[{"department":[{"_id":"NiBa"},{"_id":"CaGu"}],"year":"2013","month":"10","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152"}],"oa_version":"Submitted Version","type":"journal_article","issue":"2","_id":"2720","external_id":{"pmid":["23934880"]},"publication_status":"published","publisher":"Genetics Society of America","author":[{"first_name":"Hongan","last_name":"Long","full_name":"Long, Hongan"},{"first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953"},{"full_name":"Azevedo, Ricardo","last_name":"Azevedo","first_name":"Ricardo"},{"last_name":"Zufall","full_name":"Zufall, Rebecca","first_name":"Rebecca"}],"status":"public","abstract":[{"text":"Knowledge of the rate and fitness effects of mutations is essential for understanding the process of evolution. Mutations are inherently difficult to study because they are rare and are frequently eliminated by natural selection. In the ciliate Tetrahymena thermophila, mutations can accumulate in the germline genome without being exposed to selection. We have conducted a mutation accumulation (MA) experiment in this species. Assuming that all mutations are deleterious and have the same effect, we estimate that the deleterious mutation rate per haploid germline genome per generation is U = 0.0047 (95% credible interval: 0.0015, 0.0125), and that germline mutations decrease fitness by s = 11% when expressed in a homozygous state (95% CI: 4.4%, 27%). We also estimate that deleterious mutations are partially recessive on average (h = 0.26; 95% CI: –0.022, 0.62) and that the rate of lethal mutations is &lt;10% of the deleterious mutation rate. Comparisons between the observed evolutionary responses in the germline and somatic genomes and the results from individual-based simulations of MA suggest that the two genomes have similar mutational parameters. These are the first estimates of the deleterious mutation rate and fitness effects from the eukaryotic supergroup Chromalveolata and are within the range of those of other eukaryotes.","lang":"eng"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3781978/","open_access":"1"}],"scopus_import":1,"date_updated":"2021-01-12T06:59:16Z","language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila","page":"527-540","publist_id":"4172","citation":{"short":"H. Long, T. Paixao, R. Azevedo, R. Zufall, Genetics 195 (2013) 527–540.","ista":"Long H, Paixao T, Azevedo R, Zufall R. 2013. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. 195(2), 527–540.","ieee":"H. Long, T. Paixao, R. Azevedo, and R. Zufall, “Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila,” <i>Genetics</i>, vol. 195, no. 2. Genetics Society of America, pp. 527–540, 2013.","ama":"Long H, Paixao T, Azevedo R, Zufall R. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. <i>Genetics</i>. 2013;195(2):527-540. doi:<a href=\"https://doi.org/10.1534/genetics.113.153536\">10.1534/genetics.113.153536</a>","chicago":"Long, Hongan, Tiago Paixao, Ricardo Azevedo, and Rebecca Zufall. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” <i>Genetics</i>. Genetics Society of America, 2013. <a href=\"https://doi.org/10.1534/genetics.113.153536\">https://doi.org/10.1534/genetics.113.153536</a>.","apa":"Long, H., Paixao, T., Azevedo, R., &#38; Zufall, R. (2013). Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.113.153536\">https://doi.org/10.1534/genetics.113.153536</a>","mla":"Long, Hongan, et al. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” <i>Genetics</i>, vol. 195, no. 2, Genetics Society of America, 2013, pp. 527–40, doi:<a href=\"https://doi.org/10.1534/genetics.113.153536\">10.1534/genetics.113.153536</a>."},"date_created":"2018-12-11T11:59:15Z","quality_controlled":"1","oa":1,"ec_funded":1,"article_processing_charge":"No","doi":"10.1534/genetics.113.153536","intvolume":"       195","date_published":"2013-10-01T00:00:00Z","volume":195,"day":"01","publication":"Genetics","pmid":1},{"month":"07","year":"2013","department":[{"_id":"LaEr"}],"publisher":"Springer","type":"journal_article","oa_version":"Preprint","_id":"2782","issue":"6","external_id":{"arxiv":["1207.0031"]},"publication_status":"published","author":[{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","last_name":"Erdös","full_name":"Erdös, László"},{"first_name":"Brendan","full_name":"Farrell, Brendan","last_name":"Farrell"}],"status":"public","date_updated":"2021-01-12T06:59:41Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We consider random n×n matrices of the form (XX*+YY*)^{-1/2}YY*(XX*+YY*)^{-1/2}, where X and Y have independent entries with zero mean and variance one. These matrices are the natural generalization of the Gaussian case, which are known as MANOVA matrices and which have joint eigenvalue density given by the third classical ensemble, the Jacobi ensemble. We show that, away from the spectral edge, the eigenvalue density converges to the limiting density of the Jacobi ensemble even on the shortest possible scales of order 1/n (up to log n factors). This result is the analogue of the local Wigner semicircle law and the local Marchenko-Pastur law for general MANOVA matrices.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1207.0031"}],"scopus_import":1,"page":"1003 - 1032","publist_id":"4107","title":"Local eigenvalue density for general MANOVA matrices","oa":1,"citation":{"chicago":"Erdös, László, and Brendan Farrell. “Local Eigenvalue Density for General MANOVA Matrices.” <i>Journal of Statistical Physics</i>. Springer, 2013. <a href=\"https://doi.org/10.1007/s10955-013-0807-8\">https://doi.org/10.1007/s10955-013-0807-8</a>.","apa":"Erdös, L., &#38; Farrell, B. (2013). Local eigenvalue density for general MANOVA matrices. <i>Journal of Statistical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s10955-013-0807-8\">https://doi.org/10.1007/s10955-013-0807-8</a>","mla":"Erdös, László, and Brendan Farrell. “Local Eigenvalue Density for General MANOVA Matrices.” <i>Journal of Statistical Physics</i>, vol. 152, no. 6, Springer, 2013, pp. 1003–32, doi:<a href=\"https://doi.org/10.1007/s10955-013-0807-8\">10.1007/s10955-013-0807-8</a>.","ieee":"L. Erdös and B. Farrell, “Local eigenvalue density for general MANOVA matrices,” <i>Journal of Statistical Physics</i>, vol. 152, no. 6. Springer, pp. 1003–1032, 2013.","short":"L. Erdös, B. Farrell, Journal of Statistical Physics 152 (2013) 1003–1032.","ista":"Erdös L, Farrell B. 2013. Local eigenvalue density for general MANOVA matrices. Journal of Statistical Physics. 152(6), 1003–1032.","ama":"Erdös L, Farrell B. Local eigenvalue density for general MANOVA matrices. <i>Journal of Statistical Physics</i>. 2013;152(6):1003-1032. doi:<a href=\"https://doi.org/10.1007/s10955-013-0807-8\">10.1007/s10955-013-0807-8</a>"},"date_created":"2018-12-11T11:59:34Z","arxiv":1,"quality_controlled":"1","doi":"10.1007/s10955-013-0807-8","volume":152,"day":"18","publication":"Journal of Statistical Physics","intvolume":"       152","date_published":"2013-07-18T00:00:00Z"},{"title":"High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects","department":[{"_id":"BjHo"}],"year":"2013","month":"06","publist_id":"4081","issue":"6","_id":"2806","quality_controlled":"1","publication_status":"published","date_created":"2018-12-11T11:59:42Z","citation":{"short":"K. Avila, B. Hof, Review of Scientific Instruments 84 (2013).","ieee":"K. Avila and B. Hof, “High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects,” <i>Review of Scientific Instruments</i>, vol. 84, no. 6. American Institute of Physics, 2013.","ista":"Avila K, Hof B. 2013. High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects. Review of Scientific Instruments. 84(6), 065106.","ama":"Avila K, Hof B. High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects. <i>Review of Scientific Instruments</i>. 2013;84(6). doi:<a href=\"https://doi.org/10.1063/1.4807704\">10.1063/1.4807704</a>","chicago":"Avila, Kerstin, and Björn Hof. “High-Precision Taylor-Couette Experiment to Study Subcritical Transitions and the Role of Boundary Conditions and Size Effects.” <i>Review of Scientific Instruments</i>. American Institute of Physics, 2013. <a href=\"https://doi.org/10.1063/1.4807704\">https://doi.org/10.1063/1.4807704</a>.","apa":"Avila, K., &#38; Hof, B. (2013). High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects. <i>Review of Scientific Instruments</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4807704\">https://doi.org/10.1063/1.4807704</a>","mla":"Avila, Kerstin, and Björn Hof. “High-Precision Taylor-Couette Experiment to Study Subcritical Transitions and the Role of Boundary Conditions and Size Effects.” <i>Review of Scientific Instruments</i>, vol. 84, no. 6, 065106, American Institute of Physics, 2013, doi:<a href=\"https://doi.org/10.1063/1.4807704\">10.1063/1.4807704</a>."},"oa_version":"None","type":"journal_article","article_number":"065106","publisher":"American Institute of Physics","author":[{"first_name":"Kerstin","full_name":"Avila, Kerstin","last_name":"Avila"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"}],"status":"public","doi":"10.1063/1.4807704","date_published":"2013-06-06T00:00:00Z","scopus_import":1,"abstract":[{"text":"A novel Taylor-Couette system has been constructed for investigations of transitional as well as high Reynolds number turbulent flows in very large aspect ratios. The flexibility of the setup enables studies of a variety of problems regarding hydrodynamic instabilities and turbulence in rotating flows. The inner and outer cylinders and the top and bottom endplates can be rotated independently with rotation rates of up to 30 Hz, thereby covering five orders of magnitude in Reynolds numbers (Re = 101-106). The radius ratio can be easily changed, the highest realized one is η = 0.98 corresponding to an aspect ratio of 260 gap width in the vertical and 300 in the azimuthal direction. For η &lt; 0.98 the aspect ratio can be dynamically changed during measurements and complete transparency in the radial direction over the full length of the cylinders is provided by the usage of a precision glass inner cylinder. The temperatures of both cylinders are controlled independently. Overall this apparatus combines an unmatched variety in geometry, rotation rates, and temperatures, which is provided by a sophisticated high-precision bearing system. Possible applications are accurate studies of the onset of turbulence and spatio-temporal intermittent flow patterns in very large domains, transport processes of turbulence at high Re, the stability of Keplerian flows for different boundary conditions, and studies of baroclinic instabilities.","lang":"eng"}],"intvolume":"        84","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T06:59:50Z","volume":84,"day":"06","publication":"Review of Scientific Instruments"},{"doi":"10.1145/2488608.2488683","file_date_updated":"2020-07-14T12:45:48Z","has_accepted_license":"1","date_published":"2013-06-01T00:00:00Z","day":"01","publication":"45th Annual ACM Symposium on theory of computing","title":"Extending continuous maps: Polynomiality and undecidability","page":"595 - 604","publist_id":"4078","date_created":"2018-12-11T11:59:42Z","citation":{"ama":"Čadek M, Krcál M, Matoušek J, Vokřínek L, Wagner U. Extending continuous maps: Polynomiality and undecidability. In: <i>45th Annual ACM Symposium on Theory of Computing</i>. ACM; 2013:595-604. doi:<a href=\"https://doi.org/10.1145/2488608.2488683\">10.1145/2488608.2488683</a>","ista":"Čadek M, Krcál M, Matoušek J, Vokřínek L, Wagner U. 2013. Extending continuous maps: Polynomiality and undecidability. 