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Aguilar, Gustavo; Vigano, M Alessandra; Affolter, Markus; Matsuda, Shinya; 4 (2019). Reflections on the use of protein binders to study protein function in developmental biology. Wiley interdisciplinary reviews. Developmental biology, e356.

Aguilar, Gustavo; Matsuda, Shinya; Vigano, M Alessandra; Affolter, Markus (2019). Using Nanobodies to Study Protein Function in Developing Organisms. Antibodies, 8 (16), 1-11.


Sickmann, Michéle; Affolter, Markus; Müller, Martin (2018). Characterization of the new bithorax allele Ubx bx-Basel. Drosophila Information Service, Mutation Notes, 101 (December2018), 76-80.

Vigano, M Alessandra; Bieli, Dimitri; Schaefer, Jonas V; Jakob, Roman P; Matsuda, Shinya; Maier, Timm; Plückthun, Andreas; Affolter, Markus (2018). Correction: DARPins recognizing mTFP1 as novel reagents for; in vitro; and; in vivo; protein manipulations (doi:10.1242/bio.036749). Biology open, 7 (12), bio036749.

Postika, Nikolay; Metzler, Mario; Affolter, Markus; Müller, Martin; Schedl, Paul; Georgiev, Pavel; Kyrchanova, Olga (2018). Boundaries mediate long-distance interactions between enhancers and promoters in the Drosophila Bithorax complex. PLoS Genet, 14 (12), e1007702.

Hübner, Kathleen; Cabochette, Pauline; Diéguez-Hurtado, Rodrigo; Wiesner, Cora; Wakayama, Yuki; Grassme, Kathrin S; Hubert, Marvin; Guenther, Stefan; Belting, Heinz-Georg; Affolter, Markus; Adams, Ralf H; Vanhollebeke, Benoit; Herzog, Wiebke (2018). Wnt/β-catenin signaling regulates VE-cadherin-mediated anastomosis of brain capillaries by counteracting S1pr1 signaling. Nature communications, 9 (1), 4860.

Angulo-Urarte, Ana; Casado, Pedro; Castillo, Sandra D; Kobialka, Piotr; Kotini, Maria Paraskevi; Figueiredo, Ana M; Castel, Pau; Rajeeve, Vinothini; Milà-Guasch, Maria; Millan, Jaime; Wiesner, Cora; Serra, Helena; Muixi, Laia; Casanovas, Oriol; Viñals, Francesc; Affolter, Markus; Gerhardt, Holger; Huveneers, Stephan; Belting, Heinz-Georg; Cutillas, Pedro R; Graupera, Mariona (2018). Endothelial cell rearrangements during vascular patterning require PI3-kinase-mediated inhibition of actomyosin contractility. Nature Communications, 9 (1), 4826.

Kotini, Maria Paraskevi; Mäe, Maarja Andaloussi; Belting, Heinz-Georg; Betsholtz, Christer; Affolter, Markus (2018). Sprouting and anastomosis in the Drosophila trachea and the vertebrate vasculature: Similarities and differences in cell behaviour. Vascular pharmacology, Epub.

Vigano, M Alessandra; Bieli, Dimitri; Schaefer, Jonas V; Jakob, Roman Peter; Matsuda, Shinya; Maier, Timm; Plückthun, Andreas; Affolter, Markus (2018). DARPins recognizing mTFP1 as novel reagents for in vitro and in vivo protein manipulations. Biol Open, 7 (bio036749), 1-11.

Vigano, M Alessandra; Bieli, Dimitri; Schaefer, Jonas V; Jakob, Roman P; Matsuda, Shinya; Maier, Timm; Plückthun, Andreas; Affolter, Markus (2018). DARPins recognizing mTFP1 as novel reagents for; in vitro; and; in vivo; protein manipulations. Biology open, 7 (11), bio036749.

Paatero, Ilkka; Sauteur, Loïc; Lee, Minkyoung; Lagendijk, Anne K; Heutschi, Daniel; Wiesner, Cora; Guzmán, Camilo; Bieli, Dimitri; Hogan, Benjamin M; Affolter, Markus; Belting, Heinz-Georg (2018). Junction-based lamellipodia drive endothelial cell rearrangements in vivo via a VE-cadherin-F-actin based oscillatory cell-cell interaction. Nature Comm, 9 (1), 3545.

Harmansa, Stefan; Affolter, Markus (2018). Protein binders and their applications in developmental biology. Development, 145 (2), 1-13.


Sickmann, Michèle; Gohl, Daryl M.; Affolter, Markus; Müller, Martin (2017). The Drosophila melanogaster straw locus is allelic to laccase2. Drosophila Information Service, 100, 171-174.

Paatero, I; Sauteur, L; Lee, M; Lagendijk, AK; Heutschi, D; Bieli, D; Hogan, BM; Affolter, M; Belting, HG (2017). Junction-based lamellipodia drive endothelial cell arrangements in vivo via a VE-cadherin/F-actin based oscillatory ratchet mechanism. bioRxiv, November 2017, 1-32.

Lagendijk, Anne Karine; Gomez, Guillermo A.; Baek, Sungmin; Hesselson, Daniel; Hughes, William E.; Paterson, Scott; Conway, Daniel E.; Belting, Heinz-Georg; Affolter, Markus; Smith, Kelly A.; Schwartz, Martin A.; Yap, Alpha S.; Hogan, Benjamin M. (2017). Live imaging molecular changes in junctional tension upon VE-cadherin in zebrafish. Nature Communications, 8 (1), 1402.

Roubinet, Chantal; Tsankova, Anna; Pham, Tri Thanh; Monnard, Arnaud; Caussinus, Emmanuel; Affolter, Markus; Cabernard, Clemens (2017). Spatio-temporally separated cortical flows and spindle geometry establish physical asymmetry in fly neural stem cells. Nature Communications, 8 (1), 1383.

Affolter, Markus: Fluoreszierende Eiweisse: von der Natur ins Labor, in: Füglister, Kurt M.; Hicklin, Martin; Mäser, Pascal (Ed.). (2017). natura obscura. 200 Naturforschende - 200 Naturphänomene - 200 Jahre Naturforschende Gesellschaft in Basel, Basel: Schwabe, 9-9.

Ochoa-Espinosa, Amanda; Harmansa, Stefan; Caussinus, Emmanuel; Affolter, Markus (2017). Myosin II is not required for Drosophila tracheal branch elongation and cell intercalation. Development, 144 (16), 2961-2968.

