[{"author":[{"full_name":"Rakusová, Hana","first_name":"Hana","last_name":"Rakusová"},{"last_name":"Gallego Bartolomé","first_name":"Javier","full_name":"Gallego-Bartolomé, Javier"},{"full_name":"Vanstraelen, Marleen","first_name":"Marleen","last_name":"Vanstraelen"},{"first_name":"Hélène","last_name":"Robert","full_name":"Robert, Hélène S"},{"full_name":"Alabadí, David","last_name":"Alabadí","first_name":"David"},{"first_name":"Miguel","last_name":"Blázquez","full_name":"Blázquez, Miguel A"},{"first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Eva Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí"}],"issue":"5","_id":"3094","publication":"Plant Journal","title":"Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana","month":"09","intvolume":"        67","publication_status":"published","date_created":"2018-12-11T12:01:21Z","page":"817 - 826","quality_controlled":0,"publisher":"Wiley-Blackwell","date_published":"2011-09-01T00:00:00Z","type":"journal_article","date_updated":"2021-01-12T07:41:01Z","citation":{"ista":"Rakusová H, Gallego Bartolomé J, Vanstraelen M, Robert H, Alabadí D, Blázquez M, Benková E, Friml J. 2011. Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana. Plant Journal. 67(5), 817–826.","short":"H. Rakusová, J. Gallego Bartolomé, M. Vanstraelen, H. Robert, D. Alabadí, M. Blázquez, E. Benková, J. Friml, Plant Journal 67 (2011) 817–826.","mla":"Rakusová, Hana, et al. “Polarization of PIN3 Dependent Auxin Transport for Hypocotyl Gravitropic Response in Arabidopsis Thaliana.” <i>Plant Journal</i>, vol. 67, no. 5, Wiley-Blackwell, 2011, pp. 817–26, doi:<a href=\"https://doi.org/10.1111/j.1365-313X.2011.04636.x\">10.1111/j.1365-313X.2011.04636.x</a>.","ieee":"H. Rakusová <i>et al.</i>, “Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana,” <i>Plant Journal</i>, vol. 67, no. 5. Wiley-Blackwell, pp. 817–826, 2011.","chicago":"Rakusová, Hana, Javier Gallego Bartolomé, Marleen Vanstraelen, Hélène Robert, David Alabadí, Miguel Blázquez, Eva Benková, and Jiří Friml. “Polarization of PIN3 Dependent Auxin Transport for Hypocotyl Gravitropic Response in Arabidopsis Thaliana.” <i>Plant Journal</i>. Wiley-Blackwell, 2011. <a href=\"https://doi.org/10.1111/j.1365-313X.2011.04636.x\">https://doi.org/10.1111/j.1365-313X.2011.04636.x</a>.","ama":"Rakusová H, Gallego Bartolomé J, Vanstraelen M, et al. Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana. <i>Plant Journal</i>. 2011;67(5):817-826. doi:<a href=\"https://doi.org/10.1111/j.1365-313X.2011.04636.x\">10.1111/j.1365-313X.2011.04636.x</a>","apa":"Rakusová, H., Gallego Bartolomé, J., Vanstraelen, M., Robert, H., Alabadí, D., Blázquez, M., … Friml, J. (2011). Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana. <i>Plant Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1365-313X.2011.04636.x\">https://doi.org/10.1111/j.1365-313X.2011.04636.x</a>"},"year":"2011","abstract":[{"text":"Summary Gravitropism aligns plant growth with gravity. It involves gravity perception and the asymmetric distribution of the phytohormone auxin. Here we provide insights into the mechanism for hypocotyl gravitropic growth. We show that the Arabidopsis thaliana PIN3 auxin transporter is required for the asymmetric auxin distribution for the gravitropic response. Gravistimulation polarizes PIN3 to the bottom side of hypocotyl endodermal cells, which correlates with an increased auxin response at the lower hypocotyl side. Both PIN3 polarization and hypocotyl bending require the activity of the trafficking regulator GNOM and the protein kinase PINOID. Our data suggest that gravity-induced PIN3 polarization diverts the auxin flow to mediate the asymmetric distribution of auxin for gravitropic shoot bending.","lang":"eng"}],"publist_id":"3606","doi":"10.1111/j.1365-313X.2011.04636.x","day":"01","extern":1,"status":"public","volume":67},{"doi":" 10.1111/j.1469-8137.2011.03757.x","day":"01","abstract":[{"text":"Root system architecture depends on lateral root (LR) initiation that takes place in a relatively narrow developmental window (DW). Here, we analyzed the role of auxin gradients established along the parent root in defining this DW for LR initiation. Correlations between auxin distribution and response, and spatiotemporal control of LR initiation were analyzed in Arabidopsis thaliana and tomato (Solanum lycopersicum). In both Arabidopsis and tomato roots, a well defined zone, where auxin content and response are minimal, demarcates the position of a DW for founder cell specification and LR initiation. We show that in the zone of auxin minimum pericycle cells have highest probability to become founder cells and that auxin perception via the TIR1/AFB pathway, and polar auxin transport, are essential for the establishment of this zone. Altogether, this study reveals that the same morphogen-like molecule, auxin, can act simultaneously as a morphogenetic trigger of LR founder cell identity and as a gradient-dependent signal defining positioning of the founder cell specification. This auxin minimum zone might represent an important control mechanism ensuring the LR initiation steadiness and the acropetal LR initiation pattern. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.","lang":"eng"}],"publist_id":"3605","date_updated":"2021-01-12T07:41:01Z","citation":{"ama":"Dubrovsky J, Napsucialy Mendivil S, Duclercq J, et al. Auxin minimum defines a developmental window for lateral root initiation. <i>New Phytologist</i>. 2011;191(4):970-983. doi:<a href=\"https://doi.org/ 10.1111/j.1469-8137.2011.03757.x\"> 10.1111/j.1469-8137.2011.03757.x</a>","apa":"Dubrovsky, J., Napsucialy Mendivil, S., Duclercq, J., Cheng, Y., Shishkova, S., Ivanchenko, M., … Benková, E. (2011). Auxin minimum defines a developmental window for lateral root initiation. <i>New Phytologist</i>. Wiley-Blackwell. <a href=\"https://doi.org/ 10.1111/j.1469-8137.2011.03757.x\">https://doi.org/ 10.1111/j.1469-8137.2011.03757.x</a>","ieee":"J. Dubrovsky <i>et al.</i>, “Auxin minimum defines a developmental window for lateral root initiation,” <i>New Phytologist</i>, vol. 191, no. 4. Wiley-Blackwell, pp. 970–983, 2011.","chicago":"Dubrovsky, Joseph, Selene Napsucialy Mendivil, Jérôme Duclercq, Yan Cheng, Svetlana Shishkova, Maria Ivanchenko, Jiří Friml, Angus Murphy, and Eva Benková. “Auxin Minimum Defines a Developmental Window for Lateral Root Initiation.” <i>New Phytologist</i>. Wiley-Blackwell, 2011. <a href=\"https://doi.org/ 10.1111/j.1469-8137.2011.03757.x\">https://doi.org/ 10.1111/j.1469-8137.2011.03757.x</a>.","mla":"Dubrovsky, Joseph, et al. “Auxin Minimum Defines a Developmental Window for Lateral Root Initiation.” <i>New Phytologist</i>, vol. 191, no. 4, Wiley-Blackwell, 2011, pp. 970–83, doi:<a href=\"https://doi.org/ 10.1111/j.1469-8137.2011.03757.x\"> 10.1111/j.1469-8137.2011.03757.x</a>.","short":"J. Dubrovsky, S. Napsucialy Mendivil, J. Duclercq, Y. Cheng, S. Shishkova, M. Ivanchenko, J. Friml, A. Murphy, E. Benková, New Phytologist 191 (2011) 970–983.","ista":"Dubrovsky J, Napsucialy Mendivil S, Duclercq J, Cheng Y, Shishkova S, Ivanchenko M, Friml J, Murphy A, Benková E. 2011. Auxin minimum defines a developmental window for lateral root initiation. New Phytologist. 191(4), 970–983."},"year":"2011","date_published":"2011-01-01T00:00:00Z","type":"journal_article","volume":191,"extern":1,"status":"public","publication_status":"published","date_created":"2018-12-11T12:01:21Z","title":"Auxin minimum defines a developmental window for lateral root initiation","month":"01","intvolume":"       191","_id":"3095","publication":"New Phytologist","author":[{"first_name":"Joseph","last_name":"Dubrovsky","full_name":"Dubrovsky, Joseph G"},{"first_name":"Selene","last_name":"Napsucialy Mendivil","full_name":"Napsucialy-Mendivil, Selene"},{"first_name":"Jérôme","last_name":"Duclercq","full_name":"Duclercq, Jérôme"},{"full_name":"Cheng, Yan","last_name":"Cheng","first_name":"Yan"},{"first_name":"Svetlana","last_name":"Shishkova","full_name":"Shishkova, Svetlana O"},{"first_name":"Maria","last_name":"Ivanchenko","full_name":"Ivanchenko, Maria G"},{"first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Murphy","first_name":"Angus","full_name":"Murphy, Angus S"},{"last_name":"Benková","first_name":"Eva","full_name":"Eva Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"issue":"4","publisher":"Wiley-Blackwell","page":"970 - 983","quality_controlled":0},{"month":"09","title":"Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization","intvolume":"        16","publication_status":"published","oa_version":"None","date_created":"2018-12-11T12:01:21Z","author":[{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","last_name":"Wabnik","first_name":"Krzysztof T","full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560"},{"full_name":"Kleine Vehn, Jürgen","first_name":"Jürgen","last_name":"Kleine Vehn"},{"last_name":"Govaerts","first_name":"Willy","full_name":"Govaerts, Willy"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"}],"issue":"9","publication":"Trends in Plant Science","_id":"3096","publisher":"Cell Press","language":[{"iso":"eng"}],"page":"468 - 475","quality_controlled":"1","abstract":[{"text":"Carrier-dependent, intercellular auxin transport is central to the developmental patterning of higher plants (tracheophytes). The evolution of this polar auxin transport might be linked to the translocation of some PIN auxin efflux carriers from their presumably ancestral localization at the endoplasmic reticulum (ER) to the polar domains at the plasma membrane. Here we propose an eventually ancient mechanism of intercellular auxin distribution by ER-localized auxin transporters involving intracellular auxin retention and switch-like release from the ER. The proposed model integrates feedback circuits utilizing the conserved nuclear auxin signaling for the regulation of PIN transcription and a hypothetical ER-based signaling for the regulation of PIN-dependent transport activity at the ER. Computer simulations of the model revealed its plausibility for generating auxin channels and localized auxin maxima highlighting the possibility of this alternative mechanism for polar auxin transport.","lang":"eng"}],"publist_id":"3604","doi":"10.1016/j.tplants.2011.05.002","day":"01","date_published":"2011-09-01T00:00:00Z","type":"journal_article","date_updated":"2021-01-12T07:41:01Z","year":"2011","citation":{"ieee":"K. T. Wabnik, J. Kleine Vehn, W. Govaerts, and J. Friml, “Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization,” <i>Trends in Plant Science</i>, vol. 16, no. 9. Cell Press, pp. 468–475, 2011.","chicago":"Wabnik, Krzysztof T, Jürgen Kleine Vehn, Willy Govaerts, and Jiří Friml. “Prototype Cell-to-Cell Auxin Transport Mechanism by Intracellular Auxin Compartmentalization.” <i>Trends in Plant Science</i>. Cell Press, 2011. <a href=\"https://doi.org/10.1016/j.tplants.2011.05.002\">https://doi.org/10.1016/j.tplants.2011.05.002</a>.","ama":"Wabnik KT, Kleine Vehn J, Govaerts W, Friml J. Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization. <i>Trends in Plant Science</i>. 2011;16(9):468-475. doi:<a href=\"https://doi.org/10.1016/j.tplants.2011.05.002\">10.1016/j.tplants.2011.05.002</a>","apa":"Wabnik, K. T., Kleine Vehn, J., Govaerts, W., &#38; Friml, J. (2011). Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization. <i>Trends in Plant Science</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tplants.2011.05.002\">https://doi.org/10.1016/j.tplants.2011.05.002</a>","ista":"Wabnik KT, Kleine Vehn J, Govaerts W, Friml J. 2011. Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization. Trends in Plant Science. 16(9), 468–475.","mla":"Wabnik, Krzysztof T., et al. “Prototype Cell-to-Cell Auxin Transport Mechanism by Intracellular Auxin Compartmentalization.” <i>Trends in Plant Science</i>, vol. 16, no. 9, Cell Press, 2011, pp. 468–75, doi:<a href=\"https://doi.org/10.1016/j.tplants.2011.05.002\">10.1016/j.tplants.2011.05.002</a>.","short":"K.T. Wabnik, J. Kleine Vehn, W. Govaerts, J. Friml, Trends in Plant Science 16 (2011) 468–475."},"extern":"1","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":16},{"publication":"Developmental Cell","_id":"3097","author":[{"id":"3F45B078-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavy","first_name":"Peter","full_name":"Peter Marhavy","orcid":"0000-0001-5227-5741"},{"full_name":"Bielach, Agnieszka","last_name":"Bielach","first_name":"Agnieszka"},{"full_name":"Abas, Lindy","last_name":"Abas","first_name":"Lindy"},{"first_name":"Anas","last_name":"Abuzeineh","full_name":"Abuzeineh, Anas"},{"last_name":"Duclercq","first_name":"Jérôme","full_name":"Duclercq, Jérôme"},{"first_name":"Hirokazu","last_name":"Tanaka","full_name":"Tanaka, Hirokazu"},{"last_name":"Pařezová","first_name":"Markéta","full_name":"Pařezová, Markéta"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kleine-Vehn, Jürgen","first_name":"Jürgen","last_name":"Kleine Vehn"},{"first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Eva Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"issue":"4","publication_status":"published","date_created":"2018-12-11T12:01:22Z","month":"10","title":"Cytokinin modulates endocytic trafficking of PIN1 auxin efflux carrier to control plant organogenesis","intvolume":"        21","page":"796 - 804","quality_controlled":0,"publisher":"Cell Press","date_updated":"2021-01-12T07:41:02Z","year":"2011","citation":{"ieee":"P. Marhavý <i>et al.</i>, “Cytokinin modulates endocytic trafficking of PIN1 auxin efflux carrier to control plant organogenesis,” <i>Developmental Cell</i>, vol. 21, no. 4. Cell Press, pp. 796–804, 2011.","chicago":"Marhavý, Peter, Agnieszka Bielach, Lindy Abas, Anas Abuzeineh, Jérôme Duclercq, Hirokazu Tanaka, Markéta Pařezová, et al. “Cytokinin Modulates Endocytic Trafficking of PIN1 Auxin Efflux Carrier to Control Plant Organogenesis.” <i>Developmental Cell</i>. Cell Press, 2011. <a href=\"https://doi.org/10.1016/j.devcel.2011.08.014\">https://doi.org/10.1016/j.devcel.2011.08.014</a>.","apa":"Marhavý, P., Bielach, A., Abas, L., Abuzeineh, A., Duclercq, J., Tanaka, H., … Benková, E. (2011). Cytokinin modulates endocytic trafficking of PIN1 auxin efflux carrier to control plant organogenesis. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2011.08.014\">https://doi.org/10.1016/j.devcel.2011.08.014</a>","ama":"Marhavý P, Bielach A, Abas L, et al. Cytokinin modulates endocytic trafficking of PIN1 auxin efflux carrier to control plant organogenesis. <i>Developmental Cell</i>. 2011;21(4):796-804. doi:<a href=\"https://doi.org/10.1016/j.devcel.2011.08.014\">10.1016/j.devcel.2011.08.014</a>","ista":"Marhavý P, Bielach A, Abas L, Abuzeineh A, Duclercq J, Tanaka H, Pařezová M, Petrášek J, Friml J, Kleine Vehn J, Benková E. 2011. Cytokinin modulates endocytic trafficking of PIN1 auxin efflux carrier to control plant organogenesis. Developmental Cell. 21(4), 796–804.","short":"P. Marhavý, A. Bielach, L. Abas, A. Abuzeineh, J. Duclercq, H. Tanaka, M. Pařezová, J. Petrášek, J. Friml, J. Kleine Vehn, E. Benková, Developmental Cell 21 (2011) 796–804.","mla":"Marhavý, Peter, et al. “Cytokinin Modulates Endocytic Trafficking of PIN1 Auxin Efflux Carrier to Control Plant Organogenesis.” <i>Developmental Cell</i>, vol. 21, no. 4, Cell Press, 2011, pp. 796–804, doi:<a href=\"https://doi.org/10.1016/j.devcel.2011.08.014\">10.1016/j.devcel.2011.08.014</a>."},"date_published":"2011-10-18T00:00:00Z","type":"journal_article","doi":"10.1016/j.devcel.2011.08.014","day":"18","abstract":[{"text":"Cytokinin is an important regulator of plant growth and development. In Arabidopsis thaliana, the two-component phosphorelay mediated through a family of histidine kinases and response regulators is recognized as the principal cytokinin signal transduction mechanism activating the complex transcriptional response to control various developmental processes. Here, we identified an alternative mode of cytokinin action that uses endocytic trafficking as a means to direct plant organogenesis. This activity occurs downstream of known cytokinin receptors but through a branch of the cytokinin signaling pathway that does not involve transcriptional regulation. We show that cytokinin regulates endocytic recycling of the auxin efflux carrier PINFORMED1 (PIN1) by redirecting it for lytic degradation in vacuoles. Stimulation of the lytic PIN1 degradation is not a default effect for general downregulation of proteins from plasma membranes, but a specific mechanism to rapidly modulate the auxin distribution in cytokinin-mediated developmental processes.","lang":"eng"}],"publist_id":"3603","volume":21,"extern":1,"status":"public"},{"publist_id":"3601","abstract":[{"text":"Cell polarity reflected by asymmetric distribution of proteins at the plasma membrane is a fundamental feature of unicellular and multicellular organisms. It remains conceptually unclear how cell polarity is kept in cell wall-encapsulated plant cells. We have used super-resolution and semi-quantitative live-cell imaging in combination with pharmacological, genetic, and computational approaches to reveal insights into the mechanism of cell polarity maintenance in Arabidopsis thaliana. We show that polar-competent PIN transporters for the phytohormone auxin are delivered to the center of polar domains by super-polar recycling. Within the plasma membrane, PINs are recruited into non-mobile membrane clusters and their lateral diffusion is dramatically reduced, which ensures longer polar retention. At the circumventing edges of the polar domain, spatially defined internalization of escaped cargos occurs by clathrin-dependent endocytosis. Computer simulations confirm that the combination of these processes provides a robust mechanism for polarity maintenance in plant cells. Moreover, our study suggests that the regulation of lateral diffusion and spatially defined endocytosis, but not super-polar exocytosis have primary importance for PIN polarity maintenance.","lang":"eng"}],"day":"25","doi":"10.1038/msb.2011.72","type":"journal_article","date_published":"2011-10-25T00:00:00Z","year":"2011","citation":{"mla":"Kleine Vehn, Jürgen, et al. “Recycling, Clustering and Endocytosis Jointly Maintain PIN Auxin Carrier Polarity at the Plasma Membrane.” <i>Molecular Systems Biology</i>, vol. 7, Nature Publishing Group, 2011, doi:<a href=\"https://doi.org/10.1038/msb.2011.72\">10.1038/msb.2011.72</a>.","short":"J. Kleine Vehn, K.T. Wabnik, A. Martinière, Ł. Łangowski, K. Willig, S. Naramoto, J. Leitner, H. Tanaka, S. Jakobs, S. Robert, C. Luschnig, W. Govaerts, S. Hell, J. Runions, J. Friml, Molecular Systems Biology 7 (2011).","ista":"Kleine Vehn J, Wabnik KT, Martinière A, Łangowski Ł, Willig K, Naramoto S, Leitner J, Tanaka H, Jakobs S, Robert S, Luschnig C, Govaerts W, Hell S, Runions J, Friml J. 2011. Recycling, clustering and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane. Molecular Systems Biology. 7.","apa":"Kleine Vehn, J., Wabnik, K. T., Martinière, A., Łangowski, Ł., Willig, K., Naramoto, S., … Friml, J. (2011). Recycling, clustering and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane. <i>Molecular Systems Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/msb.2011.72\">https://doi.org/10.1038/msb.2011.72</a>","ama":"Kleine Vehn J, Wabnik KT, Martinière A, et al. Recycling, clustering and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane. <i>Molecular Systems Biology</i>. 2011;7. doi:<a href=\"https://doi.org/10.1038/msb.2011.72\">10.1038/msb.2011.72</a>","chicago":"Kleine Vehn, Jürgen, Krzysztof T Wabnik, Alexandre Martinière, Łukasz Łangowski, Katrin Willig, Satoshi Naramoto, Johannes Leitner, et al. “Recycling, Clustering and Endocytosis Jointly Maintain PIN Auxin Carrier Polarity at the Plasma Membrane.” <i>Molecular Systems Biology</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/msb.2011.72\">https://doi.org/10.1038/msb.2011.72</a>.","ieee":"J. Kleine Vehn <i>et al.