45th Annual ACM Symposium on theory of computing. STOC: Symposium on the Theory of Computing, 595–604.","short":"M. Čadek, M. Krcál, J. Matoušek, L. Vokřínek, U. Wagner, in:, 45th Annual ACM Symposium on Theory of Computing, ACM, 2013, pp. 595–604.","ieee":"M. Čadek, M. Krcál, J. Matoušek, L. Vokřínek, and U. Wagner, “Extending continuous maps: Polynomiality and undecidability,” in <i>45th Annual ACM Symposium on theory of computing</i>, Palo Alto, CA, United States, 2013, pp. 595–604.","apa":"Čadek, M., Krcál, M., Matoušek, J., Vokřínek, L., &#38; Wagner, U. (2013). Extending continuous maps: Polynomiality and undecidability. In <i>45th Annual ACM Symposium on theory of computing</i> (pp. 595–604). Palo Alto, CA, United States: ACM. <a href=\"https://doi.org/10.1145/2488608.2488683\">https://doi.org/10.1145/2488608.2488683</a>","chicago":"Čadek, Martin, Marek Krcál, Jiří Matoušek, Lukáš Vokřínek, and Uli Wagner. “Extending Continuous Maps: Polynomiality and Undecidability.” In <i>45th Annual ACM Symposium on Theory of Computing</i>, 595–604. ACM, 2013. <a href=\"https://doi.org/10.1145/2488608.2488683\">https://doi.org/10.1145/2488608.2488683</a>.","mla":"Čadek, Martin, et al. “Extending Continuous Maps: Polynomiality and Undecidability.” <i>45th Annual ACM Symposium on Theory of Computing</i>, ACM, 2013, pp. 595–604, doi:<a href=\"https://doi.org/10.1145/2488608.2488683\">10.1145/2488608.2488683</a>."},"conference":{"start_date":"2013-06-01","name":"STOC: Symposium on the Theory of Computing","end_date":"2013-06-04","location":"Palo Alto, CA, United States"},"quality_controlled":"1","oa":1,"author":[{"first_name":"Martin","last_name":"Čadek","full_name":"Čadek, Martin"},{"last_name":"Krcál","full_name":"Krcál, Marek","first_name":"Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jiří","last_name":"Matoušek","full_name":"Matoušek, Jiří"},{"first_name":"Lukáš","full_name":"Vokřínek, Lukáš","last_name":"Vokřínek"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner","full_name":"Wagner, Uli"}],"status":"public","abstract":[{"lang":"eng","text":"We consider several basic problems of algebraic topology, with connections to combinatorial and geometric questions, from the point of view of computational complexity. The extension problem asks, given topological spaces X; Y , a subspace A ⊆ X, and a (continuous) map f : A → Y , whether f can be extended to a map X → Y . For computational purposes, we assume that X and Y are represented as finite simplicial complexes, A is a subcomplex of X, and f is given as a simplicial map. In this generality the problem is undecidable, as follows from Novikov's result from the 1950s on uncomputability of the fundamental group π1(Y ). We thus study the problem under the assumption that, for some k ≥ 2, Y is (k - 1)-connected; informally, this means that Y has \\no holes up to dimension k-1&quot; (a basic example of such a Y is the sphere Sk). We prove that, on the one hand, this problem is still undecidable for dimX = 2k. On the other hand, for every fixed k ≥ 2, we obtain an algorithm that solves the extension problem in polynomial time assuming Y (k - 1)-connected and dimX ≤ 2k - 1. For dimX ≤ 2k - 2, the algorithm also provides a classification of all extensions up to homotopy (continuous deformation). This relies on results of our SODA 2012 paper, and the main new ingredient is a machinery of objects with polynomial-time homology, which is a polynomial-time analog of objects with effective homology developed earlier by Sergeraert et al. We also consider the computation of the higher homotopy groups πk(Y ), k ≥ 2, for a 1-connected Y . Their computability was established by Brown in 1957; we show that πk(Y ) can be computed in polynomial time for every fixed k ≥ 2. On the other hand, Anick proved in 1989 that computing πk(Y ) is #P-hard if k is a part of input, where Y is a cell complex with certain rather compact encoding. We strengthen his result to #P-hardness for Y given as a simplicial complex. "}],"scopus_import":1,"date_updated":"2021-01-12T06:59:51Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"department":[{"_id":"UlWa"},{"_id":"HeEd"}],"month":"06","year":"2013","file":[{"date_updated":"2020-07-14T12:45:48Z","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:14:29Z","file_size":447945,"checksum":"06c2ce5c1135fbc1f71ca15eeb242dcf","file_name":"IST-2016-533-v1+1_Extending_continuous_maps_polynomiality_and_undecidability.pdf","relation":"main_file","creator":"system","file_id":"5081"}],"ddc":["510"],"oa_version":"Submitted Version","type":"conference","_id":"2807","publication_status":"published","pubrep_id":"533","publisher":"ACM"},{"publisher":"American Society of Plant Biologists","issue":"3","_id":"2808","publication_status":"published","external_id":{"pmid":["23669745"]},"type":"journal_article","oa_version":"Submitted Version","year":"2013","month":"07","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:59:51Z","scopus_import":1,"abstract":[{"text":"In order to establish a reference for analysis of the function of auxin and the auxin biosynthesis regulators SHORT INTERNODE/ STYLISH (SHI/STY) during Physcomitrella patens reproductive development, we have described male (antheridial) and female (archegonial) development in detail, including temporal and positional information of organ initiation. This has allowed us to define discrete stages of organ morphogenesis and to show that reproductive organ development in P. patens is highly organized and that organ phyllotaxis differs between vegetative and reproductive development. Using the PpSHI1 and PpSHI2 reporter and knockout lines, the auxin reporters GmGH3pro:GUS and PpPINApro:GFP-GUS, and the auxin-conjugating transgene PpSHI2pro:IAAL, we could show that the PpSHI genes, and by inference also auxin, play important roles for reproductive organ development in moss. The PpSHI genes are required for the apical opening of the reproductive organs, the final differentiation of the egg cell, and the progression of canal cells into a cell death program. The apical cells of the archegonium, the canal cells, and the egg cell are also sites of auxin responsiveness and are affected by reduced levels of active auxin, suggesting that auxin mediates PpSHI function in the reproductive organs.","lang":"eng"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3707547/","open_access":"1"}],"author":[{"first_name":"Katarina","full_name":"Landberg, Katarina","last_name":"Landberg"},{"first_name":"Eric","last_name":"Pederson","full_name":"Pederson, Eric"},{"first_name":"Tom","last_name":"Viaene","full_name":"Viaene, Tom"},{"first_name":"Behruz","full_name":"Bozorg, Behruz","last_name":"Bozorg"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"first_name":"Henrik","full_name":"Jönsson, Henrik","last_name":"Jönsson"},{"first_name":"Mattias","full_name":"Thelander, Mattias","last_name":"Thelander"},{"first_name":"Eva","full_name":"Sundberg, Eva","last_name":"Sundberg"}],"status":"public","oa":1,"quality_controlled":"1","citation":{"mla":"Landberg, Katarina, et al. “The Moss Physcomitrella Patens Reproductive Organ Development Is Highly Organized, Affected by the Two SHI/STY Genes and by the Level of Active Auxin in the SHI/STY Expression Domain.” <i>Plant Physiology</i>, vol. 162, no. 3, American Society of Plant Biologists, 2013, pp. 1406–19, doi:<a href=\"https://doi.org/10.1104/pp.113.214023\">10.1104/pp.113.214023</a>.","chicago":"Landberg, Katarina, Eric Pederson, Tom Viaene, Behruz Bozorg, Jiří Friml, Henrik Jönsson, Mattias Thelander, and Eva Sundberg. “The Moss Physcomitrella Patens Reproductive Organ Development Is Highly Organized, Affected by the Two SHI/STY Genes and by the Level of Active Auxin in the SHI/STY Expression Domain.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1104/pp.113.214023\">https://doi.org/10.1104/pp.113.214023</a>.","apa":"Landberg, K., Pederson, E., Viaene, T., Bozorg, B., Friml, J., Jönsson, H., … Sundberg, E. (2013). The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1104/pp.113.214023\">https://doi.org/10.1104/pp.113.214023</a>","ista":"Landberg K, Pederson E, Viaene T, Bozorg B, Friml J, Jönsson H, Thelander M, Sundberg E. 2013. The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain. Plant Physiology. 162(3), 1406–1419.","short":"K. Landberg, E. Pederson, T. Viaene, B. Bozorg, J. Friml, H. Jönsson, M. Thelander, E. Sundberg, Plant Physiology 162 (2013) 1406–1419.","ieee":"K. Landberg <i>et al.</i>, “The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain,” <i>Plant Physiology</i>, vol. 162, no. 3. American Society of Plant Biologists, pp. 1406–1419, 2013.","ama":"Landberg K, Pederson E, Viaene T, et al. The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain. <i>Plant Physiology</i>. 2013;162(3):1406-1419. doi:<a href=\"https://doi.org/10.1104/pp.113.214023\">10.1104/pp.113.214023</a>"},"date_created":"2018-12-11T11:59:42Z","publist_id":"4079","page":"1406 - 1419","title":"The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain","pmid":1,"volume":162,"day":"03","publication":"Plant Physiology","date_published":"2013-07-03T00:00:00Z","intvolume":"       162","doi":"10.1104/pp.113.214023"},{"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1371/journal.pgen.1003580","file_date_updated":"2020-07-14T12:45:48Z","has_accepted_license":"1","intvolume":"         9","date_published":"2013-06-27T00:00:00Z","publication":"PLoS Genetics","day":"27","volume":9,"title":"Environmental dependence of genetic constraint","publist_id":"4075","citation":{"ista":"de Vos M, Poelwijk F, Battich N, Ndika J, Tans S. 2013. Environmental dependence of genetic constraint. PLoS Genetics. 