[{"month":"11","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"language":[{"iso":"eng"}],"doi":"10.1093/molbev/msu312","license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2020-07-14T12:45:19Z","publist_id":"5257","publication_status":"published","department":[{"_id":"HaJa"}],"publisher":"Oxford University Press","year":"2014","date_updated":"2021-01-12T06:53:34Z","date_created":"2018-12-11T11:54:19Z","volume":32,"author":[{"full_name":"Risso, Valeria","last_name":"Risso","first_name":"Valeria"},{"first_name":"Fadia","last_name":"Manssour Triedo","full_name":"Manssour Triedo, Fadia"},{"last_name":"Delgado Delgado","first_name":"Asuncion","full_name":"Delgado Delgado, Asuncion"},{"last_name":"Arco","first_name":"Rocio","full_name":"Arco, Rocio"},{"last_name":"Barroso Deljesús","first_name":"Alicia","full_name":"Barroso Deljesús, Alicia"},{"full_name":"Inglés Prieto, Álvaro","orcid":"0000-0002-5409-8571","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","last_name":"Inglés Prieto","first_name":"Álvaro"},{"full_name":"Godoy Ruiz, Raquel","last_name":"Godoy Ruiz","first_name":"Raquel"},{"full_name":"Gavira, Josè","last_name":"Gavira","first_name":"Josè"},{"first_name":"Eric","last_name":"Gaucher","full_name":"Gaucher, Eric"},{"full_name":"Ibarra Molero, Beatriz","last_name":"Ibarra Molero","first_name":"Beatriz"},{"first_name":"Jose","last_name":"Sánchez Ruiz","full_name":"Sánchez Ruiz, Jose"}],"scopus_import":1,"day":"12","has_accepted_license":"1","page":"440 - 455","publication":"Molecular Biology and Evolution","citation":{"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.","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.","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","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","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.","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."},"date_published":"2014-11-12T00:00:00Z","type":"journal_article","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"}],"issue":"2","title":"Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history","status":"public","ddc":["571"],"intvolume":" 32","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"1844","file":[{"file_id":"5247","relation":"main_file","date_updated":"2020-07-14T12:45:19Z","date_created":"2018-12-12T10:16:56Z","checksum":"06215318e66be8f3e0c33abb07e9d3da","file_name":"IST-2016-430-v1+1_Mol_Biol_Evol-2015-Risso-440-55.pdf","access_level":"open_access","creator":"system","file_size":1545246,"content_type":"application/pdf"}],"oa_version":"Published Version","pubrep_id":"430"},{"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.","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.","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.","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."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1310.7004"}],"oa":1,"publication":"Discrete & Computational Geometry","page":"64 - 79","date_published":"2014-11-14T00:00:00Z","doi":"10.1007/s00454-014-9646-x","language":[{"iso":"eng"}],"scopus_import":1,"month":"11","day":"14","year":"2014","_id":"1842","acknowledgement":"Marek Krčál was supported by the ERC Advanced Grant No. 267165.","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"intvolume":" 53","publisher":"Springer","title":"On the geometric ramsey number of outerplanar graphs","status":"public","publication_status":"published","author":[{"first_name":"Josef","last_name":"Cibulka","full_name":"Cibulka, Josef"},{"last_name":"Gao","first_name":"Pu","full_name":"Gao, Pu"},{"full_name":"Krcál, Marek","first_name":"Marek","last_name":"Krcál","id":"33E21118-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Valla, Tomáš","first_name":"Tomáš","last_name":"Valla"},{"first_name":"Pavel","last_name":"Valtr","full_name":"Valtr, Pavel"}],"oa_version":"Submitted Version","volume":53,"date_updated":"2021-01-12T06:53:33Z","date_created":"2018-12-11T11:54:18Z","type":"journal_article","publist_id":"5260","issue":"1","abstract":[{"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.","lang":"eng"}]},{"file_date_updated":"2020-07-14T12:45:19Z","publist_id":"5246","author":[{"first_name":"Paul","last_name":"Guerrero","full_name":"Guerrero, Paul"},{"full_name":"Auzinger, Thomas","last_name":"Auzinger","first_name":"Thomas","orcid":"0000-0002-1546-3265","id":"4718F954-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wimmer, Michael","last_name":"Wimmer","first_name":"Michael"},{"full_name":"Jeschke, Stefan","first_name":"Stefan","last_name":"Jeschke","id":"44D6411A-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:54:22Z","date_updated":"2021-01-12T06:53:38Z","volume":34,"year":"2014","publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"Wiley","month":"11","doi":"10.1111/cgf.12509","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","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"}],"issue":"1","type":"journal_article","pubrep_id":"574","file":[{"file_id":"5182","relation":"main_file","checksum":"91946bfc509c77f5fd3151a3ff2b2c8f","date_updated":"2020-07-14T12:45:19Z","date_created":"2018-12-12T10:15:58Z","access_level":"open_access","file_name":"IST-2016-574-v1+1_Guerrero-2014-TPS-paper.pdf","creator":"system","content_type":"application/pdf","file_size":24817484}],"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1854","status":"public","ddc":["000"],"title":"Partial shape matching using transformation parameter similarity","intvolume":" 34","day":"05","has_accepted_license":"1","scopus_import":1,"date_published":"2014-11-05T00:00:00Z","publication":"Computer Graphics Forum","citation":{"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.","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.","short":"P. Guerrero, T. Auzinger, M. Wimmer, S. Jeschke, Computer Graphics Forum 34 (2014) 239–252.","ista":"Guerrero P, Auzinger T, Wimmer M, Jeschke S. 2014. Partial shape matching using transformation parameter similarity. Computer Graphics Forum. 