[{"author":[{"last_name":"Baek","full_name":"Baek, SeungTae","first_name":"Seungtae"},{"last_name":"Kerjan","full_name":"Kerjan, Géraldine","first_name":"Géraldine"},{"first_name":"Stephanie","full_name":"Bielas, Stephanie L","last_name":"Bielas"},{"full_name":"Lee, Jieun","last_name":"Lee","first_name":"Jieun"},{"full_name":"Fenstermaker, Ali G","last_name":"Fenstermaker","first_name":"Ali"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","orcid":"0000-0002-7673-7178","full_name":"Gaia Novarino","last_name":"Novarino"},{"first_name":"Joseph","full_name":"Gleeson, Joseph G","last_name":"Gleeson"}],"publist_id":"5322","title":"Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation","citation":{"chicago":"Baek, Seungtae, Géraldine Kerjan, Stephanie Bielas, Jieun Lee, Ali Fenstermaker, Gaia Novarino, and Joseph Gleeson. “Off-Target Effect of Doublecortin Family ShRNA on Neuronal Migration Associated with Endogenous MicroRNA Dysregulation.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.04.036.","ista":"Baek S, Kerjan G, Bielas S, Lee J, Fenstermaker A, Novarino G, Gleeson J. 2014. Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. 82(6), 1255–1262.","mla":"Baek, Seungtae, et al. “Off-Target Effect of Doublecortin Family ShRNA on Neuronal Migration Associated with Endogenous MicroRNA Dysregulation.” Neuron, vol. 82, no. 6, Elsevier, 2014, pp. 1255–62, doi:10.1016/j.neuron.2014.04.036.","apa":"Baek, S., Kerjan, G., Bielas, S., Lee, J., Fenstermaker, A., Novarino, G., & Gleeson, J. (2014). Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.04.036","ama":"Baek S, Kerjan G, Bielas S, et al. Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. 2014;82(6):1255-1262. doi:10.1016/j.neuron.2014.04.036","ieee":"S. Baek et al., “Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation,” Neuron, vol. 82, no. 6. Elsevier, pp. 1255–1262, 2014.","short":"S. Baek, G. Kerjan, S. Bielas, J. Lee, A. Fenstermaker, G. Novarino, J. Gleeson, Neuron 82 (2014) 1255–1262."},"date_updated":"2021-01-12T06:53:13Z","extern":1,"type":"journal_article","status":"public","_id":"1791","page":"1255 - 1262","date_published":"2014-06-18T00:00:00Z","doi":"10.1016/j.neuron.2014.04.036","volume":82,"issue":"6","date_created":"2018-12-11T11:54:01Z","year":"2014","publication_status":"published","day":"18","publication":"Neuron","quality_controlled":0,"publisher":"Elsevier","month":"06","intvolume":" 82","abstract":[{"text":"Acute gene inactivation using short hairpin RNA (shRNA, knockdown) in developing brain is a powerful technique to study genetic function; however, discrepancies between knockdown and knockout murine phenotypes have left unanswered questions. For example, doublecortin (Dcx) knockdown but not knockout shows a neocortical neuronal migration phenotype. Here we report that in utero electroporation of shRNA, but not siRNA or miRNA, to Dcx demonstrates a migration phenotype in Dcx knockouts akin to the effect in wild-type mice, suggestingshRNA-mediated off-target toxicity. This effect wasnot limited to Dcx, as it was observed in Dclk1 knockouts, as well as with a fraction of scrambled shRNAs, suggesting a sequence-dependent but not sequence-specific effect. Profiling RNAs from electroporated cells showed a defect in endogenous let7 miRNA levels, and disruption of let7 or Dicer recapitulated the migration defect. The results suggest that shRNA-mediated knockdown can produce untoward migration effects by altering endogenous miRNA pathways.","lang":"eng"}],"acknowledgement":"This work was supported by the National Institutes of Health R01NS41537. G.K. was supported by an EMBO Long Term Fellowship, S.L.B. by the A.P. Giannini Fellowship, and A.G.F. by the Brain Behavior Research Foundation"},{"_id":"1806","status":"public","type":"book_chapter","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:53:19Z","citation":{"ieee":"P. Baster and J. Friml, “Auxin on the road navigated by cellular PIN polarity,” in Auxin and Its Role in Plant Development, E. Zažímalová, J. Petrášek, and E. Benková, Eds. Springer, 2014, pp. 143–170.","short":"P. Baster, J. Friml, in:, E. Zažímalová, J. Petrášek, E. Benková (Eds.), Auxin and Its Role in Plant Development, Springer, 2014, pp. 143–170.","apa":"Baster, P., & Friml, J. (2014). Auxin on the road navigated by cellular PIN polarity. In E. Zažímalová, J. Petrášek, & E. Benková (Eds.), Auxin and Its Role in Plant Development (pp. 143–170). Springer. https://doi.org/10.1007/978-3-7091-1526-8_8","ama":"Baster P, Friml J. Auxin on the road navigated by cellular PIN polarity. In: Zažímalová E, Petrášek J, Benková E, eds. Auxin and Its Role in Plant Development. Springer; 2014:143-170. doi:10.1007/978-3-7091-1526-8_8","mla":"Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN Polarity.” Auxin and Its Role in Plant Development, edited by Eva Zažímalová et al., Springer, 2014, pp. 143–70, doi:10.1007/978-3-7091-1526-8_8.","ista":"Baster P, Friml J. 2014.Auxin on the road navigated by cellular PIN polarity. In: Auxin and Its Role in Plant Development. , 143–170.","chicago":"Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN Polarity.” In Auxin and Its Role in Plant Development, edited by Eva Zažímalová, Jan Petrášek, and Eva Benková, 143–70. Springer, 2014. https://doi.org/10.1007/978-3-7091-1526-8_8."