9(6), e1003580.","short":"M. de Vos, F. Poelwijk, N. Battich, J. Ndika, S. Tans, PLoS Genetics 9 (2013).","ieee":"M. de Vos, F. Poelwijk, N. Battich, J. Ndika, and S. Tans, “Environmental dependence of genetic constraint,” <i>PLoS Genetics</i>, vol. 9, no. 6. Public Library of Science, 2013.","ama":"de Vos M, Poelwijk F, Battich N, Ndika J, Tans S. Environmental dependence of genetic constraint. <i>PLoS Genetics</i>. 2013;9(6). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1003580\">10.1371/journal.pgen.1003580</a>","chicago":"Vos, Marjon de, Frank Poelwijk, Nico Battich, Joseph Ndika, and Sander Tans. “Environmental Dependence of Genetic Constraint.” <i>PLoS Genetics</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pgen.1003580\">https://doi.org/10.1371/journal.pgen.1003580</a>.","apa":"de Vos, M., Poelwijk, F., Battich, N., Ndika, J., &#38; Tans, S. (2013). Environmental dependence of genetic constraint. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1003580\">https://doi.org/10.1371/journal.pgen.1003580</a>","mla":"de Vos, Marjon, et al. “Environmental Dependence of Genetic Constraint.” <i>PLoS Genetics</i>, vol. 9, no. 6, e1003580, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1003580\">10.1371/journal.pgen.1003580</a>."},"date_created":"2018-12-11T11:59:43Z","quality_controlled":"1","oa":1,"article_number":"e1003580","status":"public","author":[{"last_name":"De Vos","full_name":"De Vos, Marjon","first_name":"Marjon","id":"3111FFAC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Poelwijk, Frank","last_name":"Poelwijk","first_name":"Frank"},{"last_name":"Battich","full_name":"Battich, Nico","first_name":"Nico"},{"last_name":"Ndika","full_name":"Ndika, Joseph","first_name":"Joseph"},{"last_name":"Tans","full_name":"Tans, Sander","first_name":"Sander"}],"license":"https://creativecommons.org/licenses/by/4.0/","abstract":[{"text":"The epistatic interactions that underlie evolutionary constraint have mainly been studied for constant external conditions. However, environmental changes may modulate epistasis and hence affect genetic constraints. Here we investigate genetic constraints in the adaptive evolution of a novel regulatory function in variable environments, using the lac repressor, LacI, as a model system. We have systematically reconstructed mutational trajectories from wild type LacI to three different variants that each exhibit an inverse response to the inducing ligand IPTG, and analyzed the higher-order interactions between genetic and environmental changes. We find epistasis to depend strongly on the environment. As a result, mutational steps essential to inversion but inaccessible by positive selection in one environment, become accessible in another. We present a graphical method to analyze the observed complex higher-order interactions between multiple mutations and environmental change, and show how the interactions can be explained by a combination of mutational effects on allostery and thermodynamic stability. This dependency of genetic constraint on the environment should fundamentally affect evolutionary dynamics and affects the interpretation of phylogenetic data.","lang":"eng"}],"scopus_import":1,"date_updated":"2021-01-12T06:59:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"department":[{"_id":"ToBo"}],"month":"06","year":"2013","oa_version":"Published Version","type":"journal_article","file":[{"file_size":474655,"checksum":"7a4736dd80496d29ff6908b6f2329b4e","date_created":"2018-12-12T10:08:51Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:48Z","file_id":"4713","creator":"system","relation":"main_file","file_name":"IST-2016-412-v1+1_journal.pgen.1003580.pdf"}],"ddc":["570"],"publication_status":"published","issue":"6","_id":"2810","publisher":"Public Library of Science","pubrep_id":"412"},{"status":"public","author":[{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","last_name":"Hof","orcid":"0000-0003-2057-2754"}],"scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1306.5890","open_access":"1"}],"abstract":[{"text":"In pipe, channel, and boundary layer flows turbulence first occurs intermittently in space and time: at moderate Reynolds numbers domains of disordered turbulent motion are separated by quiescent laminar regions. Based on direct numerical simulations of pipe flow we argue here that the spatial intermittency has its origin in a nearest neighbor interaction between turbulent regions. We further show that in this regime turbulent flows are intrinsically intermittent with a well-defined equilibrium turbulent fraction but without ever assuming a steady pattern. This transition scenario is analogous to that found in simple models such as coupled map lattices. The scaling observed implies that laminar intermissions of the turbulent flow will persist to arbitrarily large Reynolds numbers.","lang":"eng"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:59:53Z","department":[{"_id":"BjHo"}],"project":[{"name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425","grant_number":"306589"}],"year":"2013","month":"06","external_id":{"arxiv":["1306.5890"]},"publication_status":"published","_id":"2811","issue":"6","type":"journal_article","oa_version":"Preprint","publisher":"American Institute of Physics","ec_funded":1,"doi":"10.1103/PhysRevE.87.063012","date_published":"2013-06-18T00:00:00Z","intvolume":"        87","day":"18","publication":"Physical Review E","volume":87,"title":"Nature of laminar-turbulence intermittency in shear flows","publist_id":"4074","arxiv":1,"quality_controlled":"1","date_created":"2018-12-11T11:59:43Z","citation":{"mla":"Avila, Marc, and Björn Hof. “Nature of Laminar-Turbulence Intermittency in Shear Flows.” <i>Physical Review E</i>, vol. 87, no. 6, 063012, American Institute of Physics, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">10.1103/PhysRevE.87.063012</a>.","apa":"Avila, M., &#38; Hof, B. (2013). Nature of laminar-turbulence intermittency in shear flows. <i>Physical Review E</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">https://doi.org/10.1103/PhysRevE.87.063012</a>","chicago":"Avila, Marc, and Björn Hof. “Nature of Laminar-Turbulence Intermittency in Shear Flows.” <i>Physical Review E</i>. American Institute of Physics, 2013. <a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">https://doi.org/10.1103/PhysRevE.87.063012</a>.","ama":"Avila M, Hof B. Nature of laminar-turbulence intermittency in shear flows. <i>Physical Review E</i>. 2013;87(6). doi:<a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">10.1103/PhysRevE.87.063012</a>","short":"M. Avila, B. Hof, Physical Review E 87 (2013).","ista":"Avila M, Hof B. 2013. Nature of laminar-turbulence intermittency in shear flows. Physical Review E. 87(6), 063012.","ieee":"M. Avila and B. Hof, “Nature of laminar-turbulence intermittency in shear flows,” <i>Physical Review E</i>, vol. 87, no. 6. American Institute of Physics, 2013."},"oa":1,"article_number":"063012"},{"publist_id":"4072","page":"117 - 125","month":"06","year":"2013","department":[{"_id":"HeEd"}],"title":"Homological reconstruction and simplification in R3","oa":1,"publisher":"ACM","quality_controlled":"1","publication_status":"published","conference":{"end_date":"2013-06-20","location":"Rio de Janeiro, Brazil","start_date":"2013-06-17","name":"SoCG: Symposium on Computational Geometry"},"_id":"2812","oa_version":"Submitted Version","type":"conference","citation":{"mla":"Attali, Dominique, et al. “Homological Reconstruction and Simplification in R3.” <i>Proceedings of the 29th Annual Symposium on Computational Geometry</i>, ACM, 2013, pp. 117–25, doi:<a href=\"https://doi.org/10.1145/2462356.2462373\">10.1145/2462356.2462373</a>.","chicago":"Attali, Dominique, Ulrich Bauer, Olivier Devillers, Marc Glisse, and André Lieutier. “Homological Reconstruction and Simplification in R3.” In <i>Proceedings of the 29th Annual Symposium on Computational Geometry</i>, 117–25. ACM, 2013. <a href=\"https://doi.org/10.1145/2462356.2462373\">https://doi.org/10.1145/2462356.2462373</a>.","apa":"Attali, D., Bauer, U., Devillers, O., Glisse, M., &#38; Lieutier, A. (2013). Homological reconstruction and simplification in R3. In <i>Proceedings of the 29th annual symposium on Computational Geometry</i> (pp. 117–125). Rio de Janeiro, Brazil: ACM. <a href=\"https://doi.org/10.1145/2462356.2462373\">https://doi.org/10.1145/2462356.2462373</a>","ista":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. 2013. Homological reconstruction and simplification in R3. Proceedings of the 29th annual symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 117–125.","short":"D. Attali, U. Bauer, O. Devillers, M. Glisse, A. Lieutier, in:, Proceedings of the 29th Annual Symposium on Computational Geometry, ACM, 2013, pp. 117–125.","ieee":"D. Attali, U. Bauer, O. Devillers, M. Glisse, and A. Lieutier, “Homological reconstruction and simplification in R3,” in <i>Proceedings of the 29th annual symposium on Computational Geometry</i>, Rio de Janeiro, Brazil, 2013, pp. 117–125.","ama":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. Homological reconstruction and simplification in R3. In: <i>Proceedings of the 29th Annual Symposium on Computational Geometry</i>. ACM; 2013:117-125. doi:<a href=\"https://doi.org/10.1145/2462356.2462373\">10.1145/2462356.2462373</a>"},"date_created":"2018-12-11T11:59:44Z","doi":"10.1145/2462356.2462373","status":"public","author":[{"first_name":"Dominique","full_name":"Attali, Dominique","last_name":"Attali"},{"last_name":"Bauer","full_name":"Bauer, Ulrich","orcid":"0000-0002-9683-0724","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich"},{"last_name":"Devillers","full_name":"Devillers, Olivier","first_name":"Olivier"},{"last_name":"Glisse","full_name":"Glisse, Marc","first_name":"Marc"},{"first_name":"André","last_name":"Lieutier","full_name":"Lieutier, André"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"day":"01","publication":"Proceedings of the 29th annual symposium on Computational Geometry","acknowledgement":"Some of the authors were partially supported by the GIGA ANR grant (contract ANR-09-BLAN-0331-01) and the European project CG-Learning (contract 255827).","date_updated":"2023-02-23T10:15:15Z","date_published":"2013-06-01T00:00:00Z","scopus_import":1,"related_material":{"record":[{"relation":"later_version","status":"public","id":"1805"}]},"main_file_link":[{"open_access":"1","url":"http://hal.archives-ouvertes.fr/hal-00833791/"}],"abstract":[{"lang":"eng","text":"We consider the problem of deciding whether the persistent homology group of a simplicial pair (K, L) can be realized as the homology H* (X) of some complex X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded in ℝ3. As a consequence, we show that it is NP-hard to simplify level and sublevel sets of scalar functions on S3 within a given tolerance constraint. This problem has relevance to the visualization of medical images by isosurfaces. We also show an implication to the theory of well groups of scalar functions: not every well group can be realized by some level set, and deciding whether a well group can be realized is NP-hard."