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Selected Publications

Betge, J., Rindtorff, N., Sauer, J., Rauscher, B., Dingert, C., Gaitantzi, H., Herweck, F., Srour-Mhanna, K., Miersch, T., Valentini, E., Boonekamp, K.E., Hauber, V., Gutting, T., Frank, L., Belle, S., Gaiser, T., Buchholz, I., Jesenofsky, R., Härtel, N., Zhan, T., Fischer, B., Breitkopf-Heinlein, K., Burgermeister, E., Ebert, M.P., Boutros, M. (2022). The drug-induced phenotypic landscape of colorectal cancer organoids. Nature Communications. 13:3135.

Zhou, J., Valentini, E., Boutros, M. (2021). Microenvironmental innate immune signaling and cell mechanical responses promote tumor growth. Developmental Cell 56:1884-1899.e5.

Zhan, T., Ambrosi, G., Wandmacher, A.M., Rauscher, B., Betge, J., Rindtorff, N., Häussler, R.S., Hinsenkamp, I., Bamberg, L., Hessling, B., Müller-Decker, K., Erdmann, G., Burgermeister, E., Ebert, M.P., Boutros, M. (2019). MEK inhibitors activate Wnt signalling and induce stem cell plasticity in colorectal cancer. Nature Communications 10:2197.

Rauscher, B., Heigwer, F., Henkel, L., Hielscher, T., Voloshanenko, O., Boutros, M. (2018). Toward an integrated map of genetic interactions in cancer cells. Molecular Systems Biology 14:e7656.

Billmann, M., Chaudhary, V., ElMaghraby, M.F., Fischer, B., Boutros, M. (2017). Widespread Rewiring of Genetic Networks upon Cancer Signaling Pathway Activation. Cell Systems S2405-4712:30485-4.

Voloshanenko, O., Erdmann, G., Dubash, T.D., Augustin, I., Metzig, M., Moffa, G., Hundsrucker, C., Kerr, G., Sandmann, T., Anchang, B., Demir, K., Boehm, C., Leible, S., Ball, C.R., Glimm, H., Spang, R., Boutros, M. (2013). Wnt secretion is required to maintain high levels of Wnt activity in colon cancer cells. Nature Communications 4:2610.

Laufer, C., Fischer, B., Billmann, M., Huber, W., Boutros, M. (2013). Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping. Nature Methods 10:427–431.

Gross, J., Chaudhary, V., Bartscherer, K., Boutros, M. (2012). Active Wnt proteins aresecreted on exosomes. Nature Cell Biology 14:1036-45.

Bartscherer, K., Pelte, N., Ingelfinger, D., Boutros, M. (2006). Secretion of Wnt ligands requires Evi, a conserved transmembrane protein. Cell 125:523-33.

Boutros, M., Kiger, A., Armknecht, S., Kerr, K., Hild, M., Koch, B., Haas, S., HD FlyArray, Paro, R., Perrimon, N. (2004). Genome-wide RNAi Analysis of Cell Growth and Viability in Drosophila. Science 303:832-835.

Boutros, M., Mihaly, J., Bouwmeester, T., Mlodzik, M. (2000). Signaling specificity by Frizzled receptors in Drosophila. Science 288:1825-8.

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.



Complete List of Publications


Bamberg, L.V., Heigwer, F., Wandmacher, A.M., Singh, A., Betge, J., Rindtorff, N., Werner, J., Josten, J., Skabkina, O.V., Hinsenkamp, I., Erdmann, G., Röcken, C., Ebert, M.P., Burgermeister, E., Zhan, T., Boutros, M. (2022). Targeting euchromatic histone lysine methyltransferases sensitizes colorectal cancer to histone deacetylase inhibitors. Int J Cancer. 151:1586-1601.

Solary, E., Blanc, P., Boutros, M., Girvalaki, C., Locatelli, F., Medema, R.H., Nagy, P., Tabernero, J. (2022)., a European initiative to UNderstand CANcer. Cancer Discov. 8:CD-22-0970.

Imkeller, K., Ambrosi, G., Klemm, N., Claveras Cabezudo, A., Henkel, L., Huber, W., Boutros, M. (2022). Metabolic balance in colorectal cancer is maintained by optimal Wnt signaling levels. Mol Syst Biol. 18:e10874.

Schubert, A., Voloshanenko, O., Ragaller, F., Gmach, P., Kranz, D., Scheeder, C., Miersch, T., Schulz, M., Trümper, L., Binder, C., Lampe, M., Engel, U., Boutros, M. (2022). Superresolution microscopy localizes endogenous Dvl2 to Wnt signaling-responsive biomolecular condensates. Proc Natl Acad Sci U S A. 119:e2122476119.

Betge, J., Rindtorff, N., Sauer, J., Rauscher, B., Dingert, C., Gaitantzi, H., Herweck, F., Srour-Mhanna, K., Miersch, T., Valentini, E., Boonekamp, K.E., Hauber, V., Gutting, T., Frank, L., Belle, S., Gaiser, T., Buchholz, I., Jesenofsky, R., Härtel, N., Zhan, T., Fischer, B., Breitkopf-Heinlein, K., Burgermeister, E., Ebert, M.P., Boutros, M. (2022). The drug-induced phenotypic landscape of colorectal cancer organoids. Nat Commun. 13:3135.

Sorrentino, A., Menevse, A.N., Michels, T., Volpin, V., Durst, F.C., Sax, J., Xydia, M., Hussein, A., Stamova, S., Spoerl, S., Heuschneider, N., Muehlbauer, J., Jeltsch, K.M., Rathinasamy, A., Werner-Klein, M., Breinig, M., Mikietyn, D., Kohler, C., Poschke, I., Purr, S., Reidell, O., Martins Freire, C., Offringa, R., Gebhard, C., Spang, R., Rehli, M., Boutros, M., Schmidl, C., Khandelwal, N., Beckhove, P. (2022). Salt-inducible kinase 3 protects tumor cells from cytotoxic T-cell attack by promoting TNF-induced NF-κB activation. J Immunother Cancer. 10:e004258.

Echle, A., Ghaffari Laleh, N., Quirke, P., Grabsch, H.I., Muti, H.S., Saldanha, O.L., Brockmoeller, S.F., van den Brandt, P.A., Hutchins, G.G.A., Richman, S.D., Horisberger, K., Galata, C., Ebert, M.P., Eckardt, M., Boutros, M., Horst, D., Reissfelder, C., Alwers, E., Brinker, T.J., Langer, R., Jenniskens, J.C.A., Offermans, K., Mueller, W., Gray, R., Gruber, S.B., Greenson, J.K., Rennert, G., Bonner, J.D., Schmolze, D., Chang-Claude, J., Brenner, H., Trautwein, C., Boor, P., Jaeger, D., Gaisa, N.T., Hoffmeister, M., West, N.P., Kather, J.N. (2022). Artificial intelligence for detection of microsatellite instability in colorectal cancer-a multicentric analysis of a pre-screening tool for clinical application. ESMO Open. 7:100400.

Port, F., Boutros, M. (2022). Tissue-Specific CRISPR-Cas9 Screening in Drosophila. Methods Mol Biol. 2540:157-176.