},"editor":[{"last_name":"Zažímalová","full_name":"Zažímalová, Eva","first_name":"Eva"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"title":"Auxin on the road navigated by cellular PIN polarity","department":[{"_id":"JiFr"}],"publist_id":"5304","author":[{"id":"3028BD74-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel","last_name":"Baster","full_name":"Baster, Pawel"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"oa_version":"None","abstract":[{"lang":"eng","text":"The generation of asymmetry, at both cellular and tissue level, is one of the most essential capabilities of all eukaryotic organisms. It mediates basically all multicellular development ranging from embryogenesis and de novo organ formation till responses to various environmental stimuli. In plants, the awe-inspiring number of such processes is regulated by phytohormone auxin and its directional, cell-to-cell transport. The mediators of this transport, PIN auxin transporters, are asymmetrically localized at the plasma membrane, and this polar localization determines the directionality of intercellular auxin flow. Thus, auxin transport contributes crucially to the generation of local auxin gradients or maxima, which instruct given cell to change its developmental program. Here, we introduce and discuss the molecular components and cellular mechanisms regulating the generation and maintenance of cellular PIN polarity, as the general hallmarks of cell polarity in plants."}],"month":"04","quality_controlled":"1","scopus_import":1,"publisher":"Springer","day":"01","language":[{"iso":"eng"}],"publication":"Auxin and Its Role in Plant Development","year":"2014","publication_status":"published","date_published":"2014-04-01T00:00:00Z","doi":"10.1007/978-3-7091-1526-8_8","date_created":"2018-12-11T11:54:07Z","page":"143 - 170"},{"ddc":["000"],"date_updated":"2021-01-12T06:53:23Z","department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:45:17Z","_id":"1816","pubrep_id":"443","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","language":[{"iso":"eng"}],"file":[{"checksum":"be45c133ab4d43351260e21beaa8f4b1","file_id":"4704","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:08:43Z","file_name":"IST-2016-443-v1+1_S0218195914500034.pdf","creator":"system","date_updated":"2020-07-14T12:45:17Z","file_size":991734}],"publication_status":"published","volume":24,"issue":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Watermarking techniques for vector graphics dislocate vertices in order to embed imperceptible, yet detectable, statistical features into the input data. The embedding process may result in a change of the topology of the input data, e.g., by introducing self-intersections, which is undesirable or even disastrous for many applications. In this paper we present a watermarking framework for two-dimensional vector graphics that employs conventional watermarking techniques but still provides the guarantee that the topology of the input data is preserved. The geometric part of this framework computes so-called maximum perturbation regions (MPR) of vertices. We propose two efficient algorithms to compute MPRs based on Voronoi diagrams and constrained triangulations. Furthermore, we present two algorithms to conditionally correct the watermarked data in order to increase the watermark embedding capacity and still guarantee topological correctness. While we focus on the watermarking of input formed by straight-line segments, one of our approaches can also be extended to circular arcs. We conclude the paper by demonstrating and analyzing the applicability of our framework in conjunction with two well-known watermarking techniques."}],"intvolume":" 24","month":"03","scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Huber S, Held M, Meerwald P, Kwitt R. Topology-preserving watermarking of vector graphics. International Journal of Computational Geometry and Applications. 