}]},{"department":[{"_id":"BjHo"}],"month":"06","year":"2013","_id":"2813","issue":"26","publication_status":"published","external_id":{"pmid":["23757498"]},"oa_version":"Submitted Version","type":"journal_article","publisher":"National Academy of Sciences","author":[{"full_name":"Samanta, Devranjan","last_name":"Samanta","first_name":"Devranjan"},{"first_name":"Yves","last_name":"Dubief","full_name":"Dubief, Yves"},{"first_name":"Markus","last_name":"Holzner","full_name":"Holzner, Markus"},{"first_name":"Christof","last_name":"Schäfer","full_name":"Schäfer, Christof"},{"first_name":"Alexander","last_name":"Morozov","full_name":"Morozov, Alexander"},{"first_name":"Christian","last_name":"Wagner","full_name":"Wagner, Christian"},{"orcid":"0000-0003-2057-2754","last_name":"Hof","full_name":"Hof, Björn","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"status":"public","scopus_import":1,"abstract":[{"text":"Turbulence is ubiquitous in nature, yet even for the case of ordinary Newtonian fluids like water, our understanding of this phenomenon is limited. Many liquids of practical importance are more complicated (e.g., blood, polymer melts, paints), however; they exhibit elastic as well as viscous characteristics, and the relation between stress and strain is nonlinear. We demonstrate here for a model system of such complex fluids that at high shear rates, turbulence is not simply modified as previously believed but is suppressed and replaced by a different type of disordered motion, elasto-inertial turbulence. Elasto-inertial turbulence is found to occur at much lower Reynolds numbers than Newtonian turbulence, and the dynamical properties differ significantly. The friction scaling observed coincides with the so-called &quot;maximum drag reduction&quot; asymptote, which is exhibited by a wide range of viscoelastic fluids.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3696777/"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:59:54Z","title":"Elasto-inertial turbulence","publist_id":"4073","page":"10557 - 10562","quality_controlled":"1","date_created":"2018-12-11T11:59:44Z","citation":{"ista":"Samanta D, Dubief Y, Holzner M, Schäfer C, Morozov A, Wagner C, Hof B. 2013. Elasto-inertial turbulence. PNAS. 110(26), 10557–10562.","short":"D. Samanta, Y. Dubief, M. Holzner, C. Schäfer, A. Morozov, C. Wagner, B. Hof, PNAS 110 (2013) 10557–10562.","ieee":"D. Samanta <i>et al.</i>, “Elasto-inertial turbulence,” <i>PNAS</i>, vol. 110, no. 26. National Academy of Sciences, pp. 10557–10562, 2013.","ama":"Samanta D, Dubief Y, Holzner M, et al. Elasto-inertial turbulence. <i>PNAS</i>. 2013;110(26):10557-10562. doi:<a href=\"https://doi.org/10.1073/pnas.1219666110\">10.1073/pnas.1219666110</a>","chicago":"Samanta, Devranjan, Yves Dubief, Markus Holzner, Christof Schäfer, Alexander Morozov, Christian Wagner, and Björn Hof. “Elasto-Inertial Turbulence.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1219666110\">https://doi.org/10.1073/pnas.1219666110</a>.","apa":"Samanta, D., Dubief, Y., Holzner, M., Schäfer, C., Morozov, A., Wagner, C., &#38; Hof, B. (2013). Elasto-inertial turbulence. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1219666110\">https://doi.org/10.1073/pnas.1219666110</a>","mla":"Samanta, Devranjan, et al. “Elasto-Inertial Turbulence.” <i>PNAS</i>, vol. 110, no. 26, National Academy of Sciences, 2013, pp. 10557–62, doi:<a href=\"https://doi.org/10.1073/pnas.1219666110\">10.1073/pnas.1219666110</a>."},"oa":1,"doi":"10.1073/pnas.1219666110","date_published":"2013-06-25T00:00:00Z","intvolume":"       110","pmid":1,"volume":110,"publication":"PNAS","day":"25"},{"title":"The complexity of coverage","publist_id":"4070","page":"165 - 185","quality_controlled":"1","arxiv":1,"citation":{"apa":"Chatterjee, K., Alfaro, L., &#38; Majumdar, R. (2013). The complexity of coverage. <i>International Journal of Foundations of Computer Science</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0129054113400066\">https://doi.org/10.1142/S0129054113400066</a>","chicago":"Chatterjee, Krishnendu, Luca Alfaro, and Ritankar Majumdar. “The Complexity of Coverage.” <i>International Journal of Foundations of Computer Science</i>. World Scientific Publishing, 2013. <a href=\"https://doi.org/10.1142/S0129054113400066\">https://doi.org/10.1142/S0129054113400066</a>.","mla":"Chatterjee, Krishnendu, et al. “The Complexity of Coverage.” <i>International Journal of Foundations of Computer Science</i>, vol. 24, no. 2, World Scientific Publishing, 2013, pp. 165–85, doi:<a href=\"https://doi.org/10.1142/S0129054113400066\">10.1142/S0129054113400066</a>.","ama":"Chatterjee K, Alfaro L, Majumdar R. The complexity of coverage. <i>International Journal of Foundations of Computer Science</i>. 2013;24(2):165-185. doi:<a href=\"https://doi.org/10.1142/S0129054113400066\">10.1142/S0129054113400066</a>","short":"K. Chatterjee, L. Alfaro, R. Majumdar, International Journal of Foundations of Computer Science 24 (2013) 165–185.","ista":"Chatterjee K, Alfaro L, Majumdar R. 2013. The complexity of coverage. International Journal of Foundations of Computer Science. 24(2), 165–185.","ieee":"K. Chatterjee, L. Alfaro, and R. Majumdar, “The complexity of coverage,” <i>International Journal of Foundations of Computer Science</i>, vol. 24, no. 2. World Scientific Publishing, pp. 165–185, 2013."},"date_created":"2018-12-11T11:59:44Z","oa":1,"ec_funded":1,"doi":"10.1142/S0129054113400066","date_published":"2013-02-01T00:00:00Z","intvolume":"        24","volume":24,"publication":"International Journal of Foundations of Computer Science","day":"01","department":[{"_id":"KrCh"}],"month":"02","year":"2013","project":[{"grant_number":"S11407","name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"issue":"2","_id":"2814","publication_status":"published","external_id":{"arxiv":["0804.4525"]},"type":"journal_article","oa_version":"Preprint","publisher":"World Scientific Publishing","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Luca","full_name":"Alfaro, Luca","last_name":"Alfaro"},{"first_name":"Ritankar","last_name":"Majumdar","full_name":"Majumdar, Ritankar"}],"status":"public","scopus_import":1,"abstract":[{"lang":"eng","text":"We study the problem of generating a test sequence that achieves maximal coverage for a reactive system under test. We formulate the problem as a repeated game between the tester and the system, where the system state space is partitioned according to some coverage criterion and the objective of the tester is to maximize the set of partitions (or coverage goals) visited during the game. We show the complexity of the maximal coverage problem for non-deterministic systems is PSPACE-complete, but is NP-complete for deterministic systems. For the special case of non-deterministic systems with a re-initializing &quot;reset&quot; action, which represent running a new test input on a re-initialized system, we show that the complexity is coNP-complete. Our proof technique for reset games uses randomized testing strategies that circumvent the exponentially large memory requirement of deterministic testing strategies. We also discuss the memory requirement for deterministic strategies and extensions of our results to other models, such as pushdown systems and timed systems."}],"main_file_link":[{"url":"https://arxiv.org/abs/0804.4525","open_access":"1"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:59:54Z"},{"publist_id":"3991","page":"797 - 822","title":"Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions","oa":1,"citation":{"apa":"Edelsbrunner, H., Fasy, B. T., &#38; Rote, G. (2013). Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-013-9517-x\">https://doi.org/10.1007/s00454-013-9517-x</a>","chicago":"Edelsbrunner, Herbert, Brittany Terese Fasy, and Günter Rote. “Add Isotropic Gaussian Kernels at Own Risk: More and More Resilient Modes in Higher Dimensions.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2013. <a href=\"https://doi.org/10.1007/s00454-013-9517-x\">https://doi.org/10.1007/s00454-013-9517-x</a>.","mla":"Edelsbrunner, Herbert, et al. “Add Isotropic Gaussian Kernels at Own Risk: More and More Resilient Modes in Higher Dimensions.” <i>Discrete &#38; Computational Geometry</i>, vol. 49, no. 4, Springer, 2013, pp. 797–822, doi:<a href=\"https://doi.org/10.1007/s00454-013-9517-x\">10.1007/s00454-013-9517-x</a>.","ama":"Edelsbrunner H, Fasy BT, Rote G. Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. <i>Discrete &#38; Computational Geometry</i>. 2013;49(4):797-822. doi:<a href=\"https://doi.org/10.1007/s00454-013-9517-x\">10.1007/s00454-013-9517-x</a>","short":"H. Edelsbrunner, B.T. Fasy, G. Rote, Discrete &#38; Computational Geometry 49 (2013) 797–822.","ista":"Edelsbrunner H, Fasy BT, Rote G. 2013. Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. Discrete &#38; Computational Geometry. 49(4), 797–822.","ieee":"H. Edelsbrunner, B. T. Fasy, and G. Rote, “Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions,” <i>Discrete &#38; Computational Geometry</i>, vol. 49, no. 4. Springer, pp. 797–822, 2013."