Neufeldt, C.J., Cerikanm, B., Cortese, M., Frankish, J., Lee, J.Y., Plociennikowska, A., Heigwer, F., Prasad, V., Joecks, S., Burkart, S.S., Zander, D.Y., Subramanian, B., Gimi, R., Padmanabhan, S., Iyer, R., Gendarme, M., El Debs, B., Halama, N., Merle, U., Boutros, M., Binder, M., Bartenschlager, R. (2022). SARS-CoV-2 infection induces a pro-inflammatory cytokine response through cGAS-STING and NF-κB. Commun Biol. 5:45.

Ambrosi, G., Voloshanenko, O., Eckert, A.F., Kranz, D., Nienhaus, G.U., Boutros, M. (2022). Allele-specific endogenous tagging and quantitative analysis of β-catenin in colorectal cancer cells. eLife. 11:e64498.

Bahuguna, S., Atilano, M., Glittenberg, M., Lee, D., Arora, S., Wang, L., Zhou, J., Redhai, S., Boutros, M., Ligoxygakis, P. (2022). Bacterial recognition by PGRP-SA and downstream signalling by Toll/DIF sustain commensal gut bacteria in Drosophila. PLoS Genet. 18:e1009992.


Bahuguna, S., Redhai, S., Zhou, J., Wang, T., Port, F., Boutros, M. (2021). Conditional CRISPR-Cas Genome Editing in Drosophila to Generate Intestinal Tumors. Cells. 10:3156.

Wolf, L.M., Lambert, A.M., Haenlin, J., Boutros, M. (2021). EVI/WLS function is regulated by ubiquitylation and is linked to ER-associated degradation by ERLIN2. J Cell Sci. 134:jcs257790.

Zhou, J., Valentini, E., Boutros, M. (2021). Microenvironmental innate immune signaling and cell mechanical responses promote tumor growth. Dev Cell. 56:1884-1899.e5.

Graf, F., Horn, P., Ho, A.D., Boutros, M., Maercker, C. (2021). The extracellular matrix proteins type I collagen, type III collagen, fibronectin, and laminin 421 stimulate migration of cancer cells. FASEB J. 35:e21692.

Inverso, D., Shi, J., Lee, K.H., Jakab, M., Ben-Moshe, S., Kulkarni, S.R., Schneider, M., Wang, G., Komeili, M., Vélez, P.A., Riedel, M., Spegg, C., Ruppert, T., Schaeffer-Reiss, C., Helm, D., Singh, I., Boutros, M., Chintharlapalli, S., Heikenwalder, M., Itzkovitz, S., Augustin, H.G. (2021). A spatial vascular transcriptomic, proteomic, and phosphoproteomic atlas unveils an angiocrine Tie-Wnt signaling axis in the liver. Dev Cell. 56:1677-1693.e10.

Redhai, S., Boutros, M. (2021). The Role of Organelles in Intestinal Function, Physiology, and Disease. Trends Cell Biol. 31:485-499.

Gutting, T., Hauber, V., Pahl, J., Klapproth, K., Wu, W., Dobrota, I., Herweck, F., Reichling, J., Helm, L., Schroeder, T., Li, B., Weidner, P., Zhan, T., Eckardt, M., Betge, J., Belle, S., Sticht, C., Gaiser, T., Boutros, M., Ebert, M.P.A., Cerwenka, A., Burgermeister, E. (2021). PPARγ induces PD-L1 expression in MSS+ colorectal cancer cells. Oncoimmunology. 10:1906500.

Zhan, T., Faehling, V., Rauscher, B., Betge, J., Ebert, M.P., Boutros, M. (2021). Multi-omics integration identifies a selective vulnerability of colorectal cancer subtypes to YM155. Int J Cancer. 148:1948-1963.

Kohrs, F.E., Daumann, I.M., Pavlovic, B., Jin, E.J., Kiral, F.R., Lin, S.C., Port, F., Wolfenberg, H., Mathejczyk, T.F., Linneweber, G.A., Chan, C.C., Boutros, M., Hiesinger, P.R. (2021). Systematic functional analysis of rab GTPases reveals limits of neuronal robustness to environmental challenges in flies. eLife. 10:e59594.

Schubert, A., Boutros, M. (2021). Extracellular vesicles and oncogenic signaling. Mol Oncol. 15:3-26.

Heigwer, F., Boutros, M. (2021). Cloud-Based Design of Short Guide RNA (sgRNA) Libraries for CRISPR Experiments. Methods Mol Biol. 2162:3-22.

Bock, C., Boutros, M., Camp, J.G., Clarke, L., Clevers, H., Knoblich, J.A., Liberali, P., Regev, A., Rios, A.C., Stegle, O., Stunnenberg, H.G., Teichmann, S.A., Treutlein, B., Vries, R.G.J.; Human Cell Atlas 'Biological Network' Organoids. (2021). The Organoid Cell Atlas. Nat Biotechnol. 39:13-17.


Lin, Y.C., Haas, A., Bufe, A., Parbin, S., Hennecke, M., Voloshanenko, O., Gross, J., Boutros, M., Acebron, S.P., Bastians, H. (2020). Wnt10b-GSK3β-dependent Wnt/STOP signaling prevents aneuploidy in human somatic cells. Life Sci Alliance. 4:e202000855.

Henkel, L., Rauscher, B., Schmitt, B., Winter, J., Boutros, M. (2020). Genome-scale CRISPR screening at high sensitivity with an empirically designed sgRNA library. BMC Biol. 18:174.

Conlon, T.M., John-Schuster, G., Heide, D., Pfister, D., Lehmann, M., Hu, Y., Ertüz, Z., Lopez, MA., Ansari, M., Strunz, M., Mayr, C., Angelidis, I., Ciminieri, C., Costa, R., Kohlhepp, M.S., Guillot, A., Günes, G., Jeridi, A., Funk, M.C., Beroshvili, G., Prokosch, S., Hetzer, J., Verleden, S.E., Alsafadi, H., Lindner, M., Burgstaller, G., Becker, L., Irmler, M., Dudek, M., Janzen, J., Goffin, E., Gosens, R., Knolle, P., Pirotte, B., Stoeger, T., Beckers, J., Wagner, D., Singh, I., Theis, F.J., de Angelis, M.H., O'Connor, T., Tacke, F., Boutros, M., Dejardin, E., Eickelberg, O., Schiller, H.B., Königshoff, M., Heikenwalder, M., Yildirim, A.Ö. (2020). Inhibition of LTβR signalling activates WNT-induced regeneration in lung. Nature. 588:151-156.

Port, F., Starostecka, M., Boutros, M. (2020). Multiplexed conditional genome editing with Cas12a in Drosophila. Proc Natl Acad Sci U S A. 117:22890-22899.

Volpin, V., Michels, T., Sorrentino, A., Menevse, A.N., Knoll, G., Ditz, M., Milenkovic, V.M., Chen, C.Y., Rathinasamy, A., Griewank, K., Boutros, M., Haferkamp, S., Berneburg, M., Wetzel, C.H., Seckinger, A., Hose, D., Goldschmidt, H., Ehrenschwender, M., Witzens-Harig, M., Szoor, A., Vereb, G., Khandelwal, N., Beckhove, P. (2020). CAMK1D Triggers Immune Resistance of Human Tumor Cells Refractory to Anti-PD-L1 Treatment. Cancer Immunol Res. 8:1163-1179.