Matsuda, Shinya; Affolter, Markus (2017). Dpp from the anterior stripe of cells is crucial for the growth of the Drosophila wing disc. eLife, 6, e22319.

Matsuda, Shinya; Affolter, Markus (2017). Dpp from the anterior stripe of cells is crucial for the growth of the; Drosophila; wing disc. eLife, 6, e22319.

Harmansa, Stefan; Alborelli, Ilaria; Bieli, Dimitri; Caussinus, Emmanuel; Affolter, Markus (2017). A nanobody-based toolset to investigate the role of protein localization and dispersal in Drosophila. eLife, 6, 22549.

Nakajima, Hiroyuki; Yamamoto, Kimiko; Agarwala, Sobhika; Terai, Kenta; Fukui, Hajime; Fukuhara, Shigetomo; Ando, Koji; Miyazaki, Takahiro; Yokota, Yasuhiro; Schmelzer, Etienne; Belting, Heinz-Georg; Affolter, Markus; Lecaudey, Virginie; Mochizuki, Naoki (2017). Flow-Dependent Endothelial YAP Regulation Contributes to Vessel Maintenance. Developmental Cell, 40 (6), 523-536.e6.

Sauteur, Loïc; Affolter, Markus; Belting, Heinz-Georg (2017). Distinct and redundant functions of Esam and VE-cadherin during vascular morphogenesis. Development, 144 (8), 1554-1565.

Tsachaki, Maria; Meyer, Arne; Weger, Benjamin; Kratschmar, Denise V.; Tokarz, Janina; Adamski, Jerzy; Belting, Heinz-Georg; Affolter, Markus; Dickmeis, Thomas; Odermatt, Alex (2017). Absence of 11-keto reduction of cortisone and 11-ketotestosterone in the model organism zebrafish. Journal of Endocrinology, 232 (2), 323-335.


Pasakarnis, Laurynas; Frei, Erich; Caussinus, Emmanuel; Affolter, Markus; Brunner, Damian (2016). Amnioserosa cell constriction but not epidermal actin cable tension autonomously drives dorsal closure. NATURE CELL BIOLOGY, 18 (11), 1161-1172.

Caussinus, Emmanuel; Affolter, Markus (2016). deGradFP: A System to Knockdown GFP-Tagged Proteins. Methods in Molecular Biology, 1478, 177-187.

Betz, Charles; Lenard, Anna; Belting, Heinz-Georg; Affolter, Markus (2016). Cell behaviors and dynamics during angiogenesis. Development, 143 (13), 2249-60.

Aydogan, Vahap; Belting, Heinz-Georg; Affolter, Markus (2016). Mapping the molecular steps of secretory-lysosome-driven tracheal tube fusion. Nature Cell Biology, 18 (7), 720-2.

Bieli, D; Alborelli, I; Harmansa, S; Matsuda, S; Caussinus, E; Affolter, M; 6 (2016). Development and Application of Functionalized Protein Binders in Multicellular Organisms. International review of cell and molecular biology, 325, 181-213.

Affolter, Markus (2016). Seeing is Believing, or How GFP Changed My Approach to Science. Current topics in developmental biology, 116, 1-16.

Matsuda, Shinya; Harmansa, Stefan; Affolter, Markus (2016). BMP morphogen gradients in flies. Cytokine & Growth Factor Reviews, 27, 119-27.

Matsuda, Shinya; Harmansa, Stefan; Affolter, Markus (2016). BMP morphogen gradients in flies. Cytokine & growth factor reviews, 27, 119-27.


Ittig, Simon J.; Schmutz, Christoph; Kasper, Christoph A.; Amstutz, Marlise; Schmidt, Alexander; Sauteur, Loic; Vigano, M. Alessandra; Low, Shyan Huey; Affolter, Markus; Cornelis, Guy R.; Nigg, Erich A.; Arrieumerlou, Cecile (2015). A bacterial type III secretion-based protein delivery tool for broad applications in cell biology. The Journal of cell biology, 211 (4), 913-931.

Harmansa, Stefan; Hamaratoglu, Fisun; Affolter, Markus; Caussinus, Emmanuel (2015). Dpp spreading is required for medial but not for lateral wing disc growth. Nature, 527 (7578), 317-22.

Bieli, Dimitri; Kanca, Oguz; Requena, David; Hamaratoglu, Fisun; Gohl, Daryl; Schedl, Paul; Affolter, Markus; Slattery, Matthew; Müller, Martin; Estella, Carlos (2015). Establishment of a Developmental Compartment Requires Interactions between Three Synergistic Cis-regulatory Modules. PLoS genetics, 11 (10), e1005376.

Bürglin, Thomas R.; Affolter, Markus (2015). Homeodomain proteins: an update. Chromosoma, 125 (3), 497-521.

Aydogan, Vahap; Lenard, Anna; Denes, Alexandru Stefan; Sauteur, Loic; Belting, Heinz-Georg; Affolter, Markus (2015). Endothelial cell division in angiogenic sprouts of differing cellular architecture. Biology open, 4 (10), 1259-69.

Affolter, Markus; Nigg, Erich A. (2015). In memoriam - Walter J. Gehring. Chromosoma, 124 (3), 291-291.

Denes, Alexandru Stefan; Kanca, Oguz; Affolter, Markus (2015). A cellular process that includes asymmetric cytokinesis remodels the dorsal tracheal branches in Drosophila larvae. Development, 142 (10), 1794-1805.

Lenard, Anna; Daetwyler, Stephan; Betz, Charles; Ellertsdottir, Elin; Belting, Heinz-Georg; Huisken, Jan; Affolter, Markus (2015). Endothelial Cell Self-fusion during Vascular Pruning. PLoS biology, 13 (4), e1002126.

Bieli, Dimitri; Kanca, Oguz; Gohl, Daryl; Denes, Alexandru; Schedl, Paul; Affolter, Markus; Mueller, Martin (2015). The drosophila melanogaster mutants apblot and apXasta affect an essential apterous wing enhancer. G3 : Genes, Genomes, Genetics, 5 (6), 1129-1143.

