[{"isi":1,"month":"04","date_updated":"2025-09-22T07:45:33Z","date_created":"2018-12-11T11:51:34Z","issue":"16","project":[{"name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152"},{"call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"scopus_import":"1","volume":113,"article_type":"original","page":"4422 - 4427","author":[{"full_name":"Paixao, Tiago","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"publication_status":"published","external_id":{"pmid":["27044080"],"isi":["000374393800056"]},"publist_id":"5886","language":[{"iso":"eng"}],"year":"2016","publication":"PNAS","citation":{"mla":"Paixao, Tiago, and Nicholas H. Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” <i>PNAS</i>, vol. 113, no. 16, National Academy of Sciences, 2016, pp. 4422–27, doi:<a href=\"https://doi.org/10.1073/pnas.1518830113\">10.1073/pnas.1518830113</a>.","ista":"Paixao T, Barton NH. 2016. The effect of gene interactions on the long-term response to selection. PNAS. 113(16), 4422–4427.","ieee":"T. Paixao and N. H. Barton, “The effect of gene interactions on the long-term response to selection,” <i>PNAS</i>, vol. 113, no. 16. National Academy of Sciences, pp. 4422–4427, 2016.","ama":"Paixao T, Barton NH. The effect of gene interactions on the long-term response to selection. <i>PNAS</i>. 2016;113(16):4422-4427. doi:<a href=\"https://doi.org/10.1073/pnas.1518830113\">10.1073/pnas.1518830113</a>","short":"T. Paixao, N.H. Barton, PNAS 113 (2016) 4422–4427.","chicago":"Paixao, Tiago, and Nicholas H Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” <i>PNAS</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1518830113\">https://doi.org/10.1073/pnas.1518830113</a>.","apa":"Paixao, T., &#38; Barton, N. H. (2016). The effect of gene interactions on the long-term response to selection. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1518830113\">https://doi.org/10.1073/pnas.1518830113</a>"},"oa":1,"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843425/"}],"doi":"10.1073/pnas.1518830113","pmid":1,"abstract":[{"text":"The role of gene interactions in the evolutionary process has long\r\nbeen controversial. Although some argue that they are not of\r\nimportance, because most variation is additive, others claim that\r\ntheir effect in the long term can be substantial. Here, we focus on\r\nthe long-term effects of genetic interactions under directional\r\nselection assuming no mutation or dominance, and that epistasis is\r\nsymmetrical overall. We ask by how much the mean of a complex\r\ntrait can be increased by selection and analyze two extreme\r\nregimes, in which either drift or selection dominate the dynamics\r\nof allele frequencies. In both scenarios, epistatic interactions affect\r\nthe long-term response to selection by modulating the additive\r\ngenetic variance. When drift dominates, we extend Robertson\r\n’\r\ns\r\n[Robertson A (1960)\r\nProc R Soc Lond B Biol Sci\r\n153(951):234\r\n−\r\n249]\r\nargument to show that, for any form of epistasis, the total response\r\nof a haploid population is proportional to the initial total genotypic\r\nvariance. In contrast, the total response of a diploid population is\r\nincreased by epistasis, for a given initial genotypic variance. When\r\nselection dominates, we show that the total selection response can\r\nonly be increased by epistasis when s\r\nome initially deleterious alleles\r\nbecome favored as the genetic background changes. We find a sim-\r\nple approximation for this effect and show that, in this regime, it is\r\nthe structure of the genotype - phenotype map that matters and not\r\nthe variance components of the population.","lang":"eng"}],"publisher":"National Academy of Sciences","corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","title":"The effect of gene interactions on the long-term response to selection","day":"19","intvolume":"       113","ec_funded":1,"department":[{"_id":"NiBa"},{"_id":"CaGu"}],"_id":"1359","type":"journal_article","date_published":"2016-04-19T00:00:00Z","status":"public","article_processing_charge":"No"},{"isi":1,"month":"10","date_updated":"2025-09-22T07:44:59Z","date_created":"2018-12-11T11:51:34Z","issue":"10","scopus_import":"1","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"volume":144,"page":"4501 - 4513","author":[{"full_name":"Akopyan, Arseniy","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","last_name":"Akopyan"},{"last_name":"Balitskiy","first_name":"Alexey","full_name":"Balitskiy, Alexey"},{"full_name":"Karasev, Roman","first_name":"Roman","last_name":"Karasev"},{"full_name":"Sharipova, Anastasia","first_name":"Anastasia","last_name":"Sharipova"}],"publication_status":"published","publist_id":"5885","external_id":{"isi":["000383054200034"],"arxiv":["1401.0442"]},"language":[{"iso":"eng"}],"year":"2016","publication":"Proceedings of the American Mathematical Society","citation":{"apa":"Akopyan, A., Balitskiy, A., Karasev, R., &#38; Sharipova, A. (2016). Elementary approach to closed billiard trajectories in asymmetric normed spaces. <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/proc/13062\">https://doi.org/10.1090/proc/13062</a>","mla":"Akopyan, Arseniy, et al. “Elementary Approach to Closed Billiard Trajectories in Asymmetric Normed Spaces.” <i>Proceedings of the American Mathematical Society</i>, vol. 144, no. 10, American Mathematical Society, 2016, pp. 4501–13, doi:<a href=\"https://doi.org/10.1090/proc/13062\">10.1090/proc/13062</a>.","ama":"Akopyan A, Balitskiy A, Karasev R, Sharipova A. Elementary approach to closed billiard trajectories in asymmetric normed spaces. <i>Proceedings of the American Mathematical Society</i>. 2016;144(10):4501-4513. doi:<a href=\"https://doi.org/10.1090/proc/13062\">10.1090/proc/13062</a>","ista":"Akopyan A, Balitskiy A, Karasev R, Sharipova A. 2016. Elementary approach to closed billiard trajectories in asymmetric normed spaces. Proceedings of the American Mathematical Society. 144(10), 4501–4513.","ieee":"A. Akopyan, A. Balitskiy, R. Karasev, and A. Sharipova, “Elementary approach to closed billiard trajectories in asymmetric normed spaces,” <i>Proceedings of the American Mathematical Society</i>, vol. 144, no. 10. American Mathematical Society, pp. 4501–4513, 2016.","chicago":"Akopyan, Arseniy, Alexey Balitskiy, Roman Karasev, and Anastasia Sharipova. “Elementary Approach to Closed Billiard Trajectories in Asymmetric Normed Spaces.” <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society, 2016. <a href=\"https://doi.org/10.1090/proc/13062\">https://doi.org/10.1090/proc/13062</a>.","short":"A. Akopyan, A. Balitskiy, R. Karasev, A. Sharipova, Proceedings of the American Mathematical Society 144 (2016) 4501–4513."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1401.0442"}],"oa_version":"Preprint","doi":"10.1090/proc/13062","abstract":[{"text":"We apply the technique of Károly Bezdek and Daniel Bezdek to study billiard trajectories in convex bodies, when the length is measured with a (possibly asymmetric) norm. We prove a lower bound for the length of the shortest closed billiard trajectory, related to the non-symmetric Mahler problem. With this technique we are able to give short and elementary proofs to some known results. ","lang":"eng"}],"publisher":"American Mathematical Society","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","arxiv":1,"title":"Elementary approach to closed billiard trajectories in asymmetric normed spaces","day":"01","ec_funded":1,"intvolume":"       144","acknowledgement":"The first and third authors were supported by the Dynasty Foundation. The first, second and third authors were supported by the Russian Foundation for Basic Re- search grant 15-31-20403 (mol a ved).","department":[{"_id":"HeEd"}],"_id":"1360","type":"journal_article","date_published":"2016-10-01T00:00:00Z","status":"public","article_processing_charge":"No"},{"article_number":"a78","oa":1,"has_accepted_license":"1","oa_version":"Published Version","doi":"10.1145/2897824.2925899","pubrep_id":"637","abstract":[{"lang":"eng","text":"We propose a novel surface-only technique for simulating incompressible, inviscid and uniform-density liquids with surface tension in three dimensions. The liquid surface is captured by a triangle mesh on which a Lagrangian velocity field is stored. Because advection of the velocity field may violate the incompressibility condition, we devise an orthogonal projection technique to remove the divergence while requiring the evaluation of only two boundary integrals. The forces of surface tension, gravity, and solid contact are all treated by a boundary element solve, allowing us to perform detailed simulations of a wide range of liquid phenomena, including waterbells, droplet and jet collisions, fluid chains, and crown splashes."}],"publisher":"ACM","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"11","title":"Surface only liquids","ec_funded":1,"intvolume":"        35","_id":"1361","ddc":["000"],"department":[{"_id":"ChWo"}],"alternative_title":["ACM Transactions on Graphics"],"date_published":"2016-07-11T00:00:00Z","type":"conference","status":"public","article_processing_charge":"No","conference":{"location":"Anaheim, CA, USA","start_date":"2016-07-24","end_date":"2016-07-28","name":"ACM SIGGRAPH"},"date_updated":"2025-09-22T07:44:26Z","isi":1,"month":"07","project":[{"call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"scopus_import":"1","issue":"4","file":[{"date_updated":"2020-07-14T12:44:46Z","creator":"system","file_size":10561865,"checksum":"6d662893bd447d4f575b4961a2247811","access_level":"open_access","date_created":"2018-12-12T10:08:01Z","content_type":"application/pdf","file_id":"4660","relation":"main_file","file_name":"IST-2016-637-v1+1_2016_Da_SOL.pdf"}],"date_created":"2018-12-11T11:51:35Z","volume":35,"file_date_updated":"2020-07-14T12:44:46Z","author":[{"last_name":"Da","first_name":"Fang","full_name":"Da, Fang"},{"full_name":"Hahn, David","id":"357A6A66-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Hahn"},{"last_name":"Batty","first_name":"Christopher","full_name":"Batty, Christopher"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","last_name":"Wojtan"},{"full_name":"Grinspun, Eitan","first_name":"Eitan","last_name":"Grinspun"}],"publication_status":"published","external_id":{"isi":["000380112400048"]},"publist_id":"5881","language":[{"iso":"eng"}],"year":"2016","citation":{"chicago":"Da, Fang, David Hahn, Christopher Batty, Chris Wojtan, and Eitan Grinspun. “Surface Only Liquids,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2897824.2925899\">https://doi.org/10.1145/2897824.2925899</a>.","short":"F. Da, D. Hahn, C. Batty, C. Wojtan, E. Grinspun, in:, ACM, 2016.","ista":"Da F, Hahn D, Batty C, Wojtan C, Grinspun E. 2016. Surface only liquids. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, a78.","ieee":"F. Da, D. Hahn, C. Batty, C. Wojtan, and E. Grinspun, “Surface only liquids,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4.","ama":"Da F, Hahn D, Batty C, Wojtan C, Grinspun E. Surface only liquids. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2897824.2925899\">10.1145/2897824.2925899</a>","mla":"Da, Fang, et al. <i>Surface Only Liquids</i>. Vol. 35, no. 4, a78, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2897824.2925899\">10.1145/2897824.2925899</a>.","apa":"Da, F., Hahn, D., Batty, C., Wojtan, C., &#38; Grinspun, E. (2016). Surface only liquids (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2897824.2925899\">https://doi.org/10.1145/2897824.2925899</a>"}},{"acknowledged_ssus":[{"_id":"ScienComp"}],"pubrep_id":"631","abstract":[{"lang":"eng","text":"When aiming to seamlessly integrate a fluid simulation into a larger scenario (like an open ocean), careful attention must be paid to boundary conditions. In particular, one must implement special &quot;non-reflecting&quot; boundary conditions, which dissipate out-going waves as they exit the simulation. Unfortunately, the state of the art in non-reflecting boundary conditions (perfectly-matched layers, or PMLs) only permits trivially simple inflow/outflow conditions, so there is no reliable way to integrate a fluid simulation into a more complicated environment like a stormy ocean or a turbulent river. This paper introduces the first method for combining nonreflecting boundary conditions based on PMLs with inflow/outflow boundary conditions that vary arbitrarily throughout space and time. Our algorithm is a generalization of stateof- the-art mean-flow boundary conditions in the computational fluid dynamics literature, and it allows for seamless integration of a fluid simulation into much more complicated environments. Our method also opens the door for previously-unseen postprocess effects like retroactively changing the location of solid obstacles, and locally increasing the visual detail of a pre-existing simulation."}],"corr_author":"1","publisher":"ACM","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","license":"https://creativecommons.org/licenses/by/4.0/","article_number":"96","oa":1,"oa_version":"Published Version","has_accepted_license":"1","doi":"10.1145/2897824.2925963","alternative_title":["ACM Transactions on Graphics"],"date_published":"2016-07-11T00:00:00Z","type":"conference","status":"public","article_processing_charge":"No","day":"11","title":"Generalized non-reflecting boundaries for fluid re-simulation","ec_funded":1,"intvolume":"        35","acknowledgement":"We thank the IST Austria Visual Computing group for helpful feedback throughout the project. ","ddc":["000"],"_id":"1363","department":[{"_id":"ChWo"}],"file":[{"relation":"main_file","file_name":"IST-2016-631-v1+2_a96-bojsen-hansen.pdf","checksum":"140b5532f0a2a006a0149cab7c73c17c","access_level":"open_access","date_created":"2018-12-12T10:13:00Z","file_id":"4981","content_type":"application/pdf","file_size":12422760,"date_updated":"2020-07-14T12:44:47Z","creator":"system"}],"project":[{"name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"issue":"4","scopus_import":"1","date_created":"2018-12-11T11:51:35Z","volume":35,"file_date_updated":"2020-07-14T12:44:47Z","author":[{"id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4417-3224","first_name":"Morten","last_name":"Bojsen-Hansen","full_name":"Bojsen-Hansen, Morten"},{"full_name":"Wojtan, Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"conference":{"end_date":"2016-07-28","start_date":"2016-07-24","location":"Anaheim, CA, USA","name":"ACM SIGGRAPH"},"date_updated":"2025-09-22T07:43:01Z","month":"07","isi":1,"year":"2016","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"M. Bojsen-Hansen, C. Wojtan, in:, ACM, 2016.","chicago":"Bojsen-Hansen, Morten, and Chris Wojtan. “Generalized Non-Reflecting Boundaries for Fluid Re-Simulation,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2897824.2925963\">https://doi.org/10.1145/2897824.2925963</a>.","ista":"Bojsen-Hansen M, Wojtan C. 2016. Generalized non-reflecting boundaries for fluid re-simulation. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 96.","ieee":"M. Bojsen-Hansen and C. Wojtan, “Generalized non-reflecting boundaries for fluid re-simulation,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4.","ama":"Bojsen-Hansen M, Wojtan C. Generalized non-reflecting boundaries for fluid re-simulation. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2897824.2925963\">10.1145/2897824.2925963</a>","mla":"Bojsen-Hansen, Morten, and Chris Wojtan. <i>Generalized Non-Reflecting Boundaries for Fluid Re-Simulation</i>. Vol. 35, no. 4, 96, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2897824.2925963\">10.1145/2897824.2925963</a>.","apa":"Bojsen-Hansen, M., &#38; Wojtan, C. (2016). Generalized non-reflecting boundaries for fluid re-simulation (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2897824.2925963\">https://doi.org/10.1145/2897824.2925963</a>"},"publication_status":"published","external_id":{"isi":["000380112400066"]},"publist_id":"5879","language":[{"iso":"eng"}]},{"volume":35,"date_created":"2018-12-11T11:51:36Z","scopus_import":"1","issue":"4","file":[{"relation":"main_file","file_name":"IST-2017-763-v1+1_wirebending.pdf","access_level":"open_access","checksum":"d00c2664a43d945df8876ea0193734e3","content_type":"application/pdf","file_id":"4853","date_created":"2018-12-12T10:11:01Z","file_size":44766392,"date_updated":"2020-07-14T12:44:47Z","creator":"system"}],"project":[{"grant_number":"645599","call_identifier":"H2020","_id":"25082902-B435-11E9-9278-68D0E5697425","name":"Soft-bodied intelligence for Manipulation"}],"author":[{"full_name":"Miguel Villalba, Eder","last_name":"Miguel Villalba","first_name":"Eder","orcid":"0000-0001-5665-0430","id":"3FB91342-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lepoutre","first_name":"Mathias","full_name":"Lepoutre, Mathias"},{"full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385"}],"file_date_updated":"2020-07-14T12:44:47Z","month":"07","isi":1,"date_updated":"2025-09-22T07:42:15Z","conference":{"name":"ACM SIGGRAPH","location":"Anaheim, CA, USA","start_date":"2016-07-24","end_date":"2016-07-28"},"year":"2016","citation":{"apa":"Miguel Villalba, E., Lepoutre, M., &#38; Bickel, B. (2016). Computational design of stable planar-rod structures (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2897824.2925978\">https://doi.org/10.1145/2897824.2925978</a>","short":"E. Miguel Villalba, M. Lepoutre, B. Bickel, in:, ACM, 2016.","chicago":"Miguel Villalba, Eder, Mathias Lepoutre, and Bernd Bickel. “Computational Design of Stable Planar-Rod Structures,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2897824.2925978\">https://doi.org/10.1145/2897824.2925978</a>.","mla":"Miguel Villalba, Eder, et al. <i>Computational Design of Stable Planar-Rod Structures</i>. Vol. 35, no. 4, 86, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2897824.2925978\">10.1145/2897824.2925978</a>.","ama":"Miguel Villalba E, Lepoutre M, Bickel B. Computational design of stable planar-rod structures. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2897824.2925978\">10.1145/2897824.2925978</a>","ieee":"E. Miguel Villalba, M. Lepoutre, and B. Bickel, “Computational design of stable planar-rod structures,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4.","ista":"Miguel Villalba E, Lepoutre M, Bickel B. 2016. Computational design of stable planar-rod structures. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 86."},"external_id":{"isi":["000380112400056"]},"publist_id":"5878","publication_status":"published","language":[{"iso":"eng"}],"abstract":[{"text":"We present a computational method for designing wire sculptures consisting of interlocking wires. Our method allows the computation of aesthetically pleasing structures that are structurally stable, efficiently fabricatable with a 2D wire bending machine, and assemblable without the need of additional connectors. Starting from a set of planar contours provided by the user, our method automatically tests for the feasibility of a design, determines a discrete ordering of wires at intersection points, and optimizes for the rest shape of the individual wires to maximize structural stability under frictional contact. In addition to their application to art, wire sculptures present an extremely efficient and fast alternative for low-fidelity rapid prototyping because manufacturing time and required material linearly scales with the physical size of objects. We demonstrate the effectiveness of our approach on a varied set of examples, all of which we fabricated.","lang":"eng"}],"pubrep_id":"763","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","publisher":"ACM","corr_author":"1","oa":1,"article_number":"86","doi":"10.1145/2897824.2925978","has_accepted_license":"1","oa_version":"Preprint","type":"conference","alternative_title":["ACM Transactions on Graphics"],"date_published":"2016-07-01T00:00:00Z","article_processing_charge":"No","status":"public","intvolume":"        35","ec_funded":1,"title":"Computational design of stable planar-rod structures","day":"01","department":[{"_id":"BeBi"}],"_id":"1364","ddc":["006"],"acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 645599."