2014;24(1):61-86. doi:10.1142/S0218195914500034","apa":"Huber, S., Held, M., Meerwald, P., & Kwitt, R. (2014). Topology-preserving watermarking of vector graphics. International Journal of Computational Geometry and Applications. World Scientific Publishing. https://doi.org/10.1142/S0218195914500034","short":"S. Huber, M. Held, P. Meerwald, R. Kwitt, International Journal of Computational Geometry and Applications 24 (2014) 61–86.","ieee":"S. Huber, M. Held, P. Meerwald, and R. Kwitt, “Topology-preserving watermarking of vector graphics,” International Journal of Computational Geometry and Applications, vol. 24, no. 1. World Scientific Publishing, pp. 61–86, 2014.","mla":"Huber, Stefan, et al. “Topology-Preserving Watermarking of Vector Graphics.” International Journal of Computational Geometry and Applications, vol. 24, no. 1, World Scientific Publishing, 2014, pp. 61–86, doi:10.1142/S0218195914500034.","ista":"Huber S, Held M, Meerwald P, Kwitt R. 2014. Topology-preserving watermarking of vector graphics. International Journal of Computational Geometry and Applications. 24(1), 61–86.","chicago":"Huber, Stefan, Martin Held, Peter Meerwald, and Roland Kwitt. “Topology-Preserving Watermarking of Vector Graphics.” International Journal of Computational Geometry and Applications. World Scientific Publishing, 2014. https://doi.org/10.1142/S0218195914500034."},"title":"Topology-preserving watermarking of vector graphics","publist_id":"5290","author":[{"id":"4700A070-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","orcid":"0000-0002-8871-5814","full_name":"Huber, Stefan","last_name":"Huber"},{"first_name":"Martin","last_name":"Held","full_name":"Held, Martin"},{"full_name":"Meerwald, Peter","last_name":"Meerwald","first_name":"Peter"},{"first_name":"Roland","last_name":"Kwitt","full_name":"Kwitt, Roland"}],"publication":"International Journal of Computational Geometry and Applications","day":"16","year":"2014","has_accepted_license":"1","date_created":"2018-12-11T11:54:10Z","doi":"10.1142/S0218195914500034","date_published":"2014-03-16T00:00:00Z","page":"61 - 86","acknowledgement":"Work by Martin Held and Stefan Huber was supported by Austrian Science Fund (FWF): L367-N15 and P25816-N15.","oa":1,"quality_controlled":"1","publisher":"World Scientific Publishing"},{"publisher":"American Institute of Physics","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2014","day":"26","publication":"Journal of Mathematical Physics","doi":"10.1063/1.4881536","date_published":"2014-06-26T00:00:00Z","date_created":"2018-12-11T11:54:11Z","article_number":"1.4881536","project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov Approximation.” Journal of Mathematical Physics, vol. 55, no. 7, 1.4881536, American Institute of Physics, 2014, doi:10.1063/1.4881536.","apa":"Seiringer, R. (2014). Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4881536","ama":"Seiringer R. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. 2014;55(7). doi:10.1063/1.4881536","ieee":"R. Seiringer, “Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation,” Journal of Mathematical Physics, vol. 55, no. 7. American Institute of Physics, 2014.","short":"R. Seiringer, Journal of Mathematical Physics 55 (2014).","chicago":"Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov Approximation.” Journal of Mathematical Physics. American Institute of Physics, 2014. https://doi.org/10.1063/1.4881536.","ista":"Seiringer R. 2014. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. 55(7), 1.4881536."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"publist_id":"5285","title":"Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation","abstract":[{"text":"We review recent progress towards a rigorous understanding of the Bogoliubov approximation for bosonic quantum many-body systems. We focus, in particular, on the excitation spectrum of a Bose gas in the mean-field (Hartree) limit. A list of open problems will be discussed at the end.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"month":"06","intvolume":" 55","publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"ed0efc93c10f1341155f0316af617b82","file_id":"5172","file_size":269171,"date_updated":"2020-07-14T12:45:17Z","creator":"system","file_name":"IST-2016-532-v1+1_J._Mathematical_Phys._2014_Seiringer.pdf","date_created":"2018-12-12T10:15:49Z"}],"language":[{"iso":"eng"}],"issue":"7","volume":55,"_id":"1821","type":"journal_article","status":"public","pubrep_id":"532","date_updated":"2021-01-12T06:53:25Z","ddc":["510","530"],"file_date_updated":"2020-07-14T12:45:17Z","department":[{"_id":"RoSe"}]},{"citation":{"ama":"Jakšić V, Pillet C, Seiringer R. Introduction. Journal of Mathematical Physics. 