Zhan, T., Belle, S., Valentini, E., Herrmann, S., Miersch, T., Li, M., Gaiser, T., Boutros, M., Ebert, M.P., Betge, J. (2020). Cancer-Associated Mutations in Normal Colorectal Mucosa Adjacent to Sporadic Neoplasia. Clin Transl Gastroenterol. 11:e00212.

Funk, M.C., Zhou, J., Boutros, M. (2020). Ageing, metabolism and the intestine. EMBO Rep. 21:e50047.

Gaub, A., Sheikh, B.N., Basilicata, M.F., Vincent, M., Nizon, M., Colson, C., Bird, M.J., Bradner, J.E., Thevenon, J., Boutros, M., Akhtar, A. (2020). Evolutionary conserved NSL complex/BRD4 axis controls transcription activation via histone acetylation. Nat Commun. 11:2243.

Wesslowski, J., Kozielewicz, P., Wang, X., Cui, H., Schihada, H., Kranz, D., Karuna, M.P., Levkin, P., Gross, J.C., Boutros, M., Schulte, G., Davidson, G. (2020). eGFP-tagged Wnt-3a enables functional analysis of Wnt trafficking and signaling and kinetic assessment of Wnt binding to full-length Frizzled. J Biol Chem. 295:8759-8774.

Michels, B.E., Mosa, M.H., Streibl, B.I., Zhan, T., Menche, C., Abou-El-Ardat, K., Darvishi, T., Członka, E., Wagner, S., Winter, J., Medyouf, H., Boutros ,M., Farin, H.F. (2020). Pooled In Vitro and In Vivo CRISPR-Cas9 Screening Identifies Tumor Suppressors in Human Colon Organoids. Cell Stem Cell. 26:782-792.e7.

Cammarata-Mouchtouris, A., Nguyen, X.H., Acker, A., Bonnay, F., Goto, A., Orian, A., Fauvarque, M.O., Boutros, M., Reichhart, J.M., Matt, N. (2020). Hyd ubiquitinates the NF-κB co-factor Akirin to operate an effective immune response in Drosophila. PLoS Pathog. 16:e1008458.

Bajic, D., Niemann, A., Hillmer, A.-K., Mejias-Luque, R., Bluemel, S., Docampo, M. Funk, M. C., Tonin, E., Boutros, M., Schnabl, B., Busch, D. H., Miki, T., Schmid, R. M., van den Brink, M., Gerhard, M., Stein-Thoeringer, C. K. (2020). Gut microbiota derived propionate regulates the expression of Reg3 mucosal lectins and ameliorates experimental colitis in mice. J Crohns Colitis pii: jjaa065. 

Port., F., Strein, C., Stricker, M., Rauscher, B., Heigwer, F., Zhou, J., Beyersdörffer, C., Frei, J., Hess, A., Kern, K., Malamud, R., Pavlovic, B., Rädecke, K., Schmitt, L., Voos, L., Valentini, E., Boutros, M. (2020). A large-scale resource for tissue-specific CRISPR mutagenesis in Drosophila. eLife 13:9. pii: e53865.

Zhou, J., Boutros, M. (2020). JNK-dependent intestinal barrier failure disrupts host-microbe homeostasis during tumorigenesis. Proceedings of the National Academy of Sciences pii: 201913976.

Imkeller, K., Ambrosi, G., Boutros, M., Huber, W. (2020). gscreend: modelling asymmetric count ratios in CRISPR screens to decrease experiment size and improve phenotype detection. Genome Biology 21:53.

Worst, T.S., Previti, C., Nitschke, K., Diessl, N., Gross, J.C., Hoffmann, L., Frey, L., Thomas, V., Kahlert, C., Bieback, K., Crigna, A.T., Fricke, F., Porubsky S, Westhoff N, Hardenberg JV, Nuhn P, Erben P, Michel M.S., Boutros M. (2020). miR-10a-5p and miR-29b-3p as Extracellular Vesicle-Associated Prostate Cancer Detection Markers. Cancers. 12:43


Bageritz, J., Willnow, P., Valentini, E., Leible, S., Boutros, M., Teleman, A.A. (2019). Gene expression atlas of a developing tissue by single cell expression correlation analysis. Nature Methods 16:750-756.

Rad, R., Boutros, M. (2019). Functionalizing cancer genomes in the era of big data. Current Opinions in Genetics and Development 54:iii-vi.

Chaudhary, V., Hingole, S., Frei, J., Port, F., Strutt, D., Boutros, M. (2019). Robust Wnt signaling is maintained by a Wg protein gradient and Fz2 receptor activity in the developing Drosophila wing. Development 146:dev174789.

Chaudhary, V., Boutros, M. (2019). Exocyst-mediated apical Wg secretion activates signaling in the Drosophila wing epithelium. PLoS Genetics 15:e1008351.

Herrmann, S., Zhan, T., Betge, J., Rauscher, B., Belle, S., Gutting, T., Schulte, N., Jesenofsky, R., Härtel, N., Gaiser, T., Hofheinz, R.D., Ebert, M.P., Boutros, M. (2019). Detection of mutational patterns in cell-free DNA of colorectal cancer by custom amplicon sequencing. Molecular Oncology 13:1669-1683.

Zhan, T., Ambrosi, G., Wandmacher, A.M., Rauscher, B., Betge, J., Rindtorff, N., Häussler, R.S., Hinsenkamp, I., Bamberg, L., Hessling, B., Müller-Decker, K., Erdmann, G., Burgermeister, E., Ebert, M.P., Boutros, M. (2019). MEK inhibitors activate Wnt signalling and induce stem cell plasticity in colorectal cancer. Nat Commun 10:2197.

Henkel, L., Rauscher, B., Boutros, M. (2019). Context-dependent genetic interactions in cancer. Curr Opin Genet Dev 54:73-82.

Nitschke, K., Erben, P., Waldbillig, F., Abdelhadi, A., Weis, C.A., Gottschalt, M., Wahby, S., Nuhn, P., Boutros, M., Michel, M.S., von Hardenberg, J., Worst, T.S. (2019). Clinical relevance of gene expression in localized and metastatic prostate cancer exemplified by FABP5. World J Urol. 38:637-645


Heigwer, F., Scheeder, C., Miersch ,T., Schmitt, B., Blass, C., Pour Jamnani, M.V., Boutros, M. (2018). Time-resolved mapping of genetic interactions to model rewiring of signaling pathways. eLife 7. pii: e40174.