},"date_created":"2018-12-11T11:59:44Z","quality_controlled":"1","doi":"10.1007/s00454-013-9517-x","article_processing_charge":"No","acknowledgement":"This research is partially supported by the National Science Foundation (NSF) under Grant DBI-0820624, by the European Science Foundation under the Research Networking Programme, and the Russian Government Project 11.G34.31.0053.","day":"01","publication":"Discrete & Computational Geometry","volume":49,"intvolume":"        49","date_published":"2013-06-01T00:00:00Z","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"year":"2013","month":"06","department":[{"_id":"HeEd"}],"article_type":"original","publisher":"Springer","oa_version":"Published Version","type":"journal_article","publication_status":"published","issue":"4","_id":"2815","status":"public","author":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"full_name":"Fasy, Brittany Terese","last_name":"Fasy","id":"F65D502E-E68D-11E9-9252-C644099818F6","first_name":"Brittany Terese"},{"first_name":"Günter","last_name":"Rote","full_name":"Rote, Günter"}],"date_updated":"2023-02-23T11:13:49Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1007/s00454-013-9517-x","open_access":"1"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"3134"}]},"abstract":[{"text":"The fact that a sum of isotropic Gaussian kernels can have more modes than kernels is surprising. Extra (ghost) modes do not exist in ℝ1 and are generally not well studied in higher dimensions. We study a configuration of n+1 Gaussian kernels for which there are exactly n+2 modes. We show that all modes lie on a finite set of lines, which we call axes, and study the restriction of the Gaussian mixture to these axes in order to discover that there are an exponential number of critical points in this configuration. Although the existence of ghost modes remained unknown due to the difficulty of finding examples in ℝ2, we show that the resilience of ghost modes grows like the square root of the dimension. In addition, we exhibit finite configurations of isotropic Gaussian kernels with superlinearly many modes.","lang":"eng"}],"scopus_import":"1"},{"citation":{"ieee":"I. Božić <i>et al.</i>, “Evolutionary dynamics of cancer in response to targeted combination therapy,” <i>eLife</i>, vol. 2. eLife Sciences Publications, 2013.","short":"I. Božić, J. Reiter, B. Allen, T. Antal, K. Chatterjee, P. Shah, Y. Moon, A. Yaqubie, N. Kelly, D. Le, E. Lipson, P. Chapman, L. Diaz, B. Vogelstein, M. Nowak, ELife 2 (2013).","ista":"Božić I, Reiter J, Allen B, Antal T, Chatterjee K, Shah P, Moon Y, Yaqubie A, Kelly N, Le D, Lipson E, Chapman P, Diaz L, Vogelstein B, Nowak M. 2013. Evolutionary dynamics of cancer in response to targeted combination therapy. eLife. 2, e00747.","ama":"Božić I, Reiter J, Allen B, et al. Evolutionary dynamics of cancer in response to targeted combination therapy. <i>eLife</i>. 2013;2. doi:<a href=\"https://doi.org/10.7554/eLife.00747\">10.7554/eLife.00747</a>","mla":"Božić, Ivana, et al. “Evolutionary Dynamics of Cancer in Response to Targeted Combination Therapy.” <i>ELife</i>, vol. 2, e00747, eLife Sciences Publications, 2013, doi:<a href=\"https://doi.org/10.7554/eLife.00747\">10.7554/eLife.00747</a>.","chicago":"Božić, Ivana, Johannes Reiter, Benjamin Allen, Tibor Antal, Krishnendu Chatterjee, Preya Shah, Yo Moon, et al. “Evolutionary Dynamics of Cancer in Response to Targeted Combination Therapy.” <i>ELife</i>. eLife Sciences Publications, 2013. <a href=\"https://doi.org/10.7554/eLife.00747\">https://doi.org/10.7554/eLife.00747</a>.","apa":"Božić, I., Reiter, J., Allen, B., Antal, T., Chatterjee, K., Shah, P., … Nowak, M. (2013). Evolutionary dynamics of cancer in response to targeted combination therapy. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.00747\">https://doi.org/10.7554/eLife.00747</a>"},"date_created":"2018-12-11T11:59:45Z","quality_controlled":"1","oa":1,"article_number":"e00747","title":"Evolutionary dynamics of cancer in response to targeted combination therapy","publist_id":"3985","has_accepted_license":"1","intvolume":"         2","date_published":"2013-06-25T00:00:00Z","publication":"eLife","day":"25","volume":2,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.7554/eLife.00747","file_date_updated":"2020-07-14T12:45:49Z","type":"journal_article","oa_version":"Published Version","ddc":["570","610"],"file":[{"file_name":"IST-2013-134-v1+1_e00747.full.pdf","relation":"main_file","file_id":"4967","creator":"system","date_updated":"2020-07-14T12:45:49Z","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:12:48Z","file_size":3358321,"checksum":"2c38c47815eacd8fa66cb8b404cf7c61"}],"publication_status":"published","_id":"2816","publisher":"eLife Sciences Publications","pubrep_id":"134","department":[{"_id":"KrCh"}],"year":"2013","month":"06","related_material":{"record":[{"id":"1400","status":"public","relation":"dissertation_contains"}]},"abstract":[{"lang":"eng","text":"In solid tumors, targeted treatments can lead to dramatic regressions, but responses are often short-lived because resistant cancer cells arise. The major strategy proposed for overcoming resistance is combination therapy. We present a mathematical model describing the evolutionary dynamics of lesions in response to treatment. We first studied 20 melanoma patients receiving vemurafenib. We then applied our model to an independent set of pancreatic, colorectal, and melanoma cancer patients with metastatic disease. We find that dual therapy results in long-term disease control for most patients, if there are no single mutations that cause cross-resistance to both drugs; in patients with large disease burden, triple therapy is needed. We also find that simultaneous therapy with two drugs is much more effective than sequential therapy. Our results provide realistic expectations for the efficacy of new drug combinations and inform the design of trials for new cancer therapeutics."}],"scopus_import":1,"date_updated":"2023-09-07T11:40:43Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"status":"public","author":[{"first_name":"Ivana","last_name":"Božić","full_name":"Božić, Ivana"},{"orcid":"0000-0002-0170-7353","last_name":"Reiter","full_name":"Reiter, Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes"},{"last_name":"Allen","full_name":"Allen, Benjamin","first_name":"Benjamin"},{"first_name":"Tibor","full_name":"Antal, Tibor","last_name":"Antal"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Preya","last_name":"Shah","full_name":"Shah, Preya"},{"last_name":"Moon","full_name":"Moon, Yo","first_name":"Yo"},{"full_name":"Yaqubie, Amin","last_name":"Yaqubie","first_name":"Amin"},{"first_name":"Nicole","full_name":"Kelly, Nicole","last_name":"Kelly"},{"first_name":"Dung","last_name":"Le","full_name":"Le, Dung"},{"full_name":"Lipson, Evan","last_name":"Lipson","first_name":"Evan"},{"first_name":"Paul","last_name":"Chapman","full_name":"Chapman, Paul"},{"first_name":"Luis","full_name":"Diaz, Luis","last_name":"Diaz"},{"last_name":"Vogelstein","full_name":"Vogelstein, Bert","first_name":"Bert"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}]},{"author":[{"first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","last_name":"Novak","orcid":"0000-0002-2519-824X"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"status":"public","scopus_import":1,"abstract":[{"text":"The basic idea of evolutionary game theory is that payoff determines reproductive rate. Successful individuals have a higher payoff and produce more offspring. But in evolutionary and ecological situations there is not only reproductive rate but also carrying capacity. Individuals may differ in their exposure to density limiting effects. Here we explore an alternative approach to evolutionary game theory by assuming that the payoff from the game determines the carrying capacity of individual phenotypes. Successful strategies are less affected by density limitation (crowding) and reach higher equilibrium abundance. We demonstrate similarities and differences between our framework and the standard replicator equation. Our equation is defined on the positive orthant, instead of the simplex, but has the same equilibrium points as the replicator equation. Linear stability analysis produces the classical conditions for asymptotic stability of pure strategies, but the stability properties of internal equilibria can differ in the two frameworks. For example, in a two-strategy game with an internal equilibrium that is always stable under the replicator equation, the corresponding equilibrium can be unstable in the new framework resulting in a limit cycle.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2025-05-28T11:42:43Z","department":[{"_id":"NiBa"},{"_id":"KrCh"}],"year":"2013","month":"10","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"_id":"2817","publication_status":"published","ddc":["000"],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5110","creator":"system","file_name":"IST-2016-400-v1+1_1-s2.0-S0022519313002609-main.pdf","date_created":"2018-12-12T10:14:54Z","file_size":834604,"checksum":"3c29059ab03a4b8f97a07646b817ddbb","date_updated":"2020-07-14T12:45:49Z","access_level":"open_access","content_type":"application/pdf"}],"pubrep_id":"400","publisher":"Elsevier","ec_funded":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2020-07-14T12:45:49Z","doi":"10.1016/j.jtbi.2013.05.029","date_published":"2013-10-07T00:00:00Z","intvolume":"       334","has_accepted_license":"1","volume":334,"day":"07","publication":"Journal of Theoretical Biology","title":"Density games","publist_id":"3984","page":"26 - 34","quality_controlled":"1","date_created":"2018-12-11T11:59:45Z","citation":{"chicago":"Novak, Sebastian, Krishnendu Chatterjee, and Martin Nowak. “Density Games.” <i>Journal of Theoretical Biology</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.jtbi.2013.05.029\">https://doi.org/10.1016/j.jtbi.2013.05.029</a>.","apa":"Novak, S., Chatterjee, K., &#38; Nowak, M. (2013). Density games. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2013.05.029\">https://doi.org/10.1016/j.jtbi.2013.05.029</a>","mla":"Novak, Sebastian, et al. “Density Games.” <i>Journal of Theoretical Biology</i>, vol. 334, Elsevier, 2013, pp. 26–34, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2013.05.029\">10.1016/j.jtbi.2013.05.029</a>.","ieee":"S. Novak, K. Chatterjee, and M. Nowak, “Density games,” <i>Journal of Theoretical Biology</i>, vol. 334. Elsevier, pp. 26–34, 2013.","short":"S. Novak, K. Chatterjee, M. Nowak, Journal of Theoretical Biology 334 (2013) 26–34.","ista":"Novak S, Chatterjee K, Nowak M. 2013. Density games. Journal of Theoretical Biology. 334, 26–34.","ama":"Novak S, Chatterjee K, Nowak M. Density games. <i>Journal of Theoretical Biology</i>. 2013;334:26-34. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2013.05.029\">10.1016/j.jtbi.2013.05.029</a>"},"oa":1},{"department":[{"_id":"GaTk"}],"year":"2013","month":"07","_id":"2818","issue":"7","external_id":{"arxiv":["1209.0121"]},"publication_status":"published","oa_version":"Preprint","type":"journal_article","publisher":"MIT Press ","author":[{"full_name":"Rajan, Kanaka","last_name":"Rajan","first_name":"Kanaka"},{"last_name":"Marre","full_name":"Marre, Olivier","first_name":"Olivier"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455"}],"status":"public","scopus_import":1,"abstract":[{"text":"Models of neural responses to stimuli with complex spatiotemporal correlation structure often assume that neurons are selective for only a small number of linear projections of a potentially high-dimensional input. In this review, we explore recent modeling approaches where the neural response depends on the quadratic form of the input rather than on its linear projection, that is, the neuron is sensitive to the local covariance structure of the signal preceding the spike. To infer this quadratic dependence in the presence of arbitrary (e.g., naturalistic) stimulus distribution, we review several inference methods, focusing in particular on two information theory–based approaches (maximization of stimulus energy and of noise entropy) and two likelihood-based approaches (Bayesian spike-triggered covariance and extensions of generalized linear models). We analyze the formal relationship between the likelihood-based and information-based approaches to demonstrate how they lead to consistent inference. We demonstrate the practical feasibility of these procedures by using model neurons responding to a flickering variance stimulus.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1209.0121"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T06:59:56Z","title":"Learning quadratic receptive fields from neural responses to natural stimuli","page":"1661 - 1692","publist_id":"3983","arxiv":1,"quality_controlled":"1","citation":{"ama":"Rajan K, Marre O, Tkačik G. Learning quadratic receptive fields from neural responses to natural stimuli. <i>Neural Computation</i>. 2013;25(7):1661-1692. doi:<a href=\"https://doi.org/10.1162/NECO_a_00463\">10.1162/NECO_a_00463</a>","short":"K. Rajan, O. Marre, G. Tkačik, Neural Computation 25 (2013) 1661–1692.","ista":"Rajan K, Marre O, Tkačik G. 2013. Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. 25(7), 1661–1692.","ieee":"K. Rajan, O. Marre, and G. Tkačik, “Learning quadratic receptive fields from neural responses to natural stimuli,” <i>Neural Computation</i>, vol. 25, no. 7. MIT Press , pp. 1661–1692, 2013.","mla":"Rajan, Kanaka, et al. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” <i>Neural Computation</i>, vol. 25, no. 7, MIT Press , 2013, pp. 1661–92, doi:<a href=\"https://doi.org/10.1162/NECO_a_00463\">10.1162/NECO_a_00463</a>.","apa":"Rajan, K., Marre, O., &#38; Tkačik, G. (2013). Learning quadratic receptive fields from neural responses to natural stimuli. <i>Neural Computation</i>. MIT Press . <a href=\"https://doi.org/10.1162/NECO_a_00463\">https://doi.org/10.1162/NECO_a_00463</a>","chicago":"Rajan, Kanaka, Olivier Marre, and Gašper Tkačik. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” <i>Neural Computation</i>. MIT Press , 2013. <a href=\"https://doi.org/10.1162/NECO_a_00463\">https://doi.org/10.1162/NECO_a_00463</a>."},"date_created":"2018-12-11T11:59:45Z","oa":1,"doi":"10.1162/NECO_a_00463","date_published":"2013-07-01T00:00:00Z","intvolume":"        25","volume":25,"day":"01","publication":"Neural Computation"},{"title":"Quantitative timed simulation functions and refinement metrics for real-time systems","page":"273 - 282","publist_id":"3982","citation":{"chicago":"Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Timed Simulation Functions and Refinement Metrics for Real-Time Systems.” In <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i>, 1:273–82. Springer, 2013. <a href=\"https://doi.org/10.1145/2461328.2461370\">https://doi.org/10.1145/2461328.2461370</a>.","apa":"Chatterjee, K., &#38; Prabhu, V. (2013). Quantitative timed simulation functions and refinement metrics for real-time systems. In <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i> (Vol. 1, pp. 273–282). Philadelphia, PA USA: Springer. <a href=\"https://doi.org/10.1145/2461328.2461370\">https://doi.org/10.1145/2461328.2461370</a>","mla":"Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Timed Simulation Functions and Refinement Metrics for Real-Time Systems.” <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i>, vol. 1, Springer, 2013, pp. 273–82, doi:<a href=\"https://doi.org/10.1145/2461328.2461370\">10.1145/2461328.2461370</a>.","ista":"Chatterjee K, Prabhu V. 2013. Quantitative timed simulation functions and refinement metrics for real-time systems. Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control vol. 1, 273–282.","ieee":"K. Chatterjee and V. Prabhu, “Quantitative timed simulation functions and refinement metrics for real-time systems,” in <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i>, Philadelphia, PA USA, 2013, vol. 1, pp. 273–282.","short":"K. Chatterjee, V. Prabhu, in:, Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, Springer, 2013, pp. 273–282.","ama":"Chatterjee K, Prabhu V. Quantitative timed simulation functions and refinement metrics for real-time systems. In: <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i>. Vol 1. Springer; 2013:273-282. doi:<a href=\"https://doi.org/10.1145/2461328.2461370\">10.1145/2461328.2461370</a>"},"date_created":"2018-12-11T11:59:46Z","conference":{"location":"Philadelphia, PA USA","end_date":"2013-04-11","start_date":"2013-04-08","name":"HSCC: Hybrid Systems - Computation and Control"},"quality_controlled":"1","oa":1,"ec_funded":1,"doi":"10.1145/2461328.2461370","intvolume":"         1","date_published":"2013-04-01T00:00:00Z","volume":1,"publication":"Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control","day":"01","acknowledgement":"This work has been financially supported in part by the European Commission FP7-ICT Cognitive Systems, Interaction, and Robotics under the contract # 270180 (NOP-TILUS); by Fundacao para Ciencia e Tecnologia under project PTDC/EEA-CRO/104901/2008 (Modeling and control of Networked vehicle systems in persistent autonomous operations); by Austrian Science Fund (FWF) Grant No P 23499-N23 on Modern Graph Algorithmic Techniques in Formal Verification; FWF NFN Grant No S11407-N23 (RiSE); ERC Start grant (279307: Graph Games); and the Microsoft faculty fellows award","department":[{"_id":"KrCh"}],"year":"2013","month":"04","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"type":"conference","oa_version":"Preprint","_id":"2819","publication_status":"published","publisher":"Springer","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Vinayak","last_name":"Prabhu","full_name":"Prabhu, Vinayak"}],"status":"public","abstract":[{"lang":"eng","text":"We introduce quantatitive timed refinement metrics and quantitative timed simulation functions, incorporating zenoness checks, for timed systems. These functions assign positive real numbers between zero and infinity which quantify the timing mismatches between two timed systems, amongst non-zeno runs. We quantify timing mismatches in three ways: (1) the maximum timing mismatch that can arise, (2) the &quot;steady-state&quot; maximum timing mismatches, where initial transient timing mismatches are ignored; and (3) the (long-run) average timing mismatches amongst two systems. These three kinds of mismatches constitute three important types of timing differences. Our event times are the global times, measured from the start of the system execution, not just the time durations of individual steps. We present algorithms over timed automata for computing the three quantitative simulation functions to within any desired degree of accuracy. In order to compute the values of the quantitative simulation functions, we use a game theoretic formulation. We introduce two new kinds of objectives for two player games on finite state game graphs: (1) eventual debit-sum level objectives, and (2) average debit-sum level objectives. We present algorithms for computing the optimal values for these objectives for player 1, and then use these algorithms to compute the values of the quantitative timed simulation functions. "}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1212.6556"}],"scopus_import":1,"date_updated":"2021-01-12T06:59:56Z","language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"publist_id":"3981","page":"163 - 172","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"S11407","name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"month":"04","year":"2013","publication_identifier":{"isbn":["978-1-4503-1567-8 "]},"department":[{"_id":"KrCh"}],"title":"Automated analysis of real-time scheduling using graph games","publisher":"ACM","publication_status":"published","quality_controlled":"1","_id":"2820","conference":{"name":"HSCC: Hybrid Systems - Computation and Control","start_date":"2013-04-08","location":"Philadelphia, PA, United States","end_date":"2013-04-11"},"oa_version":"None","type":"conference","date_created":"2018-12-11T11:59:46Z","citation":{"ama":"Chatterjee K, Kößler A, Schmid U. Automated analysis of real-time scheduling using graph games. In: <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i>. ACM; 2013:163-172. doi:<a href=\"https://doi.org/10.1145/2461328.2461356\">10.1145/2461328.2461356</a>","ista":"Chatterjee K, Kößler A, Schmid U. 2013. Automated analysis of real-time scheduling using graph games. Proceedings of the 16th International conference on Hybrid systems: Computation and control. HSCC: Hybrid Systems - Computation and Control, 163–172.","ieee":"K. Chatterjee, A. Kößler, and U. Schmid, “Automated analysis of real-time scheduling using graph games,” in <i>Proceedings of the 16th International conference on Hybrid systems: Computation and control</i>, Philadelphia, PA, United States, 2013, pp. 163–172.","short":"K. Chatterjee, A. Kößler, U. Schmid, in:, Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, ACM, 2013, pp. 163–172.","mla":"Chatterjee, Krishnendu, et al. “Automated Analysis of Real-Time Scheduling Using Graph Games.” <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i>, ACM, 2013, pp. 163–72, doi:<a href=\"https://doi.org/10.1145/2461328.2461356\">10.1145/2461328.2461356</a>.","apa":"Chatterjee, K., Kößler, A., &#38; Schmid, U. (2013). Automated analysis of real-time scheduling using graph games. In <i>Proceedings of the 16th International conference on Hybrid systems: Computation and control</i> (pp. 163–172). Philadelphia, PA, United States: ACM. <a href=\"https://doi.org/10.1145/2461328.2461356\">https://doi.org/10.1145/2461328.2461356</a>","chicago":"Chatterjee, Krishnendu, Alexander Kößler, and Ulrich Schmid. “Automated Analysis of Real-Time Scheduling Using Graph Games.” In <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i>, 163–72. ACM, 2013. <a href=\"https://doi.org/10.1145/2461328.2461356\">https://doi.org/10.1145/2461328.2461356</a>."