2014;55(7). doi:10.1063/1.4884877","apa":"Jakšić, V., Pillet, C., & Seiringer, R. (2014). Introduction. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4884877","ieee":"V. Jakšić, C. Pillet, and R. Seiringer, “Introduction,” Journal of Mathematical Physics, vol. 55, no. 7. American Institute of Physics, 2014.","short":"V. Jakšić, C. Pillet, R. Seiringer, Journal of Mathematical Physics 55 (2014).","mla":"Jakšić, Vojkan, et al. “Introduction.” Journal of Mathematical Physics, vol. 55, no. 7, 075101, American Institute of Physics, 2014, doi:10.1063/1.4884877.","ista":"Jakšić V, Pillet C, Seiringer R. 2014. Introduction. Journal of Mathematical Physics. 55(7), 075101.","chicago":"Jakšić, Vojkan, Claude Pillet, and Robert Seiringer. “Introduction.” Journal of Mathematical Physics. American Institute of Physics, 2014. https://doi.org/10.1063/1.4884877."},"date_updated":"2021-01-12T06:53:25Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5284","author":[{"first_name":"Vojkan","full_name":"Jakšić, Vojkan","last_name":"Jakšić"},{"first_name":"Claude","last_name":"Pillet","full_name":"Pillet, Claude"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"department":[{"_id":"RoSe"}],"title":"Introduction","_id":"1822","article_number":"075101","type":"journal_article","status":"public","year":"2014","publication_status":"published","day":"01","language":[{"iso":"eng"}],"publication":"Journal of Mathematical Physics","issue":"7","volume":55,"date_published":"2014-07-01T00:00:00Z","doi":"10.1063/1.4884877","date_created":"2018-12-11T11:54:12Z","oa_version":"None","publisher":"American Institute of Physics","quality_controlled":"1","scopus_import":1,"month":"07","intvolume":" 55"},{"month":"01","intvolume":" 97","quality_controlled":"1","alternative_title":["Springer Tracts in Advanced Robotics"],"publisher":"Springer","scopus_import":1,"oa_version":"None","abstract":[{"lang":"eng","text":"Hitting and batting tasks, such as tennis forehands, ping-pong strokes, or baseball batting, depend on predictions where the ball can be intercepted and how it can properly be returned to the opponent. These predictions get more accurate over time, hence the behaviors need to be continuously modified. As a result, movement templates with a learned global shape need to be adapted during the execution so that the racket reaches a target position and velocity that will return the ball over to the other side of the net or court. It requires altering learned movements to hit a varying target with the necessary velocity at a specific instant in time. Such a task cannot be incorporated straightforwardly in most movement representations suitable for learning. For example, the standard formulation of the dynamical system based motor primitives (introduced by Ijspeert et al (2002b)) does not satisfy this property despite their flexibility which has allowed learning tasks ranging from locomotion to kendama. In order to fulfill this requirement, we reformulate the Ijspeert framework to incorporate the possibility of specifying a desired hitting point and a desired hitting velocity while maintaining all advantages of the original formulation.We show that the proposed movement template formulation works well in two scenarios, i.e., for hitting a ball on a string with a table tennis racket at a specified velocity and for returning balls launched by a ball gun successfully over the net using forehand movements."}],"doi":"10.1007/978-3-319-03194-1_3","date_published":"2014-01-01T00:00:00Z","volume":97,"date_created":"2018-12-11T11:54:14Z","page":"69 - 82","day":"01","language":[{"iso":"eng"}],"publication":"Learning Motor Skills","publication_status":"published","year":"2014","status":"public","type":"book_chapter","series_title":"From Algorithms to Robot Experiments","_id":"1829","editor":[{"first_name":"Jens","full_name":"Kober, Jens","last_name":"Kober"},{"first_name":"Jan","last_name":"Peters","full_name":"Peters, Jan"}],"title":"Movement templates for learning of hitting and batting","department":[{"_id":"ChLa"}],"author":[{"last_name":"Muelling","full_name":"Muelling, Katharina","first_name":"Katharina"},{"first_name":"Oliver","last_name":"Kroemer","full_name":"Kroemer, Oliver"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"},{"first_name":"Bernhard","full_name":"Schölkopf, Bernhard","last_name":"Schölkopf"}],"publist_id":"5274","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Muelling, Katharina, Oliver Kroemer, Christoph Lampert, and Bernhard Schölkopf. “Movement Templates for Learning of Hitting and Batting.” In Learning Motor Skills, edited by Jens Kober and Jan Peters, 97:69–82. From Algorithms to Robot Experiments. Springer, 