Scheeder, C., Heigwer, F., Boutros, M. (2018). Machine learning and image-based profiling in drug discovery. Curr Opin Syst Biol 10:43-52

Tamirisa, S., Papagiannouli, F., Rempel, E., Ermakova, O., Trost, N., Zhou, J., Mundorf, J., Brunel, S., Ruhland, N., Boutros, M., Lohmann, J.U., Lohmann, I. (2018). Decoding the Regulatory Logic of the Drosophila Male Stem Cell System. Cell Rep 24:3072-3086

Mattila, J., Kokki, K., Hietakangas, V., Boutros, M. (2018). Stem Cell Intrinsic Hexosamine Metabolism Regulates Intestinal Adaptation to Nutrient Content. Dev Cell 47:112-121.e3

Trost, N., Rempel, E., Ermakova, O., Tamirisa, S., Pârcălăbescu, L., Boutros, M., Lohmann, J.U., Lohmann, I. (2018). WEADE: A workflow for enrichment analysis and data exploration. PLoS One 13:e0204016

Klingenberg, M., Groß, M., Goyal, A., Polycarpou-Schwarz, M., Miersch, T., Ernst, A.S., Leupold, J., Patil, N., Warnken, U., Allgayer, H., Longerich, T., Schirmacher, P., Boutros, M., Diederichs, S. (2018). The lncRNA CASC9 and RNA binding protein HNRNPL form a complex and co-regulate genes linked to AKT signaling. Hepatology 68:1817-1832

Kober, K.I., Cano, A., Géraud, C., Sipilä, K., Mobasseri, S.A., Philippeos, C., Pisco, A.O., Stannard, A., Martin, A., Salvador, F., Santos, V., Boutros, M., Rognoni, E., Watt, F.M. (2018). Loxl2 is dispensable for dermal development, homeostasis and tumour stroma formation. PLoS One 13:e0199679

Shen, J., Najafi, S., Stable, S., Fabian, J., Koeneke, E., Kolbinger, F.R., Wrobel, J.K., Meder, B., Distel, M., Heimburg, T., Sippl, W., Jung, M., Peterziel, H., Kranz, D., Boutros, M., Westermann, F., Witt, O., Oehme, I. (2018). A kinome-wide RNAi screen identifies ALK as a target to sensitize neuroblastoma cells for HDAC8-inhibitor treatment. Cell Death Differ 25:2053-2070

Dix, C.L., Matthews, H.K., Uroz, M., McLaren, S., Wolf, L., Heatley, N., Win, Z., Almada, P., Henriques, R., Boutros, M., Trepat, X., Baum, B. (2018). The Role of Mitotic Cell-Substrate Adhesion Re-modeling in Animal Cell Division. Dev Cell 45:132-45 e3

Zhan, T., Rindtorff, N., Betge, J., Ebert, M.P., Boutros, M. (2018). CRISPR/Cas9 for cancer research and therapy. Semin Cancer Biol pii: S1044-579X(17)30274-2

Heigwer, F., Port, F., Boutros, M. (2018). RNA Interference (RNAi) Screening in Drosophila. Genetics 208:853-74

Buljan, M., Blattmann, P., Aebersold, R., Boutros, M. (2018). Systematic characterization of pan-cancer mutation clusters. Mol Syst Biol 14:e7974

Glaeser, K., Urban, M., Fenech, E., Voloshanenko, O., Kranz, D., Lari, F., Christianson, J.C., Boutros, M. (2018). ERAD-dependent control of the Wnt secretory factor Evi. EMBO J 37

Rauscher, B., Heigwer, F., Henkel, L., Hielscher, T., Voloshanenko, O., Boutros, M. (2018). Toward an integrated map of genetic interactions in cancer cells. Mol Syst Biol 14:e7656

Voloshanenko, O., Schwartz, U., Kranz, D., Rauscher, B., Linnebacher, M., Augustin, I., Boutros, M. (2018). beta-catenin-independent regulation of Wnt target genes by RoR2 and ATF2/ATF4 in colon cancer cells. Sci Rep 8:3178

Leibing, T., Geraud, C., Augustin, I., Boutros, M., Augustin, H.G., Okun, J.G., Langhans, C.D., Zierow, J., Wohlfeil, S.A., Olsavszky, V., Schledzewski, K., Goerdt, S., Koch, P.S. (2018). Angiocrine Wnt signaling controls liver growth and metabolic maturation in mice. Hepatology 68:707-722

Galata, C., Hirsch, D., Reindl, W., Post, S., Kienle, P., Boutros, M., Gaiser, T., Horisberger, K. (2017). Clinical and Histopathologic Features of Colorectal Adenocarcinoma in Crohn's Disease. J Clin Gastroenterol 52:635-640

Billmann, M., Chaudhary, V., ElMaghraby, M.F., Fischer, B., Boutros, M. (2018). Widespread Rewiring of Genetic Networks upon Cancer Signaling Pathway Activation. Cell Syst 6:52-64 e4


Voloshanenko, O., Gmach, P., Winter, J., Kranz, D., Boutros, M. (2017). Mapping of Wnt-Frizzled interactions by multiplex CRISPR targeting of receptor gene families. FASEB J 31:4832-44

Meyer, I.S., Jungmann, A., Dieterich, C., Zhang, M., Lasitschka, F., Werkmeister, S., Haas, J., Muller, O.J., Boutros, M., Nahrendorf, M., Katus, H.A., Hardt, S.E., Leuschner, F. (2017). The cardiac microenvironment uses non-canonical WNT signaling to activate monocytes after myocardial infarction. EMBO Mol Med 9:1279-93

Menck, K., Sonmezer, C., Worst, T.S., Schulz, M., Dihazi, G.H., Streit, F., Erdmann, G., Kling, S., Boutros, M., Binder, C., Gross, J.C. (2017). Neutral sphingomyelinases control extracellular vesicles budding from the plasma membrane. J Extracell Vesicles 6:1378056

Larribere, L., Galach, M., Novak, D., Arevalo, K., Volz, H.C., Stark, H.J., Boukamp, P., Boutros, M., Utikal, J. (2017). An RNAi Screen Reveals an Essential Role for HIPK4 in Human Skin Epithelial Differentiation from iPSCs. Stem Cell Reports 9:1234-45

Merk, K., Breinig, M., Bottcher, R., Krebs, S., Blum, H., Boutros, M., Forstemann, K. (2017). Splicing stimulates siRNA formation at Drosophila DNA double-strand breaks. PLoS Genet 13:e1006861

Notzold, L., Frank, L., Gandhi, M., Polycarpou-Schwarz, M., Gross, M., Gunkel, M., Beil, N., Erfle, H., Harder, N., Rohr, K., Trendel, J., Krijgsveld, J., Longerich, T., Schirmacher, P., Boutros, M., Erhardt, S., Diederichs, S. (2017). The long non-coding RNA LINC00152 is essential for cell cycle progression through mitosis in HeLa cells. Sci Rep 7:2265

Rauscher, B., Valentini, E., Hardeland, U., Boutros, M. (2017). Phenotype Databases for Genetic Screens in Human Cells. J Biotechnol

Strassburger, K., Lorbeer, F.K., Lutz, M., Graf, F., Boutros, M., Teleman, A.A. (2017). Oxygenation and adenosine deaminase support growth and proliferation of ex vivo cultured Drosophila wing imaginal discs. Development 144:2529-38

Scheeder, C., Heigwer, F., Boutros, M. (2017). HTSvis: a web app for exploratory data analysis and visualization of arrayed high-throughput screens. Bioinformatics

