[{"isi":1,"arxiv":1,"publication":"Discrete Applied Mathematics","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","project":[{"grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425","name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF"}],"oa":1,"day":"30","doi":"10.1016/j.dam.2018.12.025","date_published":"2019-04-30T00:00:00Z","intvolume":"       259","article_type":"original","publication_identifier":{"issn":["0166-218X"]},"year":"2019","title":"Thrackles: An improved upper bound","author":[{"orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","full_name":"Fulek, Radoslav","first_name":"Radoslav"},{"first_name":"János","full_name":"Pach, János","last_name":"Pach"}],"page":"266-231","related_material":{"record":[{"status":"public","id":"433","relation":"earlier_version"}]},"date_updated":"2026-04-16T09:48:11Z","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","oa_version":"Preprint","volume":259,"department":[{"_id":"UlWa"}],"publisher":"Elsevier","main_file_link":[{"url":"https://arxiv.org/abs/1708.08037","open_access":"1"}],"citation":{"short":"R. Fulek, J. Pach, Discrete Applied Mathematics 259 (2019) 266–231.","ama":"Fulek R, Pach J. Thrackles: An improved upper bound. <i>Discrete Applied Mathematics</i>. 2019;259(4):266-231. doi:<a href=\"https://doi.org/10.1016/j.dam.2018.12.025\">10.1016/j.dam.2018.12.025</a>","ieee":"R. Fulek and J. Pach, “Thrackles: An improved upper bound,” <i>Discrete Applied Mathematics</i>, vol. 259, no. 4. Elsevier, pp. 266–231, 2019.","apa":"Fulek, R., &#38; Pach, J. (2019). Thrackles: An improved upper bound. <i>Discrete Applied Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.dam.2018.12.025\">https://doi.org/10.1016/j.dam.2018.12.025</a>","chicago":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound.” <i>Discrete Applied Mathematics</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.dam.2018.12.025\">https://doi.org/10.1016/j.dam.2018.12.025</a>.","ista":"Fulek R, Pach J. 2019. Thrackles: An improved upper bound. Discrete Applied Mathematics. 259(4), 266–231.","mla":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound.” <i>Discrete Applied Mathematics</i>, vol. 259, no. 4, Elsevier, 2019, pp. 266–231, doi:<a href=\"https://doi.org/10.1016/j.dam.2018.12.025\">10.1016/j.dam.2018.12.025</a>."},"abstract":[{"lang":"eng","text":"A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is [Formula presented](n−1), and that this bound is best possible for infinitely many values of n."}],"type":"journal_article","quality_controlled":"1","_id":"5857","month":"04","scopus_import":"1","issue":"4","publication_status":"published","date_created":"2019-01-20T22:59:17Z","external_id":{"isi":["000466061100020"],"arxiv":["1708.08037"]}},{"oa_version":"Preprint","related_material":{"record":[{"id":"10035","relation":"dissertation_contains","status":"public"}]},"page":"317-346","date_updated":"2026-04-16T09:52:04Z","author":[{"id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","full_name":"Fuchsbauer, Georg","last_name":"Fuchsbauer","first_name":"Georg"},{"orcid":"0009-0006-6812-7317","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","last_name":"Kamath Hosdurg","full_name":"Kamath Hosdurg, Chethan","first_name":"Chethan"},{"full_name":"Klein, Karen","last_name":"Klein","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"}],"title":"Adaptively secure proxy re-encryption","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","intvolume":"     11443","date_published":"2019-04-06T00:00:00Z","day":"06","doi":"10.1007/978-3-030-17259-6_11","oa":1,"ec_funded":1,"year":"2019","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783030172589"]},"isi":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","project":[{"name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020"}],"date_created":"2019-05-13T08:13:46Z","publication_status":"published","external_id":{"isi":["001299215500011"]},"alternative_title":["LNCS"],"conference":{"end_date":"2019-04-17","start_date":"2019-04-14","location":"Beijing, China","name":"PKC: Public-Key Cryptograhy"},"_id":"6430","scopus_import":"1","month":"04","quality_controlled":"1","type":"conference","abstract":[{"lang":"eng","text":"A proxy re-encryption (PRE) scheme is a public-key encryption scheme that allows the holder of a key pk to derive a re-encryption key for any other key 𝑝𝑘′. This re-encryption key lets anyone transform ciphertexts under pk into ciphertexts under 𝑝𝑘′ without having to know the underlying message, while transformations from 𝑝𝑘′ to pk should not be possible (unidirectional). Security is defined in a multi-user setting against an adversary that gets the users’ public keys and can ask for re-encryption keys and can corrupt users by requesting their secret keys. Any ciphertext that the adversary cannot trivially decrypt given the obtained secret and re-encryption keys should be secure.\r\n\r\nAll existing security proofs for PRE only show selective security, where the adversary must first declare the users it wants to corrupt. This can be lifted to more meaningful adaptive security by guessing the set of corrupted users among the n users, which loses a factor exponential in  Open image in new window , rendering the result meaningless already for moderate Open image in new window .\r\n\r\nJafargholi et al. (CRYPTO’17) proposed a framework that in some cases allows to give adaptive security proofs for schemes which were previously only known to be selectively secure, while avoiding the exponential loss that results from guessing the adaptive choices made by an adversary. We apply their framework to PREs that satisfy some natural additional properties. Concretely, we give a more fine-grained reduction for several unidirectional PREs, proving adaptive security at a much smaller loss. The loss depends on the graph of users whose edges represent the re-encryption keys queried by the adversary. For trees and chains the loss is quasi-polynomial in the size and for general graphs it is exponential in their depth and indegree (instead of their size as for previous reductions). Fortunately, trees and low-depth graphs cover many, if not most, interesting applications.\r\n\r\nOur results apply e.g. to the bilinear-map based PRE schemes by Ateniese et al. (NDSS’05 and CT-RSA’09), Gentry’s FHE-based scheme (STOC’09) and the LWE-based scheme by Chandran et al. (PKC’14)."}],"citation":{"ama":"Fuchsbauer G, Kamath Hosdurg C, Klein K, Pietrzak KZ. Adaptively secure proxy re-encryption. In: Vol 11443. Springer Nature; 2019:317-346. doi:<a href=\"https://doi.org/10.1007/978-3-030-17259-6_11\">10.1007/978-3-030-17259-6_11</a>","ieee":"G. Fuchsbauer, C. Kamath Hosdurg, K. Klein, and K. Z. Pietrzak, “Adaptively secure proxy re-encryption,” presented at the PKC: Public-Key Cryptograhy, Beijing, China, 2019, vol. 11443, pp. 317–346.","apa":"Fuchsbauer, G., Kamath Hosdurg, C., Klein, K., &#38; Pietrzak, K. Z. (2019). Adaptively secure proxy re-encryption (Vol. 11443, pp. 317–346). Presented at the PKC: Public-Key Cryptograhy, Beijing, China: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-17259-6_11\">https://doi.org/10.1007/978-3-030-17259-6_11</a>","ista":"Fuchsbauer G, Kamath Hosdurg C, Klein K, Pietrzak KZ. 2019. Adaptively secure proxy re-encryption. PKC: Public-Key Cryptograhy, LNCS, vol. 11443, 317–346.","chicago":"Fuchsbauer, Georg, Chethan Kamath Hosdurg, Karen Klein, and Krzysztof Z Pietrzak. “Adaptively Secure Proxy Re-Encryption,” 11443:317–46. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-17259-6_11\">https://doi.org/10.1007/978-3-030-17259-6_11</a>.","mla":"Fuchsbauer, Georg, et al. <i>Adaptively Secure Proxy Re-Encryption</i>. Vol. 11443, Springer Nature, 2019, pp. 317–46, doi:<a href=\"https://doi.org/10.1007/978-3-030-17259-6_11\">10.1007/978-3-030-17259-6_11</a>.","short":"G. Fuchsbauer, C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, in:, Springer Nature, 2019, pp. 317–346."},"department":[{"_id":"KrPi"}],"volume":11443,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2018/426"}],"publisher":"Springer Nature"},{"publisher":"Springer","volume":58,"department":[{"_id":"JaMa"}],"citation":{"mla":"Erbar, Matthias, et al. “On the Geometry of Geodesics in Discrete Optimal Transport.” <i>Calculus of Variations and Partial Differential Equations</i>, vol. 58, no. 1, 19, Springer, 2019, doi:<a href=\"https://doi.org/10.1007/s00526-018-1456-1\">10.1007/s00526-018-1456-1</a>.","chicago":"Erbar, Matthias, Jan Maas, and Melchior Wirth. “On the Geometry of Geodesics in Discrete Optimal Transport.” <i>Calculus of Variations and Partial Differential Equations</i>. Springer, 2019. <a href=\"https://doi.org/10.1007/s00526-018-1456-1\">https://doi.org/10.1007/s00526-018-1456-1</a>.","ista":"Erbar M, Maas J, Wirth M. 2019. On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. 58(1), 19.","apa":"Erbar, M., Maas, J., &#38; Wirth, M. (2019). On the geometry of geodesics in discrete optimal transport. <i>Calculus of Variations and Partial Differential Equations</i>. Springer. <a href=\"https://doi.org/10.1007/s00526-018-1456-1\">https://doi.org/10.1007/s00526-018-1456-1</a>","ieee":"M. Erbar, J. Maas, and M. Wirth, “On the geometry of geodesics in discrete optimal transport,” <i>Calculus of Variations and Partial Differential Equations</i>, vol. 58, no. 1. Springer, 2019.","ama":"Erbar M, Maas J, Wirth M. On the geometry of geodesics in discrete optimal transport. <i>Calculus of Variations and Partial Differential Equations</i>. 2019;58(1). doi:<a href=\"https://doi.org/10.1007/s00526-018-1456-1\">10.1007/s00526-018-1456-1</a>","short":"M. Erbar, J. Maas, M. Wirth, Calculus of Variations and Partial Differential Equations 58 (2019)."},"abstract":[{"lang":"eng","text":"We consider the space of probability measures on a discrete set X, endowed with a dynamical optimal transport metric. Given two probability measures supported in a subset Y⊆X, it is natural to ask whether they can be connected by a constant speed geodesic with support in Y at all times. Our main result answers this question affirmatively, under a suitable geometric condition on Y introduced in this paper. The proof relies on an extension result for subsolutions to discrete Hamilton-Jacobi equations, which is of independent interest."}],"type":"journal_article","quality_controlled":"1","month":"02","issue":"1","scopus_import":"1","_id":"73","external_id":{"arxiv":["1805.06040"],"isi":["000452849400001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2018-12-11T11:44:29Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","license":"https://creativecommons.org/licenses/by/4.0/","project":[{"name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","call_identifier":"H2020"},{"grant_number":"F06504","name":"Taming Complexity in Partial Differential Systems","_id":"260482E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"ddc":["510"],"isi":1,"publication":"Calculus of Variations and Partial Differential Equations","arxiv":1,"article_number":"19","article_type":"original","publication_identifier":{"issn":["0944-2669"]},"year":"2019","ec_funded":1,"oa":1,"file":[{"file_name":"2018_Calculus_Erbar.pdf","date_created":"2019-01-28T15:37:11Z","creator":"dernst","file_size":645565,"access_level":"open_access","date_updated":"2020-07-14T12:47:55Z","file_id":"5895","checksum":"ba05ac2d69de4c58d2cd338b63512798","content_type":"application/pdf","relation":"main_file"}],"day":"01","doi":"10.1007/s00526-018-1456-1","date_published":"2019-02-01T00:00:00Z","intvolume":"        58","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:55Z","title":"On the geometry of geodesics in discrete optimal transport","author":[{"first_name":"Matthias","full_name":"Erbar, Matthias","last_name":"Erbar"},{"orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"last_name":"Wirth","full_name":"Wirth, Melchior","first_name":"Melchior"}],"date_updated":"2026-04-16T09:51:42Z","oa_version":"Published Version"},{"title":"Automatic time-unbounded reachability analysis of hybrid systems","author":[{"first_name":"Mirco","last_name":"Giacobbe","full_name":"Giacobbe, Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8180-0904"}],"page":"132","date_updated":"2026-04-16T09:55:03Z","related_material":{"record":[{"id":"647","relation":"part_of_dissertation","status":"public"},{"id":"631","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"140","status":"public"}]},"status":"public","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:43Z","has_accepted_license":"1","article_processing_charge":"No","oa_version":"Published Version","supervisor":[{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","ddc":["000"],"doi":"10.15479/AT:ISTA:6894","day":"30","file":[{"file_id":"6916","date_updated":"2020-07-14T12:47:43Z","relation":"main_file","checksum":"773beaf4a85dc2acc2c12b578fbe1965","content_type":"application/pdf","file_size":4100685,"creator":"mgiacobbe","file_name":"giacobbe_thesis.pdf","date_created":"2019-09-27T14:15:05Z","access_level":"open_access"},{"access_level":"closed","date_created":"2019-09-27T14:22:04Z","file_name":"giacobbe_thesis_src.tar.gz","creator":"mgiacobbe","file_size":7959732,"checksum":"97f1c3da71feefd27e6e625d32b4c75b","content_type":"application/gzip","relation":"source_file","date_updated":"2020-07-14T12:47:43Z","file_id":"6917"}],"oa":1,"date_published":"2019-09-30T00:00:00Z","degree_awarded":"PhD","year":"2019","publication_identifier":{"eissn":["2663-337X"]},"_id":"6894","month":"09","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2019-09-22T14:08:44Z","alternative_title":["ISTA Thesis"],"department":[{"_id":"ToHe"}],"publisher":"Institute of Science and Technology Austria","corr_author":"1","type":"dissertation","abstract":[{"text":"Hybrid automata combine finite automata and dynamical systems, and model the interaction of digital with physical systems. Formal analysis that can guarantee the safety of all behaviors or rigorously witness failures, while unsolvable in general, has been tackled algorithmically using, e.g., abstraction, bounded model-checking, assisted theorem proving.\r\nNevertheless, very few methods have addressed the time-unbounded reachability analysis of hybrid automata and, for current sound and automatic tools, scalability remains critical. We develop methods for the polyhedral abstraction of hybrid automata, which construct coarse overapproximations and tightens them incrementally, in a CEGAR fashion. We use template polyhedra, i.e., polyhedra whose facets are normal to a given set of directions.\r\nWhile, previously, directions were given by the user, we introduce (1) the first method\r\nfor computing template directions from spurious counterexamples, so as to generalize and\r\neliminate them. The method applies naturally to convex hybrid automata, i.e., hybrid\r\nautomata with (possibly non-linear) convex constraints on derivatives only, while for linear\r\nODE requires further abstraction. Specifically, we introduce (2) the conic abstractions,\r\nwhich, partitioning the state space into appropriate (possibly non-uniform) cones, divide\r\ncurvy trajectories into relatively straight sections, suitable for polyhedral abstractions.