Phng, Li-Kun; Gebala, Véronique; Bentley, Katie; Philippides, Andrew; Wacker, Andrin; Mathivet, Thomas; Sauteur, Loïc; Stanchi, Fabio; Belting, Heinz-Georg; Affolter, Markus; Gerhardt, Holger (2015). Formin-mediated actin polymerization at endothelial junctions is required for vessel lumen formation and stabilization. Developmental cell, 32 (1), 123-32.

Affolter, Markus (2015).Nachruf auf Walter J. Gehring. Zoologie: Mitteilungen der Deutschen Zoologischen Gesellschaft, 2015, 73-80.


Brauchle, Michael; Hansen, Simon; Caussinus, Emmanuel; Lenard, Anna; Ochoa-Espinosa, Amanda; Scholz, Oliver; Sprecher, Simon G; Plückthun, Andreas; Affolter, Markus (2014). Protein interference applications in cellular and developmental biology using DARPins that recognize GFP and mCherry. Biology open, 3 (12), 1252-61.

Sauteur, Loïc; Krudewig, Alice; Herwig, Lukas; Ehrenfeuchter, Nikolaus; Lenard, Anna; Affolter, Markus; Belting, Heinz-Georg (2014). Cdh5/VE-cadherin Promotes Endothelial Cell Interface Elongation via Cortical Actin Polymerization during Angiogenic Sprouting. Cell reports, 9 (2), 504-13.

Santos, M Emília; Braasch, Ingo; Boileau, Nicolas; Meyer, Britta S; Sauteur, Loïc; Böhne, Astrid; Belting, Heinz-Georg; Affolter, Markus; Salzburger, Walter; 9 Santos, M. Emilia; Meyer, Britta S.; Sauteur, Loic; Boehne, Astrid (2014). The evolution of cichlid fish egg-spots is linked with a cis-regulatory change. Nature Communications, 5, 5149.

De Smet, Frederik; Tembuyser, Bieke; Lenard, Anna; Claes, Filip; Zhang, Jie; Michielsen, Christof; Van Schepdael, Ann; Herbert, Jean-Marc; Bono, Françoise; Affolter, Markus; Dewerchin, Mieke; Carmeliet, Peter (2014). Fibroblast Growth Factor Signaling Affects Vascular Outgrowth and Is Required for the Maintenance of Blood Vessel Integrity. Chemistry & biology, 21 (10), 1310-1317.

Affolter, Markus; Wüthrich, Kurt (2014). Walter Jakob Gehring: a Master of Developmental Biology. Proceedings of the National Academy of Sciences of the United States of America, 111 (35), 12574-5.

Affolter, M; Müller M, (2014). Walter Jakob Gehring (1939-2014). Dev Cell, 30 (2), 120-122.

Pyrowolakis, George (2014). Dpp/BMP signaling in flies: from molecules to biology. Seminars in cell & developmental biology, 32, 128-36.

Hultin, Sara; Zheng, Yujuan; Mojallal, Mahdi; Vertuani, Simona; Gentili, Christian; Balland, Martial; Milloud, Rachel; Belting, Heinz-Georg; Affolter, Markus; Helker, Christian S M; Adams, Ralf H; Herzog, Wiebke; Uhlen, Per; Majumdar, Arindam; Holmgren, Lars (2014). AmotL2 Links VE-cadherin to Contractile Actin Fibres Necessary for Aortic Lumen Expansion. Nature communications, 5, 3743.

Kanca, Oguz; Ochoa-Espinosa, Amanda; Affolter, Markus (2014). IV. Tools and Methods for Studying Cell Migration and Cell Rearrangement in Tissue and Organ Development. Methods, 68 (1), 228-32.

Kanca, Oguz; Caussinus, Emmanuel; Denes, Alexandru S; Percival-Smith, Anthony; Affolter, Markus (2014). Raeppli: a whole-tissue labeling tool for live imaging of Drosophila development. Development, 141 (2), 472-80.


Caussinus, Emmanuel; Kanca, Oguz; Affolter, Markus (2013). Protein knockouts in living eukaryotes using deGradFP and green fluorescent protein fusion targets. Current protocols in protein science, 73 (30.2), Unit30.2.

Lenard, Anna; Affolter, Markus (2013). Tugging organs into place. Developmental cell, 27 (3), 243-244.

Kochhan, Eva; Lenard, Anna; Ellertsdottir, Elin; Herwig, Lukas; Affolter, Markus; Belting, Heinz-Georg; Siekmann, Arndt F. (2013). Blood Flow Changes Coincide with Cellular Rearrangements during Blood Vessel Pruning in Zebrafish Embryos. PLoS ONE, 8 (10), e75060.

Hayashi, Makoto; Majumdar, Arindam; Li, Xiujuan; Adler, Jeremy; Sun, Zuyue; Vertuani, Simona; Hellberg, Carina; Mellberg, Sofie; Koch, Sina; Dimberg, Anna; Koh, Gou Young; Dejana, Elisabetta; Belting, Heinz-Georg; Affolter, Markus; Thurston, Gavin; Holmgren, Lars; Vestweber, Dietmar; Claesson-Welsh, Lena (2013). VE-PTP regulates VEGFR2 activity in stalk cells to establish endothelial cell polarity and lumen formation. Nature communications, 4, 1672.

Lenard, Anna; Ellertsdottir, Elin; Herwig, Lukas; Krudewig, Alice; Sauteur, Loïc; Belting, Heinz-Georg; Affolter, Markus (2013). In Vivo Analysis Reveals a Highly Stereotypic Morphogenetic Pathway of Vascular Anastomosis. Developmental cell, 25 (5), 492-506.

Helker, Christian S M; Schuermann, Annika; Karpanen, Terhi; Zeuschner, Dagmar; Belting, Heinz-Georg; Affolter, Markus; Schulte-Merker, Stefan; Herzog, Wiebke (2013). The Zebrafish Common Cardinal Veins Develop by a Novel Mechanism: Lumen Ensheathment. Development, 140 (13), 2776-86.

Siekmann, Arndt F.; Affolter, Markus; Belting, Heinz-Georg (2013). The Tip Cell Concept Ten Years After : New Players Tune in for a Common Theme. Experimental cell research, 319 (9), 1255-1263.


Baer, Magdalena M.; Palm, Wilhelm; Eaton, Suzanne; Leptin, Maria; Affolter, Markus (2012). Microsomal triacylglycerol transfer protein (MTP) is required cell autonomously to expand tracheal lumen in Drosophila. Journal of cell science, 125 (24), 6038-6048.

