Cell Biology (Affolter)

Battaglioni, S. (2025) Exploring the landscape of mTOR substrates: identification of two novel targets. Doctoral Thesis.

Soussi, G. (2025) TBX3 restricts anterior gene expression from the posterior mesenchyme to protect posterior identity that is promoted by HAND2. Doctoral Thesis.

Bao, Mengjing et al. (2024) ‘In vivo regulation of an endogenously-tagged protein by a light-regulated kinase’, bioRxiv [Preprint]. bioRxiv: Cold Spring Harbor Laboratory (bioRxiv). Available at: https://doi.org/10.1101/2024.11.27.625702.

Yin, Jianmin et al. (2024) ‘Initiation of lumen formation from junctions via differential actomyosin contractility regulated by dynamic recruitment of Rasip1’, Nature Communications, 15(1). Available at: https://doi.org/10.1038/s41467-024-54143-y.

Yin, Jianmin et al. (2024) ‘Oscillatory contractile forces refine endothelial cell-cell interactions for continuous lumen formation governed by Heg1/Ccm1’, Angiogenesis, (August 2024), pp. 1–16. Available at: https://doi.org/10.1007/s10456-024-09945-5.

Aguilar, Gustavo et al. (2024) ‘Protocol for generating in-frame seamless knockins in Drosophila using the SEED/Harvest technology’, STAR Protocols. 10.07.2024, 5(3). Available at: https://doi.org/10.1016/j.xpro.2024.102932.

Schnider, Sophie T. et al. (2024) ‘Functionalized Protein Binders in Developmental Biology’, Annual Review of Cell and Developmental Biology, 40(1), pp. 119–142. Available at: https://doi.org/10.1146/annurev-cellbio-112122-025214.

Aguilar, Gustavo et al. (2024) ‘Seamless knockins in Drosophila via CRISPR-triggered single-strand annealing’, Developmental Cell. 05.07.2024, (October 2024), p. Online ahead of print. Available at: https://doi.org/10.1016/j.devcel.2024.06.004.

Aguilar Ortega, G. (2024) Engineering ‘Drosophila’ development at the gene and protein levels. Doctoral Thesis.

Bauer, M. (2024) Analysis of morphogen function in Drosophila melanogaster. Doctoral Thesis.

Görsch, E. (2024) Characterization of the laminin receptors integrin α3β1, integrin α6β1, integrin α7β1 and basal cell adhesion molecule in acute myeloid leukemia. Doctoral Thesis.

Gundel, K.I. (2024) Investigating the role of PI3-Kinase α in endothelial cell rearrangements during vascular morphogenesis. Doctoral Thesis.

Kasamkattil, J. (2024) Engineering human nasal chondrocyte spheroids, towards regeneration of the intervertebral disc . Doctoral Thesis.

Reggio, D. (2024) The dynamic transcriptional landscape of intussusceptive angiogenesis. Doctoral Thesis.

Santhosh, S. (2024) Sexual selection mechanisms in a simultaneously hermaphroditic flatworm. Doctoral Thesis.

Aguilar, Gustavo et al. (2023) ‘Transcriptional control of compartmental boundary positioning during Drosophila wing development’. eLife. Available at: https://doi.org/10.7554/elife.91713.1.

Aguilar, Gustavo et al. (2023) ‘Transcriptional control of compartmental boundary positioning during Drosophila wing development’. bioRxiv Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2023.08.05.552106.

Bauer, Milena et al. (2023) ‘Heterodimerization-dependent secretion of bone morphogenetic proteins in Drosophila’, Developmental Cell, Online Ahead of Print, p. Epub. Available at: https://doi.org/10.1016/j.devcel.2023.03.008.

Blumer, S. (2023) Deciphering the role of fibrosis-specific alveolar basal cells in idiopathic pulmonary fibrosis. Doctoral Thesis.

Born, Gordian et al. (2023) ‘No apparent role for the Wari insulator in transcriptional regulation of the endogenous white gene of Drosophila melanogaster’, microPublication Biology, 2023, pp. 000702–000702. Available at: https://doi.org/10.17912/micropub.biology.000702.

Dönges, L. (2023) Modelling and targeting osteoarthritis using human progenitor cell-derived cartilage organoids. Doctoral Thesis.

Hadji Rasouliha, S. (2023) Role of cellular trafficking on Dpp morphogen gradient formation and signaling. Doctoral Thesis.

Hadji Rasouliha, Sheida et al. (2023) ‘Shaping and interpretation of Dpp morphogen gradient by endocytic trafficking’. bioRxiv. Available at: https://doi.org/10.1101/2023.03.27.534445.