2014. https://doi.org/10.1007/978-3-319-03194-1_3.","ista":"Muelling K, Kroemer O, Lampert C, Schölkopf B. 2014.Movement templates for learning of hitting and batting. In: Learning Motor Skills. Springer Tracts in Advanced Robotics, vol. 97, 69–82.","mla":"Muelling, Katharina, et al. “Movement Templates for Learning of Hitting and Batting.” Learning Motor Skills, edited by Jens Kober and Jan Peters, vol. 97, Springer, 2014, pp. 69–82, doi:10.1007/978-3-319-03194-1_3.","short":"K. Muelling, O. Kroemer, C. Lampert, B. Schölkopf, in:, J. Kober, J. Peters (Eds.), Learning Motor Skills, Springer, 2014, pp. 69–82.","ieee":"K. Muelling, O. Kroemer, C. Lampert, and B. Schölkopf, “Movement templates for learning of hitting and batting,” in Learning Motor Skills, vol. 97, J. Kober and J. Peters, Eds. Springer, 2014, pp. 69–82.","ama":"Muelling K, Kroemer O, Lampert C, Schölkopf B. Movement templates for learning of hitting and batting. In: Kober J, Peters J, eds. Learning Motor Skills. Vol 97. From Algorithms to Robot Experiments. Springer; 2014:69-82. doi:10.1007/978-3-319-03194-1_3","apa":"Muelling, K., Kroemer, O., Lampert, C., & Schölkopf, B. (2014). Movement templates for learning of hitting and batting. In J. Kober & J. Peters (Eds.), Learning Motor Skills (Vol. 97, pp. 69–82). Springer. https://doi.org/10.1007/978-3-319-03194-1_3"},"date_updated":"2021-01-12T06:53:28Z"},{"scopus_import":1,"intvolume":" 32","month":"11","abstract":[{"text":"Local protein interactions ("molecular context" effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different amino acid. It has been recently debated whether these preferences remain approximately constant during evolution or whether, due to coevolution of sites, they change strongly. Such research highlights an unresolved and fundamental issue with far-reaching implications for phylogenetic analysis and molecular evolution modeling. Here, we take advantage of the recent availability of phenotypically supported laboratory resurrections of Precambrian thioredoxins and β-lactamases to experimentally address the change of site-specific amino acid preferences over long geological timescales. Extensive mutational analyses support the notion that evolutionary adjustment to a new amino acid may occur, but to a large extent this is insufficient to erase the primitive preference for amino acid replacements. Generally, site-specific amino acid preferences appear to remain conserved throughout evolutionary history despite local sequence divergence. We show such preference conservation to be readily understandable in molecular terms and we provide crystallographic evidence for an intriguing structural-switch mechanism: Energetic preference for an ancestral amino acid in a modern protein can be linked to reorganization upon mutation to the ancestral local structure around the mutated site. Finally, we point out that site-specific preference conservation naturally leads to one plausible evolutionary explanation for the existence of intragenic global suppressor mutations.","lang":"eng"}],"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc/4.0/","issue":"2","volume":32,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:45:19Z","file_size":1545246,"date_created":"2018-12-12T10:16:56Z","file_name":"IST-2016-430-v1+1_Mol_Biol_Evol-2015-Risso-440-55.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5247","checksum":"06215318e66be8f3e0c33abb07e9d3da"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"journal_article","pubrep_id":"430","status":"public","_id":"1844","department":[{"_id":"HaJa"}],"file_date_updated":"2020-07-14T12:45:19Z","date_updated":"2021-01-12T06:53:34Z","ddc":["571"],"oa":1,"quality_controlled":"1","publisher":"Oxford University Press","page":"440 - 455","date_created":"2018-12-11T11:54:19Z","doi":"10.1093/molbev/msu312","date_published":"2014-11-12T00:00:00Z","year":"2014","has_accepted_license":"1","publication":"Molecular Biology and Evolution","day":"12","publist_id":"5257","author":[{"first_name":"Valeria","last_name":"Risso","full_name":"Risso, Valeria"},{"first_name":"Fadia","full_name":"Manssour Triedo, Fadia","last_name":"Manssour Triedo"},{"first_name":"Asuncion","full_name":"Delgado Delgado, Asuncion","last_name":"Delgado Delgado"},{"first_name":"Rocio","last_name":"Arco","full_name":"Arco, Rocio"},{"full_name":"Barroso Deljesús, Alicia","last_name":"Barroso Deljesús","first_name":"Alicia"},{"first_name":"Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","last_name":"Inglés Prieto","orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro"},{"first_name":"Raquel","full_name":"Godoy Ruiz, Raquel","last_name":"Godoy Ruiz"},{"first_name":"Josè","full_name":"Gavira, Josè","last_name":"Gavira"},{"full_name":"Gaucher, Eric","last_name":"Gaucher","first_name":"Eric"},{"first_name":"Beatriz","last_name":"Ibarra Molero","full_name":"Ibarra Molero, Beatriz"},{"last_name":"Sánchez Ruiz","full_name":"Sánchez Ruiz, Jose","first_name":"Jose"}],"title":"Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history","citation":{"apa":"Risso, V., Manssour Triedo, F., Delgado Delgado, A., Arco, R., Barroso Deljesús, A., Inglés Prieto, Á., … Sánchez Ruiz, J. (2014). Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msu312","ama":"Risso V, Manssour Triedo F, Delgado Delgado A, et al. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution. 2014;32(2):440-455. doi:10.1093/molbev/msu312","ieee":"V. Risso et al., “Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history,” Molecular Biology and Evolution, vol. 32, no. 2. Oxford University Press, pp. 440–455, 2014.","short":"V. Risso, F. Manssour Triedo, A. Delgado Delgado, R. Arco, A. Barroso Deljesús, Á. Inglés Prieto, R. Godoy Ruiz, J. Gavira, E. Gaucher, B. Ibarra Molero, J. Sánchez Ruiz, Molecular Biology and Evolution 32 (2014) 440–455.","mla":"Risso, Valeria, et al. “Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History.” Molecular Biology and Evolution, vol. 32, no. 2, Oxford University Press, 2014, pp. 440–55, doi:10.1093/molbev/msu312.","ista":"Risso V, Manssour Triedo F, Delgado Delgado A, Arco R, Barroso Deljesús A, Inglés Prieto Á, Godoy Ruiz R, Gavira J, Gaucher E, Ibarra Molero B, Sánchez Ruiz J. 2014. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution. 32(2), 440–455.","chicago":"Risso, Valeria, Fadia Manssour Triedo, Asuncion Delgado Delgado, Rocio Arco, Alicia Barroso Deljesús, Álvaro Inglés Prieto, Raquel Godoy Ruiz, et al. “Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History.” Molecular Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/molbev/msu312."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"date_updated":"2021-01-12T06:53:33Z","citation":{"ama":"Cibulka J, Gao P, Krcál M, Valla T, Valtr P. On the geometric ramsey number of outerplanar graphs. Discrete & Computational Geometry. 2014;53(1):64-79. doi:10.1007/s00454-014-9646-x","apa":"Cibulka, J., Gao, P., Krcál, M., Valla, T., & Valtr, P. (2014). On the geometric ramsey number of outerplanar graphs. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-014-9646-x","ieee":"J. Cibulka, P. Gao, M. Krcál, T. Valla, and P. Valtr, “On the geometric ramsey number of outerplanar graphs,” Discrete & Computational Geometry, vol. 53, no. 1. Springer, pp. 64–79, 2014.","short":"J. Cibulka, P. Gao, M. Krcál, T. Valla, P. Valtr, Discrete & Computational Geometry 53 (2014) 64–79.","mla":"Cibulka, Josef, et al. “On the Geometric Ramsey Number of Outerplanar Graphs.” Discrete & Computational Geometry, vol. 53, no. 1, Springer, 2014, pp. 64–79, doi:10.1007/s00454-014-9646-x.","ista":"Cibulka J, Gao P, Krcál M, Valla T, Valtr P. 2014. On the geometric ramsey number of outerplanar graphs. Discrete & Computational Geometry. 53(1), 64–79.","chicago":"Cibulka, Josef, Pu Gao, Marek Krcál, Tomáš Valla, and Pavel Valtr. “On the Geometric Ramsey Number of Outerplanar Graphs.” Discrete & Computational Geometry. Springer, 2014. https://doi.org/10.1007/s00454-014-9646-x."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Josef","last_name":"Cibulka","full_name":"Cibulka, Josef"},{"first_name":"Pu","full_name":"Gao, Pu","last_name":"Gao"},{"first_name":"Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87","full_name":"Krcál, Marek","last_name":"Krcál"},{"full_name":"Valla, Tomáš","last_name":"Valla","first_name":"Tomáš"},{"first_name":"Pavel","full_name":"Valtr, Pavel","last_name":"Valtr"}],"publist_id":"5260","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"title":"On the geometric ramsey number of outerplanar graphs","_id":"1842","type":"journal_article","status":"public","year":"2014","publication_status":"published","publication":"Discrete & Computational Geometry","language":[{"iso":"eng"}],"day":"14","page":"64 - 79","date_created":"2018-12-11T11:54:18Z","issue":"1","volume":53,"date_published":"2014-11-14T00:00:00Z","doi":"10.1007/s00454-014-9646-x","abstract":[{"lang":"eng","text":"We prove polynomial upper bounds of geometric Ramsey numbers of pathwidth-2 outerplanar triangulations in both convex and general cases. We also prove that the geometric Ramsey numbers of the ladder graph on 2n vertices are bounded by O(n3) and O(n10), in the convex and general case, respectively. We then apply similar methods to prove an (Formula presented.) upper bound on the Ramsey number of a path with n ordered vertices."