Ellertsdottir, Elin; Berthold, Peter R.; Bouzaffour, Mohamed; Dufourcq, Pascale; Trayer, Vincent; Gauron, Carole; Vriz, Sophie; Affolter, Markus; Rampon, Christine (2012). Developmental Role of Zebrafish Protease-Activated Receptor 1 (PAR1) in the Cardio-Vascular System. PLoS ONE, 7 (7), e42131.

Ochoa-Espinosa, Amanda; Affolter, Markus (2012). Branching morphogenesis : from cells to organs and back. Cold Spring Harbor Perspectives in Biology, 4 (10), 1-15.

Wang, Shuoshuo; Meyer, Heiko; Ochoa-Espinosa, Amanda; Buchwald, Ulf; Onel, Susanne; Altenhein, Benjamin; Heinisch, Jürgen J; Affolter, Markus; Paululat, Achim (2012). GBF1 (Gartenzwerg)-dependent secretion is required for Drosophila tubulogenesis. Journal of cell science, 125 (Pt2), 461-72.

Caussinus, Emmanuel; Kanca, Oguz; Affolter, Markus (2012). Fluorescent fusion protein knockout mediated by anti-GFP nanobody. Nature structural & molecular biology, 19 (1), 117-21.

Ochoa-Espinosa, Amanda; Baer, Magdalena M; Affolter, Markus (2012). Tubulogenesis: Src42A Goes to Great Lengths in Tube Elongation. Current biology, 22 (11), R446-9.

Ochoa-Espinosa, Amanda; Affolter, Markus: Branching Morphogenesis: From Cells to Organs and BackMammalian Development: Networks, Switches, and Morphogenetic Processes, Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 81-94.


Gutnick, Amos; Blechman, Janna; Kaslin, Jan; Herwig, Lukas; Belting, Heinz-Georg; Affolter, Markus; Bonkowsky, Joshua L; Levkowitz, Gil (2011). The hypothalamic neuropeptide oxytocin is required for formation of the neurovascular interface of the pituitary. Developmental cell, 21 (4), 642-54.

Vermot, Julien; Affolter, Markus (2011). Modeling new conceptual interpretations of development. Development, 138 (19), 4111-5.

Totong, Ronald; Schell, Thomas; Lescroart, Fabienne; Ryckebüsch, Lucile; Lin, Yi-Fan; Zygmunt, Tomasz; Herwig, Lukas; Krudewig, Alice; Gershoony, Dafna; Belting, Heinz-Georg; Affolter, Markus; Torres-Vázquez, Jesús; Yelon, Deborah (2011). The novel transmembrane protein Tmem2 is essential for coordination of myocardial and endocardial morphogenesis. Development, 138 (19), 4199-205.

Zygmunt, Tomasz; Gay, Carl Michael; Blondelle, Jordan; Singh, Manvendra K; Flaherty, Kathleen McCrone; Means, Paula Casey; Herwig, Lukas; Krudewig, Alice; Belting, Heinz-Georg; Affolter, Markus; Epstein, Jonathan A; Torres-Vázquez, Jesús (2011). Semaphorin-PlexinD1 Signaling Limits Angiogenic potential via the VEGF Decoy Receptor sFlt1. Developmental cell, 21 (2), 301-14.

Schulz, Joachim G; Ceulemans, Helga; Caussinus, Emmanuel; Baietti, Maria F; Affolter, Markus; Hassan, Bassem A; David, Guido (2011). Drosophila syndecan regulates tracheal cell migration by stabilizing Robo levels. EMBO reports, 12 (10), 1039-46.

Schwank, Gerald; Dalessi, Sascha; Yang, Schu-Fee; Yagi, Ryohei; de Lachapelle, Aitana Morton; Affolter, Markus; Bergmann, Sven; Basler, Konrad (2011). Formation of long range Dpp morphogen gradient. PLoS biology, 9 (7), e1001111.

Affolter, Markus; Basler, Konrad (2011). Cytonemes Show Their Colors. Science, 332 (6027), 312-313.

Vuilleumier, Robin; Affolter, Markus; Pyrowolakis, George (2011). Pentagone: patrolling BMP morphogen signaling. Fly, 5 (3), 210-4.

Hamaratoglu, Fisun; de Lachapelle, Aitana Morton; Pyrowolakis, George; Bergmann, Sven; Affolter, Markus (2011). Dpp signaling activity requires Pentagone to scale with tissue size in the growing Drosophila wing imaginal disc. PLoS biology, 9 (10), e1001182.

Herwig, Lukas; Blum, Yannick; Krudewig, Alice; Ellertsdottir, Elin; Lenard, Anna; Belting, Heinz-Georg; Affolter, Markus (2011). Distinct cellular mechanisms of blood vessel fusion in the zebrafish embryo. Current biology, 21 (22), 1942-8.


Oggier, Daniela M; Lenard, Anna; Küry, Michael; Hoeger, Birgit; Affolter, Markus; Fent, Karl (2010). Effects of the protein kinase inhibitor PKC412 on gene expression and link to physiological effects in zebrafish Danio rerio eleuthero-embryos. Toxicological sciences, 119 (1), 104-15.

Vuilleumier, Robin; Springhorn, Alexander; Patterson, Lucy; Koidl, Stefanie; Hammerschmidt, Matthias; Affolter, Markus; Pyrowolakis, George (2010). Control of Dpp morphogen signalling by a secreted feedback regulator. Nature Cell Biology, 12 (6), 611-7.

Ellertsdóttir, Elín; Lenard, Anna; Blum, Yannick; Krudewig, Alice; Herwig, Lukas; Affolter, Markus; Belting, Heinz-Georg (2010). Vascular Morphogenesis in the Zebrafish Embryo. Developmental biology, 341 (1), 56-65.

Chanut-Delalande, H.; Jung, A. C.; Baer, M. M.; Lin, L.; Payre, F.; Affolter, M. (2010). The Hrs/Stam complex acts as a positive and negative regulator of RTK signaling during Drosophila development. PLoS ONE, 5 (4).

Ninov, Nikolay; Menezes-Cabral, Sofia; Prat-Rojo, Carla; Manjón, Cristina; Weiss, Alexander; Pyrowolakis, George; Affolter, Markus; Martín-Blanco, Enrique (2010). Dpp Signaling Directs Cell Motility and Invasiveness during Epithelial Morphogenesis. Current biology, 20 (6), 513-20.