Heutschi, D. (2023) Genetic analysis of genes linked to lumen formation in the zebrafish vasculature. Doctoral Thesis.

Heutschi, Daniel et al. (2023) ‘Genetic analysis of rab7 mutants in zebrafish’. bioRxiv. Available at: https://doi.org/10.1101/2023.03.09.531857.

Kemmler, Cassie L. et al. (2023) ‘Next-generation plasmids for transgenesis in zebrafish and beyond’, Development, 150(8), pp. 1–54. Available at: https://doi.org/10.1242/dev.201531.

Matsuda, Shinya and Affolter, Markus (2023) ‘Is Drosophila Dpp/BMP morphogen spreading required for wing patterning and growth?’, BioEssays : news and reviews in molecular, cellular and developmental biology, p. e2200218. Available at: https://doi.org/10.1002/bies.202200218.

Ridwan, Sharif M. et al. (2023) ‘Diffusing fraction of niche BMP ligand safeguards stem-cell differentiation’. bioRxiv. Available at: https://doi.org/10.1101/2022.09.13.507868.

Simon, Niklas et al. (2023) ‘Dally is not essential for Dpp spreading or internalization but for Dpp stability by antagonizing Tkv-mediated Dpp internalization’. bioRxiv. Available at: https://doi.org/10.1101/2023.01.15.524087.

Aguilar, Gustavo et al. (2022) ‘In vivo seamless genetic engineering via CRISPR-triggered single-strand annealing’, bioRxiv [Preprint]. Cold Spring Harbor Laboratory (bioRxiv). Available at: https://doi.org/10.1101/2022.06.17.496589.

Aguilar, Gustavo et al. (2022) ‘In vivo seamless genetic engineering via CRISPR-triggered single-strand annealing’. bioRxiv. Available at: https://doi.org/10.1101/2022.06.17.496589v1.

Bauer, Milena et al. (2022) ‘Heterodimerization-dependent secretion of BMPs in Drosophila’. bioRxiv. Available at: https://doi.org/10.1101/2022.08.04.502599.

Gili Solé, L. (2022) Role of perfusion in the generation of stromal vascular fraction-based patches with angiogenic potential. Doctoral Thesis.

Kemmler Cassie L: Moran, MoHannah R. et al. (2022) ‘Next-generation plasmids for transgenesis in zebrafish and beyond’. bioRxiv. Available at: https://doi.org/10.1101/2022.12.13.520107.

Kotini, Maria P. et al. (2022) ‘Vinculin controls endothelial cell junction dynamics during vascular lumen formation’, Cell reports, 39(2), p. 110658. Available at: https://doi.org/10.1016/j.celrep.2022.110658.

Lepeta, Katarzyna et al. (2022) ‘Studying Protein Function Using Nanobodies and Other Protein Binders in Drosophila’, Methods in Molecular Biology, 2540, pp. 219–237. Available at: https://doi.org/10.1007/978-1-0716-2541-5_10.

Lepeta, Katarzyna et al. (2022) ‘Engineered kinases as a tool for phosphorylation of selected targets in vivo’, Journal of Cell Biology, 221(10), p. e202106179. Available at: https://doi.org/10.1083/jcb.202106179.

Matsuda, Shinya et al. (2022) ‘Nanobody-Based GFP Traps to Study Protein Localization and Function in Developmental Biology’, Methods in Molecular Biology, 2446, pp. 581–593. Available at: https://doi.org/10.1007/978-1-0716-2075-5_30.

Matsuda, Shinya et al. (2022) ‘Author Correction: Asymmetric requirement of Dpp/BMP morphogen dispersal in the Drosophila wing disc’, Nature Communications, 13(1), p. 389. Available at: https://doi.org/10.1038/s41467-021-27680-z.

Mesrouze, Yannick et al. (2022) ‘The role of lysine palmitoylation/myristoylation in the function of the TEAD transcription factors’, Scientific Reports, 12(1), p. 4984. Available at: https://doi.org/10.1038/s41598-022-09127-7.

Rouchon, A. (2022) VEGF decoration of fibrin scaffolds for in vitro and in vivo engineering of vascularized tissues. Doctoral Thesis.

Simon, N. (2022) Dpp dispersal in the Drosophila melanogaster wing disc. Doctoral Thesis.