34(1), 239–252.","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","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.","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"},"page":"239 - 252"},{"_id":"1852","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis","status":"public","intvolume":" 24","oa_version":"Submitted Version","type":"journal_article","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."}],"issue":"19","publication":"Current Biology","citation":{"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.","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.","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.","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","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.","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.","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"},"page":"2335 - 2342","date_published":"2014-10-06T00:00:00Z","scopus_import":1,"day":"06","acknowledgement":"This work was funded by grants from EraSysBio+ (iSAM) and ERC (Morphodynamics). ","year":"2014","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Cell Press","author":[{"last_name":"Sassi","first_name":"Massimiliano","full_name":"Sassi, Massimiliano"},{"full_name":"Ali, Olivier","first_name":"Olivier","last_name":"Ali"},{"first_name":"Frédéric","last_name":"Boudon","full_name":"Boudon, Frédéric"},{"full_name":"Cloarec, Gladys","first_name":"Gladys","last_name":"Cloarec"},{"full_name":"Abad, Ursula","first_name":"Ursula","last_name":"Abad"},{"full_name":"Cellier, Coralie","first_name":"Coralie","last_name":"Cellier"},{"last_name":"Chen","first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Xu"},{"full_name":"Gilles, Benjamin","first_name":"Benjamin","last_name":"Gilles"},{"full_name":"Milani, Pascale","first_name":"Pascale","last_name":"Milani"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"full_name":"Vernoux, Teva","last_name":"Vernoux","first_name":"Teva"},{"full_name":"Godin, Christophe","first_name":"Christophe","last_name":"Godin"},{"full_name":"Hamant, Olivier","last_name":"Hamant","first_name":"Olivier"},{"full_name":"Traas, Jan","last_name":"Traas","first_name":"Jan"}],"date_updated":"2021-01-12T06:53:37Z","date_created":"2018-12-11T11:54:22Z","volume":24,"publist_id":"5248","main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-01074821"}],"oa":1,"quality_controlled":"1","doi":"10.1016/j.cub.2014.08.036","language":[{"iso":"eng"}],"month":"10"},{"month":"02","day":"03","quality_controlled":"1","page":"85 - 90","citation":{"mla":"Jha, Susmit, et al. Game Theoretic Secure Localization in Wireless Sensor Networks. IEEE, 2014, pp. 85–90, doi:10.1109/IOT.2014.7030120.","short":"S. Jha, S. Tripakis, S. Seshia, K. Chatterjee, in:, IEEE, 2014, pp. 85–90.","chicago":"Jha, Susmit, Stavros Tripakis, Sanjit Seshia, and Krishnendu Chatterjee. “Game Theoretic Secure Localization in Wireless Sensor Networks,” 85–90. IEEE, 2014. https://doi.org/10.1109/IOT.2014.7030120.","ama":"Jha S, Tripakis S, Seshia S, Chatterjee K. Game theoretic secure localization in wireless sensor networks. In: IEEE; 2014:85-90. doi:10.1109/IOT.2014.7030120","ista":"Jha S, Tripakis S, Seshia S, Chatterjee K. 2014. Game theoretic secure localization in wireless sensor networks. IOT: Internet of Things, 85–90.","apa":"Jha, S., Tripakis, S., Seshia, S., & Chatterjee, K. (2014). Game theoretic secure localization in wireless sensor networks (pp. 85–90). Presented at the IOT: Internet of Things, Cambridge, USA: IEEE. https://doi.org/10.1109/IOT.2014.7030120","ieee":"S. Jha, S. Tripakis, S. Seshia, and K. Chatterjee, “Game theoretic secure localization in wireless sensor networks,” presented at the IOT: Internet of Things, Cambridge, USA, 2014, pp. 85–90."},"language":[{"iso":"eng"}],"conference":{"name":"IOT: Internet of Things","end_date":"2014-10-08","location":"Cambridge, USA","start_date":"2014-10-06"},"date_published":"2014-02-03T00:00:00Z","doi":"10.1109/IOT.2014.7030120","type":"conference","abstract":[{"text":"Wireless sensor networks (WSNs) composed of low-power, low-cost sensor nodes are expected to form the backbone of future intelligent networks for a broad range of civil, industrial and military applications. These sensor nodes are often deployed through random spreading, and function in dynamic environments. Many applications of WSNs such as pollution tracking, forest fire detection, and military surveillance require knowledge of the location of constituent nodes. But the use of technologies such as GPS on all nodes is prohibitive due to power and cost constraints. So, the sensor nodes need to autonomously determine their locations. Most localization techniques use anchor nodes with known locations to determine the position of remaining nodes. Localization techniques have two conflicting requirements. On one hand, an ideal localization technique should be computationally simple and on the other hand, it must be resistant to attacks that compromise anchor nodes. In this paper, we propose a computationally light-weight game theoretic secure localization technique and demonstrate its effectiveness in comparison to existing techniques.","lang":"eng"}],"publist_id":"5247","title":"Game theoretic secure localization in wireless sensor networks","status":"public","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"IEEE","_id":"1853","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2014","date_created":"2018-12-11T11:54:22Z","date_updated":"2021-01-12T06:53:38Z","oa_version":"None","author":[{"last_name":"Jha","first_name":"Susmit","full_name":"Jha, Susmit"},{"last_name":"Tripakis","first_name":"Stavros","full_name":"Tripakis, Stavros"},{"last_name":"Seshia","first_name":"Sanjit","full_name":"Seshia, Sanjit"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"}]}]