</i>, “Recycling, clustering and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane,” <i>Molecular Systems Biology</i>, vol. 7. Nature Publishing Group, 2011."},"date_updated":"2021-01-12T07:41:02Z","status":"public","extern":1,"volume":7,"intvolume":"         7","title":"Recycling, clustering and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane","month":"10","date_created":"2018-12-11T12:01:22Z","publication_status":"published","author":[{"last_name":"Kleine Vehn","first_name":"Jürgen","full_name":"Kleine-Vehn, Jürgen"},{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof T","last_name":"Wabnik","orcid":"0000-0001-7263-0560","full_name":"Krzysztof Wabnik"},{"first_name":"Alexandre","last_name":"Martinière","full_name":"Martinière, Alexandre"},{"full_name":"Łangowski, Łukasz","last_name":"Łangowski","first_name":"Łukasz"},{"first_name":"Katrin","last_name":"Willig","full_name":"Willig, Katrin"},{"full_name":"Naramoto, Satoshi","first_name":"Satoshi","last_name":"Naramoto"},{"full_name":"Leitner, Johannes","last_name":"Leitner","first_name":"Johannes"},{"full_name":"Tanaka, Hirokazu","first_name":"Hirokazu","last_name":"Tanaka"},{"last_name":"Jakobs","first_name":"Stefan","full_name":"Jakobs, Stefan"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"},{"full_name":"Luschnig, Christian","first_name":"Christian","last_name":"Luschnig"},{"full_name":"Govaerts, Willy J","last_name":"Govaerts","first_name":"Willy"},{"first_name":"Stefan","last_name":"Hell","full_name":"Hell, Stefan W"},{"full_name":"Runions, John","last_name":"Runions","first_name":"John"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","first_name":"Jirí","last_name":"Friml"}],"publication":"Molecular Systems Biology","_id":"3098","publisher":"Nature Publishing Group","quality_controlled":0},{"quality_controlled":0,"page":"17850 - 17855","publisher":"National Academy of Sciences","issue":"43","author":[{"full_name":"Drakakaki, Georgia","first_name":"Georgia","last_name":"Drakakaki"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"},{"full_name":"Szatmári, Anna-Maria","first_name":"Anna","last_name":"Szatmári"},{"full_name":"Brown, Michelle Q","last_name":"Brown","first_name":"Michelle"},{"full_name":"Nagawa, Shingo","first_name":"Shingo","last_name":"Nagawa"},{"last_name":"Van Damme","first_name":"Daniël","full_name":"Van Damme, Daniël"},{"last_name":"Leonard","first_name":"Marylin","full_name":"Leonard, Marylin"},{"first_name":"Zhenbiao","last_name":"Yang","full_name":"Yang, Zhenbiao"},{"full_name":"Girke, Thomas","first_name":"Thomas","last_name":"Girke"},{"last_name":"Schmid","first_name":"Sandra","full_name":"Schmid, Sandra L"},{"full_name":"Russinova, Eugenia","last_name":"Russinova","first_name":"Eugenia"},{"orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Natasha","last_name":"Raikhel","full_name":"Raikhel, Natasha V"},{"full_name":"Hicks, Glen R","first_name":"Glen","last_name":"Hicks"}],"publication":"PNAS","_id":"3099","intvolume":"       108","month":"10","title":"Clusters of bioactive compounds target dynamic endomembrane networks in vivo","date_created":"2018-12-11T12:01:23Z","publication_status":"published","status":"public","extern":1,"volume":108,"type":"journal_article","date_published":"2011-10-25T00:00:00Z","citation":{"chicago":"Drakakaki, Georgia, Stéphanie Robert, Anna Szatmári, Michelle Brown, Shingo Nagawa, Daniël Van Damme, Marylin Leonard, et al. “Clusters of Bioactive Compounds Target Dynamic Endomembrane Networks in Vivo.” <i>PNAS</i>. National Academy of Sciences, 2011. <a href=\"https://doi.org/10.1073/pnas.1108581108\">https://doi.org/10.1073/pnas.1108581108</a>.","ieee":"G. Drakakaki <i>et al.</i>, “Clusters of bioactive compounds target dynamic endomembrane networks in vivo,” <i>PNAS</i>, vol. 108, no. 43. National Academy of Sciences, pp. 17850–17855, 2011.","ama":"Drakakaki G, Robert S, Szatmári A, et al. Clusters of bioactive compounds target dynamic endomembrane networks in vivo. <i>PNAS</i>. 2011;108(43):17850-17855. doi:<a href=\"https://doi.org/10.1073/pnas.1108581108\">10.1073/pnas.1108581108</a>","apa":"Drakakaki, G., Robert, S., Szatmári, A., Brown, M., Nagawa, S., Van Damme, D., … Hicks, G. (2011). Clusters of bioactive compounds target dynamic endomembrane networks in vivo. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1108581108\">https://doi.org/10.1073/pnas.1108581108</a>","ista":"Drakakaki G, Robert S, Szatmári A, Brown M, Nagawa S, Van Damme D, Leonard M, Yang Z, Girke T, Schmid S, Russinova E, Friml J, Raikhel N, Hicks G. 2011. Clusters of bioactive compounds target dynamic endomembrane networks in vivo. PNAS. 108(43), 17850–17855.","mla":"Drakakaki, Georgia, et al. “Clusters of Bioactive Compounds Target Dynamic Endomembrane Networks in Vivo.” <i>PNAS</i>, vol. 108, no. 43, National Academy of Sciences, 2011, pp. 17850–55, doi:<a href=\"https://doi.org/10.1073/pnas.1108581108\">10.1073/pnas.1108581108</a>.","short":"G. Drakakaki, S. Robert, A. Szatmári, M. Brown, S. Nagawa, D. Van Damme, M. Leonard, Z. Yang, T. Girke, S. Schmid, E. Russinova, J. Friml, N. Raikhel, G. Hicks, PNAS 108 (2011) 17850–17855."},"year":"2011","date_updated":"2021-01-12T07:41:02Z","publist_id":"3602","abstract":[{"text":"Endomembrane trafficking relies on the coordination of a highly complex, dynamic network of intracellular vesicles. Understanding the network will require a dissection of cargo and vesicle dynamics at the cellular level in vivo. This is also a key to establishing a link between vesicular networks and their functional roles in development. We used a high-content intracellular screen to discover small molecules targeting endomembrane trafficking in vivo in a complex eukaryote, Arabidopsis thaliana. Tens of thousands of molecules were prescreened and a selected subset was interrogated against a panel of plasma membrane (PM) and other endomembrane compartment markers to identify molecules that altered vesicle trafficking. The extensive image dataset was transformed by a flexible algorithm into a marker-by-phenotype-by-treatment time matrix and revealed groups of molecules that induced similar subcellular fingerprints (clusters). This matrix provides a platform for a systems view of trafficking. Molecules from distinct clusters presented avenues and enabled an entry point to dissect recycling at the PM, vacuolar sorting, and cell-plate maturation. Bioactivity in human cells indicated the value of the approach to identifying small molecules that are active in diverse organisms for biology and drug discovery.","lang":"eng"}],"day":"25","doi":"10.1073/pnas.1108581108"},{"quality_controlled":0,"page":"3430 - 3441","publisher":"Wiley-Blackwell","issue":"16","author":[{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"full_name":"Coppens, Frederik","first_name":"Frederik","last_name":"Coppens"},{"first_name":"Eunkyoung","last_name":"Lee","full_name":"Lee, EunKyoung"},{"full_name":"Donner, Tyler J","first_name":"Tyler","last_name":"Donner"},{"full_name":"Xie, Zidian","last_name":"Xie","first_name":"Zidian"},{"full_name":"Van Isterdael, Gert","first_name":"Gert","last_name":"Van Isterdael"},{"last_name":"Dhondt","first_name":"Stijn","full_name":"Dhondt, Stijn"},{"full_name":"De Winter, Freya","last_name":"De Winter","first_name":"Freya"},{"full_name":"De Rybel, Bert","first_name":"Bert","last_name":"De Rybel"},{"first_name":"Marnik","last_name":"Vuylsteke","full_name":"Vuylsteke, Marnik"},{"first_name":"Lieven","last_name":"De Veylder","full_name":"De Veylder, Lieven"},{"orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Inzé, Dirk","last_name":"Inzé","first_name":"Dirk"},{"first_name":"Erich","last_name":"Grotewold","full_name":"Grotewold, Erich"},{"first_name":"Enrico","last_name":"Scarpella","full_name":"Scarpella, Enrico"},{"first_name":"Fred","last_name":"Sack","full_name":"Sack, Fred"},{"full_name":"Beemster, Gerrit T","last_name":"Beemster","first_name":"Gerrit"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"}],"publication":"EMBO Journal","_id":"3100","intvolume":"        30","month":"08","title":"Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis ","date_created":"2018-12-11T12:01:23Z","publication_status":"published","status":"public","extern":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3160660/"}],"volume":30,"type":"journal_article","date_published":"2011-08-17T00:00:00Z","citation":{"ista":"Vanneste S, Coppens F, Lee E, Donner T, Xie Z, Van Isterdael G, Dhondt S, De Winter F, De Rybel B, Vuylsteke M, De Veylder L, Friml J, Inzé D, Grotewold E, Scarpella E, Sack F, Beemster G, Beeckman T. 2011. Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis . EMBO Journal. 30(16), 3430–3441.","mla":"Vanneste, Steffen, et al. “Developmental Regulation of CYCA2s Contributes to Tissue-Specific Proliferation in Arabidopsis .” <i>EMBO Journal</i>, vol. 30, no. 16, Wiley-Blackwell, 2011, pp. 3430–41, doi:<a href=\"https://doi.org/10.1038/emboj.2011.240\">10.1038/emboj.2011.240</a>.","short":"S. Vanneste, F. Coppens, E. Lee, T. Donner, Z. Xie, G. Van Isterdael, S. Dhondt, F. De Winter, B. De Rybel, M. Vuylsteke, L. De Veylder, J. Friml, D. Inzé, E. Grotewold, E. Scarpella, F. Sack, G. Beemster, T. Beeckman, EMBO Journal 30 (2011) 3430–3441.","chicago":"Vanneste, Steffen, Frederik Coppens, Eunkyoung Lee, Tyler Donner, Zidian Xie, Gert Van Isterdael, Stijn Dhondt, et al. “Developmental Regulation of CYCA2s Contributes to Tissue-Specific Proliferation in Arabidopsis .” <i>EMBO Journal</i>. Wiley-Blackwell, 2011. <a href=\"https://doi.org/10.1038/emboj.2011.240\">https://doi.org/10.1038/emboj.2011.240</a>.","ieee":"S. Vanneste <i>et al.</i>, “Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis ,” <i>EMBO Journal</i>, vol. 30, no. 16. Wiley-Blackwell, pp. 3430–3441, 2011.","apa":"Vanneste, S., Coppens, F., Lee, E., Donner, T., Xie, Z., Van Isterdael, G., … Beeckman, T. (2011). Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis . <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/emboj.2011.240\">https://doi.org/10.1038/emboj.2011.240</a>","ama":"Vanneste S, Coppens F, Lee E, et al. Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis . <i>EMBO Journal</i>. 2011;30(16):3430-3441. doi:<a href=\"https://doi.org/10.1038/emboj.2011.240\">10.1038/emboj.2011.240</a>"},"year":"2011","date_updated":"2021-01-12T07:41:04Z","oa":1,"publist_id":"3600","abstract":[{"text":"In multicellular organisms, morphogenesis relies on a strict coordination in time and space of cell proliferation and differentiation. In contrast to animals, plant development displays continuous organ formation and adaptive growth responses during their lifespan relying on a tight coordination of cell proliferation. How developmental signals interact with the plant cell-cycle machinery is largely unknown. Here, we characterize plant A2-type cyclins, a small gene family of mitotic cyclins, and show how they contribute to the fine-tuning of local proliferation during plant development. Moreover, the timely repression of CYCA2;3 expression in newly formed guard cells is shown to require the stomatal transcription factors FOUR LIPS/MYB124 and MYB88, providing a direct link between developmental programming and cell-cycle exit in plants. Thus, transcriptional downregulation of CYCA2s represents a critical mechanism to coordinate proliferation during plant development.","lang":"eng"}],"day":"17","doi":"10.1038/emboj.2011.240"},{"page":"1711 - 1722","quality_controlled":0,"publisher":"Nature Publishing Group","author":[{"last_name":"Zwiewka","first_name":"Marta","full_name":"Zwiewka, Marta"},{"full_name":"Feraru, Elena","first_name":"Elena","last_name":"Feraru"},{"full_name":"Möller, Barbara","last_name":"Möller","first_name":"Barbara"},{"full_name":"Hwang, Inhwan","last_name":"Hwang","first_name":"Inhwan"},{"full_name":"Feraru, Mugurel I","last_name":"Feraru","first_name":"Mugurel"},{"last_name":"Kleine Vehn","first_name":"Jürgen","full_name":"Kleine-Vehn, Jürgen"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596"}],"issue":"12","publication":"Cell Research","_id":"3101","month":"01","title":"The AP 3 adaptor complex is required for vacuolar function in Arabidopsis","intvolume":"        21","publication_status":"published","date_created":"2018-12-11T12:01:23Z","extern":1,"status":"public","volume":21,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3357998/","open_access":"1"}],"date_published":"2011-01-01T00:00:00Z","type":"journal_article","date_updated":"2021-01-12T07:41:04Z","citation":{"ista":"Zwiewka M, Feraru E, Möller B, Hwang I, Feraru M, Kleine Vehn J, Weijers D, Friml J. 2011. The AP 3 adaptor complex is required for vacuolar function in Arabidopsis. Cell Research. 21(12), 1711–1722.","short":"M. Zwiewka, E. Feraru, B. Möller, I. Hwang, M. Feraru, J. Kleine Vehn, D. Weijers, J. Friml, Cell Research 21 (2011) 1711–1722.","mla":"Zwiewka, Marta, et al. “The AP 3 Adaptor Complex Is Required for Vacuolar Function in Arabidopsis.” <i>Cell Research</i>, vol. 21, no. 12, Nature Publishing Group, 2011, pp. 1711–22, doi:<a href=\"https://doi.org/10.1038/cr.2011.99\">10.1038/cr.2011.99</a>.","ieee":"M. Zwiewka <i>et al.</i>, “The AP 3 adaptor complex is required for vacuolar function in Arabidopsis,” <i>Cell Research</i>, vol. 21, no. 12. Nature Publishing Group, pp. 1711–1722, 2011.","chicago":"Zwiewka, Marta, Elena Feraru, Barbara Möller, Inhwan Hwang, Mugurel Feraru, Jürgen Kleine Vehn, Dolf Weijers, and Jiří Friml. “The AP 3 Adaptor Complex Is Required for Vacuolar Function in Arabidopsis.” <i>Cell Research</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/cr.2011.99\">https://doi.org/10.1038/cr.2011.99</a>.","ama":"Zwiewka M, Feraru E, Möller B, et al. The AP 3 adaptor complex is required for vacuolar function in Arabidopsis. <i>Cell Research</i>. 2011;21(12):1711-1722. doi:<a href=\"https://doi.org/10.1038/cr.2011.99\">10.1038/cr.2011.99</a>","apa":"Zwiewka, M., Feraru, E., Möller, B., Hwang, I., Feraru, M., Kleine Vehn, J., … Friml, J. (2011). The AP 3 adaptor complex is required for vacuolar function in Arabidopsis. <i>Cell Research</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/cr.2011.99\">https://doi.org/10.1038/cr.2011.99</a>"},"year":"2011","abstract":[{"text":"Subcellular trafficking is required for a multitude of functions in eukaryotic cells. It involves regulation of cargo sorting, vesicle formation, trafficking and fusion processes at multiple levels. Adaptor protein (AP) complexes are key regulators of cargo sorting into vesicles in yeast and mammals but their existence and function in plants have not been demonstrated. Here we report the identification of the protein-affected trafficking 4 (pat4) mutant defective in the putative δ subunit of the AP-3 complex. pat4 and pat2, a mutant isolated from the same GFP imaging-based forward genetic screen that lacks a functional putative AP-3 β, as well as dominant negative AP-3 μ transgenic lines display undistinguishable phenotypes characterized by largely normal morphology and development, but strong intracellular accumulation of membrane proteins in aberrant vacuolar structures. All mutants are defective in morphology and function of lytic and protein storage vacuoles (PSVs) but show normal sorting of reserve proteins to PSVs. Immunoprecipitation experiments and genetic studies revealed tight functional and physical associations of putative AP-3 β and AP-3 δ subunits. Furthermore, both proteins are closely linked with putative AP-3 μ and σ subunits and several components of the clathrin and dynamin machineries. Taken together, these results demonstrate that AP complexes, similar to those in other eukaryotes, exist in plants, and that AP-3 plays a specific role in the regulation of biogenesis and function of vacuoles in plant cells. © 2011 IBCB, SIBS, CAS All rights reserved","lang":"eng"}],"oa":1,"publist_id":"3597","doi":"10.1038/cr.2011.99","day":"01"},{"volume":23,"status":"public","extern":1,"year":"2011","citation":{"ieee":"B. Berckmans <i>et al.</i>, “Auxin Dependent cell cycle reactivation through transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins,” <i>Plant Cell</i>, vol. 23, no. 10. American Society of Plant Biologists, pp. 3671–3683, 2011.","chicago":"Berckmans, Barbara, Valya Vassileva, Stephan Schmid, Sara Maes, Boris Parizot, Satoshi Naramoto, Zoltan Magyar, et al. “Auxin Dependent Cell Cycle Reactivation through Transcriptional Regulation of Arabidopsis E2Fa by Lateral Organ Boundary Proteins.” <i>Plant Cell</i>. American Society of Plant Biologists, 2011. <a href=\"https://doi.org/10.1105/tpc.111.088377\">https://doi.org/10.1105/tpc.111.088377</a>.","ama":"Berckmans B, Vassileva V, Schmid S, et al. Auxin Dependent cell cycle reactivation through transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins. <i>Plant Cell</i>. 2011;23(10):3671-3683. doi:<a href=\"https://doi.org/10.1105/tpc.111.088377\">10.1105/tpc.111.088377</a>","apa":"Berckmans, B., Vassileva, V., Schmid, S., Maes, S., Parizot, B., Naramoto, S., … De Veyldera, L. (2011). Auxin Dependent cell cycle reactivation through transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.111.088377\">https://doi.org/10.1105/tpc.111.088377</a>","ista":"Berckmans B, Vassileva V, Schmid S, Maes S, Parizot B, Naramoto S, Magyar Z, Lessa Alvim Kamei C, Koncz C, Bögre L, Persiau G, De Jaeger G, Friml J, Simon R, Beeckman T, De Veyldera L. 2011. Auxin Dependent cell cycle reactivation through transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins. Plant Cell. 23(10), 3671–3683.","mla":"Berckmans, Barbara, et al. “Auxin Dependent Cell Cycle Reactivation through Transcriptional Regulation of Arabidopsis E2Fa by Lateral Organ Boundary Proteins.” <i>Plant Cell</i>, vol. 23, no. 10, American Society of Plant Biologists, 2011, pp. 3671–83, doi:<a href=\"https://doi.org/10.1105/tpc.111.088377\">10.1105/tpc.111.088377</a>.","short":"B. Berckmans, V. Vassileva, S. Schmid, S. Maes, B. Parizot, S. Naramoto, Z. Magyar, C. Lessa Alvim Kamei, C. Koncz, L. Bögre, G. Persiau, G. De Jaeger, J. Friml, R. Simon, T. Beeckman, L. De Veyldera, Plant Cell 23 (2011) 3671–3683."},"date_updated":"2021-01-12T07:41:04Z","type":"journal_article","date_published":"2011-10-14T00:00:00Z","day":"14","doi":"10.1105/tpc.111.088377","publist_id":"3598","abstract":[{"lang":"eng","text":"Multicellular organisms depend on cell production, cell fate specification, and correct patterning to shape their adult body. In plants, auxin plays a prominent role in the timely coordination of these different cellular processes. A well-studied example is lateral root initiation, in which auxin triggers founder cell specification and cell cycle activation of xylem pole–positioned pericycle cells. Here, we report that the E2Fa transcription factor of Arabidopsis thaliana is an essential component that regulates the asymmetric cell division marking lateral root initiation. Moreover, we demonstrate that E2Fa expression is regulated by the LATERAL ORGAN BOUNDARY DOMAIN18/LATERAL ORGAN BOUNDARY DOMAIN33 (LBD18/LBD33) dimer that is, in turn, regulated by the auxin signaling pathway. LBD18/LBD33 mediates lateral root organogenesis through E2Fa transcriptional activation, whereas E2Fa expression under control of the LBD18 promoter eliminates the need for LBD18. Besides lateral root initiation, vascular patterning is disrupted in E2Fa knockout plants, similarly as it is affected in auxin signaling and lbd mutants, indicating that the transcriptional induction of E2Fa through LBDs represents a general mechanism for auxin-dependent cell cycle activation. Our data illustrate how a conserved mechanism driving cell cycle entry has been adapted evolutionarily to connect auxin signaling with control of processes determining plant architecture. "}],"quality_controlled":0,"page":"3671 - 3683","publisher":"American Society of Plant Biologists","_id":"3102","publication":"Plant Cell","issue":"10","author":[{"full_name":"Berckmans, Barbara","last_name":"Berckmans","first_name":"Barbara"},{"full_name":"Vassileva, Valya","first_name":"Valya","last_name":"Vassileva"},{"first_name":"Stephan","last_name":"Schmid","full_name":"Schmid, Stephan