}],"acknowledgement":"Marek Krčál was supported by the ERC Advanced Grant No. 267165.","oa_version":"Submitted Version","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1310.7004"}],"publisher":"Springer","scopus_import":1,"intvolume":" 53","month":"11"},{"volume":34,"issue":"1","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_size":24817484,"date_updated":"2020-07-14T12:45:19Z","creator":"system","file_name":"IST-2016-574-v1+1_Guerrero-2014-TPS-paper.pdf","date_created":"2018-12-12T10:15:58Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5182","checksum":"91946bfc509c77f5fd3151a3ff2b2c8f"}],"scopus_import":1,"intvolume":" 34","month":"11","abstract":[{"text":"In this paper, we present a method for non-rigid, partial shape matching in vector graphics. Given a user-specified query region in a 2D shape, similar regions are found, even if they are non-linearly distorted. Furthermore, a non-linear mapping is established between the query regions and these matches, which allows the automatic transfer of editing operations such as texturing. This is achieved by a two-step approach. First, pointwise correspondences between the query region and the whole shape are established. The transformation parameters of these correspondences are registered in an appropriate transformation space. For transformations between similar regions, these parameters form surfaces in transformation space, which are extracted in the second step of our method. The extracted regions may be related to the query region by a non-rigid transform, enabling non-rigid shape matching. In this paper, we present a method for non-rigid, partial shape matching in vector graphics. Given a user-specified query region in a 2D shape, similar regions are found, even if they are non-linearly distorted. Furthermore, a non-linear mapping is established between the query regions and these matches, which allows the automatic transfer of editing operations such as texturing. This is achieved by a two-step approach. First, pointwise correspondences between the query region and the whole shape are established. The transformation parameters of these correspondences are registered in an appropriate transformation space. For transformations between similar regions, these parameters form surfaces in transformation space, which are extracted in the second step of our method. The extracted regions may be related to the query region by a non-rigid transform, enabling non-rigid shape matching.","lang":"eng"}],"oa_version":"Submitted Version","department":[{"_id":"ChWo"}],"file_date_updated":"2020-07-14T12:45:19Z","date_updated":"2021-01-12T06:53:38Z","ddc":["000"],"type":"journal_article","pubrep_id":"574","status":"public","_id":"1854","page":"239 - 252","date_created":"2018-12-11T11:54:22Z","doi":"10.1111/cgf.12509","date_published":"2014-11-05T00:00:00Z","year":"2014","has_accepted_license":"1","publication":"Computer Graphics Forum","day":"05","oa":1,"quality_controlled":"1","publisher":"Wiley","publist_id":"5246","author":[{"first_name":"Paul","last_name":"Guerrero","full_name":"Guerrero, Paul"},{"id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Auzinger","full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265"},{"first_name":"Michael","last_name":"Wimmer","full_name":"Wimmer, Michael"},{"full_name":"Jeschke, Stefan","last_name":"Jeschke","first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87"}],"title":"Partial shape matching using transformation parameter similarity","citation":{"mla":"Guerrero, Paul, et al. “Partial Shape Matching Using Transformation Parameter Similarity.” Computer Graphics Forum, vol. 34, no. 1, Wiley, 2014, pp. 239–52, doi:10.1111/cgf.12509.","ama":"Guerrero P, Auzinger T, Wimmer M, Jeschke S. Partial shape matching using transformation parameter similarity. Computer Graphics Forum. 2014;34(1):239-252. doi:10.1111/cgf.12509","apa":"Guerrero, P., Auzinger, T., Wimmer, M., & Jeschke, S. (2014). Partial shape matching using transformation parameter similarity. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.12509","short":"P. Guerrero, T. Auzinger, M. Wimmer, S. Jeschke, Computer Graphics Forum 34 (2014) 239–252.","ieee":"P. Guerrero, T. Auzinger, M. Wimmer, and S. Jeschke, “Partial shape matching using transformation parameter similarity,” Computer Graphics Forum, vol. 34, no. 1. Wiley, pp. 239–252, 2014.","chicago":"Guerrero, Paul, Thomas Auzinger, Michael Wimmer, and Stefan Jeschke. “Partial Shape Matching Using Transformation Parameter Similarity.” Computer Graphics Forum. Wiley, 2014. https://doi.org/10.1111/cgf.12509.","ista":"Guerrero P, Auzinger T, Wimmer M, Jeschke S. 2014. Partial shape matching using transformation parameter similarity. Computer Graphics Forum. 