Fernandes, Isabelle; Chanut-Delalande, Hélène; Ferrer, Pierre; Latapie, Yvan; Waltzer, Lucas; Affolter, Markus; Payre, François; Plaza, Serge (2010). Zona Pellucida Domain Proteins Remodel the Apical Compartment for Localized Cell Shape Changes. Developmental cell, 18 (1), 64-76.

Li, Keguo; Blum, Yannick; Verma, Anjali; Liu, Zhong; Pramanik, Kallal; Leigh, Noah R.; Chun, Chang Z.; Samant, Ganesh V.; Zhao, Baofeng; Garnaas, Maija K.; Horswill, Mark A.; Stanhope, Stephen A.; North, Paula E.; Miao, Robert Q.; Wilkinson, George A.; Affolter, Markus; Ramchandran, Ramani (2010). A non-coding antisense RNA in tie-1 locus regulates tie-1 function in vivo. Blood, 115 (1), 133-139.

Baer, Magdalena M; Bilstein, Andreas; Caussinus, Emmanuel; Csiszar, Agnes; Affolter, Markus; Leptin, Maria (2010). The role of apoptosis in shaping the tracheal system in the Drosophila embryo. Mechanisms of Development, 127 (1-2), 28-35.

Affolter, M (2010).Basel Biozentrum, a state-of-the-art institute. Swiss Label Spécial CHUV, COM Consulting SA, 2/2010, 34-35.

Weiss, Alexander; Charbonnier, Enrica; Ellertsdottir, Elin; Tsirigos, Aristotelis; Wolf, Christian; Schuh, Reinhard; Pyrowolakis, George; Affolter, Markus (2010). A conserved activation element in BMP signaling during Drosophila development. Nature structural & molecular biology, 17 (1), 69-U91.


Affolter, Markus; Zeller, Rolf; Caussinus, Emmanuel (2009). Tissue remodelling through branching morphogenesis. Nature reviews. Molecular cell biology, 10 (12), 831-42.

Hamaratoglu, Fisun; Basler, Konrad; Affolter, Markus (2009). Confronting morphogen gradients : how important are they for growth?. Science Signaling, 2 (94), pe67.

Affolter, Markus; Zeller, Rolf (2009). From cells to organs : new insight into organ morphogenesis. Current opinion in genetics & development, 19 (5), 421-3.

Baer, Magdalena M; Chanut-Delalande, Helene; Affolter, Markus (2009). Cellular and molecular mechanisms underlying the formation of biological tubes. Current topics in developmental biology, 89, 137-62.

Grieder, Nicole C; Morata, Gines; Affolter, Markus; Gehring, Walter J (2009). Spalt major controls the development of the notum and of wing hinge primordia of the Drosophila melanogaster wing imaginal disc. Developmental biology, 329 (2), 315-26.

Kleaveland, Benjamin; Zheng, Xiangjian; Liu, Jian J; Blum, Yannick; Tung, Jennifer J; Zou, Zhiying; Sweeney, Shawn M; Chen, Mei; Guo, Lili; Lu, Min-min; Zhou, Diane; Kitajewski, Jan; Affolter, Markus; Ginsberg, Mark H; Kahn, Mark L (2009). Regulation of cardiovascular development and integrity by the heart of glass-cerebral cavernous malformation protein pathway. Nature medicine, 15 (2), 169-76.

Affolter, Markus (2009). The Dawn of Life - Cells into Organs. , Leonardo Film GmbH, Oldenburg, Germany...

Affolter, Markus (2009). Ich will die Studierenden begeistern : [Interview]. , Interpharma.


Gohl, D.; Muller, M.; Pirrotta, V.; Affolter, M.; Schedl, P. (2008). Enhancer blocking and transvection at the Drosophila apterous locus. Genetics, 178 (1), 127-43.

Affolter M, (2008). Migration als treibende Kraft in der Organogenese. Nova Acta Leopoldina, Natur und Migration, NF97 (358), 115-131.

Affolter, Markus; Caussinus, Emmanuel (2008). Tracheal branching morphogenesis in Drosophila : new insights into cell behaviour and organ architecture. Development, 135 (12), 2055-64.

Caussinus, Emmanuel; Colombelli, Julien; Affolter, Markus (2008). Tip-cell migration controls stalk-cell intercalation during Drosophila tracheal tube elongation. Current biology, 18 (22), 1727-34.

Blum, Yannick; Belting, Heinz-Georg; Ellertsdottir, Elin; Herwig, Lukas; Lüders, Florian; Affolter, Markus (2008). Complex cell rearrangements during intersegmental vessel sprouting and vessel fusion in the zebrafish embryo. Developmental biology, 316 (2), 312-22.

Affolter, Markus; Slattery, Matthew; Mann, Richard S. (2008). A lexicon for homeodomain-DNA recognition. Cell, 133 (7), 1133-1135.

Affolter, Markus; Pyrowolakis, George; Weiss, Alexander; Basler, Konrad (2008). Signal-induced repression : the exception or the rule in developmental signaling?. Developmental cell, 15 (1), 11-22.

Grieder, N. C.; Caussinus, E.; Parker, D. S.; Cadigan, K.; Affolter, M.; Luschnig, S. (2008). gammaCOP is required for apical protein secretion and epithelial morphogenesis in Drosophila melanogaster. PLoS ONE, 3 (9), e3241.


Merabet, Samir; Saadaoui, Mehdi; Sambrani, Nagraj; Hudry, Bruno; Pradel, Jacques; Affolter, Markus; Graba, Yacine (2007). A unique Extradenticle recruitment mode in the Drosophila Hox protein Ultrabithorax. Proceedings of the National Academy of Sciences of the United States of America, 104 (43), 16946-51.

Belting, Heinz-Georg; Affolter, Markus (2007). It takes guts to make a single lumen. Nature Cell Biology, 9 (8), 880-1.

Chanut-Delalande, H.; Jung, A. C.; Lin, L.; Baer, M. M.; Bilstein, A.; Cabernard, C.; Leptin, M.; Affolter, M. (2007). A genetic mosaic analysis with a repressible cell marker screen to identify genes involved in tracheal cell migration during Drosophila air sac morphogenesis. Genetics, 176 (4), 2177-2187.