Worst, T.S., von Hardenberg, J., Gross, J.C., Erben, P., Schnoelzer, M., Hausser, I., Bugert, P., Michel, M.S., Boutros, M. (2017). A database-augmented, exosome-based mass spectrometry approach exemplarily identifies circulating claudin 3 as biomarker in prostate cancer. Mol Cell Proteomics 16:998-1008

Zhou, J., Edgar, B.A., Boutros, M. (2017). ATF3 acts as a rheostat to control JNK signalling during intestinal regeneration. Nat Commun 8:14289

Billmann, M., Boutros, M. (2017). Systematic epistatic mapping of cellular processes. Cell Div 12:2

Seiler, J., Breinig, M., Caudron-Herger, M., Polycarpou-Schwarz, M., Boutros, M., Diederichs, S. (2017). The lncRNA VELUCT strongly regulates viability of lung cancer cells despite its extremely low abundance. Nucleic Acids Res 45:5458-69

Baliga, N.S., Bjorkegren, J.L., Boeke, J.D., Boutros, M., Crawford, N.P., Dudley, A.M., Farber, C.R., Jones, A., Levey, A.I., Lusis, A.J., Mak, H.C., Nadeau, J.H., Noyes, M.B., Petretto, E., Seyfried, N.T., Steinmetz, L.M., Vonesch, S.C. (2017). The State of Systems Genetics in 2017. Cell Syst 4:7-15

Zhan, T., Rindtorff, N., Boutros, M. (2017). Wnt signaling in cancer. Oncogene 36:1461-73

Augustin, I., Dewi, D.L., Hundshammer, J., Erdmann, G., Kerr, G., Boutros, M. (2017). Autocrine Wnt regulates the survival and genomic stability of embryonic stem cells. Sci Signal 10

Rauscher, B., Heigwer, F., Breinig, M., Winter, J., Boutros, M. (2017). GenomeCRISPR - a database for high-throughput CRISPR/Cas9 screens. Nucleic Acids Res 45:D679-D86


Billmann, M., Boutros, M. (2016). Methods for High-Throughput RNAi Screening in Drosophila Cells. Methods Mol Biol 1478:95-116

Augustin, I., Dewi, D.L., Hundshammer, J., Rempel, E., Brunk, F., Boutros, M. (2016). Immune cell recruitment in teratomas is impaired by increased Wnt secretion. Stem Cell Res 17:607-15

Billmann, M., Horn, T., Fischer, B., Sandmann, T., Huber, W., Boutros, M. (2016). A genetic interaction map of cell cycle regulators. Mol Biol Cell 27:1397-407

Costanzo, M., VanderSluis, B., Koch, E.N., Baryshnikova, A., Pons, C., Tan, G., Wang, W., Usaj, M., Hanchard, J., Lee, S.D., Pelechano, V., Styles, E.B., Billmann, M., van Leeuwen, J., van Dyk, N., Lin, Z.Y., Kuzmin, E., Nelson, J., Piotrowski, J.S., Srikumar, T., Bahr, S., Chen, Y., Deshpande, R., Kurat, C.F., Li, S.C., Li, Z., Usaj, M.M., Okada, H., Pascoe, N., San Luis, B.J., Sharifpoor, S., Shuteriqi, E., Simpkins, S.W., Snider, J., Suresh, H.G., Tan, Y., Zhu, H., Malod-Dognin, N., Janjic, V., Przulj, N., Troyanskaya, O.G., Stagljar, I., Xia, T., Ohya, Y., Gingras, A.C., Raught, B., Boutros, M., Steinmetz, L.M., Moore, C.L., Rosebrock, A.P., Caudy, A.A., Myers, C.L., Andrews, B., Boone, C. (2016). A global genetic interaction network maps a wiring diagram of cellular function. Science 353 pii: aaf1420

Konotop, G., Bausch, E., Nagai, T., Turchinovich, A., Becker, N., Benner, A., Boutros, M., Mizuno, K., Kramer, A., Raab, M.S. (2016). Pharmacological Inhibition of Centrosome Clustering by Slingshot-Mediated Cofilin Activation and Actin Cortex Destabilization. Cancer Res 76:6690-6700

Zhan, T., Boutros, M. (2016). Towards a compendium of essential genes - From model organisms to synthetic lethality in cancer cells. Crit Rev Biochem Mol Biol 51:74-85

Glaeser, K., Boutros, M., Gross, J.C. (2016). Biochemical Methods to Analyze Wnt Protein Secretion. Methods Mol Biol 1481:17-28

Gilbert, D.F., Boutros, M. (2016). A Protocol for a High-Throughput Multiplex Cell Viability Assay. Methods Mol Biol 1470:75-84

Tsokanos, F.F., Albert, M.A., Demetriades, C., Spirohn, K., Boutros, M., Teleman, A.A. (2016). eIF4A inactivates TORC1 in response to amino acid starvation. EMBO J35:1058-76

Heigwer, F., Zhan, T., Breinig, M., Winter, J., Brugemann, D., Leible, S., Boutros, M. (2016). CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries. Genome Biol 17:55.

Moffa, G., Erdmann, G., Voloshanenko, O., Hundsrucker, C., Sadeh, M.J., Boutros, M., Spang, R. (2016). Refining Pathways: A Model Comparison Approach. PLoS One 11:e0155999.

Chatterjee, N., Tian, M., Spirohn, K., Boutros, M., Bohmann, D. (2016). Keap1-Independent Regulation of Nrf2 Activity by Protein Acetylation and a BET Bromodomain Protein. PLoS Genet 12:e1006072.

Boutros, M., Niehrs, C. (2016). Sticking Around: Short-Range Activity of Wnt Ligands. Dev Cell 36:485-6.

Billmann, M., Horn, T., Fischer, B., Sandmann, T., Huber, W., Boutros, M. (2016). A genetic interaction map of cell cycle regulators. Mol Biol Cell 27:1397-407

Lamiable, O., Kellenberger, C., Kemp, C., Troxler, L., Pelte, N., Boutros, M., Marques, J.T., Daeffler, L., Hoffmann, J.A., Roussel, A., Imler, J.L. (2016). Cytokine Diedel and a viral homologue suppress the IMD pathway in Drosophila. Proc Natl Acad Sci U S A 113:698-703.

Li, X., Chatterjee, N., Spirohn, K., Boutros, M., Bohmann, D. (2016). Cdk12 Is A Gene-Selective RNA Polymerase II Kinase That Regulates a Subset of the Transcriptome, Including Nrf2 Target Genes. Sci Rep 6:21455.

Schafer, M., Oeing, C.U., Rohm, M., Baysal-Temel, E., Lehmann, L.H., Bauer, R., Volz, H.C., Boutros, M., Sohn, D., Sticht, C., Gretz, N., Eichelbaum, K., Werner, T., Hirt, M.N., Eschenhagen, T., Muller-Decker, K., Strobel, O., Hackert, T., Krijgsveld, J., Katus, H.A., Berriel Diaz, M., Backs, J., Herzig, S. (2016). Ataxin-10 is part of a cachexokine cocktail triggering cardiac metabolic dysfunction in cancer cachexia. Mol Metab 5:67-78.