34(1), 239–252."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Sassi, Massimiliano, Olivier Ali, Frédéric Boudon, Gladys Cloarec, Ursula Abad, Coralie Cellier, Xu Chen, et al. “An Auxin-Mediated Shift toward Growth Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2014.08.036.","ista":"Sassi M, Ali O, Boudon F, Cloarec G, Abad U, Cellier C, Chen X, Gilles B, Milani P, Friml J, Vernoux T, Godin C, Hamant O, Traas J. 2014. An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. Current Biology. 24(19), 2335–2342.","mla":"Sassi, Massimiliano, et al. “An Auxin-Mediated Shift toward Growth Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” Current Biology, vol. 24, no. 19, Cell Press, 2014, pp. 2335–42, doi:10.1016/j.cub.2014.08.036.","ieee":"M. Sassi et al., “An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis,” Current Biology, vol. 24, no. 19. Cell Press, pp. 2335–2342, 2014.","short":"M. Sassi, O. Ali, F. Boudon, G. Cloarec, U. Abad, C. Cellier, X. Chen, B. Gilles, P. Milani, J. Friml, T. Vernoux, C. Godin, O. Hamant, J. Traas, Current Biology 24 (2014) 2335–2342.","ama":"Sassi M, Ali O, Boudon F, et al. An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. Current Biology. 2014;24(19):2335-2342. doi:10.1016/j.cub.2014.08.036","apa":"Sassi, M., Ali, O., Boudon, F., Cloarec, G., Abad, U., Cellier, C., … Traas, J. (2014). An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2014.08.036"},"title":"An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis","publist_id":"5248","author":[{"first_name":"Massimiliano","last_name":"Sassi","full_name":"Sassi, Massimiliano"},{"first_name":"Olivier","full_name":"Ali, Olivier","last_name":"Ali"},{"last_name":"Boudon","full_name":"Boudon, Frédéric","first_name":"Frédéric"},{"last_name":"Cloarec","full_name":"Cloarec, Gladys","first_name":"Gladys"},{"first_name":"Ursula","full_name":"Abad, Ursula","last_name":"Abad"},{"last_name":"Cellier","full_name":"Cellier, Coralie","first_name":"Coralie"},{"last_name":"Chen","full_name":"Chen, Xu","first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Benjamin","full_name":"Gilles, Benjamin","last_name":"Gilles"},{"last_name":"Milani","full_name":"Milani, Pascale","first_name":"Pascale"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"first_name":"Teva","last_name":"Vernoux","full_name":"Vernoux, Teva"},{"first_name":"Christophe","last_name":"Godin","full_name":"Godin, Christophe"},{"full_name":"Hamant, Olivier","last_name":"Hamant","first_name":"Olivier"},{"last_name":"Traas","full_name":"Traas, Jan","first_name":"Jan"}],"acknowledgement":"This work was funded by grants from EraSysBio+ (iSAM) and ERC (Morphodynamics). ","oa":1,"quality_controlled":"1","publisher":"Cell Press","publication":"Current Biology","day":"06","year":"2014","date_created":"2018-12-11T11:54:22Z","doi":"10.1016/j.cub.2014.08.036","date_published":"2014-10-06T00:00:00Z","page":"2335 - 2342","_id":"1852","status":"public","type":"journal_article","date_updated":"2021-01-12T06:53:37Z","department":[{"_id":"JiFr"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"To control morphogenesis, molecular regulatory networks have to interfere with the mechanical properties of the individual cells of developing organs and tissues, but how this is achieved is not well known. We study this issue here in the shoot meristem of higher plants, a group of undifferentiated cells where complex changes in growth rates and directions lead to the continuous formation of new organs [1, 2]. Here, we show that the plant hormone auxin plays an important role in this process via a dual, local effect on the extracellular matrix, the cell wall, which determines cell shape. Our study reveals that auxin not only causes a limited reduction in wall stiffness but also directly interferes with wall anisotropy via the regulation of cortical microtubule dynamics. We further show that to induce growth isotropy and organ outgrowth, auxin somehow interferes with the cortical microtubule-ordering activity of a network of proteins, including AUXIN BINDING PROTEIN 1 and KATANIN 1. Numerical simulations further indicate that the induced isotropy is sufficient to amplify the effects of the relatively minor changes in wall stiffness to promote organogenesis and the establishment of new growth axes in a robust manner."}],"intvolume":" 24","month":"10","main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-01074821","open_access":"1"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","issue":"19","volume":24}]