},{"citation":{"chicago":"Alwen, Joel F, and Jeremiah Blocki. “Efficiently Computing Data-Independent Memory-Hard Functions,” 9815:241–71. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-53008-5_9\">https://doi.org/10.1007/978-3-662-53008-5_9</a>.","short":"J.F. Alwen, J. Blocki, in:, Springer, 2016, pp. 241–271.","mla":"Alwen, Joel F., and Jeremiah Blocki. <i>Efficiently Computing Data-Independent Memory-Hard Functions</i>. Vol. 9815, Springer, 2016, pp. 241–71, doi:<a href=\"https://doi.org/10.1007/978-3-662-53008-5_9\">10.1007/978-3-662-53008-5_9</a>.","ieee":"J. F. Alwen and J. Blocki, “Efficiently computing data-independent memory-hard functions,” presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, USA, 2016, vol. 9815, pp. 241–271.","ama":"Alwen JF, Blocki J. Efficiently computing data-independent memory-hard functions. In: Vol 9815. Springer; 2016:241-271. doi:<a href=\"https://doi.org/10.1007/978-3-662-53008-5_9\">10.1007/978-3-662-53008-5_9</a>","ista":"Alwen JF, Blocki J. 2016. Efficiently computing data-independent memory-hard functions. CRYPTO: International Cryptology Conference, LNCS, vol. 9815, 241–271.","apa":"Alwen, J. F., &#38; Blocki, J. (2016). Efficiently computing data-independent memory-hard functions (Vol. 9815, pp. 241–271). Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-662-53008-5_9\">https://doi.org/10.1007/978-3-662-53008-5_9</a>"},"year":"2016","language":[{"iso":"eng"}],"external_id":{"isi":["000416104300009"]},"publist_id":"5876","publication_status":"published","author":[{"id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F","last_name":"Alwen","full_name":"Alwen, Joel F"},{"full_name":"Blocki, Jeremiah","last_name":"Blocki","first_name":"Jeremiah"}],"page":"241 - 271","volume":9815,"scopus_import":"1","date_created":"2018-12-11T11:51:36Z","date_updated":"2025-09-22T07:41:33Z","isi":1,"month":"08","conference":{"location":"Santa Barbara, CA, USA","end_date":"2016-08-18","start_date":"2016-08-14","name":"CRYPTO: International Cryptology Conference"},"article_processing_charge":"No","status":"public","alternative_title":["LNCS"],"date_published":"2016-08-01T00:00:00Z","type":"conference","_id":"1365","department":[{"_id":"KrPi"}],"intvolume":"      9815","day":"01","title":"Efficiently computing data-independent memory-hard functions","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Springer","abstract":[{"text":"A memory-hard function (MHF) f is equipped with a space cost σ and time cost τ parameter such that repeatedly computing fσ,τ on an application specific integrated circuit (ASIC) is not economically advantageous relative to a general purpose computer. Technically we would like that any (generalized) circuit for evaluating an iMHF fσ,τ has area × time (AT) complexity at Θ(σ2 ∗ τ). A data-independent MHF (iMHF) has the added property that it can be computed with almost optimal memory and time complexity by an algorithm which accesses memory in a pattern independent of the input value. Such functions can be specified by fixing a directed acyclic graph (DAG) G on n = Θ(σ ∗ τ) nodes representing its computation graph. In this work we develop new tools for analyzing iMHFs. First we define and motivate a new complexity measure capturing the amount of energy (i.e. electricity) required to compute a function. We argue that, in practice, this measure is at least as important as the more traditional AT-complexity. Next we describe an algorithm A for repeatedly evaluating an iMHF based on an arbitrary DAG G. We upperbound both its energy and AT complexities per instance evaluated in terms of a certain combinatorial property of G. Next we instantiate our attack for several general classes of DAGs which include those underlying many of the most important iMHF candidates in the literature. In particular, we obtain the following results which hold for all choices of parameters σ and τ (and thread-count) such that n = σ ∗ τ. -The Catena-Dragonfly function of [FLW13] has AT and energy complexities O(n1.67). -The Catena-Butterfly function of [FLW13] has complexities is O(n1.67). -The Double-Buffer and the Linear functions of [CGBS16] both have complexities in O(n1.67). -The Argon2i function of [BDK15] (winner of the Password Hashing Competition [PHC]) has complexities O(n7/4 log(n)). -The Single-Buffer function of [CGBS16] has complexities O(n7/4 log(n)). -Any iMHF can be computed by an algorithm with complexities O(n2/ log1 −ε(n)) for all ε &gt; 0. In particular when τ = 1 this shows that the goal of constructing an iMHF with AT-complexity Θ(σ2 ∗ τ ) is unachievable. Along the way we prove a lemma upper-bounding the depth-robustness of any DAG which may prove to be of independent interest.","lang":"eng"}],"doi":"10.1007/978-3-662-53008-5_9","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://eprint.iacr.org/2016/115"}],"oa":1},{"article_processing_charge":"No","status":"public","alternative_title":["LNCS"],"date_published":"2016-05-01T00:00:00Z","type":"conference","_id":"1366","department":[{"_id":"KrPi"}],"ec_funded":1,"intvolume":"      9665","day":"01","title":"Provably robust sponge-based PRNGs and KDFs","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","publisher":"Springer","abstract":[{"text":"We study the problem of devising provably secure PRNGs with input based on the sponge paradigm. Such constructions are very appealing, as efficient software/hardware implementations of SHA-3 can easily be translated into a PRNG in a nearly black-box way. The only existing sponge-based construction, proposed by Bertoni et al. (CHES 2010), fails to achieve the security notion of robustness recently considered by Dodis et al. (CCS 2013), for two reasons: (1) The construction is deterministic, and thus there are high-entropy input distributions on which the construction fails to extract random bits, and (2) The construction is not forward secure, and presented solutions aiming at restoring forward security have not been rigorously analyzed. We propose a seeded variant of Bertoni et al.’s PRNG with input which we prove secure in the sense of robustness, delivering in particular concrete security bounds. On the way, we make what we believe to be an important conceptual contribution, developing a variant of the security framework of Dodis et al. tailored at the ideal permutation model that captures PRNG security in settings where the weakly random inputs are provided from a large class of possible adversarial samplers which are also allowed to query the random permutation. As a further application of our techniques, we also present an efficient sponge-based key-derivation function (which can be instantiated from SHA-3 in a black-box fashion), which we also prove secure when fed with samples from permutation-dependent distributions.","lang":"eng"}],"doi":"10.1007/978-3-662-49890-3_4","oa_version":"Preprint","main_file_link":[{"url":"https://eprint.iacr.org/2016/169/20160219:201940","open_access":"1"}],"oa":1,"citation":{"chicago":"Gazi, Peter, and Stefano Tessaro. “Provably Robust Sponge-Based PRNGs and KDFs,” 9665:87–116. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-49890-3_4\">https://doi.org/10.1007/978-3-662-49890-3_4</a>.","short":"P. Gazi, S. Tessaro, in:, Springer, 2016, pp. 87–116.","ama":"Gazi P, Tessaro S. Provably robust sponge-based PRNGs and KDFs. In: Vol 9665. Springer; 2016:87-116. doi:<a href=\"https://doi.org/10.1007/978-3-662-49890-3_4\">10.1007/978-3-662-49890-3_4</a>","ieee":"P. Gazi and S. Tessaro, “Provably robust sponge-based PRNGs and KDFs,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Vienna, Austria, 2016, vol. 9665, pp. 87–116.","ista":"Gazi P, Tessaro S. 2016. Provably robust sponge-based PRNGs and KDFs. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 9665, 87–116.","mla":"Gazi, Peter, and Stefano Tessaro. <i>Provably Robust Sponge-Based PRNGs and KDFs</i>. Vol. 9665, Springer, 2016, pp. 87–116, doi:<a href=\"https://doi.org/10.1007/978-3-662-49890-3_4\">10.1007/978-3-662-49890-3_4</a>.","apa":"Gazi, P., &#38; Tessaro, S. (2016). Provably robust sponge-based PRNGs and KDFs (Vol. 9665, pp. 87–116). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Vienna, Austria: Springer. <a href=\"https://doi.org/10.1007/978-3-662-49890-3_4\">https://doi.org/10.1007/978-3-662-49890-3_4</a>"},"year":"2016","language":[{"iso":"eng"}],"external_id":{"isi":["000389727400004"]},"publist_id":"5872","publication_status":"published","author":[{"last_name":"Gazi","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Gazi, Peter"},{"full_name":"Tessaro, Stefano","last_name":"Tessaro","first_name":"Stefano"}],"page":"87 - 116","volume":9665,"project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"259668","name":"Provable Security for Physical Cryptography"}],"scopus_import":"1","date_created":"2018-12-11T11:51:36Z","date_updated":"2025-09-22T07:40:51Z","month":"05","isi":1,"conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques","location":"Vienna, Austria","start_date":"2016-05-08","end_date":"2016-05-12"}},{"author":[{"first_name":"Marcin","last_name":"Wysokiński","full_name":"Wysokiński, Marcin"},{"full_name":"Kaczmarczyk, Jan","orcid":"0000-0002-1629-3675","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Kaczmarczyk"},{"last_name":"Spałek","first_name":"Jozef","full_name":"Spałek, Jozef"}],"volume":94,"issue":"2","scopus_import":"1","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_created":"2018-12-11T11:51:37Z","date_updated":"2025-09-22T07:40:18Z","isi":1,"month":"07","citation":{"chicago":"Wysokiński, Marcin, Jan Kaczmarczyk, and Jozef Spałek. “Correlation Driven d Wave Superconductivity in Anderson Lattice Model: Two Gaps.