Scholz, B., Korn, C., Wojtarowicz, J., Mogler, C., Augustin, I., Boutros, M., Niehrs, C., Augustin, H.G. (2016). Endothelial RSPO3 Controls Vascular Stability and Pruning through Non-canonical WNT/Ca(2+)/NFAT Signaling. Dev Cell 36:79-93.

Winter, J., Breinig, M., Heigwer, F., Brugemann, D., Leible, S., Pelz, O., Zhan, T., Boutros, M. (2016). caRpools: an R package for exploratory data analysis and documentation of pooled CRISPR/Cas9 screens. Bioinformatics 32:632-4.


Boutros, M., Heigwer, F., Laufer, C. (2015). Microscopy-Based High-Content Screening. Cell 163:1314-25.

Breinig, M., Klein, F.A., Huber, W., Boutros, M. (2015). A chemical-genetic interaction map of small molecules using high-throughput imaging in cancer cells. Mol Syst Biol 11:846.

Brunk, F., Augustin, I., Meister, M., Boutros, M., Kyewski, B. (2015). Thymic Epithelial Cells Are a Nonredundant Source of Wnt Ligands for Thymus Development. J Immunol 195:5261-71.

Zhan, T., Boutros, M. (2015). Towards a compendium of essential genes - From model organisms to synthetic lethality in cancer cells. Crit Rev Biochem Mol Biol 1-12.

Erdmann, G., Suchanek, M., Horn, P., Graf, F., Volz, C., Horn, T., Zhang, X., Wagner, W., Ho, A.D., Boutros, M. (2015). Functional fingerprinting of human mesenchymal stem cells using high-throughput RNAi screening. Genome Medicine 7:46.

Betge, J., Kerr, G., Miersch, T., Leible, S., Erdmann, G., Galata, C.L., Zhan, T., Gaiser, T., Post, S., Ebert, M.P., Horisberger, K., Boutros, M. (2015). Amplicon sequencing of colorectal cancer: variant calling in frozen and formalin-fixed samples. PLoS One 10:e0127146.

Tiebe, M., Lutz, M., De La Garza, A., Buechling, T., Boutros, M., Teleman, A.A. (2015). REPTOR and REPTOR-BP Regulate Organismal Metabolism and Transcription Downstream of TORC1. Developmental Cell 33:272-84.

Fischer, B., Sandmann, T., Horn, T., Billmann, M., Chaudhary, V., Huber, W., Boutros, M. (2015). A map of directional genetic interactions in a metazoan cell. eLife 4.

Khandelwal, N., Breinig, M., Speck, T., Michels, T., Kreutzer, C., Sorrentino, A., Sharma, A.K., Umansky, L., Conrad, H., Poschke, I., Offringa, R., König, R., Bernhard, H., Machlenkin, A., Boutros, M., Beckhove, P. (2015). A high-throughput RNAi screen for detection of immune-checkpoint molecules that mediate tumor resistance to cytotoxic T lymphocytes. EMBO Molecular Medicine 7:450-63.

Guida, C., Altamura, S., Klein, F.A., Galy, B., Boutros, M., Ulmer, A.J., Hentze, M.W., Muckenthaler, M.U. (2015). A novel inflammatory pathway mediating rapid hepcidin-independent hypoferremia. Blood 125:2265-75.

Zhou, J., Florescu, S., Boettcher, A., Luo, L., Dutta, D., Kerr, G., Cai, Y., Edgar, B.A., Boutros, M. (2015). Dpp/Gbb signaling is required for normal intestinal regeneration during infection. Developmental Biology 399:189-203.


Laufer, C., Fischer, B., Huber, W., Boutros, M. (2014). Measuring genetic interactions in human cells by RNAi and imaging. Nature Protocols 9(10):2341-2353

Schmidt, E.E., Banos, M.S., Smith, J.A., Birmingham, A., Boutros, M., Shamu, C.E. (2014). Public Repositories for RNAi Screening Data. In: Frontiers in RNAi / Tripp, R.A., Karpilow, J.M., Bentham eBooks

Jankovics, F., Henn, L., Bujna, Á., Vilmos, P., Spirohn, K., Boutros, M., Erdélyi, M. (2014). Functional analysis of the Drosophila embryonic germ cell transcriptome by RNA interference. PLoS One 9(6):e98579.

Kumar, S., Žigman, M., Patel, T.R., Trageser, B., Gross, J.C., Rahm, K., Boutros, M., Gradl, D., Steinbeisser, H., Holstein, T., Stetefeld, J., Özbek, S. (2014). Molecular dissection of Wnt3a-Frizzled8 interaction reveals essential and modulatory determinants of Wnt signaling activity. BMC Biol 12:44.

Korn, C., Scholz, B., Hu, J., Srivastava, K., Wojtarowicz, J., Arnsperger, T., Adams, R.H., Boutros, M., Augustin, H.G., Augustin, I. (2014). Endothelial cell-derived non-canonical Wnt ligands control vascular pruning in angiogenesis. Development 141(8):1757-66.

Heigwer, F., Kerr, G., Boutros, M. (2014). E-CRISP: fast CRISPR target site identification. Nature Methods 11(2):122-3.

Kranz, D., Boutros, M. (2014). A synthetic lethal screen identifies FAT1 as an antagonist of caspase-8 in extrinsic apoptosis. EMBO Journal 33(3):181-97.

Mleczko-Sanecka, K., Roche, F., da Silva, A.R., Call, D., D'Alessio, F., Ragab, A., Lapinski, P.E., Ummanni, R., Korf, U., Oakes, C., Damm, G., D'Alessandro, L.A., Klingmüller, U., King, P.D., Boutros, M., Hentze, M.W., Muckenthaler, M.U. (2014). Unbiased RNAi screen for hepcidin regulators links hepcidin suppression to the proliferative Ras/RAF and the nutrient-dependent mTOR signaling pathways. Blood 123(10):1574-85.


Zhang, X., Boutros, M. (2013). A novel phenotypic dissimilarity method for image-based high-throughput screens. BMC Bioinformatics 14:336.

Voloshanenko, O., Erdmann, G., Dubash, T.D., Augustin, I., Metzig, M., Moffa, G., Hundsrucker, C., Kerr, G., Sandmann, T., Anchang, B., Demir, K., Boehm, C., Leible, S., Ball, C.R., Glimm, H., Spang, R., Boutros, M. (2013). Wnt secretion is required to maintain high levels of Wnt activity in colon cancer cells. Nature Communications 4:2610.

Demir, K., Kirsch, N., Beretta, C.A., Erdmann, G., Ingelfinger, D., Moro, E., Argenton, F., Carl, M., Niehrs, C., Boutros, M. (2013). RAB8B is required for activity and caveolar endocytosis of LRP6. Cell Reports 4(6):1224-34.

Börner, K., Niopek, D., Cotugno, G., Kaldenbach, M., Pankert, T., Willemsen, J., Zhang, X., Schürmann, N., Mockenhaupt, S., Serva, A., Hiet, M.S., Wiedtke, E., Castoldi, M., Starkuviene, V., Erfle, H., Gilbert, D.F., Bartenschlager, R., Boutros, M., Binder, M., Streetz, K., Kräusslich, H.G., Grimm, D. (2013). Robust RNAi enhancement via human Argonaute-2 overexpression from plasmids, viral vectors and cell lines. Nucleic Acids Research 41(21):e199.