\r\nFinally, we introduce (3) space-time interpolation, which, combining interval arithmetic\r\nand template refinement, computes appropriate (possibly non-uniform) time partitioning\r\nand template directions along spurious trajectories, so as to eliminate them.\r\nWe obtain sound and automatic methods for the reachability analysis over dense\r\nand unbounded time of convex hybrid automata and hybrid automata with linear ODE.\r\nWe build prototype tools and compare—favorably—our methods against the respective\r\nstate-of-the-art tools, on several benchmarks.","lang":"eng"}],"citation":{"short":"M. Giacobbe, Automatic Time-Unbounded Reachability Analysis of Hybrid Systems, Institute of Science and Technology Austria, 2019.","mla":"Giacobbe, Mirco. <i>Automatic Time-Unbounded Reachability Analysis of Hybrid Systems</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6894\">10.15479/AT:ISTA:6894</a>.","ista":"Giacobbe M. 2019. Automatic time-unbounded reachability analysis of hybrid systems. Institute of Science and Technology Austria.","chicago":"Giacobbe, Mirco. “Automatic Time-Unbounded Reachability Analysis of Hybrid Systems.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6894\">https://doi.org/10.15479/AT:ISTA:6894</a>.","ieee":"M. Giacobbe, “Automatic time-unbounded reachability analysis of hybrid systems,” Institute of Science and Technology Austria, 2019.","apa":"Giacobbe, M. (2019). <i>Automatic time-unbounded reachability analysis of hybrid systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6894\">https://doi.org/10.15479/AT:ISTA:6894</a>","ama":"Giacobbe M. Automatic time-unbounded reachability analysis of hybrid systems. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6894\">10.15479/AT:ISTA:6894</a>"}},{"publication":"17th International Conference on Computational Methods in Systems Biology","isi":1,"project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211"},{"grant_number":"24573","name":"Design principles underlying genetic switch architecture","_id":"251EE76E-B435-11E9-9278-68D0E5697425"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.1007/978-3-030-31304-3_9","day":"17","intvolume":"     11773","date_published":"2019-09-17T00:00:00Z","year":"2019","publication_identifier":{"issn":["0302-9743"],"eisbn":["9783030313043"],"eissn":["1611-3349"],"isbn":["9783030313036"]},"title":"Transient memory in gene regulation","author":[{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C","first_name":"Calin C"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"id":"46613666-F248-11E8-B48F-1D18A9856A87","last_name":"Igler","full_name":"Igler, Claudia","orcid":"0000-0001-7777-546X","first_name":"Claudia"},{"last_name":"Petrov","full_name":"Petrov, Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9041-0905","first_name":"Tatjana"},{"first_name":"Ali","last_name":"Sezgin","full_name":"Sezgin, Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87"}],"page":"155-187","date_updated":"2026-04-16T10:26:49Z","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","oa_version":"None","volume":11773,"department":[{"_id":"CaGu"},{"_id":"ToHe"}],"publisher":"Springer Nature","type":"conference","abstract":[{"lang":"eng","text":"The expression of a gene is characterised by its transcription factors and the function processing them. If the transcription factors are not affected by gene products, the regulating function is often represented as a combinational logic circuit, where the outputs (product) are determined by current input values (transcription factors) only, and are hence independent on their relative arrival times. However, the simultaneous arrival of transcription factors (TFs) in genetic circuits is a strong assumption, given that the processes of transcription and translation of a gene into a protein introduce intrinsic time delays and that there is no global synchronisation among the arrival times of different molecular species at molecular targets.\r\n\r\nIn this paper, we construct an experimentally implementable genetic circuit with two inputs and a single output, such that, in presence of small delays in input arrival, the circuit exhibits qualitatively distinct observable phenotypes. In particular, these phenotypes are long lived transients: they all converge to a single value, but so slowly, that they seem stable for an extended time period, longer than typical experiment duration. We used rule-based language to prototype our circuit, and we implemented a search for finding the parameter combinations raising the phenotypes of interest.\r\n\r\nThe behaviour of our prototype circuit has wide implications. First, it suggests that GRNs can exploit event timing to create phenotypes. Second, it opens the possibility that GRNs are using event timing to react to stimuli and memorise events, without explicit feedback in regulation. From the modelling perspective, our prototype circuit demonstrates the critical importance of analysing the transient dynamics at the promoter binding sites of the DNA, before applying rapid equilibrium assumptions."}],"citation":{"ista":"Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. 2019. Transient memory in gene regulation. 17th International Conference on Computational Methods in Systems Biology. CMSB: Computational Methods in Systems Biology, LNCS, vol. 11773, 155–187.","chicago":"Guet, Calin C, Thomas A Henzinger, Claudia Igler, Tatjana Petrov, and Ali Sezgin. “Transient Memory in Gene Regulation.” In <i>17th International Conference on Computational Methods in Systems Biology</i>, 11773:155–87. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-31304-3_9\">https://doi.org/10.1007/978-3-030-31304-3_9</a>.","mla":"Guet, Calin C., et al. “Transient Memory in Gene Regulation.” <i>17th International Conference on Computational Methods in Systems Biology</i>, vol. 11773, Springer Nature, 2019, pp. 155–87, doi:<a href=\"https://doi.org/10.1007/978-3-030-31304-3_9\">10.1007/978-3-030-31304-3_9</a>.","apa":"Guet, C. C., Henzinger, T. A., Igler, C., Petrov, T., &#38; Sezgin, A. (2019). Transient memory in gene regulation. In <i>17th International Conference on Computational Methods in Systems Biology</i> (Vol. 11773, pp. 155–187). Trieste, Italy: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-31304-3_9\">https://doi.org/10.1007/978-3-030-31304-3_9</a>","ieee":"C. C. Guet, T. A. Henzinger, C. Igler, T. Petrov, and A. Sezgin, “Transient memory in gene regulation,” in <i>17th International Conference on Computational Methods in Systems Biology</i>, Trieste, Italy, 2019, vol. 11773, pp. 155–187.","ama":"Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. Transient memory in gene regulation. In: <i>17th International Conference on Computational Methods in Systems Biology</i>. Vol 11773. Springer Nature; 2019:155-187. doi:<a href=\"https://doi.org/10.1007/978-3-030-31304-3_9\">10.1007/978-3-030-31304-3_9</a>","short":"C.C. Guet, T.A. Henzinger, C. Igler, T. Petrov, A. Sezgin, in:, 17th International Conference on Computational Methods in Systems Biology, Springer Nature, 2019, pp. 155–187."