database for cell-based RNAi phenotypes. Nucleic Acid Research D492-7
2006
Boutros, M., Bras, L., Huber, W. (2006). Analysis of cell-based RNAi screens. Genome Biology R66 link website
Echeverri C.J., Beachy, P.A., Baum, B., Boutros, M., Buchholz, F., Chanda, S.K., Downward, J., Ellenberg, J., Fraser, A.G., Hacohen, N., Hahn, W.C., Jackson, A.L., Kiger, A., Linsley, P.S., Lum, L., Ma, Y., Mathey-Prevot, B., Root, D.E., Sabatini, D.M., Taipale, J., Perrimon, N., Bernards, R. (2006). Minimizing the risk of reporting false positives in large-scale RNAi screens. Nature Methods 3:777-9.
Bartscherer, K., Pelte, N., Ingelfinger, D., Boutros, M. (2006). Secretion of Wnt ligands requires Evi, a conserved transmembrane protein. Cell 125:523-33.
Fuchs, F., Boutros, M. (2006). Cellular phenotyping by RNAi. Brief Funct Genomic Proteomic 5:52-6.
2005
Gesellchen, V., Kuttenkeuler, D., Steckel, M., Pelte, N., Boutros, M. (2005). An RNAi screen identified a Role for IAP2 in Innate Immune Response in Drosophila. EMBO reports 6:979-984.
Muller, P., Kuttenkeuler, D., Gesellchen, V., Zeidler, M., Boutros, M. (2005). Identification of JAK/STAT signaling components by genome-wide RNAi. Nature 436:871-5. supplemental material
Arziman, Z., Horn, T., Boutros, M. (2005). E-RNAi: A web application to design optimized RNAi constructs. Nucleic Acids Research 33:W582-88. website
Armknecht, S., Boutros, M., Kiger, A., Nybakken, K., Mathey-Prevot, B., Perrimon, N. (2005). High-throughput RNA interference screens in Drosophila tissue culture cells. Methods Enzymology 392:55-73.
Choe, S. E., Boutros, M., Michelson, A.M., Church, G.M., Halfon, M.S. (2005). Preferred analysis methods for Affymetrix GeneChips revealed by a wholly-defined control dataset. Genome Biology R5. link
2004
Kuttenkeuler, D., Boutros, M. (2004). Genome-wide RNAi as a route to gene function in Drosophila. Brief Funct Genomic Proteomic 3:168-76.
Gesellchen, V., Boutros, M. (2004). Managing the genome: microRNAs in Drosophila. Differentiation 72:74-80.
Boutros, M., Kiger, A., Armknecht, S., Kerr, K., Hild, M., Koch, B., Haas, S., Heidelberg FlyArray, Paro, R., Perrimon, N. (2004). Genome-wide RNAi Analysis of Cell Growth and Viability in Drosophila. Science 303:832-835. supplemental material
2003
Hild M., Beckmann, B., Beckmann, B., Haas, S., Koch, B., Solovyev, V., Busold, C., Fellenberg, K., Boutros, M., Vingron, M., Sauer, F., Hoheisel, J. D., Paro, R. (2003). An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome. GenomeBiology 5:R3. link website
Agaisse A., Petersen, U.-M., Boutros, M., Mathey-Prevot, B., Perrimon, N. (2003). Signaling Role of Hemocytes in Drosophila JAK/STAT-Dependent Response to Septic Injury. Developmental Cell 5:441-50.
2002
Boutros, M., Agaisse, A., Perrimon, N. (2002). Sequential activation of signaling pathways during innate immune responses in Drosophila. Developmental Cell 3:711-22. supplemental material
Moon, R.T., Bowerman, B., Boutros, M., Perrimon, N. (2002). The promise and perils of Wnt signaling through beta-catenin. Science 296:1644-6.
2001
Boutros, M., Perrimon, N. (2001). Wnt/Fz signaling pathways in Drosophila. Science Technology Knowledge Environment (STKE). link
2000
Boutros, M., J. Mihaly, T. Bouwmeester, Mlodzik, M. (2000). Signaling specificity by Frizzled receptors in Drosophila. Science 288:1825-8.
Boutros, M., Perrimon, N. (2000). Drosophila genome takes flight. Nature Cell Biology 2:E53-4.
Wilson, A.C., Boutros, M., Johnson, K.M., Herr, W. (2000). HCF Amino- and Carboxy-Terminal Subunit Association through Two Separate Sets of Interaction Modules: Involvement of Fibronectin Type 3 Repeats. Molecular and Cellular Biology 20:6721-30.
1999
Boutros, M., Mlodzik M. (1999). Dishevelled: at the crossroads of divergent intracellular signaling pathways. Mechanisms of Development 83:27-37.
Paricio N., F. Feiguin, M. Boutros, S. Eaton, Mlodzik, M. (1999). The Drosophila STE20-like kinase misshapen is required downstream of the Frizzled receptor in planar polarity signaling. EMBO Journal 18:4669-78.
1998
Boutros, M., Paricio, N., Strutt, D., Mlodzik, M. (1998). Dishevelled activates JNK and discriminates between JNK pathways in planar polarity and wingless signaling. Cell 94:109-18.
1995
Chong, J. A., Tapia-Ramirez, J., Kim, S., Toledo-Aral, J.J., Zheng, Y., Boutros, M.C., Altshuller, Y.M., Frohman, M.A., Kraner, S.D., Mandel, G. (1995). REST: A Mammalian Silencer Protein That Restricts Sodium Channel Gene Expression to Neurons. Cell 80:949-57.
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