P"},{"full_name":"Maes, Sara","last_name":"Maes","first_name":"Sara"},{"last_name":"Parizot","first_name":"Boris","full_name":"Parizot, Boris"},{"full_name":"Naramoto, Satoshi","first_name":"Satoshi","last_name":"Naramoto"},{"first_name":"Zoltan","last_name":"Magyar","full_name":"Magyar, Zoltan"},{"last_name":"Lessa Alvim Kamei","first_name":"Claire","full_name":"Lessa Alvim Kamei, Claire"},{"last_name":"Koncz","first_name":"Csaba","full_name":"Koncz, Csaba"},{"full_name":"Bögre, Laszlo","last_name":"Bögre","first_name":"Laszlo"},{"last_name":"Persiau","first_name":"Geert","full_name":"Persiau, Geert"},{"last_name":"De Jaeger","first_name":"Geert","full_name":"De Jaeger, Geert"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596"},{"full_name":"Simon, Rüdiger","last_name":"Simon","first_name":"Rüdiger"},{"full_name":"Beeckman, Tom","first_name":"Tom","last_name":"Beeckman"},{"first_name":"Lieven","last_name":"De Veyldera","full_name":"de Veyldera, Lieven"}],"date_created":"2018-12-11T12:01:24Z","publication_status":"published","intvolume":"        23","month":"10","title":"Auxin Dependent cell cycle reactivation through transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins"},{"extern":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","volume":14,"abstract":[{"lang":"eng","text":"Endocytosis in plants has an essential role not only for basic cellular functions but also for growth and development, hormonal signaling and communication with the environment including nutrient delivery, toxin avoidance, and pathogen defense. The major endocytic mechanism in plants depends on the coat protein clathrin. It starts by clathrin-coated vesicle formation at the plasma membrane, where specific cargoes are recognized and packaged for internalization. Recently, genetic, biochemical and advanced microscopy studies provided initial insights into mechanisms and roles of clathrin-mediated endocytosis in plants. Here we summarize the present state of knowledge and compare mechanisms of clathrin-mediated endocytosis in plants with animal and yeast paradigms as well as review plant-specific regulations and roles of this process."}],"publist_id":"3596","doi":"10.1016/j.pbi.2011.08.006","day":"01","date_published":"2011-12-01T00:00:00Z","type":"journal_article","date_updated":"2021-01-12T07:41:05Z","year":"2011","citation":{"apa":"Chen, X., Irani, N., &#38; Friml, J. (2011). Clathrin-mediated endocytosis: The gateway into plant cells. <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2011.08.006\">https://doi.org/10.1016/j.pbi.2011.08.006</a>","ama":"Chen X, Irani N, Friml J. Clathrin-mediated endocytosis: The gateway into plant cells. <i>Current Opinion in Plant Biology</i>. 2011;14(6):674-682. doi:<a href=\"https://doi.org/10.1016/j.pbi.2011.08.006\">10.1016/j.pbi.2011.08.006</a>","ieee":"X. Chen, N. Irani, and J. Friml, “Clathrin-mediated endocytosis: The gateway into plant cells,” <i>Current Opinion in Plant Biology</i>, vol. 14, no. 6. Elsevier, pp. 674–682, 2011.","chicago":"Chen, Xu, Niloufer Irani, and Jiří Friml. “Clathrin-Mediated Endocytosis: The Gateway into Plant Cells.” <i>Current Opinion in Plant Biology</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.pbi.2011.08.006\">https://doi.org/10.1016/j.pbi.2011.08.006</a>.","mla":"Chen, Xu, et al. “Clathrin-Mediated Endocytosis: The Gateway into Plant Cells.” <i>Current Opinion in Plant Biology</i>, vol. 14, no. 6, Elsevier, 2011, pp. 674–82, doi:<a href=\"https://doi.org/10.1016/j.pbi.2011.08.006\">10.1016/j.pbi.2011.08.006</a>.","short":"X. Chen, N. Irani, J. Friml, Current Opinion in Plant Biology 14 (2011) 674–682.","ista":"Chen X, Irani N, Friml J. 2011. Clathrin-mediated endocytosis: The gateway into plant cells. Current Opinion in Plant Biology. 14(6), 674–682."},"publisher":"Elsevier","language":[{"iso":"eng"}],"page":"674 - 682","quality_controlled":"1","month":"12","title":"Clathrin-mediated endocytosis: The gateway into plant cells","intvolume":"        14","publication_status":"published","oa_version":"None","date_created":"2018-12-11T12:01:24Z","author":[{"first_name":"Xu","last_name":"Chen","full_name":"Chen, Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Niloufer","last_name":"Irani","full_name":"Irani, Niloufer"},{"last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"issue":"6","publication":"Current Opinion in Plant Biology","_id":"3103"},{"doi":"10.1523/JNEUROSCI.0294-11.2011","day":"08","abstract":[{"lang":"eng","text":"Hippocampal sharp waves (SPWs) and associated fast (&quot;ripple&quot;) oscillations (SPW-Rs) in the CA1 region are among the most synchronous physiological patterns in the mammalian brain. Using two-dimensional arrays of electrodes for recording local field potentials and unit discharges in freely moving rats, we studied the emergence of ripple oscillations (140-220 Hz) and compared their origin and cellular-synaptic mechanisms with fast gamma oscillations (90-140 Hz). We show that (1) hippocampal SPW-Rs and fast gamma oscillations are quantitatively distinct patterns but involve the same networks and share similar mechanisms; (2) both the frequency and magnitude of fast oscillations are positively correlated with the magnitude of SPWs; (3) during both ripples and fast gamma oscillations the frequency of network oscillation is higher in CA1 than in CA3; and (4) the emergence of CA3 population bursts, a prerequisite for SPW-Rs, is biased by activity patterns in the dentate gyrus and entorhinal cortex, with the highest probability of ripples associated with an &quot;optimum&quot; level of dentate gamma power. We hypothesize that each hippocampal subnetwork possesses distinct resonant properties, tuned by the magnitude of the excitatory drive."}],"publist_id":"3559","date_updated":"2021-01-12T07:41:19Z","year":"2011","citation":{"ista":"Sullivan D, Csicsvari JL, Mizuseki K, Montgomery S, Diba K, Buzsáki G. 2011. Relationships between hippocampal sharp waves ripples and fast gamma oscillation Influence of dentate and entorhinal cortical activity. Journal of Neuroscience. 31(23), 8605–8616.","mla":"Sullivan, David, et al. “Relationships between Hippocampal Sharp Waves Ripples and Fast Gamma Oscillation Influence of Dentate and Entorhinal Cortical Activity.” <i>Journal of Neuroscience</i>, vol. 31, no. 23, Society for Neuroscience, 2011, pp. 8605–16, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0294-11.2011\">10.1523/JNEUROSCI.0294-11.2011</a>.","short":"D. Sullivan, J.L. Csicsvari, K. Mizuseki, S. Montgomery, K. Diba, G. Buzsáki, Journal of Neuroscience 31 (2011) 8605–8616.","ieee":"D. Sullivan, J. L. Csicsvari, K. Mizuseki, S. Montgomery, K. Diba, and G. Buzsáki, “Relationships between hippocampal sharp waves ripples and fast gamma oscillation Influence of dentate and entorhinal cortical activity,” <i>Journal of Neuroscience</i>, vol. 31, no. 23. Society for Neuroscience, pp. 8605–8616, 2011.","chicago":"Sullivan, David, Jozsef L Csicsvari, Kenji Mizuseki, Sean Montgomery, Kamran Diba, and György Buzsáki. “Relationships between Hippocampal Sharp Waves Ripples and Fast Gamma Oscillation Influence of Dentate and Entorhinal Cortical Activity.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2011. <a href=\"https://doi.org/10.1523/JNEUROSCI.0294-11.2011\">https://doi.org/10.1523/JNEUROSCI.0294-11.2011</a>.","ama":"Sullivan D, Csicsvari JL, Mizuseki K, Montgomery S, Diba K, Buzsáki G. Relationships between hippocampal sharp waves ripples and fast gamma oscillation Influence of dentate and entorhinal cortical activity. <i>Journal of Neuroscience</i>. 2011;31(23):8605-8616. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0294-11.2011\">10.1523/JNEUROSCI.0294-11.2011</a>","apa":"Sullivan, D., Csicsvari, J. L., Mizuseki, K., Montgomery, S., Diba, K., &#38; Buzsáki, G. (2011). Relationships between hippocampal sharp waves ripples and fast gamma oscillation Influence of dentate and entorhinal cortical activity. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.0294-11.2011\">https://doi.org/10.1523/JNEUROSCI.0294-11.2011</a>"},"date_published":"2011-06-08T00:00:00Z","type":"journal_article","volume":31,"extern":1,"status":"public","publication_status":"published","date_created":"2018-12-11T12:01:36Z","title":"Relationships between hippocampal sharp waves ripples and fast gamma oscillation Influence of dentate and entorhinal cortical activity","month":"06","intvolume":"        31","publication":"Journal of Neuroscience","_id":"3138","author":[{"first_name":"David","last_name":"Sullivan","full_name":"Sullivan, David W"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Jozsef Csicsvari","first_name":"Jozsef L","last_name":"Csicsvari"},{"full_name":"Mizuseki, Kenji","first_name":"Kenji","last_name":"Mizuseki"},{"first_name":"Sean","last_name":"Montgomery","full_name":"Montgomery, Sean M"},{"full_name":"Diba, Kamran","first_name":"Kamran","last_name":"Diba"},{"full_name":"Buzsáki, György","last_name":"Buzsáki","first_name":"György"}],"issue":"23","publisher":"Society for Neuroscience","page":"8605 - 8616","quality_controlled":0},{"publisher":"National Academy of Sciences","page":"7902 - 7907","quality_controlled":0,"month":"05","title":"Site specific integrase mediated transgenesis in mice via pronuclear injection","intvolume":"       108","publication_status":"published","date_created":"2018-12-11T12:01:39Z","author":[{"full_name":"Tasic, Bosiljka","first_name":"Bosiljka","last_name":"Tasic"},{"first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Simon Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wang","first_name":"Charlene","full_name":"Wang, Charlene"},{"full_name":"Gamboa, Matthew","last_name":"Gamboa","first_name":"Matthew"},{"full_name":"Zong, Hui","last_name":"Zong","first_name":"Hui"},{"first_name":"Yanru","last_name":"Chen Tsai","full_name":"Chen-Tsai, Yanru"},{"last_name":"Luo","first_name":"Liqun","full_name":"Luo, Liqun"}],"issue":"19","publication":"PNAS","_id":"3145","extern":1,"status":"public","volume":108,"abstract":[{"lang":"eng","text":"Microinjection of recombinant DNA into zygotic pronuclei has been widely used for producing transgenic mice. However, with this method, the insertion site, integrity, and copy number of the transgene cannot be controlled. Here, we present an integrase-based approach to produce transgenic mice via pronuclear injection, whereby an intact single-copy transgene can be inserted into predetermined chromosomal loci with high efficiency (up to 40%), and faithfully transmitted through generations. We show that neighboring transgenic elements and bacterial DNA within the transgene cause profound silencing and expression variability of the transgenic marker. Removal of these undesirable elements leads to global high-level marker expression from transgenes driven by a ubiquitous promoter. We also obtained faithful marker expression from a tissue-specific promoter. The technique presented here will greatly facilitate murine transgenesis and precise structure/function dissection of mammalian gene function and regulation in vivo."