},"quality_controlled":"1","_id":"7147","month":"09","scopus_import":"1","publication_status":"published","date_created":"2019-12-04T16:07:50Z","conference":{"start_date":"2019-09-18","name":"CMSB: Computational Methods in Systems Biology","location":"Trieste, Italy","end_date":"2019-09-20"},"alternative_title":["LNCS"],"external_id":{"isi":["000557875100009"]}},{"publication":"Evo-Devo: Non-model species in cell and developmental biology","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ddc":["570"],"day":"10","doi":"10.1007/978-3-030-23459-1_6","oa":1,"file":[{"access_level":"open_access","date_created":"2020-05-14T10:09:30Z","file_name":"2019_RESULTS_McDougall.pdf","file_size":19317348,"creator":"dernst","relation":"main_file","checksum":"7f43e1e3706d15061475c5c57efc2786","content_type":"application/pdf","file_id":"7829","date_updated":"2020-07-14T12:47:46Z"}],"intvolume":"        68","date_published":"2019-10-10T00:00:00Z","publication_identifier":{"isbn":["9783030234584"],"eissn":["1861-0412"],"eisbn":["9783030234591"],"issn":["0080-1844"]},"year":"2019","author":[{"first_name":"Alex","last_name":"McDougall","full_name":"McDougall, Alex"},{"first_name":"Janet","last_name":"Chenevert","full_name":"Chenevert, Janet"},{"first_name":"Benoit G","last_name":"Godard","full_name":"Godard, Benoit G","id":"33280250-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Remi","full_name":"Dumollard, Remi","last_name":"Dumollard"}],"title":"Emergence of embryo shape during cleavage divisions","page":"127-154","date_updated":"2026-04-16T10:26:18Z","language":[{"iso":"eng"}],"status":"public","file_date_updated":"2020-07-14T12:47:46Z","article_processing_charge":"No","has_accepted_license":"1","editor":[{"first_name":"Waclaw","last_name":"Tworzydlo","full_name":"Tworzydlo, Waclaw"},{"first_name":"Szczepan M.","full_name":"Bilinski, Szczepan M.","last_name":"Bilinski"}],"oa_version":"Submitted Version","volume":68,"department":[{"_id":"CaHe"}],"publisher":"Springer Nature","pmid":1,"abstract":[{"text":"Cells are arranged into species-specific patterns during early embryogenesis. Such cell division patterns are important since they often reflect the distribution of localized cortical factors from eggs/fertilized eggs to specific cells as well as the emergence of organismal form. However, it has proven difficult to reveal the mechanisms that underlie the emergence of cell positioning patterns that underlie embryonic shape, likely because a systems-level approach is required that integrates cell biological, genetic, developmental, and mechanical parameters. The choice of organism to address such questions is also important. Because ascidians display the most extreme form of invariant cleavage pattern among the metazoans, we have been analyzing the cell biological mechanisms that underpin three aspects of cell division (unequal cell division (UCD), oriented cell division (OCD), and asynchronous cell cycles) which affect the overall shape of the blastula-stage ascidian embryo composed of 64 cells. In ascidians, UCD creates two small cells at the 16-cell stage that in turn undergo two further successive rounds of UCD. Starting at the 16-cell stage, the cell cycle becomes asynchronous, whereby the vegetal half divides before the animal half, thus creating 24-, 32-, 44-, and then 64-cell stages. Perturbing either UCD or the alternate cell division rhythm perturbs cell position. We propose that dynamic cell shape changes propagate throughout the embryo via cell-cell contacts to create the ascidian-specific invariant cleavage pattern.","lang":"eng"}],"type":"book_chapter","citation":{"short":"A. McDougall, J. Chenevert, B.G. Godard, R. Dumollard, in:, W. Tworzydlo, S.M. Bilinski (Eds.), Evo-Devo: Non-Model Species in Cell and Developmental Biology, Springer Nature, 2019, pp. 127–154.","ista":"McDougall A, Chenevert J, Godard BG, Dumollard R. 2019.Emergence of embryo shape during cleavage divisions. In: Evo-Devo: Non-model species in cell and developmental biology. RESULTS, vol. 68, 127–154.","chicago":"McDougall, Alex, Janet Chenevert, Benoit G Godard, and Remi Dumollard. “Emergence of Embryo Shape during Cleavage Divisions.” In <i>Evo-Devo: Non-Model Species in Cell and Developmental Biology</i>, edited by Waclaw Tworzydlo and Szczepan M. Bilinski, 68:127–54. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-23459-1_6\">https://doi.org/10.1007/978-3-030-23459-1_6</a>.","mla":"McDougall, Alex, et al. “Emergence of Embryo Shape during Cleavage Divisions.” <i>Evo-Devo: Non-Model Species in Cell and Developmental Biology</i>, edited by Waclaw Tworzydlo and Szczepan M. Bilinski, vol. 68, Springer Nature, 2019, pp. 127–54, doi:<a href=\"https://doi.org/10.1007/978-3-030-23459-1_6\">10.1007/978-3-030-23459-1_6</a>.","ama":"McDougall A, Chenevert J, Godard BG, Dumollard R. Emergence of embryo shape during cleavage divisions. In: Tworzydlo W, Bilinski SM, eds. <i>Evo-Devo: Non-Model Species in Cell and Developmental Biology</i>. Vol 68. Springer Nature; 2019:127-154. doi:<a href=\"https://doi.org/10.1007/978-3-030-23459-1_6\">10.1007/978-3-030-23459-1_6</a>","ieee":"A. McDougall, J. Chenevert, B. G. Godard, and R. Dumollard, “Emergence of embryo shape during cleavage divisions,” in <i>Evo-Devo: Non-model species in cell and developmental biology</i>, vol. 68, W. Tworzydlo and S. M. Bilinski, Eds. Springer Nature, 2019, pp. 127–154.","apa":"McDougall, A., Chenevert, J., Godard, B. G., &#38; Dumollard, R. (2019). Emergence of embryo shape during cleavage divisions. In W. Tworzydlo &#38; S. M. Bilinski (Eds.), <i>Evo-Devo: Non-model species in cell and developmental biology</i> (Vol. 68, pp. 127–154). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-23459-1_6\">https://doi.org/10.1007/978-3-030-23459-1_6</a>"},"quality_controlled":"1","_id":"6987","month":"10","scopus_import":"1","publication_status":"published","date_created":"2019-11-04T16:20:19Z","external_id":{"pmid":["31598855"]},"alternative_title":["RESULTS"]},{"page":"277-291","date_updated":"2026-04-16T10:27:47Z","author":[{"full_name":"Abusalah, Hamza M","last_name":"Abusalah","id":"40297222-F248-11E8-B48F-1D18A9856A87","first_name":"Hamza M"},{"first_name":"Chethan","orcid":"0009-0006-6812-7317","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","full_name":"Kamath Hosdurg, Chethan","last_name":"Kamath Hosdurg"},{"id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","last_name":"Klein","full_name":"Klein, Karen","first_name":"Karen"},{"last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z"},{"full_name":"Walter, Michael","last_name":"Walter","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3186-2482","first_name":"Michael"}],"title":"Reversible proofs of sequential work","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","oa_version":"Submitted Version","isi":1,"publication":"Advances in Cryptology – EUROCRYPT 2019","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","project":[{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"date_published":"2019-04-24T00:00:00Z","intvolume":"     11477","oa":1,"doi":"10.1007/978-3-030-17656-3_10","day":"24","year":"2019","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"eisbn":["9783030176563"],"isbn":["9783030176556"]},"ec_funded":1,"_id":"7411","scopus_import":"1","month":"04","date_created":"2020-01-30T09:26:14Z","publication_status":"published","external_id":{"isi":["000483516200010"]},"alternative_title":["LNCS"],"conference":{"location":"Darmstadt, Germany","name":"EUROCRYPT: International Conference on the Theory and Applications of Cryptographic Techniques","start_date":"2019-05-19","end_date":"2019-05-23"},"department":[{"_id":"KrPi"}],"volume":11477,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/252"}],"publisher":"Springer International Publishing","quality_controlled":"1","citation":{"mla":"Abusalah, Hamza M., et al. “Reversible Proofs of Sequential Work.” <i>Advances in Cryptology – EUROCRYPT 2019</i>, vol. 11477, Springer International Publishing, 2019, pp. 277–91, doi:<a href=\"https://doi.org/10.1007/978-3-030-17656-3_10\">10.1007/978-3-030-17656-3_10</a>.","chicago":"Abusalah, Hamza M, Chethan Kamath Hosdurg, Karen Klein, Krzysztof Z Pietrzak, and Michael Walter. “Reversible Proofs of Sequential Work.” In <i>Advances in Cryptology – EUROCRYPT 2019</i>, 11477:277–91. Springer International Publishing, 2019. <a href=\"https://doi.org/10.1007/978-3-030-17656-3_10\">https://doi.org/10.1007/978-3-030-17656-3_10</a>.","ista":"Abusalah HM, Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. 