Heigwer, F., Kerr, G., Walther, N., Glaeser, K., Pelz, O., Breinig, M., Boutros, M. (2013). E-TALEN: a web tool to design TALENs for genome engineering. Nucleic Acids Research 41(20):e190.

Fukuyama, H., Verdier, Y., Guan, Y., Makino-Okamura, C., Shilova, V., Liu, X., Maksoud, E., Matsubayashi, J., Haddad, I., Spirohn, K., Ono, K., Hetru, C., Rossier, J., Ideker, T., Boutros, M., Vinh, J., Hoffmann, J.A. (2013). Landscape of protein-protein interactions in Drosophila immune deficiency signaling during bacterial challenge. Proceedings of the National Academy of Sciences of the United States of America 110:10717-22.

Augustin, I., Gross, J., Baumann, D., Korn, C., Kerr, G., Grigoryan, T., Mauch, C., Birchmeier, W., Boutros, M. (2013). Loss of epidermal Evi/Wls results in a phenotype resembling psoriasiform dermatitis. The Journal of Experimental Medicine 210:1761-77.

Serysheva, E., Berhane, H., Grumolato, L., Demir, K., Balmer, S., Bodak, M., Boutros, M., Aaronson, S., Mlodzik, M., Jenny, A. (2013). Wnk kinases are positive regulators of canonical Wnt/β-catenin signalling. EMBO Reports 14:718-25

Laufer, C., Fischer, B., Billmann, M., Huber, W., Boutros, M. (2013). Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping. Nature Methods 10:427-31.

Gross, J.C., Boutros, M. (2013). Secretion and extracellular space travel of Wnt proteins. Current Opinion in Genetics and Development 23(4):385-90.

Horn, T., Boutros, M. (2013). Design of RNAi Reagents for Invertebrate Model Organisms and Human Disease Vectors. Methods in Molecular Biology 942:315-46.

Schmidt, E.E., Pelz, O., Buhlmann, S., Kerr, G., Horn, T., Boutros, M. (2013). GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update. Nucleic Acids Research 41(Database issue):D1021-6.

Kuhns, S., Schmidt, K.N., Reymann, J., Gilbert, D.F., Neuner, A., Hub, B., Carvalho, R., Wiedemann, P., Zentgraf, H., Erfle, H., Klingmüller, U., Boutros, M., Pereira, G. (2013). The microtubule affinity regulating kinase MARK4 promotes axoneme extension during early ciliogenesis. The Journal of Cell Biology 200:505-22.


Page, R.M., Münch, A., Horn, T., Kuhn, P.H., Colombo, A., Reiner, O., Boutros, M., Steiner, H., Lichtenthaler, S.F., Haass, C. (2012). Loss of PAFAH1B2 reduces amyloid-β generation by promoting the degradation of amyloid precursor protein C-terminal fragments. The Journal of Neuroscience : The Official Journal of the Society for Neuroscience 32(50):18204-14.

Brechmann, M., Mock, T., Nickles, D., Kiessling, M., Weit, N., Breuer, R., Müller, W., Wabnitz, G., Frey, F., Nicolay, J.P., Booken, N., Samstag, Y., Klemke, C.D., Herling, M., Boutros, M., Krammer, P.H., Arnold, R. (2012). A PP4 holoenzyme balances physiological and oncogenic nuclear factor-kappa B signaling in T lymphocytes. Immunity 37(4):697-708.

Gross, J.C., Chaudhary, V., Bartscherer, K., Boutros, M. (2012). Active Wnt proteins are secreted on exosomes. Nature Cell Biology 14(10):1036-45.

Stender, J.D., Pascual, G., Liu, W., Kaikkonen, M.U., Do, K., Spann, N.J., Boutros, M., Perrimon, N., Rosenfeld, M.G., Glass, C.K. (2012). Control of Proinflammatory Gene Programs by Regulated Trimethylation and Demethylation of Histone H4K20. Molecular Cell 48(1):28-38.

Petrakis, S., Raskó, T., Russ, J., Friedrich, R.P., Stroedicke, M., Riechers, SP., Muehlenberg, K., Möller, A., Reinhardt, A., Vinayagam, A., Schaefer, M.H., Boutro,s M., Tricoire, H., Andrade-Navarro, MA., Wanker, E.E. (2012). Identification of human proteins that modify misfolding and proteotoxicity of pathogenic ataxin-1. PLoS Genetics 8(8):e1002897.

Demir, K., Boutros, M. (2012). Cell perturbation screens for target identification by RNAi. Methods in Molecular Biology 910:1-13.

Icardi, L., Mori, R., Gesellchen, V., Eyckerman, S., De Cauwer, L., Verhelst, J., Vercauteren, K., Saelens, X., Meuleman, P., Leroux-Roels, G., De Bosscher, K., Boutros, M., Tavernier, J. (2012). The Sin3a repressor complex is a master regulator of STAT transcriptional activity. Proceedings of the National Academy of Sciences of the United States of America 109(30):12058-63.

Nickles, D., Falschlehner, C., Metzig, M., Boutros, M. (2012). A genome-wide RNAi screen identifies CASP4 as a factor required for TNF-α signaling. Molecular and Cellular Biology 32(17):3372-81.

Erdmann, G., Volz, C., Boutros, M. (2012). Systematic approaches to dissect biological processes in stem cells by image-based screening. Biotechnology Journal 7:768-78.

Falschlehner, C., Boutros, M. (2012). Innate immunity: regulation of caspases by IAP-dependent ubiquitylation. EMBO Journal 31:2750-2752.

Sandmann, T., Boutros, M. (2012). Screens, maps & networks: from genome sequences to personalized medicine. Current Opinion in Genetics and Development 22:36-44.

Shamu, C.E., Wiemann, S., Boutros, M. (2012). On target: A public repository for large-scale RNAi experiments. Nature Cell Biology 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. (2012). The Wnt secretion protein Evi/Gpr177 promotes glioma tumorigenesis. EMBO Molecular Medicine 4:38-51.


Buechling, T., Boutros, M. (2011). Wnt signaling signaling at and above the receptor level. Current Topics in Developmental Biology 97:21-53.

Gilbert, D.F., Erdmann, G., Zhang, X., Fritzsche, A., Demir, K., Jaedicke, A., Muehlenberg, K., Wanker, E.E., Boutros, M. (2011). A Novel Multiplex Cell Viability Assay for High-Throughput RNAi Screening. PLoS One 6:e28338.

Horn, T., Boutros, M. (2011). Design of RNAi reagents for invertebrate model organisms and human disease vectors. Nature Precedings

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/β-catenin and Wnt/PCP signalling. EMBO Reports 12:1055-61.

Buechling, T., Chaudhary, V., Spirohn, K., Weiss, M., Boutros, M. (2011). p24 proteins are required for secretion of Wnt ligands. EMBO Reports 12:1265-72.

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.

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 by modulating Sec16 membrane association. EMBO Journal 30:3684-700.