},"doi":"10.1145/2461328.2461356","status":"public","ec_funded":1,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"full_name":"Kößler, Alexander","last_name":"Kößler","first_name":"Alexander"},{"full_name":"Schmid, Ulrich","last_name":"Schmid","first_name":"Ulrich"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publication":"Proceedings of the 16th International conference on Hybrid systems: Computation and control","day":"01","date_updated":"2023-09-27T12:52:38Z","date_published":"2013-04-01T00:00:00Z","scopus_import":1,"related_material":{"record":[{"id":"738","relation":"later_version","status":"public"}]},"abstract":[{"text":"In this paper, we introduce the powerful framework of graph games for the analysis of real-time scheduling with firm deadlines. We introduce a novel instance of a partial-observation game that is suitable for this purpose, and prove decidability of all the involved decision problems. We derive a graph game that allows the automated computation of the competitive ratio (along with an optimal witness algorithm for the competitive ratio) and establish an NP-completeness proof for the graph game problem. For a given on-line algorithm, we present polynomial time solution for computing (i) the worst-case utility; (ii) the worst-case utility ratio w.r.t. a clairvoyant off-line algorithm; and (iii) the competitive ratio. A major strength of the proposed approach lies in its flexibility w.r.t. incorporating additional constraints on the adversary and/or the algorithm, including limited maximum or average load, finiteness of periods of overload, etc., which are easily added by means of additional instances of standard objective functions for graph games. ","lang":"eng"}]},{"publisher":"American Society of Plant Biologists","type":"journal_article","oa_version":"Submitted Version","_id":"2821","issue":"3","publication_status":"published","external_id":{"pmid":["23524662"]},"year":"2013","month":"04","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:59:57Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Many key aspects of plant development are regulated by the polarized transport of the phytohormone auxin. Cellular auxin efflux, the rate-limiting step in this process, has been shown to rely on the coordinated action of PIN-formed (PIN) and B-type ATP binding cassette (ABCB) carriers. Here, we report that polar auxin transport in the Arabidopsis thaliana root also requires the action of a Major Facilitator Superfamily (MFS) transporter, Zinc-Induced Facilitator-Like 1 (ZIFL1). Sequencing, promoter-reporter, and fluorescent protein fusion experiments indicate that the full-length ZIFL1.1 protein and a truncated splice isoform, ZIFL1.3, localize to the tonoplast of root cells and the plasma membrane of leaf stomatal guard cells, respectively. Using reverse genetics, we show that the ZIFL1.1 transporter regulates various root auxin-related processes, while the ZIFL1.3 isoform mediates drought tolerance by regulating stomatal closure. Auxin transport and immunolocalization assays demonstrate that ZIFL1.1 indirectly modulates cellular auxin efflux during shootward auxin transport at the root tip, likely by regulating plasma membrane PIN2 abundance. Finally, heterologous expression in yeast revealed that ZIFL1.1 and ZIFL1.3 share H+-coupled K+ transport activity. Thus, by determining the subcellular and tissue distribution of two isoforms, alternative splicing dictates a dual function for the ZIFL1 transporter. We propose that this MFS carrier regulates stomatal movements and polar auxin transport by modulating potassium and proton fluxes in Arabidopsis cells."}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634696/","open_access":"1"}],"scopus_import":1,"author":[{"full_name":"Remy, Estelle","last_name":"Remy","first_name":"Estelle"},{"first_name":"Tânia","full_name":"Cabrito, Tânia","last_name":"Cabrito"},{"id":"3028BD74-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel","full_name":"Baster, Pawel","last_name":"Baster"},{"full_name":"Batista, Rita","last_name":"Batista","first_name":"Rita"},{"full_name":"Teixeira, Miguel","last_name":"Teixeira","first_name":"Miguel"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sá Correia","full_name":"Sá Correia, Isabel","first_name":"Isabel"},{"first_name":"Paula","last_name":"Duque","full_name":"Duque, Paula"}],"status":"public","oa":1,"date_created":"2018-12-11T11:59:46Z","citation":{"chicago":"Remy, Estelle, Tânia Cabrito, Pawel Baster, Rita Batista, Miguel Teixeira, Jiří Friml, Isabel Sá Correia, and Paula Duque. “A Major Facilitator Superfamily Transporter Plays a Dual Role in Polar Auxin Transport and Drought Stress Tolerance in Arabidopsis.” <i>Plant Cell</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1105/tpc.113.110353\">https://doi.org/10.1105/tpc.113.110353</a>.","apa":"Remy, E., Cabrito, T., Baster, P., Batista, R., Teixeira, M., Friml, J., … Duque, P. (2013). A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.113.110353\">https://doi.org/10.1105/tpc.113.110353</a>","mla":"Remy, Estelle, et al. “A Major Facilitator Superfamily Transporter Plays a Dual Role in Polar Auxin Transport and Drought Stress Tolerance in Arabidopsis.” <i>Plant Cell</i>, vol. 25, no. 3, American Society of Plant Biologists, 2013, pp. 901–26, doi:<a href=\"https://doi.org/10.1105/tpc.113.110353\">10.1105/tpc.113.110353</a>.","short":"E. Remy, T. Cabrito, P. Baster, R. Batista, M. Teixeira, J. Friml, I. Sá Correia, P. Duque, Plant Cell 25 (2013) 901–926.","ieee":"E. Remy <i>et al.</i>, “A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis,” <i>Plant Cell</i>, vol. 25, no. 3. American Society of Plant Biologists, pp. 901–926, 2013.","ista":"Remy E, Cabrito T, Baster P, Batista R, Teixeira M, Friml J, Sá Correia I, Duque P. 2013. A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis. Plant Cell. 25(3), 901–926.","ama":"Remy E, Cabrito T, Baster P, et al. A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis. <i>Plant Cell</i>. 2013;25(3):901-926. doi:<a href=\"https://doi.org/10.1105/tpc.113.110353\">10.1105/tpc.113.110353</a>"},"quality_controlled":"1","publist_id":"3980","page":"901 - 926","title":"A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis","volume":25,"day":"24","publication":"Plant Cell","pmid":1,"intvolume":"        25","date_published":"2013-04-24T00:00:00Z","doi":"10.1105/tpc.113.110353"},{"title":"3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture","page":"E1695 - E1704","publist_id":"3979","date_created":"2018-12-11T11:59:47Z","citation":{"apa":"Topp, C., Iyer Pascuzzi, A., Anderson, J., Lee, C., Zurek, P., Symonova, O., … Benfey, P. (2013). 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1304354110\">https://doi.org/10.1073/pnas.1304354110</a>","chicago":"Topp, Christopher, Anjali Iyer Pascuzzi, Jill Anderson, Cheng Lee, Paul Zurek, Olga Symonova, Ying Zheng, et al. “3D Phenotyping and Quantitative Trait Locus Mapping Identify Core Regions of the Rice Genome Controlling Root Architecture.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1304354110\">https://doi.org/10.1073/pnas.1304354110</a>.","mla":"Topp, Christopher, et al. “3D Phenotyping and Quantitative Trait Locus Mapping Identify Core Regions of the Rice Genome Controlling Root Architecture.” <i>PNAS</i>, vol. 110, no. 18, National Academy of Sciences, 2013, pp. E1695–704, doi:<a href=\"https://doi.org/10.1073/pnas.1304354110\">10.1073/pnas.1304354110</a>.","ama":"Topp C, Iyer Pascuzzi A, Anderson J, et al. 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. <i>PNAS</i>. 2013;110(18):E1695-E1704. doi:<a href=\"https://doi.org/10.1073/pnas.1304354110\">10.1073/pnas.1304354110</a>","ista":"Topp C, Iyer Pascuzzi A, Anderson J, Lee C, Zurek P, Symonova O, Zheng Y, Bucksch A, Mileyko Y, Galkovskyi T, Moore B, Harer J, Edelsbrunner H, Mitchell Olds T, Weitz J, Benfey P. 2013. 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. PNAS. 110(18), E1695–E1704.","short":"C. Topp, A. Iyer Pascuzzi, J. Anderson, C. Lee, P. Zurek, O. Symonova, Y. Zheng, A. Bucksch, Y. Mileyko, T. Galkovskyi, B. Moore, J. Harer, H. Edelsbrunner, T. Mitchell Olds, J. Weitz, P. Benfey, PNAS 110 (2013) E1695–E1704.","ieee":"C. Topp <i>et al.</i>, “3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture,” <i>PNAS</i>, vol. 110, no. 18. National Academy of Sciences, pp. E1695–E1704, 2013."},"quality_controlled":"1","oa":1,"doi":"10.1073/pnas.1304354110","intvolume":"       110","date_published":"2013-04-30T00:00:00Z","volume":110,"publication":"PNAS","day":"30","pmid":1,"department":[{"_id":"MaJö"},{"_id":"HeEd"}],"year":"2013","month":"04","type":"journal_article","oa_version":"Submitted Version","_id":"2822","issue":"18","external_id":{"pmid":["25673779"]},"publication_status":"published","publisher":"National Academy of Sciences","author":[{"full_name":"Topp, Christopher","last_name":"Topp","first_name":"Christopher"},{"last_name":"Iyer Pascuzzi","full_name":"Iyer Pascuzzi, Anjali","first_name":"Anjali"},{"full_name":"Anderson, Jill","last_name":"Anderson","first_name":"Jill"},{"first_name":"Cheng","last_name":"Lee","full_name":"Lee, Cheng"},{"first_name":"Paul","last_name":"Zurek","full_name":"Zurek, Paul"},{"last_name":"Symonova","full_name":"Symonova, Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","first_name":"Olga"},{"first_name":"Ying","last_name":"Zheng","full_name":"Zheng, Ying"},{"first_name":"Alexander","last_name":"Bucksch","full_name":"Bucksch, Alexander"},{"full_name":"Mileyko, Yuriy","last_name":"Mileyko","first_name":"Yuriy"},{"first_name":"Taras","last_name":"Galkovskyi","full_name":"Galkovskyi, Taras"},{"first_name":"Brad","full_name":"Moore, Brad","last_name":"Moore"},{"last_name":"Harer","full_name":"Harer, John","first_name":"John"},{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"last_name":"Mitchell Olds","full_name":"Mitchell Olds, Thomas","first_name":"Thomas"},{"first_name":"Joshua","full_name":"Weitz, Joshua","last_name":"Weitz"},{"last_name":"Benfey","full_name":"Benfey, Philip","first_name":"Philip"}],"status":"public","abstract":[{"lang":"eng","text":"Identification of genes that control root system architecture in crop plants requires innovations that enable high-throughput and accurate measurements of root system architecture through time. We demonstrate the ability of a semiautomated 3D in vivo imaging and digital phenotyping pipeline to interrogate the quantitative genetic basis of root system growth in a rice biparental mapping population, Bala x Azucena. We phenotyped &gt;1,400 3D root models and &gt;57,000 2D images for a suite of 25 traits that quantified the distribution, shape, extent of exploration, and the intrinsic size of root networks at days 12, 14, and 16 of growth in a gellan gum medium. From these data we identified 89 quantitative trait loci, some of which correspond to those found previously in soil-grown plants, and provide evidence for genetic tradeoffs in root growth allocations, such as between the extent and thoroughness of exploration. We also developed a multivariate method for generating and mapping central root architecture phenotypes and used it to identify five major quantitative trait loci (r2 = 24-37%), two of which were not identified by our univariate analysis. Our imaging and analytical platform provides a means to identify genes with high potential for improving root traits and agronomic qualities of crops."