}],"publist_id":"3549","doi":"10.1073/pnas.1019507108","day":"10","date_published":"2011-05-10T00:00:00Z","type":"journal_article","date_updated":"2021-01-12T07:41:22Z","year":"2011","citation":{"ista":"Tasic B, Hippenmeyer S, Wang C, Gamboa M, Zong H, Chen Tsai Y, Luo L. 2011. Site specific integrase mediated transgenesis in mice via pronuclear injection. PNAS. 108(19), 7902–7907.","mla":"Tasic, Bosiljka, et al. “Site Specific Integrase Mediated Transgenesis in Mice via Pronuclear Injection.” <i>PNAS</i>, vol. 108, no. 19, National Academy of Sciences, 2011, pp. 7902–07, doi:<a href=\"https://doi.org/10.1073/pnas.1019507108\">10.1073/pnas.1019507108</a>.","short":"B. Tasic, S. Hippenmeyer, C. Wang, M. Gamboa, H. Zong, Y. Chen Tsai, L. Luo, PNAS 108 (2011) 7902–7907.","chicago":"Tasic, Bosiljka, Simon Hippenmeyer, Charlene Wang, Matthew Gamboa, Hui Zong, Yanru Chen Tsai, and Liqun Luo. “Site Specific Integrase Mediated Transgenesis in Mice via Pronuclear Injection.” <i>PNAS</i>. National Academy of Sciences, 2011. <a href=\"https://doi.org/10.1073/pnas.1019507108\">https://doi.org/10.1073/pnas.1019507108</a>.","ieee":"B. Tasic <i>et al.</i>, “Site specific integrase mediated transgenesis in mice via pronuclear injection,” <i>PNAS</i>, vol. 108, no. 19. National Academy of Sciences, pp. 7902–7907, 2011.","ama":"Tasic B, Hippenmeyer S, Wang C, et al. Site specific integrase mediated transgenesis in mice via pronuclear injection. <i>PNAS</i>. 2011;108(19):7902-7907. doi:<a href=\"https://doi.org/10.1073/pnas.1019507108\">10.1073/pnas.1019507108</a>","apa":"Tasic, B., Hippenmeyer, S., Wang, C., Gamboa, M., Zong, H., Chen Tsai, Y., &#38; Luo, L. (2011). Site specific integrase mediated transgenesis in mice via pronuclear injection. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1019507108\">https://doi.org/10.1073/pnas.1019507108</a>"}},{"year":"2011","citation":{"mla":"Liu, Chong, et al. “Mosaic Analysis with Double Markers Reveals Tumor Cell of Origin in Glioma.” <i>Cell</i>, vol. 146, no. 2, Cell Press, 2011, pp. 209–21, doi:<a href=\"https://doi.org/10.1016/j.cell.2011.06.014\">10.1016/j.cell.2011.06.014</a>.","short":"C. Liu, J. Sage, M. Miller, R. Verhaak, S. Hippenmeyer, H. Vogel, O. Foreman, R. Bronson, A. Nishiyama, L. Luo, H. Zong, Cell 146 (2011) 209–221.","ista":"Liu C, Sage J, Miller M, Verhaak R, Hippenmeyer S, Vogel H, Foreman O, Bronson R, Nishiyama A, Luo L, Zong H. 2011. Mosaic analysis with double markers reveals tumor cell of origin in glioma. Cell. 146(2), 209–221.","apa":"Liu, C., Sage, J., Miller, M., Verhaak, R., Hippenmeyer, S., Vogel, H., … Zong, H. (2011). Mosaic analysis with double markers reveals tumor cell of origin in glioma. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2011.06.014\">https://doi.org/10.1016/j.cell.2011.06.014</a>","ama":"Liu C, Sage J, Miller M, et al. Mosaic analysis with double markers reveals tumor cell of origin in glioma. <i>Cell</i>. 2011;146(2):209-221. doi:<a href=\"https://doi.org/10.1016/j.cell.2011.06.014\">10.1016/j.cell.2011.06.014</a>","ieee":"C. Liu <i>et al.</i>, “Mosaic analysis with double markers reveals tumor cell of origin in glioma,” <i>Cell</i>, vol. 146, no. 2. Cell Press, pp. 209–221, 2011.","chicago":"Liu, Chong, Jonathan Sage, Michael Miller, Roel Verhaak, Simon Hippenmeyer, Hannes Vogel, Oded Foreman, et al. “Mosaic Analysis with Double Markers Reveals Tumor Cell of Origin in Glioma.” <i>Cell</i>. Cell Press, 2011. <a href=\"https://doi.org/10.1016/j.cell.2011.06.014\">https://doi.org/10.1016/j.cell.2011.06.014</a>."},"date_updated":"2021-01-12T07:41:23Z","type":"journal_article","date_published":"2011-07-22T00:00:00Z","day":"22","doi":"10.1016/j.cell.2011.06.014","publist_id":"3548","abstract":[{"text":"Cancer cell of origin is difficult to identify by analyzing cells within terminal stage tumors, whose identity could be concealed by the acquired plasticity. Thus, an ideal approach to identify the cell of origin is to analyze proliferative abnormalities in distinct lineages prior to malignancy. Here, we use mosaic analysis with double markers (MADM) in mice to model gliomagenesis by initiating concurrent p53/Nf1 mutations sporadically in neural stem cells (NSCs). Surprisingly, MADM-based lineage tracing revealed significant aberrant growth prior to malignancy only in oligodendrocyte precursor cells (OPCs), but not in any other NSC-derived lineages or NSCs themselves. Upon tumor formation, phenotypic and transcriptome analyses of tumor cells revealed salient OPC features. Finally, introducing the same p53/Nf1 mutations directly into OPCs consistently led to gliomagenesis. Our findings suggest OPCs as the cell of origin in this model, even when initial mutations occur in NSCs, and highlight the importance of analyzing premalignant stages to identify the cancer cell of origin.","lang":"eng"}],"volume":146,"status":"public","extern":1,"publication":"Cell","_id":"3147","issue":"2","author":[{"full_name":"Liu, Chong","last_name":"Liu","first_name":"Chong"},{"full_name":"Sage, Jonathan C","first_name":"Jonathan","last_name":"Sage"},{"first_name":"Michael","last_name":"Miller","full_name":"Miller, Michael R"},{"full_name":"Verhaak, Roel G","last_name":"Verhaak","first_name":"Roel"},{"orcid":"0000-0003-2279-1061","full_name":"Simon Hippenmeyer","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vogel","first_name":"Hannes","full_name":"Vogel, Hannes"},{"first_name":"Oded","last_name":"Foreman","full_name":"Foreman, Oded"},{"last_name":"Bronson","first_name":"Roderick","full_name":"Bronson, Roderick T"},{"full_name":"Nishiyama, Akiko","last_name":"Nishiyama","first_name":"Akiko"},{"first_name":"Liqun","last_name":"Luo","full_name":"Luo, Liqun"},{"full_name":"Zong, Hui","first_name":"Hui","last_name":"Zong"}],"date_created":"2018-12-11T12:01:40Z","publication_status":"published","intvolume":"       146","title":"Mosaic analysis with double markers reveals tumor cell of origin in glioma","month":"07","quality_controlled":0,"page":"209 - 221","publisher":"Cell Press"},{"author":[{"full_name":"DeGennaro, Matthew","first_name":"Matthew","last_name":"Degennaro"},{"first_name":"Thomas","last_name":"Hurd","full_name":"Hurd, Thomas R"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Daria Siekhaus","orcid":"0000-0001-8323-8353","last_name":"Siekhaus","first_name":"Daria E"},{"full_name":"Biteau, Benoit","last_name":"Biteau","first_name":"Benoit"},{"first_name":"Heinrich","last_name":"Jasper","full_name":"Jasper, Heinrich"},{"last_name":"Lehmann","first_name":"Ruth","full_name":"Lehmann, Ruth"}],"issue":"2","_id":"3154","publication":"Developmental Cell","month":"02","title":"Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion","intvolume":"        20","publication_status":"published","date_created":"2018-12-11T12:01:42Z","page":"233 - 243","quality_controlled":0,"publisher":"Cell Press","date_published":"2011-02-15T00:00:00Z","type":"journal_article","date_updated":"2021-01-12T07:41:26Z","citation":{"chicago":"Degennaro, Matthew, Thomas Hurd, Daria E Siekhaus, Benoit Biteau, Heinrich Jasper, and Ruth Lehmann. “Peroxiredoxin Stabilization of DE-Cadherin Promotes Primordial Germ Cell Adhesion.” <i>Developmental Cell</i>. Cell Press, 2011. <a href=\"https://doi.org/10.1016/j.devcel.2010.12.007\">https://doi.org/10.1016/j.devcel.2010.12.007</a>.","ieee":"M. Degennaro, T. Hurd, D. E. Siekhaus, B. Biteau, H. Jasper, and R. Lehmann, “Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion,” <i>Developmental Cell</i>, vol. 20, no. 2. Cell Press, pp. 233–243, 2011.","ama":"Degennaro M, Hurd T, Siekhaus DE, Biteau B, Jasper H, Lehmann R. Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion. <i>Developmental Cell</i>. 2011;20(2):233-243. doi:<a href=\"https://doi.org/10.1016/j.devcel.2010.12.007\">10.1016/j.devcel.2010.12.007</a>","apa":"Degennaro, M., Hurd, T., Siekhaus, D. E., Biteau, B., Jasper, H., &#38; Lehmann, R. (2011). Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2010.12.007\">https://doi.org/10.1016/j.devcel.2010.12.007</a>","ista":"Degennaro M, Hurd T, Siekhaus DE, Biteau B, Jasper H, Lehmann R. 2011. Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion. Developmental Cell. 20(2), 233–243.","mla":"Degennaro, Matthew, et al. “Peroxiredoxin Stabilization of DE-Cadherin Promotes Primordial Germ Cell Adhesion.” <i>Developmental Cell</i>, vol. 20, no. 2, Cell Press, 2011, pp. 233–43, doi:<a href=\"https://doi.org/10.1016/j.devcel.2010.12.007\">10.1016/j.devcel.2010.12.007</a>.","short":"M. Degennaro, T. Hurd, D.E. Siekhaus, B. Biteau, H. Jasper, R. Lehmann, Developmental Cell 20 (2011) 233–243."