Sandmann, T., Vogg, M.C., Owlarn, S., Boutros, M., Bartscherer, K. (2011). The head-regeneration transcriptome of the planarian Schmidtea mediterranea. Genome Biology 12:R76.

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:e17173.

Metzig, M., Nickles, D., Boutros, M. (2011). Large-scale RNAi screens to dissect TNF and NF-κB signaling pathways. Advances in Experimental Medicine and Biology 691:131-9.

Horn, T., Sandmann, T., Fischer, B., Axelsson, E., Huber, W., Boutros, M. (2011). Mapping of signaling networks through synthetic genetic interaction analysis by RNAi. Nature Methods 8:341-6.

Metzig, M., Nickles, D., Falschlehner, C., Lehmann-Koch, J., Straub, B.K., Roth, W., Boutros, M. (2011). An RNAi screen identifies USP2 as a factor required for TNF-α induced NF-κB signaling. International Journal of Cancer 129:607-18.

Ragab, A., Buechling, T., Gesellchen, V., Spirohn, K., Boettcher, A.L., Boutros, M. (2011). Drosophila Ras/MAPK signalling regulates innate immune responses in immune and intestinal stem cells. EMBO Journal 30:1123-36.

Liang, J., Fu, Y., Cruciat, C.M., 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. Molecular and Cellular Biology 31:2577-90.

Huhn, S., Ingelfinger, D., Bermejo, J.L., Bevier, M., Pardini, B., Naccarati, A., Steinke, V., Rahner, N., Holinski-Feder, E., Morak, M., Schackert, H.K., Görgens, H., Pox, C.P., Goecke, T., Kloor, M., Loeffler, M., Büttner, R., Vodickova, L., Novotny, J., Demir, K., Cruciat, C.M., 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. International Journal of Molecular Epidemiology and Genetics 2:36-50.


Gilboa, L., Boutros, M. (2010). Celebrating 100 years of Drosophila research. EMBO Reports 11:724-6.

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 29:3344-57.

Niehrs, C., Boutros., M. (2010). Trafficking, Acidification, and Growth Factors Signaling. Science Signaling 3:pe26.

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 20:1263-1268.

Horn, T., Sandmann, T., Boutros., M. (2010). Design and evaluation of genome-wide libraries for RNAi screens. Genome Biology 11:R61.

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.

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 2:33ra38.

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 18:862-76.

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.

Pelz., O., Gilsdorf, M., Boutros, M. (2010). web cellHTS2: A web application for the analysis of high-throughput screening data. BMC Bioinformatics 11:185.

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. Molecular and Cellular Biology 30:2837-48.

Falschlehner, C., Steinbrink, S., Erdmann, G., Boutros, M. (2010). High-throughput RNAi screening to dissect cellular pathways: a how-to guide. Biotechnology Journal 5:368-76.

Pau, G., Fuchs, F., Sklyar, O., Boutros, M., Huber, W. (2010). EBImage - an R package for image processing with applications to cellular phenotypes. Bioinformatics 26:979-81.

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 327:459-63.

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.

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 2:181-194.

Mleczko-Sanecka, K., Casanovas, G., Ragab, A., Breitkopf, K., Muller, A., Boutros, M., Dooley, S., Hentze, M.W., Muckenthaler, M.U. (2010). SMAD7 controls iron metabolism as a potent inhibitor of hepcidin expression. Blood 115:2657-65.


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.

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. Nature Cell Biology 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 19:1006-13.

Adell, T., Saló, 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.


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 in Molecular Biology 420:139-1353.

Mueller P., Boutros M., Zeidler, M. (2008). Identification of JAK/STAT pathway regulators-Insights from RNAi screens. Seminars in Cell and Developmental Biology 19:360-9

Boutros, M., Ahringer, J. (2008). The art and design of genetic screens: RNA interference. Nature Reviews Genetics 9:554-566.

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.

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 9:97-104.


Eulalio, A., Rehwinkel J., Stricker, M., Huntzinger, E., Yang, S.F., Doerks, T., Dorner, S., Bork, P., Boutros, M., Izaurralde, E. (2007). Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing. Genes and Development 21:2558-2570.

Horn, T., Arziman, Z., Berger J., Boutros, M. (2007). GenomeRNAi: a database for cell-based RNAi phenotypes. Nucleic Acids Research 35:D492-7.


Boutros, M., Bras, L., Huber, W. (2006). Analysis of cell-based RNAi screens. Genome Biology, 7:R66.

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. Briefings in Functional Genomics and Proteomics 5:52-6.


Gesellchen, V., Kuttenkeuler, D., Steckel, M., Pelte, N., Boutros, M. (2005). An RNA interference screen identifies Inhibitor of Apoptosis Protein 2 as a regulator of innate immune signalling in Drosophila. EMBO Reports 6:979-84.

Muller, P., D. Kuttenkeuler, V. Gesellchen, M. Zeidler, M. Boutros. (2005). Identification of JAK/STAT signaling components by genome-wide RNAi. Nature 436:871-5.

Arziman, Z., Horn, T., Boutros, M. (2005). E-RNAi: A web application to design optimized RNAi constructs. Nucleic Acids Research 33:W582-88.

Armknecht, S., M. Boutros, A. Kiger, K. Nybakken, B. Mathey-Prevot, N. Perrimon. (2005). High-throughput RNA interference screens in Drosophila tissue culture cells. Methods in 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 6:R16.


Gesellchen, V., Boutros, M. (2004). Managing the genome: microRNAs in Drosophila. Differentiation 72:74-80.

Kuttenkeuler D., Boutros, M. (2004). Genome-wide RNAi as a route to gene function in Drosophila. Briefings in Functional Genomics and Proteomics 3:168-76.

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 growth and viability in Drosophila cells. Science 303:832-835.


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. Genome Biology 5:R3.

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.


Boutros, M., Agaisse, A., Perrimon, N. (2002). Sequential activation of signaling pathways during innate immune responses in Drosophila. Developmental Cell 3:711-22.

Moon, R.T., Bowerman, B., Boutros, M., Perrimon, N. (2002). The promise and perils of Wnt signaling through beta-catenin. Science 296:1644-6.


Boutros, M., Perrimon, N. (2001). Wnt/Fz signaling pathways in Drosophila. Science Technology Knowledge Environment (STKE).


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.


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.


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.


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.


Rauscher, B., Heigwer, F., Henkel, L., Hielscher, T., Voloshanenko, O., Boutros, M. Towards an Integrated Map of Genetic Interactions in Cancer Cells. bioRxiv 120964; doi:

Winter, J., Schwering, M., Pelz, O., Rauscher, B., Zhan, T., Heigwer, F., Boutros, M. CRISPRAnalyzeR: Interactive analysis, annotation and documentation of pooled CRISPR screens. bioRxiv 109967; doi:

Volz, H.C., Heigwer, F., Wuest, T., Galach, M., Utikal, J., Katus, H.A., Boutros, M. Single-cell phenotyping of human induced pluripotent stem cells by high-throughput imaging. bioRxiv 026955; doi:

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Systems Genetics


Boutroslab Github software repository

Software developed by the lab can be downloaded from our Github respository.

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