}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378147/"}],"scopus_import":1,"date_updated":"2021-01-12T06:59:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}]},{"status":"public","author":[{"first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","last_name":"Pickup","full_name":"Pickup, Melinda"},{"last_name":"Wilson","full_name":"Wilson, Susie","first_name":"Susie"},{"last_name":"Freudenberger","full_name":"Freudenberger, David","first_name":"David"},{"last_name":"Nicholls","full_name":"Nicholls, Nick","first_name":"Nick"},{"first_name":"Lori","last_name":"Gould","full_name":"Gould, Lori"},{"last_name":"Hnatiuk","full_name":"Hnatiuk, Sarah","first_name":"Sarah"},{"first_name":"Jeni","last_name":"Delandre","full_name":"Delandre, Jeni"}],"doi":"10.1111/j.1442-9993.2012.02404.x","intvolume":"        38","abstract":[{"text":"The primary goal of restoration is to create self-sustaining ecological communities that are resilient to periodic disturbance. Currently, little is known about how restored communities respond to disturbance events such as fire and how this response compares to remnant vegetation. Following the 2003 fires in south-eastern Australia we examined the post-fire response of revegetation plantings and compared this to remnant vegetation. Ten burnt and 10 unburnt (control) sites were assessed for each of three types of vegetation (direct seeding revegetation, revegetation using nursery seedlings (tubestock) and remnant woodland). Sixty sampling sites were surveyed 6months after fire to quantify the initial survival of mid- and overstorey plant species in each type of vegetation. Three and 5years after fire all sites were resurveyed to assess vegetation structure, species diversity and vigour, as well as indicators of soil function. Overall, revegetation showed high (&gt;60%) post-fire survival, but this varied among species depending on regeneration strategy (obligate seeder or resprouter). The native ground cover, mid- and overstorey in both types of plantings showed rapid recovery of vegetation structure and cover within 3years of fire. This recovery was similar to the burnt remnant woodlands. Non-native (exotic) ground cover initially increased after fire, but was no different in burnt and unburnt sites 5years after fire. Fire had no effect on species richness, but burnt direct seeding sites had reduced species diversity (Simpson's Diversity Index) while diversity was higher in burnt remnant woodlands. Indices of soil function in all types of vegetation had recovered to levels found in unburnt sites 5years after fire. These results indicate that even young revegetation (stands &lt;10years old) showed substantial recovery from disturbance by fire. This suggests that revegetation can provide an important basis for restoring woodland communities in the fire-prone Australian environment.","lang":"eng"}],"scopus_import":1,"date_published":"2013-05-01T00:00:00Z","publication":"Austral Ecology","day":"01","volume":38,"date_updated":"2021-01-12T06:59:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"title":"Post-fire recovery of revegetated woodland communities in south-eastern Australia","page":"300 - 312","publist_id":"3978","month":"05","year":"2013","type":"journal_article","oa_version":"None","date_created":"2018-12-11T11:59:47Z","citation":{"mla":"Pickup, Melinda, et al. “Post-Fire Recovery of Revegetated Woodland Communities in South-Eastern Australia.” <i>Austral Ecology</i>, vol. 38, no. 3, Wiley-Blackwell, 2013, pp. 300–12, doi:<a href=\"https://doi.org/10.1111/j.1442-9993.2012.02404.x\">10.1111/j.1442-9993.2012.02404.x</a>.","apa":"Pickup, M., Wilson, S., Freudenberger, D., Nicholls, N., Gould, L., Hnatiuk, S., &#38; Delandre, J. (2013). Post-fire recovery of revegetated woodland communities in south-eastern Australia. <i>Austral Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1442-9993.2012.02404.x\">https://doi.org/10.1111/j.1442-9993.2012.02404.x</a>","chicago":"Pickup, Melinda, Susie Wilson, David Freudenberger, Nick Nicholls, Lori Gould, Sarah Hnatiuk, and Jeni Delandre. “Post-Fire Recovery of Revegetated Woodland Communities in South-Eastern Australia.” <i>Austral Ecology</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/j.1442-9993.2012.02404.x\">https://doi.org/10.1111/j.1442-9993.2012.02404.x</a>.","ama":"Pickup M, Wilson S, Freudenberger D, et al. Post-fire recovery of revegetated woodland communities in south-eastern Australia. <i>Austral Ecology</i>. 2013;38(3):300-312. doi:<a href=\"https://doi.org/10.1111/j.1442-9993.2012.02404.x\">10.1111/j.1442-9993.2012.02404.x</a>","ista":"Pickup M, Wilson S, Freudenberger D, Nicholls N, Gould L, Hnatiuk S, Delandre J. 2013. Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. 38(3), 300–312.","ieee":"M. Pickup <i>et al.</i>, “Post-fire recovery of revegetated woodland communities in south-eastern Australia,” <i>Austral Ecology</i>, vol. 38, no. 3. Wiley-Blackwell, pp. 300–312, 2013.","short":"M. Pickup, S. Wilson, D. Freudenberger, N. Nicholls, L. Gould, S. Hnatiuk, J. Delandre, Austral Ecology 38 (2013) 300–312."},"quality_controlled":"1","publication_status":"published","_id":"2823","issue":"3","publisher":"Wiley-Blackwell"},{"date_updated":"2021-01-12T06:59:58Z","volume":"228-229","publication":"Information and Computation","day":"24","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We study synthesis of controllers for real-time systems, where the objective is to stay in a given safe set. The problem is solved by obtaining winning strategies in the setting of concurrent two player timed automaton games with safety objectives. To prevent a player from winning by blocking time, we restrict each player to strategies that ensure that the player cannot be responsible for causing a Zeno run. We construct winning strategies for the controller which require access only to (1) the system clocks (thus, controllers which require their own internal infinitely precise clocks are not necessary), and (2) a logarithmic (in the number of clocks) number of memory bits (i.e. a linear number of memory states). Precisely, we show that for safety objectives, a memory of size (3 + lg (| C | + 1)) bits suffices for winning controller strategies, where C is the set of clocks of the timed automaton game, significantly improving the previous known exponential memory states bound. We also settle the open question of whether winning region-based strategies require memory for safety objectives by showing with an example the necessity of memory for such strategies to win for safety objectives. Finally, we show that the decision problem of determining if there exists a receptive player-1 winning strategy for safety objectives is EXPTIME-complete over timed automaton games.","lang":"eng"}],"date_published":"2013-04-24T00:00:00Z","scopus_import":1,"doi":"10.1016/j.ic.2013.04.003","ec_funded":1,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Prabhu, Vinayak","last_name":"Prabhu","first_name":"Vinayak"}],"status":"public","publisher":"Elsevier","citation":{"chicago":"Chatterjee, Krishnendu, and Vinayak Prabhu. “Synthesis of Memory-Efficient, Clock-Memory Free, and Non-Zeno Safety Controllers for Timed Systems.” <i>Information and Computation</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.ic.2013.04.003\">https://doi.org/10.1016/j.ic.2013.04.003</a>.","apa":"Chatterjee, K., &#38; Prabhu, V. (2013). Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems. <i>Information and Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ic.2013.04.003\">https://doi.org/10.1016/j.ic.2013.04.003</a>","mla":"Chatterjee, Krishnendu, and Vinayak Prabhu. “Synthesis of Memory-Efficient, Clock-Memory Free, and Non-Zeno Safety Controllers for Timed Systems.” <i>Information and Computation</i>, vol. 228–229, Elsevier, 2013, pp. 83–119, doi:<a href=\"https://doi.org/10.1016/j.ic.2013.04.003\">10.1016/j.ic.2013.04.003</a>.","ieee":"K. Chatterjee and V. Prabhu, “Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems,” <i>Information and Computation</i>, vol. 228–229. Elsevier, pp. 83–119, 2013.","short":"K. Chatterjee, V. Prabhu, Information and Computation 228–229 (2013) 83–119.","ista":"Chatterjee K, Prabhu V. 2013. Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems. Information and Computation. 228–229, 83–119.","ama":"Chatterjee K, Prabhu V. Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems. <i>Information and Computation</i>. 2013;228-229:83-119. doi:<a href=\"https://doi.org/10.1016/j.ic.2013.04.003\">10.1016/j.ic.2013.04.003</a>"},"date_created":"2018-12-11T11:59:47Z","type":"journal_article","oa_version":"None","_id":"2824","quality_controlled":"1","publication_status":"published","year":"2013","month":"04","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF","grant_number":"S11407"},{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"publist_id":"3977","page":"83-119","title":"Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems","department":[{"_id":"KrCh"}]}]