2019. Reversible proofs of sequential work. Advances in Cryptology – EUROCRYPT 2019. EUROCRYPT: International Conference on the Theory and Applications of Cryptographic Techniques, LNCS, vol. 11477, 277–291.","apa":"Abusalah, H. M., Kamath Hosdurg, C., Klein, K., Pietrzak, K. Z., &#38; Walter, M. (2019). Reversible proofs of sequential work. In <i>Advances in Cryptology – EUROCRYPT 2019</i> (Vol. 11477, pp. 277–291). Darmstadt, Germany: Springer International Publishing. <a href=\"https://doi.org/10.1007/978-3-030-17656-3_10\">https://doi.org/10.1007/978-3-030-17656-3_10</a>","ieee":"H. M. Abusalah, C. Kamath Hosdurg, K. Klein, K. Z. Pietrzak, and M. Walter, “Reversible proofs of sequential work,” in <i>Advances in Cryptology – EUROCRYPT 2019</i>, Darmstadt, Germany, 2019, vol. 11477, pp. 277–291.","ama":"Abusalah HM, Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. Reversible proofs of sequential work. In: <i>Advances in Cryptology – EUROCRYPT 2019</i>. Vol 11477. Springer International Publishing; 2019:277-291. doi:<a href=\"https://doi.org/10.1007/978-3-030-17656-3_10\">10.1007/978-3-030-17656-3_10</a>","short":"H.M. Abusalah, C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, M. Walter, in:, Advances in Cryptology – EUROCRYPT 2019, Springer International Publishing, 2019, pp. 277–291."},"type":"conference","abstract":[{"lang":"eng","text":"Proofs of sequential work (PoSW) are proof systems where a prover, upon receiving a statement χ and a time parameter T computes a proof ϕ(χ,T) which is efficiently and publicly verifiable. The proof can be computed in T sequential steps, but not much less, even by a malicious party having large parallelism. A PoSW thus serves as a proof that T units of time have passed since χ\r\n\r\nwas received.\r\n\r\nPoSW were introduced by Mahmoody, Moran and Vadhan [MMV11], a simple and practical construction was only recently proposed by Cohen and Pietrzak [CP18].\r\n\r\nIn this work we construct a new simple PoSW in the random permutation model which is almost as simple and efficient as [CP18] but conceptually very different. Whereas the structure underlying [CP18] is a hash tree, our construction is based on skip lists and has the interesting property that computing the PoSW is a reversible computation.\r\nThe fact that the construction is reversible can potentially be used for new applications like constructing proofs of replication. We also show how to “embed” the sloth function of Lenstra and Weselowski [LW17] into our PoSW to get a PoSW where one additionally can verify correctness of the output much more efficiently than recomputing it (though recent constructions of “verifiable delay functions” subsume most of the applications this construction was aiming at)."}]},{"oa_version":"None","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","author":[{"first_name":"Dejan","full_name":"Ničković, Dejan","last_name":"Ničković"},{"last_name":"Qin","full_name":"Qin, Xin","first_name":"Xin"},{"orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","full_name":"Ferrere, Thomas","first_name":"Thomas"},{"last_name":"Mateis","full_name":"Mateis, Cristinel","first_name":"Cristinel"},{"full_name":"Deshmukh, Jyotirmoy","last_name":"Deshmukh","first_name":"Jyotirmoy"}],"title":"Shape expressions for specifying and extracting signal features","page":"292-309","date_updated":"2026-04-16T10:27:14Z","year":"2019","publication_identifier":{"eisbn":["9783030320799"],"isbn":["9783030320782"],"issn":["0302-9743"]},"doi":"10.1007/978-3-030-32079-9_17","day":"01","intvolume":"     11757","date_published":"2019-10-01T00:00:00Z","project":[{"call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication":"19th International Conference on Runtime Verification","isi":1,"conference":{"name":"RV: Runtime Verification","location":"Porto, Portugal","start_date":"2019-10-08","end_date":"2019-10-11"},"alternative_title":["LNCS"],"external_id":{"isi":["000570006300017"]},"publication_status":"published","date_created":"2019-12-09T08:47:55Z","month":"10","scopus_import":"1","_id":"7159","abstract":[{"text":"Cyber-physical systems (CPS) and the Internet-of-Things (IoT) result in a tremendous amount of generated, measured and recorded time-series data. Extracting temporal segments that encode patterns with useful information out of these huge amounts of data is an extremely difficult problem. We propose shape expressions as a declarative formalism for specifying, querying and extracting sophisticated temporal patterns from possibly noisy data. Shape expressions are regular expressions with arbitrary (linear, exponential, sinusoidal, etc.) shapes with parameters as atomic predicates and additional constraints on these parameters. We equip shape expressions with a novel noisy semantics that combines regular expression matching semantics with statistical regression. We characterize essential properties of the formalism and propose an efficient approximate shape expression matching procedure. We demonstrate the wide applicability of this technique on two case studies. ","lang":"eng"}],"type":"conference","citation":{"mla":"Ničković, Dejan, et al. “Shape Expressions for Specifying and Extracting Signal Features.” <i>19th International Conference on Runtime Verification</i>, vol. 11757, Springer Nature, 2019, pp. 292–309, doi:<a href=\"https://doi.org/10.1007/978-3-030-32079-9_17\">10.1007/978-3-030-32079-9_17</a>.","ista":"Ničković D, Qin X, Ferrere T, Mateis C, Deshmukh J. 2019. Shape expressions for specifying and extracting signal features. 19th International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 11757, 292–309.","chicago":"Ničković, Dejan, Xin Qin, Thomas Ferrere, Cristinel Mateis, and Jyotirmoy Deshmukh. “Shape Expressions for Specifying and Extracting Signal Features.” In <i>19th International Conference on Runtime Verification</i>, 11757:292–309. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-32079-9_17\">https://doi.org/10.1007/978-3-030-32079-9_17</a>.","apa":"Ničković, D., Qin, X., Ferrere, T., Mateis, C., &#38; Deshmukh, J. (2019). Shape expressions for specifying and extracting signal features. In <i>19th International Conference on Runtime Verification</i> (Vol. 11757, pp. 292–309). Porto, Portugal: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-32079-9_17\">https://doi.org/10.1007/978-3-030-32079-9_17</a>","ama":"Ničković D, Qin X, Ferrere T, Mateis C, Deshmukh J. Shape expressions for specifying and extracting signal features. In: <i>19th International Conference on Runtime Verification</i>. Vol 11757. Springer Nature; 2019:292-309. doi:<a href=\"https://doi.org/10.1007/978-3-030-32079-9_17\">10.1007/978-3-030-32079-9_17</a>","ieee":"D. Ničković, X. Qin, T. Ferrere, C. Mateis, and J. Deshmukh, “Shape expressions for specifying and extracting signal features,” in <i>19th International Conference on Runtime Verification</i>, Porto, Portugal, 2019, vol. 11757, pp. 292–309.","short":"D. Ničković, X. Qin, T. Ferrere, C. Mateis, J. Deshmukh, in:, 19th International Conference on Runtime Verification, Springer Nature, 2019, pp. 292–309."