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevB.94.024517\">https://doi.org/10.1103/PhysRevB.94.024517</a>.","short":"M. Wysokiński, J. Kaczmarczyk, J. Spałek, Physical Review B - Condensed Matter and Materials Physics 94 (2016).","mla":"Wysokiński, Marcin, et al. “Correlation Driven d Wave Superconductivity in Anderson Lattice Model: Two Gaps.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 94, no. 2, 024517, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevB.94.024517\">10.1103/PhysRevB.94.024517</a>.","ieee":"M. Wysokiński, J. Kaczmarczyk, and J. Spałek, “Correlation driven d wave superconductivity in Anderson lattice model: Two gaps,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 94, no. 2. American Physical Society, 2016.","ista":"Wysokiński M, Kaczmarczyk J, Spałek J. 2016. Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. Physical Review B - Condensed Matter and Materials Physics. 94(2), 024517.","ama":"Wysokiński M, Kaczmarczyk J, Spałek J. Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2016;94(2). doi:<a href=\"https://doi.org/10.1103/PhysRevB.94.024517\">10.1103/PhysRevB.94.024517</a>","apa":"Wysokiński, M., Kaczmarczyk, J., &#38; Spałek, J. (2016). Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.94.024517\">https://doi.org/10.1103/PhysRevB.94.024517</a>"},"publication":"Physical Review B - Condensed Matter and Materials Physics","year":"2016","language":[{"iso":"eng"}],"external_id":{"isi":["000380098600005"],"arxiv":["1510.00224"]},"publist_id":"5844","publication_status":"published","arxiv":1,"quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"American Physical Society","abstract":[{"text":"Superconductivity in heavy-fermion systems has an unconventional nature and is considered to originate from the universal features of the electronic structure. Here, the Anderson lattice model is studied by means of the full variational Gutzwiller wave function incorporating nonlocal effects of the on-site interaction. We show that the d-wave superconducting ground state can be driven solely by interelectronic correlations. The proposed microscopic mechanism leads to a multigap superconductivity with the dominant contribution due to f electrons and in the dx2−y2-wave channel. Our results rationalize several important observations for CeCoIn5.","lang":"eng"}],"doi":"10.1103/PhysRevB.94.024517","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1510.00224"}],"oa_version":"Preprint","oa":1,"article_number":"024517","article_processing_charge":"No","status":"public","date_published":"2016-07-01T00:00:00Z","type":"journal_article","_id":"1368","department":[{"_id":"MiLe"}],"acknowledgement":"The  work  has  been  supported  by  the  National Science  Center  (NCN)  under  the  Grant  MAESTRO,  No.\r\nDEC-2012/04/A/ST3/00342. ","intvolume":"        94","ec_funded":1,"day":"01","title":"Correlation driven d wave superconductivity in Anderson lattice model: Two gaps"},{"type":"conference","date_published":"2016-09-15T00:00:00Z","alternative_title":["LNCS"],"status":"public","article_processing_charge":"No","title":"Seed, expand and constrain: Three principles for weakly-supervised image segmentation","day":"15","ec_funded":1,"intvolume":"      9908","department":[{"_id":"ChLa"}],"_id":"1369","abstract":[{"text":"We introduce a new loss function for the weakly-supervised training of semantic image segmentation models based on three guiding principles: to seed with weak localization cues, to expand objects based on the information about which classes can occur in an image, and to constrain the segmentations to coincide with object boundaries. We show experimentally that training a deep convolutional neural network using the proposed loss function leads to substantially better segmentations than previous state-of-the-art methods on the challenging PASCAL VOC 2012 dataset. We furthermore give insight into the working mechanism of our method by a detailed experimental study that illustrates how the segmentation quality is affected by each term of the proposed loss function as well as their combinations.","lang":"eng"}],"corr_author":"1","publisher":"Springer","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1603.06098","open_access":"1"}],"oa_version":"Preprint","doi":"10.1007/978-3-319-46493-0_42","year":"2016","citation":{"chicago":"Kolesnikov, Alexander, and Christoph Lampert. “Seed, Expand and Constrain: Three Principles for Weakly-Supervised Image Segmentation,” 9908:695–711. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-46493-0_42\">https://doi.org/10.1007/978-3-319-46493-0_42</a>.","short":"A. Kolesnikov, C. Lampert, in:, Springer, 2016, pp. 695–711.","ista":"Kolesnikov A, Lampert C. 2016. Seed, expand and constrain: Three principles for weakly-supervised image segmentation. ECCV: European Conference on Computer Vision, LNCS, vol. 9908, 695–711.","ieee":"A. Kolesnikov and C. Lampert, “Seed, expand and constrain: Three principles for weakly-supervised image segmentation,” presented at the ECCV: European Conference on Computer Vision, Amsterdam, The Netherlands, 2016, vol. 9908, pp. 695–711.","ama":"Kolesnikov A, Lampert C. Seed, expand and constrain: Three principles for weakly-supervised image segmentation. In: Vol 9908. Springer; 2016:695-711. doi:<a href=\"https://doi.org/10.1007/978-3-319-46493-0_42\">10.1007/978-3-319-46493-0_42</a>","mla":"Kolesnikov, Alexander, and Christoph Lampert. <i>Seed, Expand and Constrain: Three Principles for Weakly-Supervised Image Segmentation</i>. Vol. 9908, Springer, 2016, pp. 695–711, doi:<a href=\"https://doi.org/10.1007/978-3-319-46493-0_42\">10.1007/978-3-319-46493-0_42</a>.","apa":"Kolesnikov, A., &#38; Lampert, C. (2016). Seed, expand and constrain: Three principles for weakly-supervised image segmentation (Vol. 9908, pp. 695–711). Presented at the ECCV: European Conference on Computer Vision, Amsterdam, The Netherlands: Springer. <a href=\"https://doi.org/10.1007/978-3-319-46493-0_42\">https://doi.org/10.1007/978-3-319-46493-0_42</a>"},"publication_status":"published","external_id":{"isi":["000389385100042"],"arxiv":["1603.06098"]},"publist_id":"5842","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:51:37Z","scopus_import":"1","project":[{"name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"volume":9908,"page":"695 - 711","author":[{"full_name":"Kolesnikov, Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander","last_name":"Kolesnikov"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert"}],"conference":{"name":"ECCV: European Conference on Computer Vision","location":"Amsterdam, The Netherlands","end_date":"2016-10-14","start_date":"2016-10-11"},"isi":1,"month":"09","date_updated":"2025-09-22T07:39:37Z"},{"intvolume":"        93","title":"Phonon Josephson junction with nanomechanical resonators","day":"28","department":[{"_id":"JoFi"}],"_id":"1370","acknowledgement":"The work of S.B. has been supported by the European Commission (Belgium) via the SCALEQIT program and by the Alexander von Humboldt Foundation.  ","type":"journal_article","date_published":"2016-03-28T00:00:00Z","article_processing_charge":"No","status":"public","oa":1,"article_number":"033846","doi":"10.1103/PhysRevA.93.033846","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1601.01818"}],"oa_version":"Preprint","abstract":[{"text":"We study coherent phonon oscillations and tunneling between two coupled nonlinear nanomechanical resonators. We show that the coupling between two nanomechanical resonators creates an effective phonon Josephson junction, which exhibits two different dynamical behaviors: Josephson oscillation (phonon-Rabi oscillation) and macroscopic self-trapping (phonon blockade). Self-trapping originates from mechanical nonlinearities, meaning that when the nonlinearity exceeds its critical value, the energy exchange between the two resonators is suppressed, and phonon Josephson oscillations between them are completely blocked. An effective classical Hamiltonian for the phonon Josephson junction is derived and its mean-field dynamics is studied in phase space. Finally, we study the phonon-phonon coherence quantified by the mean fringe visibility, and show that the interaction between the two resonators may lead to the loss of coherence in the phononic junction.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","arxiv":1,"publisher":"American Physical Society","external_id":{"arxiv":["1601.01818"],"isi":["000372797700010"]},"publist_id":"5841","publication_status":"published","language":[{"iso":"eng"}],"publication":"Physical Review A - Atomic, Molecular, and Optical Physics","year":"2016","citation":{"apa":"Barzanjeh, S., &#38; Vitali, D. (2016). Phonon Josephson junction with nanomechanical resonators. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.93.033846\">https://doi.org/10.1103/PhysRevA.93.033846</a>","mla":"Barzanjeh, Shabir, and David Vitali. “Phonon Josephson Junction with Nanomechanical Resonators.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 93, no. 3, 033846, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevA.93.033846\">10.1103/PhysRevA.93.033846</a>.","ieee":"S. Barzanjeh and D. Vitali, “Phonon Josephson junction with nanomechanical resonators,” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 93, no. 3. American Physical Society, 2016.","ista":"Barzanjeh S, Vitali D. 2016. Phonon Josephson junction with nanomechanical resonators. Physical Review A - Atomic, Molecular, and Optical Physics. 93(3), 033846.","ama":"Barzanjeh S, Vitali D. Phonon Josephson junction with nanomechanical resonators. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2016;93(3). doi:<a href=\"https://doi.org/10.1103/PhysRevA.93.033846\">10.1103/PhysRevA.93.033846</a>","chicago":"Barzanjeh, Shabir, and David Vitali. “Phonon Josephson Junction with Nanomechanical Resonators.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevA.93.033846\">https://doi.org/10.1103/PhysRevA.93.033846</a>.","short":"S. Barzanjeh, D. Vitali, Physical Review A - Atomic, Molecular, and Optical Physics 93 (2016)."},"isi":1,"month":"03","date_updated":"2025-09-22T07:37:17Z","volume":93,"date_created":"2018-12-11T11:51:38Z","scopus_import":"1","issue":"3","author":[{"full_name":"Barzanjeh, Shabir","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423","first_name":"Shabir"},{"full_name":"Vitali, David","first_name":"David","last_name":"Vitali"}]},{"oa_version":"None","doi":"10.1016/j.plrev.2016.06.002","publisher":"Elsevier","corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","abstract":[{"lang":"eng","text":"Living cells can maintain their internal states, react to changing environments, grow, differentiate, divide, etc. All these processes are tightly controlled by what can be called a regulatory program. The logic of the underlying control can sometimes be guessed at by examining the network of influences amongst genetic components. Some associated gene regulatory networks have been studied in prokaryotes and eukaryotes, unveiling various structural features ranging from broad distributions of out-degrees to recurrent &quot;motifs&quot;, that is small subgraphs having a specific pattern of interactions. To understand what factors may be driving such structuring, a number of groups have introduced frameworks to model the dynamics of gene regulatory networks. In that context, we review here such in silico approaches and show how selection for phenotypes, i.e., network function, can shape network structure."}],"acknowledgement":"MZ has been supported by Polish National Science Centre Grant No. DEC-2012/07/N/NZ2/00107 and by Foundation of Polish Science award START. ","department":[{"_id":"AnKi"}],"_id":"1371","title":"Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function","day":"01","ec_funded":1,"intvolume":"        17","status":"public","article_processing_charge":"No","type":"journal_article","date_published":"2016-07-01T00:00:00Z","isi":1,"month":"07","date_updated":"2025-09-22T07:36:42Z","page":"124 - 158","author":[{"last_name":"Martin","first_name":"Olivier","full_name":"Martin, Olivier"},{"last_name":"Krzywicki","first_name":"André","full_name":"Krzywicki, André"},{"full_name":"Zagórski, Marcin P","orcid":"0000-0001-7896-7762","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin P","last_name":"Zagórski"}],"date_created":"2018-12-11T11:51:38Z","scopus_import":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"volume":17,"language":[{"iso":"eng"}],"publication_status":"published","external_id":{"isi":["000381544100029"]},"publist_id":"5840","citation":{"apa":"Martin, O., Krzywicki, A., &#38; Zagórski, M. P. (2016). Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function. <i>Physics of Life Reviews</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plrev.2016.06.002\">https://doi.org/10.1016/j.plrev.2016.06.002</a>","chicago":"Martin, Olivier, André Krzywicki, and Marcin P Zagórski. “Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function.” <i>Physics of Life Reviews</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.plrev.2016.06.002\">https://doi.org/10.1016/j.plrev.2016.06.002</a>.","short":"O. Martin, A. Krzywicki, M.P. Zagórski, Physics of Life Reviews 17 (2016) 124–158.","ista":"Martin O, Krzywicki A, Zagórski MP. 2016. Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function. Physics of Life Reviews. 17, 124–158.","ieee":"O. Martin, A. Krzywicki, and M. P. Zagórski, “Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function,” <i>Physics of Life Reviews</i>, vol. 17. Elsevier, pp. 124–158, 2016.","ama":"Martin O, Krzywicki A, Zagórski MP. Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function. <i>Physics of Life Reviews</i>. 2016;17:124-158. doi:<a href=\"https://doi.org/10.1016/j.plrev.2016.06.002\">10.1016/j.plrev.2016.06.002</a>","mla":"Martin, Olivier, et al. “Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function.” <i>Physics of Life Reviews</i>, vol. 17, Elsevier, 2016, pp. 124–58, doi:<a href=\"https://doi.org/10.1016/j.plrev.2016.06.002\">10.1016/j.plrev.2016.06.002</a>."},"year":"2016","publication":"Physics of Life Reviews"},{"publisher":"Wiley-Blackwell","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pubrep_id":"1006","abstract":[{"lang":"eng","text":"Redirection of intercellular auxin fluxes via relocalization of the PIN-FORMED 3 (PIN3) and PIN7 auxin efflux carriers has been suggested to be necessary for the root gravitropic response. Cytokinins have also been proposed to play a role in controlling root gravitropism, but conclusive evidence is lacking. We present a detailed study of the dynamics of root bending early after gravistimulation, which revealed a delayed gravitropic response in transgenic lines with depleted endogenous cytokinins (Pro35S:AtCKX) and cytokinin signaling mutants. Pro35S:AtCKX lines, as well as a cytokinin receptor mutant ahk3, showed aberrations in the auxin response distribution in columella cells consistent with defects in the auxin transport machinery. Using in vivo real-time imaging of PIN3-GFP and PIN7-GFP in AtCKX3 overexpression and ahk3 backgrounds, we observed wild-type-like relocalization of PIN proteins in the columella early after gravistimulation, with gravity-induced relocalization of PIN7 faster than that of PIN3. Nonetheless, the cellular distribution of PIN3 and PIN7 and expression of PIN7 and the auxin influx carrier AUX1 was affected in AtCKX overexpression lines. Based on the retained cytokinin sensitivity in pin3 pin4 pin7 mutant, we propose the AUX1-mediated auxin transport rather than columella-located PIN proteins as a target of endogenous cytokinins in the control of root gravitropism."}],"oa_version":"Submitted Version","has_accepted_license":"1","doi":"10.1111/nph.14049","oa":1,"status":"public","article_processing_charge":"No","date_published":"2016-10-01T00:00:00Z","type":"journal_article","acknowledgement":"Funded by Ministry of Education, Youth and Sports Czech Republic. Grant Numbers: CEITEC 2020, LQ1601, LO1204, LH14104 and The European Research Council. Grant Number: ERC-2011-StG-20101109-PSDP and The Czech Science Foundation. Grant Numbers: GAP501/11/1150, GA13-40637S, GP14-30004P","ddc":["581"],"_id":"1372","department":[{"_id":"JiFr"}],"day":"01","title":"Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis","intvolume":"       212","file_date_updated":"2020-07-14T12:44:47Z","page":"497 - 509","author":[{"last_name":"Pernisová","first_name":"Markéta","full_name":"Pernisová, Markéta"},{"id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","last_name":"Prat","full_name":"Prat, Tomas"},{"full_name":"Grones, Peter","last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"last_name":"Haruštiaková","first_name":"Danka","full_name":"Haruštiaková, Danka"},{"last_name":"Matonohova","first_name":"Martina","full_name":"Matonohova, Martina"},{"first_name":"Lukáš","last_name":"Spíchal","full_name":"Spíchal, Lukáš"},{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí"},{"full_name":"Hejátko, Jan","last_name":"Hejátko","first_name":"Jan"}],"scopus_import":"1","issue":"2","file":[{"date_created":"2018-12-12T10:14:53Z","content_type":"application/pdf","file_id":"5108","checksum":"27fd841ceaf0403559d7048ef51500f9","access_level":"open_access","file_name":"IST-2018-1006-v1+1_Pernisova_NewPhytol_2016_peer_review.pdf","relation":"main_file","creator":"system","date_updated":"2020-07-14T12:44:47Z","file_size":972763}],"date_created":"2018-12-11T11:51:38Z","volume":212,"date_updated":"2025-09-22T07:36:11Z","isi":1,"month":"10","citation":{"short":"M. Pernisová, T. Prat, P. Grones, D. Haruštiaková, M. Matonohova, L. Spíchal, T. Nodzyński, J. Friml, J. Hejátko, New Phytologist 212 (2016) 497–509.","chicago":"Pernisová, Markéta, Tomas Prat, Peter Grones, Danka Haruštiaková, Martina Matonohova, Lukáš Spíchal, Tomasz Nodzyński, Jiří Friml, and Jan Hejátko. “Cytokinins Influence Root Gravitropism via Differential Regulation of Auxin Transporter Expression and Localization in Arabidopsis.” <i>New Phytologist</i>. Wiley-Blackwell, 2016. <a href=\"https://doi.org/10.1111/nph.14049\">https://doi.org/10.1111/nph.14049</a>.","ama":"Pernisová M, Prat T, Grones P, et al. Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. <i>New Phytologist</i>. 2016;212(2):497-509. doi:<a href=\"https://doi.org/10.1111/nph.14049\">10.1111/nph.14049</a>","ieee":"M. Pernisová <i>et al.</i>, “Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis,” <i>New Phytologist</i>, vol. 212, no. 2. Wiley-Blackwell, pp. 497–509, 2016.","ista":"Pernisová M, Prat T, Grones P, Haruštiaková D, Matonohova M, Spíchal L, Nodzyński T, Friml J, Hejátko J. 2016. Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. 212(2), 497–509.","mla":"Pernisová, Markéta, et al. “Cytokinins Influence Root Gravitropism via Differential Regulation of Auxin Transporter Expression and Localization in Arabidopsis.” <i>New Phytologist</i>, vol. 212, no. 2, Wiley-Blackwell, 2016, pp. 497–509, doi:<a href=\"https://doi.org/10.1111/nph.14049\">10.1111/nph.14049</a>.","apa":"Pernisová, M., Prat, T., Grones, P., Haruštiaková, D., Matonohova, M., Spíchal, L., … Hejátko, J. (2016). Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. <i>New Phytologist</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/nph.14049\">https://doi.org/10.1111/nph.14049</a>"},"year":"2016","publication":"New Phytologist","language":[{"iso":"eng"}],"publication_status":"published","publist_id":"5839","external_id":{"isi":["000383595700023"]}},{"date_updated":"2025-09-22T07:35:28Z","isi":1,"month":"07","scopus_import":"1","date_created":"2018-12-11T11:51:39Z","volume":17,"page":"168 - 171","author":[{"last_name":"Martin","first_name":"Olivier","full_name":"Martin, Olivier"},{"id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7896-7762","first_name":"Marcin P","last_name":"Zagórski","full_name":"Zagórski, Marcin P"}],"publication_status":"published","publist_id":"5838","external_id":{"isi":["000381544100034"]},"language":[{"iso":"eng"}],"year":"2016","publication":"Physics of Life Reviews","citation":{"apa":"Martin, O., &#38; Zagórski, M. P. (2016). Network architectures and operating principles. Reply to comments on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; <i>Physics of Life Reviews</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plrev.2016.06.006\">https://doi.org/10.1016/j.plrev.2016.06.006</a>","short":"O. Martin, M.P. Zagórski, Physics of Life Reviews 17 (2016) 168–171.","chicago":"Martin, Olivier, and Marcin P Zagórski. “Network Architectures and Operating Principles. Reply to Comments on &#38;quot;Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function&#38;quot;” <i>Physics of Life Reviews</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.plrev.2016.06.006\">https://doi.org/10.1016/j.plrev.2016.06.006</a>.","mla":"Martin, Olivier, and Marcin P. Zagórski. “Network Architectures and Operating Principles. Reply to Comments on &#38;quot;Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function&#38;quot;” <i>Physics of Life Reviews</i>, vol. 17, Elsevier, 2016, pp. 168–71, doi:<a href=\"https://doi.org/10.1016/j.plrev.2016.06.006\">10.1016/j.plrev.2016.06.006</a>.","ista":"Martin O, Zagórski MP. 2016. Network architectures and operating principles. Reply to comments on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; Physics of Life Reviews. 17, 168–171.","ieee":"O. Martin and M. P. Zagórski, “Network architectures and operating principles. Reply to comments on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot;,” <i>Physics of Life Reviews</i>, vol. 17. Elsevier, pp. 168–171, 2016.","ama":"Martin O, Zagórski MP. Network architectures and operating principles. Reply to comments on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; <i>Physics of Life Reviews</i>. 2016;17:168-171. doi:<a href=\"https://doi.org/10.1016/j.plrev.2016.06.006\">10.1016/j.plrev.2016.06.006</a>"},"oa":1,"main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-01531698","open_access":"1"}],"oa_version":"Preprint","doi":"10.1016/j.plrev.2016.06.006","corr_author":"1","publisher":"Elsevier","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","title":"Network architectures and operating principles. Reply to comments on &quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&quot;","intvolume":"        17","_id":"1373","department":[{"_id":"AnKi"}],"date_published":"2016-07-01T00:00:00Z","type":"journal_article","status":"public","article_processing_charge":"No"},{"status":"public","article_processing_charge":"No","type":"journal_article","date_published":"2016-05-03T00:00:00Z","department":[{"_id":"VlKo"}],"_id":"1377","title":"Total variation on a tree","day":"03","intvolume":"         9","ec_funded":1,"publisher":"Society for Industrial and Applied Mathematics ","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"We consider the problem of minimizing the continuous valued total variation subject to different unary terms on trees and propose fast direct algorithms based on dynamic programming to solve these problems. We treat both the convex and the nonconvex case and derive worst-case complexities that are equal to or better than existing methods. We show applications to total variation based two dimensional image processing and computer vision problems based on a Lagrangian decomposition approach. The resulting algorithms are very effcient, offer a high degree of parallelism, and come along with memory requirements which are only in the order of the number of image pixels."}],"main_file_link":[{"url":"http://arxiv.org/abs/1502.07770","open_access":"1"}],"oa_version":"Preprint","doi":"10.1137/15M1010257","oa":1,"citation":{"apa":"Kolmogorov, V., Pock, T., &#38; Rolinek, M. (2016). Total variation on a tree. <i>SIAM Journal on Imaging Sciences</i>. Society for Industrial and Applied Mathematics . <a href=\"https://doi.org/10.1137/15M1010257\">https://doi.org/10.1137/15M1010257</a>","ama":"Kolmogorov V, Pock T, Rolinek M. Total variation on a tree. <i>SIAM Journal on Imaging Sciences</i>. 2016;9(2):605-636. doi:<a href=\"https://doi.org/10.1137/15M1010257\">10.1137/15M1010257</a>","ista":"Kolmogorov V, Pock T, Rolinek M. 2016. Total variation on a tree. SIAM Journal on Imaging Sciences. 9(2), 605–636.","ieee":"V. Kolmogorov, T. Pock, and M. Rolinek, “Total variation on a tree,” <i>SIAM Journal on Imaging Sciences</i>, vol. 9, no. 2. Society for Industrial and Applied Mathematics , pp. 605–636, 2016.","mla":"Kolmogorov, Vladimir, et al. “Total Variation on a Tree.” <i>SIAM Journal on Imaging Sciences</i>, vol. 9, no. 2, Society for Industrial and Applied Mathematics , 2016, pp. 605–36, doi:<a href=\"https://doi.org/10.1137/15M1010257\">10.1137/15M1010257</a>.","short":"V. Kolmogorov, T. Pock, M. Rolinek, SIAM Journal on Imaging Sciences 9 (2016) 605–636.","chicago":"Kolmogorov, Vladimir, Thomas Pock, and Michal Rolinek. “Total Variation on a Tree.” <i>SIAM Journal on Imaging Sciences</i>. Society for Industrial and Applied Mathematics , 2016. <a href=\"https://doi.org/10.1137/15M1010257\">https://doi.org/10.1137/15M1010257</a>."},"year":"2016","publication":"SIAM Journal on Imaging Sciences","language":[{"iso":"eng"}],"publication_status":"published","publist_id":"5834","external_id":{"arxiv":["1502.07770"],"isi":["000385275400005"]},"page":"605 - 636","author":[{"last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"},{"last_name":"Pock","first_name":"Thomas","full_name":"Pock, Thomas"},{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","last_name":"Rolinek","full_name":"Rolinek, Michal"}],"date_created":"2018-12-11T11:51:40Z","project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"scopus_import":"1","issue":"2","volume":9,"isi":1,"month":"05","date_updated":"2025-09-22T07:34:48Z"},{"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","pubrep_id":"623","abstract":[{"lang":"eng","text":"We give a detailed and easily accessible proof of Gromov's Topological Overlap Theorem. Let X be a finite simplicial complex or, more generally, a finite polyhedral cell complex of dimension d. Informally, the theorem states that if X has sufficiently strong higher-dimensional expansion properties (which generalize edge expansion of graphs and are defined in terms of cellular cochains of X) then X has the following topological overlap property: for every continuous map X → ℝd there exists a point p ∈ ℝd whose preimage intersects a positive fraction μ &gt; 0 of the d-cells of X. More generally, the conclusion holds if ℝd is replaced by any d-dimensional piecewise-linear (PL) manifold M, with a constant μ that depends only on d and on the expansion properties of X, but not on M."}],"doi":"10.4230/LIPIcs.SoCG.2016.35","has_accepted_license":"1","oa_version":"Published Version","oa":1,"article_processing_charge":"No","status":"public","alternative_title":["LIPIcs"],"date_published":"2016-06-01T00:00:00Z","type":"conference","_id":"1378","ddc":["510"],"department":[{"_id":"UlWa"}],"intvolume":"        51","day":"01","title":"On expansion and topological overlap","author":[{"full_name":"Dotterrer, Dominic","last_name":"Dotterrer","first_name":"Dominic"},{"full_name":"Kaufman, Tali","first_name":"Tali","last_name":"Kaufman"},{"orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","last_name":"Wagner","full_name":"Wagner, Uli"}],"file_date_updated":"2020-07-14T12:44:47Z","page":"35.1 - 35.10","volume":51,"scopus_import":"1","file":[{"creator":"system","date_updated":"2020-07-14T12:44:47Z","file_size":536923,"date_created":"2018-12-12T10:08:38Z","content_type":"application/pdf","file_id":"4699","checksum":"cee65b0e722d50f9d1cc70c90ec1d59b","access_level":"open_access","file_name":"IST-2016-623-v1+1_LIPIcs-SoCG-2016-35.pdf","relation":"main_file"}],"project":[{"_id":"25FA3206-B435-11E9-9278-68D0E5697425","grant_number":"PP00P2_138948","name":"Embeddings in Higher Dimensions: Algorithms and Combinatorics"}],"date_created":"2018-12-11T11:51:41Z","date_updated":"2025-06-03T11:41:00Z","month":"06","conference":{"location":"Medford, MA, USA","start_date":"2016-06-14","end_date":"2016-06-17","name":"SoCG: Symposium on Computational Geometry"},"citation":{"apa":"Dotterrer, D., Kaufman, T., &#38; Wagner, U. (2016). On expansion and topological overlap (Vol. 51, p. 35.1-35.10). Presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.35\">https://doi.org/10.4230/LIPIcs.SoCG.2016.35</a>","chicago":"Dotterrer, Dominic, Tali Kaufman, and Uli Wagner. “On Expansion and Topological Overlap,” 51:35.1-35.10. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.35\">https://doi.org/10.4230/LIPIcs.SoCG.2016.35</a>.","short":"D. Dotterrer, T. Kaufman, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, p. 35.1-35.10.","ista":"Dotterrer D, Kaufman T, Wagner U. 2016. On expansion and topological overlap. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 35.1-35.10.","ama":"Dotterrer D, Kaufman T, Wagner U. On expansion and topological overlap. In: Vol 51. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016:35.1-35.10. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.35\">10.4230/LIPIcs.SoCG.2016.35</a>","ieee":"D. Dotterrer, T. Kaufman, and U. Wagner, “On expansion and topological overlap,” presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA, 2016, vol. 51, p. 35.1-35.10.","mla":"Dotterrer, Dominic, et al. <i>On Expansion and Topological Overlap</i>. Vol. 51, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, p. 35.1-35.10, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.35\">10.4230/LIPIcs.SoCG.2016.35</a>."