Affolter, Markus: Klempnerarbeit im Embryo, in: Sandhoff, Konrad; Donner, Wolfgang (Ed.). (2007). Vom Urknall zum Bewusstsein - Selbstorganisation der Materie, Stuttgart: Thieme Verlag, 193-206.

Affolter, Markus; Basler, Konrad (2007). The Decapentaplegic morphogen gradient : from pattern formation to growth regulation. Nature Reviews. Genetics, 8 (9), 663-74.

Affolter, Markus; Barde, Yves (2007). Self-renewal in the fly kidney. Developmental cell, 13 (3), 321-322.


Affolter, Markus; Pyrowolakis, George (2006). eIF4A goes beyond translation. Nature Cell Biology, 8 (12), 1319-21.

Affolter, Markus (2006). Markus Affolter. Interview. Current biology, 16 (4), R111-R112.

Affolter, Markus; Mann, Richard: Hyped-up for Hox in Hyderabad : workshop on upstream and downstream of Hox genesEMBO reports, London: Nature Publishing Group, 7.

Affolter, M. (2006). Polychaetoid/ZO-1 is required for cell specification and rearrangement during Drosophila tracheal morphogenesis. Current biology, 16 (12), 1224-31.

Cordier, Florence; Hartmann, Britta; Rogowski, Marco; Affolter, Markus; Grzesiek, Stephan (2006). DNA recognition by the brinker repressor - an extreme case of coupling between binding and folding. Journal of molecular biology, 361 (4), 659-72.

Neumann, Marc; Affolter, Markus (2006). Remodelling epithelial tubes through cell rearrangements : from cells to molecules. EMBO reports, 7 (1), 36-40.


Cabernard, Clemens; Affolter, Markus (2005). Distinct roles for two receptor tyrosine kinases in epithelial branching morphogenesis in Drosophila. Developmental cell, 9 (6), 831-42.

Merabet, S. (2005). Recognition of distinct target sites by a unique Labial/Extradenticle/Homothorax complex. Development, 132 (7), 1591-600.

Jung, Alain C; Denholm, Barry; Skaer, Helen; Affolter, Markus (2005). Renal tubule development in Drosophila : a closer look at the cellular level. Journal of the American Society of Nephrology, 16 (2), 322-8.

Affolter, Markus; Weijer, Cornelis J (2005). Signaling to cytoskeletal dynamics during chemotaxis. Developmental cell, 9 (1), 19-34.

Affolter, M. (2005). The Drosophila Extradenticle and Homothorax selector proteins control branchless/FGF expression in mesodermal bridge-cells. EMBO reports, 6 (8), 762-8.


Cabernard, Clemens; Neumann, Marc; Affolter, Markus (2004). Cellular and molecular mechanisms involved in branching morphogenesis of the Drosophila tracheal system. Journal of applied physiology, 97 (6), 2347-53.

Leptin, Maria; Affolter, Markus (2004). Drosophila gastrulation : identification of a missing link. Current biology, 14 (12), R480-2.

Jaźwińska, Anna; Affolter, Markus (2004). A family of genes encoding zona pellucida (ZP) domain proteins is expressed in various epithelial tissues during Drosophila embryogenesis. Gene Expression Patterns, 4 (4), 413-21.

Petit, Valérie; Nussbaumer, Ute; Dossenbach, Caroline; Affolter, Markus (2004). Downstream-of-FGFR is a fibroblast growth factor-specific scaffolding protein and recruits Corkscrew upon receptor activation. Molecular and cellular biology, 24 (9), 3769-81.

Pyrowolakis, George; Hartmann, Britta; Müller, Bruno; Basler, Konrad; Affolter, Markus (2004). A simple molecular complex mediates widespread BMP-induced repression during Drosophila development. Developmental cell, 7 (2), 229-40.

Ribeiro, Carlos; Neumann, Marc; Affolter, Markus (2004). Genetic control of cell intercalation during tracheal morphogenesis in Drosophila. Current biology, 14 (24), 2197-207.


Groppe, Jay; Greenwald, Jason; Wiater, Ezra; Rodriguez-Leon, Joaquin; Economides, Aris N; Kwiatkowski, Witek; Baban, Kandan; Affolter, Markus; Vale, Wylie W; Izpisua Belmonte, Juan Carlos; Choe, Senyon (2003). Structural basis of BMP signaling inhibition by Noggin, a novel twelve-membered cystine knot protein. The Journal of bone and joint surgery, 85-A Suppl 3, 52-8.

Basler, K. (2003). Conversion of an extracellular Dpp/BMP morphogen gradient into an inverse transcriptional gradient. Cell, 113 (2), 221-33.

Affolter, Markus; Bellusci, Savério; Itoh, Nobuyuki; Shilo, Benny; Thiery, Jean-Paul; Werb, Zena (2003). Tube or not tube : remodeling epithelial tissues by branching morphogenesis. Developmental cell, 4 (1), 11-8.

Ribeiro, Carlos; Petit, Valérie; Affolter, Markus (2003). Signaling systems, guided cell migration, and organogenesis : insights from genetic studies in Drosophila. Developmental biology, 260 (1), 1-8.

Jaźwińska, Anna; Ribeiro, Carlos; Affolter, Markus (2003). Epithelial tube morphogenesis during Drosophila tracheal development requires Piopio, a luminal ZP protein. Nature Cell Biology, 5 (10), 895-901.


Groppe, Jay; Greenwald, Jason; Wiater, Ezra; Rodriguez-Leon, Joaquin; Economides, Aris N; Kwiatkowski, Witek; Affolter, Markus; Vale, Wylie W; Izpisua Belmonte, Juan Carlos; Choe, Senyon (2002). Structural basis of BMP signalling inhibition by the cystine knot protein Noggin. Nature, 420 (6916), 636-42.

Streit, Adrian; Kohler, Reto; Marty, Thomas; Belfiore, Marco; Takacs-Vellai, Krisztina; Vigano, Maria-Alessandra; Schnabel, Ralf; Affolter, Markus; Muller, Fritz (2002). Conserved regulation of the Caenorhabditis elegans labial/Hox1 gene ceh-13. Developmental biology, 242 (2), 96-108.

Petit, Valérie; Ribeiro, Carlos; Ebner, Andreas; Affolter, Markus (2002). Regulation of cell migration during tracheal development in Drosophila melanogaster. The International Journal of Developmental Biology, 46 (1), 125-32.