},"quality_controlled":"1","publisher":"Springer Nature","volume":11757,"department":[{"_id":"ToHe"}]},{"related_material":{"record":[{"id":"6774","relation":"part_of_dissertation","status":"public"}]},"page":"104","date_updated":"2026-04-16T12:20:40Z","author":[{"first_name":"Stephan Y","last_name":"Zhechev","full_name":"Zhechev, Stephan Y","id":"3AA52972-F248-11E8-B48F-1D18A9856A87"}],"title":"Algorithmic aspects of homotopy theory and embeddability","file_date_updated":"2020-07-14T12:47:37Z","article_processing_charge":"No","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"oa_version":"Published Version","supervisor":[{"first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","last_name":"Wagner"}],"ddc":["514"],"OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2019-08-08T00:00:00Z","doi":"10.15479/AT:ISTA:6681","day":"08","file":[{"content_type":"application/pdf","checksum":"3231e7cbfca3b5687366f84f0a57a0c0","relation":"main_file","date_updated":"2020-07-14T12:47:37Z","file_id":"6771","access_level":"open_access","creator":"szhechev","file_size":1464227,"date_created":"2019-08-07T13:02:50Z","file_name":"Stephan_Zhechev_thesis.pdf"},{"relation":"source_file","content_type":"application/octet-stream","checksum":"85d65eb27b4377a9e332ee37a70f08b6","file_id":"6772","date_updated":"2020-07-14T12:47:37Z","access_level":"closed","date_created":"2019-08-07T13:03:22Z","file_name":"Stephan_Zhechev_thesis.tex","file_size":303988,"creator":"szhechev"},{"access_level":"closed","file_name":"supplementary_material.zip","date_created":"2019-08-07T13:03:34Z","file_size":1087004,"creator":"szhechev","relation":"supplementary_material","checksum":"86b374d264ca2dd53e712728e253ee75","content_type":"application/zip","file_id":"6773","date_updated":"2020-07-14T12:47:37Z"}],"oa":1,"degree_awarded":"PhD","year":"2019","publication_identifier":{"issn":["2663-337X"]},"_id":"6681","month":"08","date_created":"2019-07-26T11:14:34Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"alternative_title":["ISTA Thesis"],"department":[{"_id":"UlWa"}],"corr_author":"1","publisher":"Institute of Science and Technology Austria","type":"dissertation","abstract":[{"text":"The first part of the thesis considers the computational aspects of the homotopy groups πd(X) of a topological space X. It is well known that there is no algorithm to decide whether the fundamental group π1(X) of a given finite simplicial complex X is trivial. On the other hand, there are several algorithms that, given a finite simplicial complex X that is simply connected (i.e., with π1(X) trivial), compute the higher homotopy group πd(X) for any given d ≥ 2.\r\nHowever, these algorithms come with a caveat: They compute the isomorphism type of πd(X), d ≥ 2 as an abstract finitely generated abelian group given by generators and relations, but they work with very implicit representations of the elements of πd(X). We present an algorithm that, given a simply connected space X, computes πd(X) and represents its elements as simplicial maps from suitable triangulations of the d-sphere Sd to X. For fixed d, the algorithm runs in time exponential in size(X), the number of simplices of X. Moreover, we prove that this is optimal: For every fixed d ≥ 2,\r\nwe construct a family of simply connected spaces X such that for any simplicial map representing a generator of πd(X), the size of the triangulation of S d on which the map is defined, is exponential in size(X).\r\nIn the second part of the thesis, we prove that the following question is algorithmically undecidable for d < ⌊3(k+1)/2⌋, k ≥ 5 and (k, d) ̸= (5, 7), which covers essentially everything outside the meta-stable range: Given a finite simplicial complex K of dimension k, decide whether there exists a piecewise-linear (i.e., linear on an arbitrarily fine subdivision of K) embedding f : K ↪→ Rd of K into a d-dimensional Euclidean space.","lang":"eng"}],"citation":{"short":"S.Y. Zhechev, Algorithmic Aspects of Homotopy Theory and Embeddability, Institute of Science and Technology Austria, 2019.","ama":"Zhechev SY. Algorithmic aspects of homotopy theory and embeddability. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6681\">10.15479/AT:ISTA:6681</a>","ieee":"S. Y. Zhechev, “Algorithmic aspects of homotopy theory and embeddability,” Institute of Science and Technology Austria, 2019.","apa":"Zhechev, S. Y. (2019). <i>Algorithmic aspects of homotopy theory and embeddability</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6681\">https://doi.org/10.15479/AT:ISTA:6681</a>","mla":"Zhechev, Stephan Y. <i>Algorithmic Aspects of Homotopy Theory and Embeddability</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6681\">10.15479/AT:ISTA:6681</a>.","chicago":"Zhechev, Stephan Y. “Algorithmic Aspects of Homotopy Theory and Embeddability.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6681\">https://doi.org/10.15479/AT:ISTA:6681</a>.","ista":"Zhechev SY. 2019. Algorithmic aspects of homotopy theory and embeddability. Institute of Science and Technology Austria."}},{"quality_controlled":"1","date_published":"2019-06-01T00:00:00Z","extern":"1","day":"01","doi":"10.1364/cleo_si.2019.sf1n.1","type":"conference","abstract":[{"text":"We demonstrate an integrated silicon photonic Markov Chain Monte Carlo sampler capable of high-probability convergence to the ground state of various 4-spin Ising graphs. Robustness to getting trapped in local minima is enhanced by experimental system noise.","lang":"eng"}],"citation":{"short":"C. Roques-Carmes, M. Prabhu, Y. Shen, N. Harris, L. Jing, J. Carolan, R. Hamerly, T. Baehr-Jones, M. Hochberg, V. Ceperic, J.D. Joannopoulos, D. Englund, M. Soljacic, in:, Conference on Lasers and Electro-Optics, Optica Publishing Group, 2019.","ieee":"C. Roques-Carmes <i>et al.</i>, “Integrated nanophotonic ising sampler,” in <i>Conference on Lasers and Electro-Optics</i>, San Jose, CA, United States, 2019.","ama":"Roques-Carmes C, Prabhu M, Shen Y, et al. Integrated nanophotonic ising sampler. In: <i>Conference on Lasers and Electro-Optics</i>. Optica Publishing Group; 2019. doi:<a href=\"https://doi.org/10.1364/cleo_si.2019.sf1n.1\">10.1364/cleo_si.2019.sf1n.1</a>","apa":"Roques-Carmes, C., Prabhu, M., Shen, Y., Harris, N., Jing, L., Carolan, J., … Soljacic, M. (2019). Integrated nanophotonic ising sampler. In <i>Conference on Lasers and Electro-Optics</i>. San Jose, CA, United States: Optica Publishing Group. <a href=\"https://doi.org/10.1364/cleo_si.2019.sf1n.1\">https://doi.org/10.1364/cleo_si.2019.sf1n.1</a>","chicago":"Roques-Carmes, Charles, Mihika Prabhu, Yichen Shen, Nicholas Harris, Li Jing, Jacques Carolan, Ryan Hamerly, et al. “Integrated Nanophotonic Ising Sampler.” In <i>Conference on Lasers and Electro-Optics</i>. Optica Publishing Group, 2019. <a href=\"https://doi.org/10.1364/cleo_si.2019.sf1n.1\">https://doi.org/10.1364/cleo_si.2019.sf1n.1</a>.","ista":"Roques-Carmes C, Prabhu M, Shen Y, Harris N, Jing L, Carolan J, Hamerly R, Baehr-Jones T, Hochberg M, Ceperic V, Joannopoulos JD, Englund D, Soljacic M. 2019. Integrated nanophotonic ising sampler. Conference on Lasers and Electro-Optics. CLEO: Science and Innovations, SF1N.1.","mla":"Roques-Carmes, Charles, et al. “Integrated Nanophotonic Ising Sampler.” <i>Conference on Lasers and Electro-Optics</i>, SF1N.1, Optica Publishing Group, 2019, doi:<a href=\"https://doi.org/10.1364/cleo_si.2019.sf1n.1\">10.1364/cleo_si.2019.sf1n.1</a>."