},"year":"2011","abstract":[{"text":"Regulated adhesion between cells and their environment is critical for normal cell migration. We have identified mutations in a gene encoding the Drosophila hydrogen peroxide (H2O2)-degrading enzyme Jafrac1, which lead to germ cell adhesion defects. During gastrulation, primordial germ cells (PGCs) associate tightly with the invaginating midgut primordium as it enters the embryo; however, in embryos from jafrac1 mutant mothers this association is disrupted, leaving some PGCs trailing on the outside of the embryo. We observed similar phenotypes in embryos from DE-cadherin/shotgun (shg) mutant mothers and were able to rescue the jafrac1 phenotype by increasing DE-cadherin levels. This and our biochemical evidence strongly suggest that Jafrac1-mediated reduction of H2O2 is required to maintain DE-cadherin protein levels in the early embryo. Our results present in vivo evidence of a peroxiredoxin regulating DE-cadherin-mediated adhesion.","lang":"eng"}],"publist_id":"3541","doi":"10.1016/j.devcel.2010.12.007","day":"15","extern":1,"status":"public","volume":20},{"quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Neural Information Processing Systems","conference":{"start_date":"2011-12-12","name":"NIPS: Neural Information Processing Systems","end_date":"2011-12-14","location":"Granada, Spain"},"_id":"3163","scopus_import":1,"author":[{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"publication_status":"published","oa_version":"None","department":[{"_id":"ChLa"}],"date_created":"2018-12-11T12:01:45Z","month":"12","title":"Maximum margin multi-label structured prediction","related_material":{"record":[{"status":"public","id":"3322","relation":"later_version"}]},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","date_updated":"2023-10-17T11:47:35Z","citation":{"ista":"Lampert C. 2011. Maximum margin multi-label structured prediction. NIPS: Neural Information Processing Systems.","short":"C. Lampert, in:, Neural Information Processing Systems, 2011.","mla":"Lampert, Christoph. <i>Maximum Margin Multi-Label Structured Prediction</i>. Neural Information Processing Systems, 2011.","chicago":"Lampert, Christoph. “Maximum Margin Multi-Label Structured Prediction.” Neural Information Processing Systems, 2011.","ieee":"C. Lampert, “Maximum margin multi-label structured prediction,” presented at the NIPS: Neural Information Processing Systems, Granada, Spain, 2011.","ama":"Lampert C. Maximum margin multi-label structured prediction. In: Neural Information Processing Systems; 2011.","apa":"Lampert, C. (2011). Maximum margin multi-label structured prediction. Presented at the NIPS: Neural Information Processing Systems, Granada, Spain: Neural Information Processing Systems."},"year":"2011","date_published":"2011-12-01T00:00:00Z","type":"conference","day":"01","abstract":[{"text":"We study multi-label prediction for structured output sets, a problem that occurs, for example, in object detection in images, secondary structure prediction in computational biology, and graph matching with symmetries. Conventional multilabel classification techniques are typically not applicable in this situation, because they require explicit enumeration of the label set, which is infeasible in case of structured outputs. Relying on techniques originally designed for single-label structured prediction, in particular structured support vector machines, results in reduced prediction accuracy, or leads to infeasible optimization problems. In this work we derive a maximum-margin training formulation for multi-label structured prediction that remains computationally tractable while achieving high prediction accuracy. It also shares most beneficial properties with single-label maximum-margin approaches, in particular formulation as a convex optimization problem, efficient working set training, and PAC-Bayesian generalization bounds.","lang":"eng"}],"publist_id":"3522"},{"conference":{"name":"MFCS: Mathematical Foundations of Computer Science"},"publisher":"Springer","page":"400 - 411","quality_controlled":0,"alternative_title":["LNCS"],"title":"Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions","month":"08","intvolume":"      6907","publication_status":"published","date_created":"2018-12-11T12:02:00Z","author":[{"last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Vladimir Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"_id":"3204","extern":1,"status":"public","volume":6907,"main_file_link":[{"open_access":"0","url":"http://arxiv.org/pdf/1007.1229v3"}],"abstract":[{"lang":"eng","text":"We introduce a new class of functions that can be minimized in polynomial time in the value oracle model. These are functions f satisfying f(x) + f(y) ≥ f(x ∏ y) + f(x ∐ y) where the domain of each variable x i corresponds to nodes of a rooted binary tree, and operations ∏,∐ are defined with respect to this tree. Special cases include previously studied L-convex and bisubmodular functions, which can be obtained with particular choices of trees. We present a polynomial-time algorithm for minimizing functions in the new class. It combines Murota's steepest descent algorithm for L-convex functions with bisubmodular minimization algorithms. "}],"publist_id":"3478","doi":"10.1007/978-3-642-22993-0_37","day":"09","date_published":"2011-08-09T00:00:00Z","type":"conference","date_updated":"2021-01-12T07:41:47Z","citation":{"apa":"Kolmogorov, V. (2011). Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions (Vol. 6907, pp. 400–411). Presented at the MFCS: Mathematical Foundations of Computer Science, Springer. <a href=\"https://doi.org/10.1007/978-3-642-22993-0_37\">https://doi.org/10.1007/978-3-642-22993-0_37</a>","ama":"Kolmogorov V. Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions. In: Vol 6907. Springer; 2011:400-411. doi:<a href=\"https://doi.org/10.1007/978-3-642-22993-0_37\">10.1007/978-3-642-22993-0_37</a>","chicago":"Kolmogorov, Vladimir. “Submodularity on a Tree: Unifying Submodularity on a Tree: Unifying L-Convex and Bisubmodular Functions Convex and Bisubmodular Functions,” 6907:400–411. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-22993-0_37\">https://doi.org/10.1007/978-3-642-22993-0_37</a>.","ieee":"V. Kolmogorov, “Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions,” presented at the MFCS: Mathematical Foundations of Computer Science, 2011, vol. 6907, pp. 400–411.","mla":"Kolmogorov, Vladimir. <i>Submodularity on a Tree: Unifying Submodularity on a Tree: Unifying L-Convex and Bisubmodular Functions Convex and Bisubmodular Functions</i>. Vol. 6907, Springer, 2011, pp. 400–11, doi:<a href=\"https://doi.org/10.1007/978-3-642-22993-0_37\">10.1007/978-3-642-22993-0_37</a>.","short":"V. Kolmogorov, in:, Springer, 2011, pp. 400–411.","ista":"Kolmogorov V. 2011. Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions. MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 6907, 400–411."},"year":"2011"},{"status":"public","extern":1,"main_file_link":[{"open_access":"0","url":"http://ttic.uchicago.edu/~dbatra/publications/assets/tbkk_icml11.pdf"}],"type":"conference","date_published":"2011-01-01T00:00:00Z","year":"2011","citation":{"chicago":"Tarlow, Daniel, Druv Batra, Pushmeet Kohli, and Vladimir Kolmogorov. “Dynamic Tree Block Coordinate Ascent,” 113–20. Omnipress, 2011.","ieee":"D. Tarlow, D. Batra, P. Kohli, and V. Kolmogorov, “Dynamic tree block coordinate ascent,” presented at the ICML: International Conference on Machine Learning, 2011, pp. 113–120.","ama":"Tarlow D, Batra D, Kohli P, Kolmogorov V. Dynamic tree block coordinate ascent. In: Omnipress; 2011:113-120.","apa":"Tarlow, D., Batra, D., Kohli, P., &#38; Kolmogorov, V. (2011). Dynamic tree block coordinate ascent (pp. 113–120). Presented at the ICML: International Conference on Machine Learning, Omnipress.","ista":"Tarlow D, Batra D, Kohli P, Kolmogorov V. 2011. Dynamic tree block coordinate ascent. ICML: International Conference on Machine Learning, 113–120.","mla":"Tarlow, Daniel, et al. <i>Dynamic Tree Block Coordinate Ascent</i>. Omnipress, 2011, pp. 113–20.","short":"D. Tarlow, D. Batra, P. Kohli, V. Kolmogorov, in:, Omnipress, 2011, pp. 113–120."},"date_updated":"2021-01-12T07:41:47Z","publist_id":"3475","abstract":[{"lang":"eng","text":"This paper proposes a novel Linear Programming (LP) based algorithm, called Dynamic Tree-Block Coordinate Ascent (DT-BCA), for performing maximum a posteriori (MAP) inference in probabilistic graphical models. Unlike traditional message passing algorithms, which operate uniformly on the whole factor graph, our method dynamically chooses regions of the factor graph on which to focus message-passing efforts. We propose two criteria for selecting regions, including an efficiently computable upper-bound on the increase in the objective possible by passing messages in any particular region. This bound is derived from the theory of primal-dual methods from combinatorial optimization, and the forest that maximizes the bounds can be chosen efficiently using a maximum-spanning-tree-like algorithm. Experimental results show that our dynamic schedules significantly speed up state-of-the-art LP-based message-passing algorithms on a wide variety of real-world problems."}],"day":"01","quality_controlled":0,"page":"113 - 120","conference":{"name":"ICML: International Conference on Machine Learning"},"publisher":"Omnipress","author":[{"last_name":"Tarlow","first_name":"Daniel","full_name":"Tarlow, Daniel"},{"full_name":"Batra, Druv","first_name":"Druv","last_name":"Batra"},{"first_name":"Pushmeet","last_name":"Kohli","full_name":"Kohli, Pushmeet"},{"full_name":"Vladimir Kolmogorov","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"_id":"3205","title":"Dynamic tree block coordinate ascent","month":"01","date_created":"2018-12-11T12:02:00Z","publication_status":"published"},{"abstract":[{"lang":"eng","text":"In this paper we address the problem of finding the most probable state of discrete Markov random field (MRF) with associative pairwise terms. Although of practical importance, this problem is known to be NP-hard in general. We propose a new type of MRF decomposition, submod-ular decomposition (SMD). Unlike existing decomposition approaches SMD decomposes the initial problem into sub-problems corresponding to a specific class label while preserving the graph structure of each subproblem. Such decomposition enables us to take into account several types of global constraints in an efficient manner. We study theoretical properties of the proposed approach and demonstrate its applicability on a number of problems."