Ebner, Andreas; Kiefer, Fabrice N; Ribeiro, Carlos; Petit, Valérie; Nussbaumer, Ute; Affolter, Markus (2002). Tracheal development in Drosophila melanogaster as a model system for studying the development of a branched organ. Gene, 287 (1-2), 55-66.

Ribeiro, Carlos; Ebner, Andreas; Affolter, Markus (2002). In vivo imaging reveals different cellular functions for FGF and Dpp signaling in tracheal branching morphogenesis. Developmental cell, 2 (5), 677-83.


Marty, T; Vigano, M A; Ribeiro, C; Nussbaumer, U; Grieder, N C; Affolter, M (2001). A HOX complex, a repressor element and a 50 bp sequence confer regional specificity to a DPP-responsive enhancer. Development, 128 (14), 2833-45.

Affolter, M; Mann, R (2001). Development : legs, eyes, or wings - selectors and signals make the difference. Science, 292 (5519), 1080-1.

Affolter, M; Marty, T; Vigano, M A; Jaźwińska, A (2001). Nuclear interpretation of Dpp signaling in Drosophila. The EMBO journal, 20 (13), 3298-305.

Dossenbach, C; Röck, S; Affolter, M (2001). Specificity of FGF signaling in cell migration in Drosophila. Development, 128 (22), 4563-72.


Sivasankaran, R; Vigano, M A; Müller, B; Affolter, M; Basler, K (2000). Direct transcriptional control of the Dpp target omb by the DNA binding protein Brinker. The EMBO journal, 19 (22), 6162-72.

Udagawa, Y; Hanai, J; Tada, K; Grieder, N C; Momoeda, M; Taketani, Y; Affolter, M; Kawabata, M; Miyazono, K (2000). Schnurri interacts with Mad in a Dpp-dependent manner. Genes to cells, 5 (5), 359-69.

Affolter, M (2000). Cell-cell interaction during Drosophila embryogenesis : novel mechanisms and molecules. Ernst Schering Research Foundation Workshop, 29 (29), 65-79.

Montagne, J. (2000). Expression of the blistered/DSRF gene is controlled by different morphogens during Drosophila trachea and wing development. Mechanisms of Development, 96 (1), 27-36.

Amherd, R; Hintermann, E; Walz, D; Affolter, M; Meyer, U A (2000). Purification, cloning, and characterization of a second arylalkylamine N-acetyltransferase from Drosophila melanogaster. DNA and cell biology, 19 (11), 697-705.

Affolter, M; Shilo, B Z (2000). Genetic control of branching morphogenesis during Drosophila tracheal development. Current opinion in cell biology, 12 (6), 731-5.

Marty, T; Müller, B; Basler, K; Affolter, M (2000). Schnurri mediates Dpp-dependent repression of brinker transcription. Nature Cell Biology, 2 (10), 745-9.


Mann, R. S. (1999). Regulation of Hox target genes by a DNA bound Homothorax/Hox/Extradenticle complex. Development, 126 (22), 5137-48.

Affolter, M; Marty, T; Vigano, M A (1999). Balancing import and export in development. Genes & development, 13 (8), 913-5.


Chen, C K; Kühnlein, R P; Eulenberg, K G; Vincent, S; Affolter, M; Schuh, R (1998). The transcription factors KNIRPS and KNIRPS RELATED control cell migration and branch morphogenesis during Drosophila tracheal development. Development, 125 (24), 4959-68.

Groppe, J; Rumpel, K; Economides, A N; Stahl, N; Sebald, W; Affolter, M (1998). Biochemical and biophysical characterization of refolded Drosophila DPP : a homolog of bone morphogenetic proteins 2 and 4. Journal of Biological Chemistry, 273 (44), 29052-65.

Mann, R S; Affolter, M (1998). Hox proteins meet more partners. Current opinion in genetics & development, 8 (4), 423-9.

Brodbeck, D; Amherd, R; Callaerts, P; Hintermann, E; Meyer, U A; Affolter, M (1998). Molecular and biochemical characterization of the aaNAT1 (Dat) locus in Drosophila melanogaster : differential expression of two gene products. DNA and cell biology, 17 (7), 621-33.

Vincent, S; Wilson, R; Coelho, C; Affolter, M; Leptin, M (1998). The Drosophila protein Dof is specifically required for FGF signaling. Molecular cell, 2 (4), 515-25.


Vincent, S; Ruberte, E; Grieder, N C; Chen, C K; Haerry, T; Schuh, R; Affolter, M (1997). DPP controls tracheal cell migration along the dorsoventral body axis of the Drosophila embryo. Development, 124 (14), 2741-50.

Yamamoto, Y; Girard, F; Bello, B; Affolter, M; Gehring, W J (1997). The cramped gene of Drosophila is a member of the Polycomb-group, and interacts with mus209, the gene encoding Proliferating Cell Nuclear Antigen. Development, 124 (17), 3385-94.

Affolter, M. (1997). Synergistic activation of a Drosophila enhancer by HOM/EXD and DPP signaling. The EMBO journal, 16 (24), 7402-10.


Guillemin, K; Groppe, J; Ducker, K; Treisman, R; Hafen, E; Affolter, M; Krasnow, M A (1996). The pruned gene encodes the Drosophila serum response factor and regulates cytoplasmic outgrowth during terminal branching of the tracheal system. Development, 122 (5), 1353-62.

Montagne, J; Groppe, J; Guillemin, K; Krasnow, M A; Gehring, W J; Affolter, M (1996). The Drosophila Serum Response Factor gene is required for the formation of intervein tissue of the wing and is allelic to blistered. Development, 122 (9), 2589-97.


Ruberte, E; Marty, T; Nellen, D; Affolter, M; Basler, K (1995). An absolute requirement for both the type II and type I receptors, punt and thick veins, for dpp signaling in vivo. Cell, 80 (6), 889-97.

Grieder, N C; Nellen, D; Burke, R; Basler, K; Affolter, M (1995). Schnurri is required for Drosophila Dpp signaling and encodes a zinc finger protein similar to the mammalian transcription factor PRDII-BF1. Cell, 81 (5), 791-800.


Basler, K. (1994). Multiple requirements for the receptor serine/threonine kinase thick veins reveal novel functions of TGF beta homologs during Drosophila embryogenesis. Development, 120 (11), 3105-17.