},"publication_identifier":{"issnl":["2162-2701"],"eisbn":["9781943580576"]},"year":"2019","article_number":"SF1N.1","publication":"Conference on Lasers and Electro-Optics","OA_type":"closed access","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Optica Publishing Group","date_created":"2026-03-30T12:22:48Z","oa_version":"None","publication_status":"published","conference":{"name":"CLEO: Science and Innovations","location":"San Jose, CA, United States","start_date":"2019-05-05","end_date":"2019-05-10"},"date_updated":"2026-05-05T06:52:44Z","_id":"21627","author":[{"full_name":"Roques-Carmes, Charles","last_name":"Roques-Carmes","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","first_name":"Charles"},{"last_name":"Prabhu","full_name":"Prabhu, Mihika","first_name":"Mihika"},{"first_name":"Yichen","full_name":"Shen, Yichen","last_name":"Shen"},{"first_name":"Nicholas","full_name":"Harris, Nicholas","last_name":"Harris"},{"full_name":"Jing, Li","last_name":"Jing","first_name":"Li"},{"first_name":"Jacques","last_name":"Carolan","full_name":"Carolan, Jacques"},{"last_name":"Hamerly","full_name":"Hamerly, Ryan","first_name":"Ryan"},{"first_name":"Tom","full_name":"Baehr-Jones, Tom","last_name":"Baehr-Jones"},{"first_name":"Michael","full_name":"Hochberg, Michael","last_name":"Hochberg"},{"first_name":"Vladimir","full_name":"Ceperic, Vladimir","last_name":"Ceperic"},{"full_name":"Joannopoulos, John D.","last_name":"Joannopoulos","first_name":"John D."},{"full_name":"Englund, Dirk","last_name":"Englund","first_name":"Dirk"},{"first_name":"Marin","full_name":"Soljacic, Marin","last_name":"Soljacic"}],"title":"Integrated nanophotonic ising sampler","scopus_import":"1","article_processing_charge":"No","month":"06","status":"public","language":[{"iso":"eng"}]},{"date_created":"2026-03-30T12:22:48Z","oa_version":"None","publication_status":"published","conference":{"end_date":"2019-05-10","name":"CLEO: Fundamental Science","location":"San Jose, CA, United States","start_date":"2019-05-05"},"date_updated":"2026-05-05T06:51:29Z","_id":"21620","title":"Photonic Recurrent Ising Sampler","author":[{"first_name":"Charles","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","last_name":"Roques-Carmes","full_name":"Roques-Carmes, Charles"},{"first_name":"Yichen","full_name":"Shen, Yichen","last_name":"Shen"},{"first_name":"Cristian","full_name":"Zanoci, Cristian","last_name":"Zanoci"},{"last_name":"Prabhu","full_name":"Prabhu, Mihika","first_name":"Mihika"},{"first_name":"Fadi","last_name":"Atieh","full_name":"Atieh, Fadi"},{"last_name":"Jing","full_name":"Jing, Li","first_name":"Li"},{"full_name":"Dubček, Tena","last_name":"Dubček","first_name":"Tena"},{"full_name":"Čeperić, Vladimir","last_name":"Čeperić","first_name":"Vladimir"},{"last_name":"Joannopoulos","full_name":"Joannopoulos, John D.","first_name":"John D."},{"first_name":"Dirk","last_name":"Englund","full_name":"Englund, Dirk"},{"full_name":"Soljačić, Marin","last_name":"Soljačić","first_name":"Marin"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","month":"06","quality_controlled":"1","date_published":"2019-06-01T00:00:00Z","abstract":[{"lang":"eng","text":"We present the Photonic Recurrent Ising Sampler (PRIS), an algorithm tailored for photonic parallel networks, that can sample distributions of arbitrary Ising problems. The PRIS finds the ground state of general Ising problems and probes critical exponents of universality classes."}],"extern":"1","type":"conference","day":"01","doi":"10.1364/cleo_qels.2019.ftu4c.2","citation":{"short":"C. Roques-Carmes, Y. Shen, C. Zanoci, M. Prabhu, F. Atieh, L. Jing, T. Dubček, V. Čeperić, J.D. Joannopoulos, D. Englund, M. Soljačić, in:, Conference on Lasers and Electro-Optics, Optica Publishing Group, 2019.","mla":"Roques-Carmes, Charles, et al. “Photonic Recurrent Ising Sampler.” <i>Conference on Lasers and Electro-Optics</i>, FTu4C.2, Optica Publishing Group, 2019, doi:<a href=\"https://doi.org/10.1364/cleo_qels.2019.ftu4c.2\">10.1364/cleo_qels.2019.ftu4c.2</a>.","ista":"Roques-Carmes C, Shen Y, Zanoci C, Prabhu M, Atieh F, Jing L, Dubček T, Čeperić V, Joannopoulos JD, Englund D, Soljačić M. 2019. Photonic Recurrent Ising Sampler. Conference on Lasers and Electro-Optics. CLEO: Fundamental Science, FTu4C.2.","chicago":"Roques-Carmes, Charles, Yichen Shen, Cristian Zanoci, Mihika Prabhu, Fadi Atieh, Li Jing, Tena Dubček, et al. “Photonic Recurrent Ising Sampler.” In <i>Conference on Lasers and Electro-Optics</i>. Optica Publishing Group, 2019. <a href=\"https://doi.org/10.1364/cleo_qels.2019.ftu4c.2\">https://doi.org/10.1364/cleo_qels.2019.ftu4c.2</a>.","ama":"Roques-Carmes C, Shen Y, Zanoci C, et al. Photonic Recurrent Ising Sampler. In: <i>Conference on Lasers and Electro-Optics</i>. Optica Publishing Group; 2019. doi:<a href=\"https://doi.org/10.1364/cleo_qels.2019.ftu4c.2\">10.1364/cleo_qels.2019.ftu4c.2</a>","apa":"Roques-Carmes, C., Shen, Y., Zanoci, C., Prabhu, M., Atieh, F., Jing, L., … Soljačić, M. (2019). Photonic Recurrent Ising Sampler. In <i>Conference on Lasers and Electro-Optics</i>. San Jose, CA, United States: Optica Publishing Group. <a href=\"https://doi.org/10.1364/cleo_qels.2019.ftu4c.2\">https://doi.org/10.1364/cleo_qels.2019.ftu4c.2</a>","ieee":"C. Roques-Carmes <i>et al.</i>, “Photonic Recurrent Ising Sampler,” in <i>Conference on Lasers and Electro-Optics</i>, San Jose, CA, United States, 2019."},"publication_identifier":{"eisbn":["9781943580576"]},"year":"2019","article_number":"FTu4C.2","publication":"Conference on Lasers and Electro-Optics","OA_type":"closed access","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Optica Publishing Group"},{"year":"2019","publication_identifier":{"eissn":["2156-017X"],"eisbn":["9781728140322"]},"day":"01","type":"conference","doi":"10.1109/iedm19573.2019.8993624","abstract":[{"lang":"eng","text":"Optical approaches to AI acceleration have gained intense interest recently due to the potentially breakthrough advantages of photonics: high bandwidth, low power consumption, and efficient data movement. We overview leading photonic AI platforms based on beamsplitter mesh networks, weight banks, and photoelectric multiplication. While the theoretical performance can be orders of magnitude beyond current state of the art, practical issues of chip area, input / output, and crosstalk paint a more nuanced near-term picture of photonic AI acceleration. Both fundamental and near-term limitations to energy efficiency are addressed, and bandwidth limitations due to temporal crosstalk are analyzed."}],"extern":"1","citation":{"short":"R. Hamerly, A. Sludds, L. Bernstein, M. Prabhu, C. Roques-Carmes, J. Carolan, Y. Yamamoto, M. Soljacic, D. Englund, in:, 2019 IEEE International Electron Devices Meeting, IEEE, 2019.","ieee":"R. Hamerly <i>et al.</i>, “Towards large-scale photonic neural-network accelerators,” in <i>2019 IEEE International Electron Devices Meeting</i>, San Francisco, CA, United States, 2019.","apa":"Hamerly, R., Sludds, A., Bernstein, L., Prabhu, M., Roques-Carmes, C., Carolan, J., … Englund, D. (2019). Towards large-scale photonic neural-network accelerators. In <i>2019 IEEE International Electron Devices Meeting</i>. San Francisco, CA, United States: IEEE. <a href=\"https://doi.org/10.1109/iedm19573.2019.8993624\">https://doi.org/10.1109/iedm19573.2019.8993624</a>","ama":"Hamerly R, Sludds A, Bernstein L, et al. Towards large-scale photonic neural-network accelerators. In: <i>2019 IEEE International Electron Devices Meeting</i>. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/iedm19573.2019.8993624\">10.1109/iedm19573.2019.8993624</a>","ista":"Hamerly R, Sludds A, Bernstein L, Prabhu M, Roques-Carmes C, Carolan J, Yamamoto Y, Soljacic M, Englund D. 2019. Towards large-scale photonic neural-network accelerators. 