Singh, S. (2022) Toolset for incorporation of unnatural amino acids into proteins expressed in mammalian cells. Doctoral Thesis.

van der Stoel, Miesje M. et al. (2022) ‘Vinculin strengthens the endothelial barrier during vascular development’, Vascular Biology, 5(1), p. e220012. Available at: https://doi.org/10.1530/vb-22-0012.

Vigano, M. Alessandra et al. (2021) ‘Protein manipulation using single copies of short peptide tags in cultured cells and in; Drosophila melanogaster;’, Development, 148(6). Available at: https://doi.org/10.1242/dev.191700.

Affolter, Markus (2021) ‘Preface’, Current Topics in Developmental Biology, 143, pp. xi–xiv. Available at: https://doi.org/10.1016/s0070-2153(21)00040-5.

Grosso, A. (2021) Vascular Endothelial Growth Factor (VEGF) and Semaphorin 3A (Sema3A) signaling for vascularized bone grafts . Doctoral Thesis.

Kotini, Maria P. et al. (2021) ‘Probing the Effects of the FGFR-Inhibitor Derazantinib on Vascular Development in Zebrafish Embryos’, Pharmaceuticals, 14(1), p. 25. Available at: https://doi.org/10.3390/ph14010025.

Lee, M. (2021) Genetic Analysis of Blood Vessel Morphogenesis: the role of Rasip1 in the regulation of junctional dynamics during angiogenic sprouting and lumen formation. Doctoral Thesis.

Lee, Minkyoung et al. (2021) ‘Control of dynamic cell behaviors during angiogenesis and anastomosis by Rasip1’, Development, 148(15), p. dev197509. Available at: https://doi.org/10.1242/dev.197509.

Matsuda, Shinya et al. (2021) ‘Asymmetric requirement of Dpp/BMP morphogen dispersal in the Drosophila wing disc’, Nature Communications, 12(1), p. 6435. Available at: https://doi.org/10.1038/s41467-021-26726-6.

Yang, Zhenguo et al. (2021) ‘The tight junctions protein Claudin-5 limits endothelial cell motility’, Journal of Cell Science, 134(1), p. jcs248237. Available at: https://doi.org/10.1242/jcs.248237.

Yin, Jianmin et al. (2021) ‘Building the complex architectures of vascular networks: Where to branch, where to connect and where to remodel?’, Current topics in developmental biology, 143, pp. 281–297. Available at: https://doi.org/10.1016/bs.ctdb.2021.01.002.

Vigano, M. Alessandra et al. (2020) ‘Protein manipulation using single copies of short peptide tags in cultured cells and in Drosophila melanogaster’, bioRxiv [Preprint]. Cold Spring Harbor Laboratory (bioRxiv). Available at: https://doi.org/10.1101/2020.04.06.027599.

Galeone, Antonio et al. (2020) ‘Regulation of BMP4/Dpp retrotranslocation and signaling by deglycosylation’, eLife, 9, p. e55596. Available at: https://doi.org/10.7554/elife.55596.

Matsuda, Shinya et al. (2020) ‘Asymmetric requirement of Dpp/BMP morphogen dispersal in the Drosophila wing disc’, bioRxiv, November, pp. 1–31. Available at: https://doi.org/10.1101/2020.11.23.394379.

Mesrouze, Yannick et al. (2020) ‘A new perspective on the evolution of the interaction between the Vg/VGLL1-3 proteins and the TEAD transcription factors’, Scientific Reports, 10, p. 17442. Available at: https://doi.org/10.1038/s41598-020-74584-x.

Wiesner, C. (2020) Analysis of junctional and F-actin dynamics during blood vessel morphogenesis. Doctoral Thesis. Available at: https://doi.org/10.5451/unibas-007208920.

Aguilar, Gustavo et al. (2019) ‘Using Nanobodies to Study Protein Function in Developing Organisms’, Antibodies, 8(1), p. 16. Available at: https://doi.org/10.3390/antib8010016.

Aguilar, Gustavo et al. (2019) ‘Reflections on the use of protein binders to study protein function in developmental biology’, WIREs Developmental Biology, 8(6), p. e356. Available at: https://doi.org/10.1002/wdev.356.

Schmelzer, E. (2019) Endo-lysosomal dynamics during transcellular lumen formation in the vasculature. Analysis of the dynamics of late endosomal, lysosomal compartments during transcellular lumen formation by high spatial and temporal resolution microscopy. Doctoral Thesis. Available at: https://doi.org/10.5451/unibas-007110979.

Vigano, M. Alessandra et al. (2018) ‘DARPins recognizing mTFP1 as novel reagents for in vitro and in vivo protein manipulations’. bioRxiv. Available at: https://doi.org/10.1101/354134.