}],"publist_id":"3476","doi":"10.1109/CVPR.2011.5995361","day":"22","date_published":"2011-08-22T00:00:00Z","type":"conference","date_updated":"2021-01-12T07:41:47Z","citation":{"short":"A. Osokin, D. Vetrov, V. Kolmogorov, in:, IEEE, 2011, pp. 1889–1896.","mla":"Osokin, Anton, et al. <i>Submodular Decomposition Framework for Inference in Associative Markov Networks with Global Constraints</i>. IEEE, 2011, pp. 1889–96, doi:<a href=\"https://doi.org/10.1109/CVPR.2011.5995361\">10.1109/CVPR.2011.5995361</a>.","ista":"Osokin A, Vetrov D, Kolmogorov V. 2011. Submodular decomposition framework for inference in associative Markov networks with global constraints. CVPR: Computer Vision and Pattern Recognition, 1889–1896.","apa":"Osokin, A., Vetrov, D., &#38; Kolmogorov, V. (2011). Submodular decomposition framework for inference in associative Markov networks with global constraints (pp. 1889–1896). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. <a href=\"https://doi.org/10.1109/CVPR.2011.5995361\">https://doi.org/10.1109/CVPR.2011.5995361</a>","ama":"Osokin A, Vetrov D, Kolmogorov V. Submodular decomposition framework for inference in associative Markov networks with global constraints. In: IEEE; 2011:1889-1896. doi:<a href=\"https://doi.org/10.1109/CVPR.2011.5995361\">10.1109/CVPR.2011.5995361</a>","chicago":"Osokin, Anton, Dmitry Vetrov, and Vladimir Kolmogorov. “Submodular Decomposition Framework for Inference in Associative Markov Networks with Global Constraints,” 1889–96. IEEE, 2011. <a href=\"https://doi.org/10.1109/CVPR.2011.5995361\">https://doi.org/10.1109/CVPR.2011.5995361</a>.","ieee":"A. Osokin, D. Vetrov, and V. Kolmogorov, “Submodular decomposition framework for inference in associative Markov networks with global constraints,” presented at the CVPR: Computer Vision and Pattern Recognition, 2011, pp. 1889–1896."},"year":"2011","extern":1,"status":"public","main_file_link":[{"open_access":"0","url":"http://arxiv.org/pdf/1103.1077v1"}],"title":"Submodular decomposition framework for inference in associative Markov networks with global constraints","month":"08","publication_status":"published","date_created":"2018-12-11T12:02:00Z","author":[{"full_name":"Osokin, Anton","last_name":"Osokin","first_name":"Anton"},{"last_name":"Vetrov","first_name":"Dmitry","full_name":"Vetrov, Dmitry"},{"last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Vladimir Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"_id":"3206","conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"publisher":"IEEE","page":"1889 - 1896","quality_controlled":0},{"conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"publisher":"IEEE","page":"2217 - 2224","quality_controlled":0,"title":"Object cosegmentation","month":"08","publication_status":"published","date_created":"2018-12-11T12:02:01Z","author":[{"full_name":"Vicente, Sara","last_name":"Vicente","first_name":"Sara"},{"full_name":"Rother, Carsten","first_name":"Carsten","last_name":"Rother"},{"full_name":"Vladimir Kolmogorov","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"_id":"3207","extern":1,"status":"public","abstract":[{"lang":"eng","text":"Cosegmentation is typically defined as the task of jointly segmenting something similar in a given set of images. Existing methods are too generic and so far have not demonstrated competitive results for any specific task. In this paper we overcome this limitation by adding two new aspects to cosegmentation: (1) the &quot;something&quot; has to be an object, and (2) the &quot;similarity&quot; measure is learned. In this way, we are able to achieve excellent results on the recently introduced iCoseg dataset, which contains small sets of images of either the same object instance or similar objects of the same class. The challenge of this dataset lies in the extreme changes in viewpoint, lighting, and object deformations within each set. We are able to considerably outperform several competitors. To achieve this performance, we borrow recent ideas from object recognition: the use of powerful features extracted from a pool of candidate object-like segmentations. We believe that our work will be beneficial to several application areas, such as image retrieval."}],"publist_id":"3477","doi":"10.1109/CVPR.2011.5995530","day":"22","date_published":"2011-08-22T00:00:00Z","type":"conference","date_updated":"2021-01-12T07:41:48Z","citation":{"ista":"Vicente S, Rother C, Kolmogorov V. 2011. Object cosegmentation. CVPR: Computer Vision and Pattern Recognition, 2217–2224.","short":"S. Vicente, C. Rother, V. Kolmogorov, in:, IEEE, 2011, pp. 2217–2224.","mla":"Vicente, Sara, et al. <i>Object Cosegmentation</i>. IEEE, 2011, pp. 2217–24, doi:<a href=\"https://doi.org/10.1109/CVPR.2011.5995530\">10.1109/CVPR.2011.5995530</a>.","chicago":"Vicente, Sara, Carsten Rother, and Vladimir Kolmogorov. “Object Cosegmentation,” 2217–24. IEEE, 2011. <a href=\"https://doi.org/10.1109/CVPR.2011.5995530\">https://doi.org/10.1109/CVPR.2011.5995530</a>.","ieee":"S. Vicente, C. Rother, and V. Kolmogorov, “Object cosegmentation,” presented at the CVPR: Computer Vision and Pattern Recognition, 2011, pp. 2217–2224.","ama":"Vicente S, Rother C, Kolmogorov V. Object cosegmentation. In: IEEE; 2011:2217-2224. doi:<a href=\"https://doi.org/10.1109/CVPR.2011.5995530\">10.1109/CVPR.2011.5995530</a>","apa":"Vicente, S., Rother, C., &#38; Kolmogorov, V. (2011). Object cosegmentation (pp. 2217–2224). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. <a href=\"https://doi.org/10.1109/CVPR.2011.5995530\">https://doi.org/10.1109/CVPR.2011.5995530</a>"},"year":"2011"},{"type":"conference","date_published":"2011-01-01T00:00:00Z","citation":{"mla":"Jain, Abhishek, and Krzysztof Z. Pietrzak. <i>Parallel Repetition for Leakage Resilience Amplification Revisited</i>. Vol. 6597, Springer, 2011, pp. 58–69, doi:<a href=\"https://doi.org/10.1007/978-3-642-19571-6_5\">10.1007/978-3-642-19571-6_5</a>.","short":"A. Jain, K.Z. Pietrzak, in:, Springer, 2011, pp. 58–69.","ista":"Jain A, Pietrzak KZ. 2011. Parallel repetition for leakage resilience amplification revisited. TCC: Theory of Cryptography Conference, LNCS, vol. 6597, 58–69.","ama":"Jain A, Pietrzak KZ. Parallel repetition for leakage resilience amplification revisited. In: Vol 6597. Springer; 2011:58-69. doi:<a href=\"https://doi.org/10.1007/978-3-642-19571-6_5\">10.1007/978-3-642-19571-6_5</a>","apa":"Jain, A., &#38; Pietrzak, K. Z. (2011). Parallel repetition for leakage resilience amplification revisited (Vol. 6597, pp. 58–69). Presented at the TCC: Theory of Cryptography Conference, Springer. <a href=\"https://doi.org/10.1007/978-3-642-19571-6_5\">https://doi.org/10.1007/978-3-642-19571-6_5</a>","chicago":"Jain, Abhishek, and Krzysztof Z Pietrzak. “Parallel Repetition for Leakage Resilience Amplification Revisited,” 6597:58–69. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-19571-6_5\">https://doi.org/10.1007/978-3-642-19571-6_5</a>.","ieee":"A. Jain and K. Z. Pietrzak, “Parallel repetition for leakage resilience amplification revisited,” presented at the TCC: Theory of Cryptography Conference, 2011, vol. 6597, pp. 58–69."},"year":"2011","date_updated":"2021-01-12T07:42:00Z","publist_id":"3443","abstract":[{"lang":"eng","text":"If a cryptographic primitive remains secure even if ℓ bits about the secret key are leaked to the adversary, one would expect that at least one of n independent instantiations of the scheme remains secure given n·ℓ bits of leakage. This intuition has been proven true for schemes satisfying some special information-theoretic properties by Alwen et al. [Eurocrypt'10]. On the negative side, Lewko and Waters [FOCS'10] construct a CPA secure public-key encryption scheme for which this intuition fails. The counterexample of Lewko and Waters leaves open the interesting possibility that for any scheme there exists a constant c&gt;0, such that n fold repetition remains secure against c·n·ℓ bits of leakage. Furthermore, their counterexample requires the n copies of the encryption scheme to share a common reference parameter, leaving open the possibility that the intuition is true for all schemes without common setup. In this work we give a stronger counterexample ruling out these possibilities. We construct a signature scheme such that: 1. a single instantiation remains secure given ℓ = log(k) bits of leakage where k is a security parameter. 2. any polynomial number of independent instantiations can be broken (in the strongest sense of key-recovery) given ℓ′ = poly(k) bits of leakage. Note that ℓ does not depend on the number of instances. The computational assumption underlying our counterexample is that non-interactive computationally sound proofs exist. Moreover, under a stronger (non-standard) assumption about such proofs, our counterexample does not require a common reference parameter. The underlying idea of our counterexample is rather generic and can be applied to other primitives like encryption schemes. © 2011 International Association for Cryptologic Research."}],"day":"01","doi":"10.1007/978-3-642-19571-6_5","status":"public","extern":1,"volume":"6597 ","author":[{"last_name":"Jain","first_name":"Abhishek","full_name":"Jain, Abhishek"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Krzysztof Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"_id":"3236","alternative_title":["LNCS"],"month":"01","title":"Parallel repetition for leakage resilience amplification revisited","date_created":"2018-12-11T12:02:11Z","publication_status":"published","quality_controlled":0,"page":"58 - 69","conference":{"name":"TCC: Theory of Cryptography Conference"},"publisher":"Springer"}]