},"related_material":{"record":[{"id":"742","status":"public","relation":"later_version"}]},"year":"2016","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"publist_id":"5833","publication_status":"published"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2016","related_material":{"record":[{"status":"public","id":"534","relation":"later_version"}]},"citation":{"short":"B. Burton, A.N. de Mesmay, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, p. 24.1-24.15.","chicago":"Burton, Benjamin, Arnaud N de Mesmay, and Uli Wagner. “Finding Non-Orientable Surfaces in 3-Manifolds,” 51:24.1-24.15. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.24\">https://doi.org/10.4230/LIPIcs.SoCG.2016.24</a>.","mla":"Burton, Benjamin, et al. <i>Finding Non-Orientable Surfaces in 3-Manifolds</i>. Vol. 51, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, p. 24.1-24.15, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.24\">10.4230/LIPIcs.SoCG.2016.24</a>.","ama":"Burton B, de Mesmay AN, Wagner U. Finding non-orientable surfaces in 3-manifolds. In: Vol 51. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016:24.1-24.15. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.24\">10.4230/LIPIcs.SoCG.2016.24</a>","ieee":"B. Burton, A. N. de Mesmay, and U. Wagner, “Finding non-orientable surfaces in 3-manifolds,” presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA, 2016, vol. 51, p. 24.1-24.15.","ista":"Burton B, de Mesmay AN, Wagner U. 2016. Finding non-orientable surfaces in 3-manifolds. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 24.1-24.15.","apa":"Burton, B., de Mesmay, A. N., &#38; Wagner, U. (2016). Finding non-orientable surfaces in 3-manifolds (Vol. 51, p. 24.1-24.15). Presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.24\">https://doi.org/10.4230/LIPIcs.SoCG.2016.24</a>"},"publication_status":"published","publist_id":"5832","language":[{"iso":"eng"}],"file":[{"file_size":574770,"date_updated":"2020-07-14T12:44:47Z","creator":"system","relation":"main_file","file_name":"IST-2016-622-v1+1_LIPIcs-SoCG-2016-24.pdf","access_level":"open_access","checksum":"f04248a61c24297cfabd30c5f8e0deb9","file_id":"4930","content_type":"application/pdf","date_created":"2018-12-12T10:12:12Z"}],"scopus_import":"1","date_created":"2018-12-11T11:51:41Z","volume":51,"page":"24.1 - 24.15","file_date_updated":"2020-07-14T12:44:47Z","author":[{"full_name":"Burton, Benjamin","first_name":"Benjamin","last_name":"Burton"},{"full_name":"De Mesmay, Arnaud N","last_name":"De Mesmay","id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87","first_name":"Arnaud N"},{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","last_name":"Wagner","full_name":"Wagner, Uli"}],"conference":{"name":"SoCG: Symposium on Computational Geometry","end_date":"2016-06-17","start_date":"2016-06-14","location":"Medford, MA, USA"},"date_updated":"2025-09-18T09:45:01Z","month":"06","alternative_title":["LIPIcs"],"date_published":"2016-06-01T00:00:00Z","type":"conference","status":"public","article_processing_charge":"No","day":"01","title":"Finding non-orientable surfaces in 3-manifolds","intvolume":"        51","_id":"1379","ddc":["510"],"department":[{"_id":"UlWa"}],"pubrep_id":"622","abstract":[{"text":"We investigate the complexity of finding an embedded non-orientable surface of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural question in low-dimensional topology, and as a first non-trivial instance of embeddability of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding to the relatively few hardness results that are currently known in 3-manifold topology. In addition, we show that the problem lies in NP when the Euler genus g is odd, and we give an explicit algorithm in this case.","lang":"eng"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"has_accepted_license":"1","oa_version":"Published Version","doi":"10.4230/LIPIcs.SoCG.2016.24"},{"type":"journal_article","date_published":"2016-06-01T00:00:00Z","article_processing_charge":"No","status":"public","intvolume":"        63","title":"On the complexity of the orbit problem","day":"01","department":[{"_id":"KrCh"}],"_id":"1380","abstract":[{"text":"We consider higher-dimensional versions of Kannan and Lipton's Orbit Problem - determining whether a target vector space V may be reached from a starting point x under repeated applications of a linear transformation A. Answering two questions posed by Kannan and Lipton in the 1980s, we show that when V has dimension one, this problem is solvable in polynomial time, and when V has dimension two or three, the problem is in NPRP.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1,"quality_controlled":"1","publisher":"ACM","oa":1,"article_number":"23","doi":"10.1145/2857050","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1303.2981"}],"oa_version":"Preprint","publication":"Journal of the ACM","year":"2016","citation":{"apa":"Chonev, V. K., Ouaknine, J., &#38; Worrell, J. (2016). On the complexity of the orbit problem. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/2857050\">https://doi.org/10.1145/2857050</a>","ama":"Chonev VK, Ouaknine J, Worrell J. On the complexity of the orbit problem. <i>Journal of the ACM</i>. 2016;63(3). doi:<a href=\"https://doi.org/10.1145/2857050\">10.1145/2857050</a>","ieee":"V. K. Chonev, J. Ouaknine, and J. Worrell, “On the complexity of the orbit problem,” <i>Journal of the ACM</i>, vol. 63, no. 3. ACM, 2016.","ista":"Chonev VK, Ouaknine J, Worrell J. 2016. On the complexity of the orbit problem. Journal of the ACM. 63(3), 23.","mla":"Chonev, Ventsislav K., et al. “On the Complexity of the Orbit Problem.” <i>Journal of the ACM</i>, vol. 63, no. 3, 23, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2857050\">10.1145/2857050</a>.","chicago":"Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On the Complexity of the Orbit Problem.” <i>Journal of the ACM</i>. ACM, 2016. <a href=\"https://doi.org/10.1145/2857050\">https://doi.org/10.1145/2857050</a>.","short":"V.K. Chonev, J. Ouaknine, J. Worrell, Journal of the ACM 63 (2016)."},"external_id":{"arxiv":["1303.2981"],"isi":["000382753300004"]},"publist_id":"5831","publication_status":"published","language":[{"iso":"eng"}],"volume":63,"date_created":"2018-12-11T11:51:41Z","scopus_import":"1","issue":"3","author":[{"full_name":"Chonev, Ventsislav K","first_name":"Ventsislav K","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Chonev"},{"first_name":"Joël","last_name":"Ouaknine","full_name":"Ouaknine, Joël"},{"full_name":"Worrell, James","first_name":"James","last_name":"Worrell"}],"isi":1,"month":"06","date_updated":"2025-09-22T07:33:47Z"},{"department":[{"_id":"UlWa"}],"ddc":["510"],"_id":"1381","intvolume":"        51","title":"Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range","day":"01","article_processing_charge":"No","status":"public","type":"conference","alternative_title":["LIPIcs"],"date_published":"2016-06-01T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2016.51","oa_version":"Published Version","has_accepted_license":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","corr_author":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","abstract":[{"text":"Motivated by Tverberg-type problems in topological combinatorics and by classical results about embeddings (maps without double points), we study the question whether a finite simplicial complex K can be mapped into double-struck Rd without higher-multiplicity intersections. We focus on conditions for the existence of almost r-embeddings, i.e., maps f : K → double-struck Rd such that f(σ1) ∩ ⋯ ∩ f(σr) = ∅ whenever σ1, ..., σr are pairwise disjoint simplices of K. Generalizing the classical Haefliger-Weber embeddability criterion, we show that a well-known necessary deleted product condition for the existence of almost r-embeddings is sufficient in a suitable r-metastable range of dimensions: If rd ≥ (r + 1) dim K + 3, then there exists an almost r-embedding K → double-struck Rd if and only if there exists an equivariant map (K)Δ r → Sr Sd(r-1)-1, where (K)Δ r is the deleted r-fold product of K, the target Sd(r-1)-1 is the sphere of dimension d(r - 1) - 1, and Sr is the symmetric group. This significantly extends one of the main results of our previous paper (which treated the special case where d = rk and dim K = (r - 1)k for some k ≥ 3), and settles an open question raised there.","lang":"eng"}],"pubrep_id":"621","language":[{"iso":"eng"}],"publist_id":"5830","publication_status":"published","citation":{"apa":"Mabillard, I., &#38; Wagner, U. (2016). Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range (Vol. 51, p. 51.1-51.12). Presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.51\">https://doi.org/10.4230/LIPIcs.SoCG.2016.51</a>","ista":"Mabillard I, Wagner U. 2016. Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 51.1-51.12.","ama":"Mabillard I, Wagner U. Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range. In: Vol 51. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016:51.1-51.12. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.51\">10.4230/LIPIcs.SoCG.2016.51</a>","ieee":"I. Mabillard and U. Wagner, “Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range,” presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA, 2016, vol. 51, p. 51.1-51.12.","mla":"Mabillard, Isaac, and Uli Wagner. <i>Eliminating Higher-Multiplicity Intersections, II. The Deleted Product Criterion in the r-Metastable Range</i>. Vol. 51, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, p. 51.1-51.12, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.51\">10.4230/LIPIcs.SoCG.2016.51</a>.","chicago":"Mabillard, Isaac, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections, II. The Deleted Product Criterion in the r-Metastable Range,” 51:51.1-51.12. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.51\">https://doi.org/10.4230/LIPIcs.SoCG.2016.51</a>.","short":"I. Mabillard, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, p. 51.1-51.12."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2016","month":"06","date_updated":"2025-06-03T11:41:20Z","conference":{"end_date":"2016-06-17","start_date":"2016-06-14","location":"Medford, MA, USA","name":"SoCG: Symposium on Computational Geometry"},"author":[{"id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","first_name":"Isaac","last_name":"Mabillard","full_name":"Mabillard, Isaac"},{"full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner"}],"file_date_updated":"2020-07-14T12:44:47Z","page":"51.1 - 51.12","volume":51,"date_created":"2018-12-11T11:51:41Z","scopus_import":"1","project":[{"name":"Embeddings in Higher Dimensions: Algorithms and Combinatorics","_id":"25FA3206-B435-11E9-9278-68D0E5697425","grant_number":"PP00P2_138948"}],"file":[{"file_name":"IST-2016-621-v1+1_LIPIcs-SoCG-2016-51.pdf","relation":"main_file","date_created":"2018-12-12T10:10:06Z","file_id":"4791","content_type":"application/pdf","checksum":"92c0c3735fe908f8ded6e484005cb3b1","access_level":"open_access","file_size":622969,"creator":"system","date_updated":"2020-07-14T12:44:47Z"}]},{"abstract":[{"text":"Background and aims Angiosperms display remarkable diversity in flower colour, implying that transitions between pigmentation phenotypes must have been common. Despite progress in understanding transitions between anthocyanin (blue, purple, pink or red) and unpigmented (white) flowers, little is known about the evolutionary patterns of flower-colour transitions in lineages with both yellow and anthocyanin-pigmented flowers. This study investigates the relative rates of evolutionary transitions between different combinations of yellow- and anthocyanin-pigmentation phenotypes in the tribe Antirrhineae. Methods We surveyed taxonomic literature for data on anthocyanin and yellow floral pigmentation for 369 species across the tribe. We then reconstructed the phylogeny of 169 taxa and used phylogenetic comparative methods to estimate transition rates among pigmentation phenotypes across the phylogeny. Key Results In contrast to previous studies we found a bias towards transitions involving a gain in pigmentation, although transitions to phenotypes with both anthocyanin and yellow taxa are nevertheless extremely rare. Despite the dominance of yellow and anthocyanin-pigmented taxa, transitions between these phenotypes are constrained to move through a white intermediate stage, whereas transitions to double-pigmentation are very rare. The most abundant transitions are between anthocyanin-pigmented and unpigmented flowers, and similarly the most abundant polymorphic taxa were those with anthocyanin-pigmented and unpigmented flowers. Conclusions Our findings show that pigment evolution is limited by the presence of other floral pigments. This interaction between anthocyanin and yellow pigments constrains the breadth of potential floral diversity observed in nature. In particular, they suggest that selection has repeatedly acted to promote the spread of single-pigmented phenotypes across the Antirrhineae phylogeny. Furthermore, the correlation between transition rates and polymorphism suggests that the forces causing and maintaining variance in the short term reflect evolutionary processes on longer time scales.","lang":"eng"}],"quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","publisher":"Oxford University Press","doi":"10.1093/aob/mcw043","oa_version":"None","date_published":"2016-06-01T00:00:00Z","type":"journal_article","article_processing_charge":"No","status":"public","intvolume":"       117","day":"01","title":"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae","_id":"1382","department":[{"_id":"NiBa"}],"acknowledgement":"We thank Melinda Pickup, Spencer Barrett, Nick Barton and four anonymous reviewers for helpful discussions on previous versions  of  this  manuscript.  We  also  thank  Jana  Porsche  for her efforts in tracking down the more obscure references.","volume":117,"scopus_import":"1","issue":"7","date_created":"2018-12-11T11:51:42Z","author":[{"last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","first_name":"Thomas","full_name":"Ellis, Thomas"},{"full_name":"Field, David","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field"}],"page":"1133 - 1140","date_updated":"2025-09-22T07:32:44Z","isi":1,"month":"06","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5550"}]},"publication":"Annals of Botany","year":"2016","citation":{"ieee":"T. Ellis and D. Field, “Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae,” <i>Annals of Botany</i>, vol. 117, no. 7. Oxford University Press, pp. 1133–1140, 2016.","ista":"Ellis T, Field D. 2016. Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. 117(7), 1133–1140.","ama":"Ellis T, Field D. Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. <i>Annals of Botany</i>. 2016;117(7):1133-1140. doi:<a href=\"https://doi.org/10.1093/aob/mcw043\">10.1093/aob/mcw043</a>","mla":"Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” <i>Annals of Botany</i>, vol. 117, no. 7, Oxford University Press, 2016, pp. 1133–40, doi:<a href=\"https://doi.org/10.1093/aob/mcw043\">10.1093/aob/mcw043</a>.","short":"T. Ellis, D. Field, Annals of Botany 117 (2016) 1133–1140.","chicago":"Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” <i>Annals of Botany</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/aob/mcw043\">https://doi.org/10.1093/aob/mcw043</a>.","apa":"Ellis, T., &#38; Field, D. (2016). Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. <i>Annals of Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/aob/mcw043\">https://doi.org/10.1093/aob/mcw043</a>"},"external_id":{"isi":["000379733800004"]},"publist_id":"5828","publication_status":"published","language":[{"iso":"eng"}]},{"date_published":"2016-07-05T00:00:00Z","type":"conference","status":"public","article_processing_charge":"No","day":"05","title":"On recurrent reachability for continuous linear dynamical systems","ec_funded":1,"_id":"1389","department":[{"_id":"KrCh"}],"abstract":[{"text":"The continuous evolution of a wide variety of systems, including continous-time Markov chains and linear hybrid automata, can be\r\ndescribed in terms of linear differential equations. In this paper we study the decision problem of whether the solution x(t) of a system of linear differential equations dx/dt = Ax reaches a target halfspace infinitely often. This recurrent reachability problem can\r\nequivalently be formulated as the following Infinite Zeros Problem: does a real-valued function f:R≥0 --&gt; R satisfying a given linear\r\ndifferential equation have infinitely many zeros? Our main decidability result is that if the differential equation has order at most 7, then the Infinite Zeros Problem is decidable. On the other hand, we show that a decision procedure for the Infinite Zeros Problem at order 9 (and above) would entail a major breakthrough in Diophantine Approximation, specifically an algorithm for computing the Lagrange constants of arbitrary real algebraic numbers to arbitrary precision.","lang":"eng"}],"publisher":"IEEE","arxiv":1,"quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1507.03632"}],"oa_version":"Preprint","doi":"10.1145/2933575.2934548","year":"2016","publication":"LICS '16","citation":{"mla":"Chonev, Ventsislav K., et al. “On Recurrent Reachability for Continuous Linear Dynamical Systems.” <i>LICS ’16</i>, IEEE, 2016, pp. 515–24, doi:<a href=\"https://doi.org/10.1145/2933575.2934548\">10.1145/2933575.2934548</a>.","ama":"Chonev VK, Ouaknine J, Worrell J. On recurrent reachability for continuous linear dynamical systems. In: <i>LICS ’16</i>. IEEE; 2016:515-524. doi:<a href=\"https://doi.org/10.1145/2933575.2934548\">10.1145/2933575.2934548</a>","ista":"Chonev VK, Ouaknine J, Worrell J. 2016. On recurrent reachability for continuous linear dynamical systems. LICS ’16. LICS: Logic in Computer Science, 515–524.","ieee":"V. K. Chonev, J. Ouaknine, and J. Worrell, “On recurrent reachability for continuous linear dynamical systems,” in <i>LICS ’16</i>, New York, NY, USA, 2016, pp. 515–524.","chicago":"Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On Recurrent Reachability for Continuous Linear Dynamical Systems.” In <i>LICS ’16</i>, 515–24. IEEE, 2016. <a href=\"https://doi.org/10.1145/2933575.2934548\">https://doi.org/10.1145/2933575.2934548</a>.","short":"V.K. Chonev, J. Ouaknine, J. Worrell, in:, LICS ’16, IEEE, 2016, pp. 515–524.","apa":"Chonev, V. K., Ouaknine, J., &#38; Worrell, J. (2016). On recurrent reachability for continuous linear dynamical systems. In <i>LICS ’16</i> (pp. 515–524). New York, NY, USA: IEEE. <a href=\"https://doi.org/10.1145/2933575.2934548\">https://doi.org/10.1145/2933575.2934548</a>"},"publication_status":"published","external_id":{"arxiv":["1507.03632"],"isi":["000387609200052"]},"publist_id":"5820","language":[{"iso":"eng"}],"project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"}],"scopus_import":"1","date_created":"2018-12-11T11:51:44Z","page":"515 - 524","author":[{"full_name":"Chonev, Ventsislav K","first_name":"Ventsislav K","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Chonev"},{"full_name":"Ouaknine, Joël","first_name":"Joël","last_name":"Ouaknine"},{"full_name":"Worrell, James","first_name":"James","last_name":"Worrell"}],"conference":{"name":"LICS: Logic in Computer Science","start_date":"2018-07-05","end_date":"2018-07-08","location":"New York, NY, USA"},"date_updated":"2025-09-22T07:31:08Z","isi":1,"month":"07"}]