Basler, K. (1994). Receptor serine/threonine kinases implicated in the control of Drosophila body pattern by decapentaplegic. Cell, 78 (2), 225-37.

Dorn, A; Affolter, M; Gehring, W J; Leupin, W (1994). Homeodomain proteins in development and therapy. Pharmacology & therapeutics, 61 (1-2), 155-84.

Gehring, W.J.; Affolter, M.; Burglin, T. (1994). Homeodomain proteins. Annual review of biochemistry, 63, 487-526.

Affolter, M; Montagne, J; Walldorf, U; Groppe, J; Kloter, U; LaRosa, M; Gehring, W J (1994). The Drosophila SRF homolog is expressed in a subset of tracheal cells and maps within a genomic region required for tracheal development. Development, 120 (4), 743-53.


Affolter, M; Walldorf, U; Kloter, U; Schier, A F; Gehring, W J (1993). Regional repression of a Drosophila POU box gene in the endoderm involves inductive interactions between germ layers. Development, 117 (4), 1199-210.


Qian, Y Q; Otting, G; Furukubo-Tokunaga, K; Affolter, M; Gehring, W J; Wüthrich, K (1992). NMR structure determination reveals that the homeodomain is connected through a flexible linker to the main body in the Drosophila Antennapedia protein. Proceedings of the National Academy of Sciences of the United States of America, 89 (22), 10738-42.

Furukubo-Tokunaga, K; Müller, M; Affolter, M; Pick, L; Kloter, U; Gehring, W J (1992). In vivo analysis of the helix-turn-helix motif of the fushi tarazu homeo domain of Drosophila melanogaster. Genes & development, 6 (6), 1082-96.

Dorn, A; Affolter, M; Müller, M; Gehring, W J; Leupin, W (1992). Distamycin-induced inhibition of homeodomain-DNA complexes. The EMBO journal, 11 (1), 279-86.


Affolter, M; Percival-Smith, A; Müller, M; Billeter, M; Qian, Y Q; Otting, G; Wüthrich, K; Gehring, W J (1991). Similarities between the homeodomain and the Hin recombinase DNA-binding domain. Cell, 64 (5), 879-80.


Affolter, M; Schier, A; Gehring, W J (1990). Homeodomain proteins and the regulation of gene expression. Current opinion in cell biology, 2 (3), 485-95.

Percival-Smith, A; Müller, M; Affolter, M; Gehring, W J (1990). The interaction with DNA of wild-type and mutant fushi tarazu homeodomains. The EMBO journal, 9 (12), 3967-74.

Otting, G; Qian, Y Q; Billeter, M; Müller, M; Affolter, M; Gehring, W J; Wüthrich, K (1990). Protein - DNA contacts in the structure of a homeodomain - DNA complex determined by nuclear magnetic resonance spectroscopy in solution. The EMBO journal, 9 (10), 3085-92.

Gehring, W J; Müller, M; Affolter, M; Percival-Smith, A; Billeter, M; Qian, Y Q; Otting, G; Wüthrich, K (1990). The structure of the homeodomain and its functional implications. Trends in Genetics, 6 (10), 323-9.

Pick, L; Schier, A; Affolter, M; Schmidt-Glenewinkel, T; Gehring, W J (1990). Analysis of the ftz upstream element : germ layer-specific enhancers are independently autoregulated. Genes & development, 4 (7), 1224-39.

Affolter, M; Percival-Smith, A; Müller, M; Leupin, W; Gehring, W J (1990). DNA binding properties of the purified Antennapedia homeodomain. Proceedings of the National Academy of Sciences of the United States of America, 87 (11), 4093-7.


Otting, G; Qian, Y Q; Müller, M; Affolter, M; Gehring, W; Wüthrich, K (1988). Secondary structure determination for the Antennapedia homeodomain by nuclear magnetic resonance and evidence for a helix-turn-helix motif. The EMBO journal, 7 (13), 4305-9.

Müller, M; Affolter, M; Leupin, W; Otting, G; Wüthrich, K; Gehring, W J (1988). Isolation and sequence-specific DNA binding of the Antennapedia homeodomain. The EMBO journal, 7 (13), 4299-304.


Affolter, M; Côté, J; Renaud, J; Ruiz-Carrillo, A (1987). Regulation of histone and beta A-globin gene expression during differentiation of chicken erythroid cells. Molecular and cellular biology, 7 (10), 3663-72.


Affolter, M; Ruiz-Carrillo, A (1986). Transcription unit of the chicken histone H5 gene and mapping of H5 pre-mRNA sequences. Journal of biological chemistry, 261 (25), 11496-502.

Affolter, M; Labbé, D; Jean, A; Raymond, M; Noël, D; Labelle, Y; Parent-Vaugeois, C; Lambert, M; Bojanowski, R; Anderson, A (1986). cDNA clones for liver cytochrome P-450s from individual aroclor-treated rats : constitutive expression of a new P-450 gene related to phenobarbital-inducible forms. DNA, 5 (3), 209-18.


Affolter, M; Ruiz-Carrillo, A (1985). L'expression des gènes et ses conséquences dans les maladies génétiques. L'Union médicale du Canada, 114 (9), 724-6.

ANDERSON, A; WAITHE, W; LABBE, D; AFFOLTER, M; LABELLE, Y (1985). Diversité des cytochromes P-450 hépatiques : rôle dans la cancérogénèse chimique. L'Union médicale du Canada, 114 (9), 731-732.


Affolter, M; Anderson, A (1984). Segmental homologies in the coding and 3' non-coding sequences of rat liver cytochrome P-450e and P-450b cDNAs and cytochrome P-450e-like genes. Biochemical and Biophysical Research Communications, 118 (2), 655-62.


Ruiz-Carrillo, A; Affolter, M; Renaud, J (1983). Genomic organization of the genes coding for the six main histones of the chicken : complete sequence of the H5 gene. Journal of molecular biology, 170 (4), 843-59.

Affolter, M; Parent-Vaugeois, C; Anderson, A (1983). Curing and induction of the Fels 1 and Fels 2 prophages in the Ames mutagen tester strains of Salmonella typhimurium. Mutation research, 110 (2), 243-62.

Affolter, M; Parent-Vaugeois, C; Anderson, A (1983). Mutagenic response of Ames strains cured of their inducible Fels 1 and Fels 2 prophages. Cancer research, 43 (2), 653-9.

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