Angulo-Urarte, Ana et al. (2018) ‘Endothelial cell rearrangements during vascular patterning require PI3-kinase-mediated inhibition of actomyosin contractility’, Nature Communications, 9(1), p. 4826. Available at: https://doi.org/10.1038/s41467-018-07172-3.

Bovo, E. (2018) Mechanisms of vascular stabilization by PDGF-BB. Doctoral Thesis. Available at: https://doi.org/10.5451/unibas-006859508.

Harmansa, Stefan and Affolter, Markus (2018) ‘Protein binders and their applications in developmental biology’, Development, 145(2), pp. 1–13. Available at: https://doi.org/10.1242/dev.148874.

Haumer, A. (2018) Prefabrication of vascularized large bone grafts. Doctoral Thesis. Available at: https://doi.org/10.5451/unibas-006855694.

Hübner, Kathleen et al. (2018) ‘Wnt/β-catenin signaling regulates VE-cadherin-mediated anastomosis of brain capillaries by counteracting S1pr1 signaling’, Nature communications, 9(1), p. 4860. Available at: https://doi.org/10.1038/s41467-018-07302-x.

Kotini, Maria Paraskevi et al. (2018) ‘Sprouting and anastomosis in the Drosophila trachea and the vertebrate vasculature: Similarities and differences in cell behaviour’, Vascular pharmacology, 112, pp. 8–16. Available at: https://doi.org/10.1016/j.vph.2018.11.002.

Monnard, A. (2018) An optogenetic tool to study asymmetric cell division. Doctoral Thesis. Available at: https://doi.org/10.5451/unibas-007110739.

Paatero, Ilkka et al. (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), p. 3545. Available at: https://doi.org/10.1038/s41467-018-05851-9.

Paczulla, A.M. (2018) Investigation of mechanisms regulating leukemogenesis using mouse xenograft models of human acute myeloid leukemia. Doctoral Thesis. Available at: https://doi.org/10.5451/unibas-007056152.

Postika, Nikolay et al. (2018) ‘Boundaries mediate long-distance interactions between enhancers and promoters in the Drosophila Bithorax complex’, PLoS Genet, 14(12), p. e1007702. Available at: https://doi.org/10.1371/journal.pgen.1007702.

Schellinx, N. (2018) Deciphering cytoskeletal junctional interactions during blood vessel morphogenesis in vivo : introduction of novel genetic tools for mosaic analysis of Cdh5/VE-cadherin regulation and function & phenotypic analysis of RadilB function in sprouting angiogenesis. Doctoral Thesis. Available at: https://doi.org/10.5451/unibas-006859937.

Sickmann, Michèle, Affolter, Markus and Müller, Martin (2018) ‘Characterization of the new bithorax allele Ubx bx-Basel’, Drosophila Information Service, 101, pp. 76–80. Available at: http://www.ou.edu/journals/dis/DIS101/DIS101.html.

Vigano, M. Alessandra et al. (2018) ‘DARPins recognizing mTFP1 as novel reagents for in vitro and in vivo protein manipulations’, Biology open, 7(11), p. bio036749. Available at: https://doi.org/10.1242/bio.036749.

Vigano, M. Alessandra et al. (2018) ‘Correction:DARPins recognizing mTFP1 as novel reagents for in vitro; and in vivo protein manipulations’, Biology open, 7(12), p. bio036749. Available at: https://doi.org/10.1242/bio.040832.

Brkić, Š. (2017) Molecular regulation of intussusceptive angiogenesis by ephrinB2/EphB4 signaling and its therapeutic potential. Doctoral Thesis. Available at: https://doi.org/10.5451/unibas-006779002.

Harmansa, Stefan et al. (2017) ‘A nanobody-based toolset to investigate the role of protein localization and dispersal in Drosophila’, eLife, 6, p. 22549. Available at: https://doi.org/10.7554/elife.22549.

Lagendijk, Anne Karine et al. (2017) ‘Live imaging molecular changes in junctional tension upon VE-cadherin in zebrafish’, Nature Communications, 8(1), p. 1402. Available at: https://doi.org/10.1038/s41467-017-01325-6.

Matsuda, Shinya and Affolter, Markus (2017) ‘Dpp from the anterior stripe of cells is crucial for the growth of the Drosophila wing disc’, eLife, 6, p. e22319. Available at: https://doi.org/10.7554/elife.22319.

Nakajima, Hiroyuki et al. (2017) ‘Flow-Dependent Endothelial YAP Regulation Contributes to Vessel Maintenance’, Developmental Cell, 40(6), pp. 523–536.e6. Available at: https://doi.org/10.1016/j.devcel.2017.02.019.

Ochoa-Espinosa, Amanda et al. (2017) ‘Myosin II is not required for Drosophila tracheal branch elongation and cell intercalation’, Development, 144(16), pp. 2961–2968. Available at: https://doi.org/10.1242/dev.148940.

Paatero, Ilkka et al. (2017) ‘Junction-based lamellipodia drive endothelial cell arrangements in vivo via a VE-cadherin/F-actin based oscillatory ratchet mechanism’, bioRxiv, pp. 1–32. Available at: https://doi.org/10.1101/212522.

Roubinet, Chantal et al. (2017) ‘Spatio-temporally separated cortical flows and spindle geometry establish physical asymmetry in fly neural stem cells’, Nature Communications, 8(1), p. 1383. Available at: https://doi.org/10.1038/s41467-017-01391-w.

Sauteur, Loïc, Affolter, Markus and Belting, Heinz-Georg (2017) ‘Distinct and redundant functions of Esam and VE-cadherin during vascular morphogenesis’, Development, 144(8), pp. 1554–1565. Available at: https://doi.org/10.1242/dev.140038.

Sickmann, Michèle et al. (2017) ‘The Drosophila melanogaster straw locus is allelic to laccase2.’, Drosophila Information Service, 100, pp. 171–174. Available at: http://www.ou.edu/journals/dis/DIS100/DIS%20100.pdf.

Tsachaki, Maria et al. (2017) ‘Absence of 11-keto reduction of cortisone and 11-ketotestosterone in the model organism zebrafish’, Journal of Endocrinology, 232(2), pp. 323–335. Available at: https://doi.org/10.1530/joe-16-0495.

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

Affolter, Markus (2016) ‘Seeing is Believing, or How GFP Changed My Approach to Science’, Current topics in developmental biology, 116, pp. 1–16. Available at: https://doi.org/10.1016/bs.ctdb.2015.12.001.

Alborelli, I. (2016) Characterization of the subcellular localization of the TGF-β receptors in the wing imaginal disc. Doctoral Thesis. Available at: https://doi.org/10.5451/unibas-006672510.

Aydogan, V. (2016) Understanding endothelial cell behaviors during sprouting angiogenesis. Doctoral Thesis. Available at: https://doi.org/10.5451/unibas-006740639.

Aydogan, Vahap, Belting, Heinz-Georg and Affolter, Markus (2016) ‘Mapping the molecular steps of secretory-lysosome-driven tracheal tube fusion’, Nature Cell Biology, 18(7), pp. 720–2. Available at: https://doi.org/10.1038/ncb3383.

Betz, Charles et al. (2016) ‘Cell behaviors and dynamics during angiogenesis’, Development, 143(13), pp. 2249–60. Available at: https://doi.org/10.1242/dev.135616.

Bieli, D. et al. (2016) ‘Development and Application of Functionalized Protein Binders in Multicellular Organisms’, International Review of Cell and Molecular Biology, 325, pp. 181–213. Available at: https://doi.org/10.1016/bs.ircmb.2016.02.006.

Caussinus, Emmanuel and Affolter, Markus (2016) ‘deGradFP: A System to Knockdown GFP-Tagged Proteins’, Methods in Molecular Biology, 1478, pp. 177–187. Available at: https://doi.org/10.1007/978-1-4939-6371-3_9.

Enderle, L. (2016) Exploring the developmental functions of fat cadherins in Drosophila and mammals. Doctoral Thesis. Available at: https://doi.org/10.5451/unibas-006624278.

Gaudiello, E. (2016) Engineering cell-based patches as controlled VEGF-releasing devices for therapeutic angiogenesis. Doctoral Thesis. Available at: https://doi.org/10.5451/unibas-006754597.

Harmansa, S. (2016) Nanobodies as novel tools to study morphogen function ‘in vivo’. Doctoral Thesis. Available at: https://doi.org/10.5451/unibas-006617662.

Matsuda, Shinya, Harmansa, Stefan and Affolter, Markus (2016) ‘BMP morphogen gradients in flies’, Cytokine & Growth Factor Reviews, 27, pp. 119–27. Available at: https://doi.org/10.1016/j.cytogfr.2015.11.003.

Metzler, M. (2016) In situ genetic dissection of the boundary element Miscadestral pigmentation in the Bithorax complex of Drosophila melanogaster. Doctoral Thesis. Available at: https://doi.org/10.5451/unibas-006699957.