2019 IEEE International Electron Devices Meeting. IEDM: International Electron Devices Meeting.","chicago":"Hamerly, R., A. Sludds, L. Bernstein, M. Prabhu, Charles Roques-Carmes, J. Carolan, Y. Yamamoto, M. Soljacic, and D. Englund. “Towards Large-Scale Photonic Neural-Network Accelerators.” In <i>2019 IEEE International Electron Devices Meeting</i>. IEEE, 2019. <a href=\"https://doi.org/10.1109/iedm19573.2019.8993624\">https://doi.org/10.1109/iedm19573.2019.8993624</a>.","mla":"Hamerly, R., et al. “Towards Large-Scale Photonic Neural-Network Accelerators.” <i>2019 IEEE International Electron Devices Meeting</i>, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/iedm19573.2019.8993624\">10.1109/iedm19573.2019.8993624</a>."},"quality_controlled":"1","date_published":"2019-12-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IEEE","publication":"2019 IEEE International Electron Devices Meeting","OA_type":"closed access","conference":{"start_date":"2019-12-07","location":"San Francisco, CA, United States","name":"IEDM: International Electron Devices Meeting","end_date":"2019-12-11"},"publication_status":"published","date_created":"2026-03-30T12:22:47Z","oa_version":"None","language":[{"iso":"eng"}],"month":"12","status":"public","scopus_import":"1","article_processing_charge":"No","author":[{"first_name":"R.","full_name":"Hamerly, R.","last_name":"Hamerly"},{"first_name":"A.","full_name":"Sludds, A.","last_name":"Sludds"},{"full_name":"Bernstein, L.","last_name":"Bernstein","first_name":"L."},{"first_name":"M.","full_name":"Prabhu, M.","last_name":"Prabhu"},{"first_name":"Charles","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","last_name":"Roques-Carmes","full_name":"Roques-Carmes, Charles"},{"first_name":"J.","last_name":"Carolan","full_name":"Carolan, J."},{"last_name":"Yamamoto","full_name":"Yamamoto, Y.","first_name":"Y."},{"first_name":"M.","full_name":"Soljacic, M.","last_name":"Soljacic"},{"first_name":"D.","last_name":"Englund","full_name":"Englund, D."}],"title":"Towards large-scale photonic neural-network accelerators","_id":"21568","date_updated":"2026-05-05T07:39:32Z"},{"date_created":"2026-05-06T10:52:25Z","publication_status":"published","scopus_import":"1","issue":"16","month":"08","_id":"21814","quality_controlled":"1","citation":{"mla":"Mostafavi, Seyed Hossein, et al. “Photoinduced Deadhesion of a Polymer Film Using a Photochromic Donor-Acceptor Stenhouse Adduct.” <i>Macromolecules</i>, vol. 52, no. 16, American Chemical Society, 2019, pp. 6311–17, doi:<a href=\"https://doi.org/10.1021/acs.macromol.9b00882\">10.1021/acs.macromol.9b00882</a>.","ista":"Mostafavi SH, Li W, Clark KD, Stricker FJ, Alaniz JR de, Bardeen CJ. 2019. Photoinduced deadhesion of a polymer film using a photochromic donor-acceptor Stenhouse adduct. Macromolecules. 52(16), 6311–6317.","chicago":"Mostafavi, Seyed Hossein, Wangxiang Li, Kyle D. Clark, Friedrich J Stricker, Javier Read de Alaniz, and Christopher J. Bardeen. “Photoinduced Deadhesion of a Polymer Film Using a Photochromic Donor-Acceptor Stenhouse Adduct.” <i>Macromolecules</i>. American Chemical Society, 2019. <a href=\"https://doi.org/10.1021/acs.macromol.9b00882\">https://doi.org/10.1021/acs.macromol.9b00882</a>.","ama":"Mostafavi SH, Li W, Clark KD, Stricker FJ, Alaniz JR de, Bardeen CJ. Photoinduced deadhesion of a polymer film using a photochromic donor-acceptor Stenhouse adduct. <i>Macromolecules</i>. 2019;52(16):6311-6317. doi:<a href=\"https://doi.org/10.1021/acs.macromol.9b00882\">10.1021/acs.macromol.9b00882</a>","apa":"Mostafavi, S. H., Li, W., Clark, K. D., Stricker, F. J., Alaniz, J. R. de, &#38; Bardeen, C. J. (2019). Photoinduced deadhesion of a polymer film using a photochromic donor-acceptor Stenhouse adduct. <i>Macromolecules</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.macromol.9b00882\">https://doi.org/10.1021/acs.macromol.9b00882</a>","ieee":"S. H. Mostafavi, W. Li, K. D. Clark, F. J. Stricker, J. R. de Alaniz, and C. J. Bardeen, “Photoinduced deadhesion of a polymer film using a photochromic donor-acceptor Stenhouse adduct,” <i>Macromolecules</i>, vol. 52, no. 16. American Chemical Society, pp. 6311–6317, 2019.","short":"S.H. Mostafavi, W. Li, K.D. Clark, F.J. Stricker, J.R. de Alaniz, C.J. Bardeen, Macromolecules 52 (2019) 6311–6317."},"abstract":[{"text":"Photoisomerization of molecules dissolved in a polymer film can modulate its properties. In a previous paper (Mostafavi, S. H.; Macromolecules 2018, 51, 2388−2394), it was found that the ultraviolet light-induced photoisomerization of spiropyran dopants could substantially increase adhesion to a glass surface. In this work, a different photochromic reaction, the visible-light-induced cyclization of a donor–acceptor Stenhouse adduct (DASA), leads to the opposite effect: the deadhesion of a polystyrene film from a clean glass surface. Measurements of the shear and pull-off adhesion strengths before and after visible irradiation show a light-induced decrease of 20–30%. The time required for delamination in water shows an even more dramatic decrease of 90%. Changes in the water contact angle and other measurements suggest that molecular-level noncovalent interactions between the polymer and glass are weakened after photoisomerization, possibly due to the molecular contraction of the DASA that disrupts the interaction between its amine groups and the surface silanols. The ability to reduce polymer adhesion using visible light enables the controlled release of dye molecules from a glass container, where these have been stored as a dry powder, into an aqueous solution. Embedding photochromic molecules in a polymer can lead to new effects that may have practical applications in stimuli-responsive materials.","lang":"eng"}],"extern":"1","type":"journal_article","publisher":"American Chemical Society","OA_type":"closed access","volume":52,"oa_version":"None","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","page":"6311-6317","date_updated":"2026-05-11T08:48:38Z","author":[{"first_name":"Seyed Hossein","full_name":"Mostafavi, Seyed Hossein","last_name":"Mostafavi"},{"full_name":"Li, Wangxiang","last_name":"Li","first_name":"Wangxiang"},{"last_name":"Clark","full_name":"Clark, Kyle D.","first_name":"Kyle D."},{"first_name":"Friedrich J","id":"7aca2cfc-46cf-11f0-abd3-8c96b5186745","full_name":"Stricker, Friedrich J","last_name":"Stricker"},{"last_name":"Alaniz","full_name":"Alaniz, Javier Read de","first_name":"Javier Read de"},{"first_name":"Christopher J.","last_name":"Bardeen","full_name":"Bardeen, Christopher J."}],"title":"Photoinduced deadhesion of a polymer film using a photochromic donor-acceptor Stenhouse adduct","article_type":"original","publication_identifier":{"eissn":["1520-5835"],"issn":["0024-9297"]},"year":"2019","date_published":"2019-08-16T00:00:00Z","intvolume":"        52","doi":"10.1021/acs.macromol.9b00882","day":"16","ddc":["540"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Macromolecules"},{"month":"05","_id":"6392","alternative_title":["IST Austria Thesis"],"publication_status":"published","date_created":"2019-05-09T19:53:00Z","publisher":"IST Austria","department":[{"_id":"ToBo"}],"citation":{"apa":"Lukacisin, M. (2019). <i>Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6392\">https://doi.org/10.15479/AT:ISTA:6392</a>","ama":"Lukacisin M. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6392\">10.15479/AT:ISTA:6392</a>","ieee":"M. Lukacisin, “Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory,” IST Austria, 2019.","chicago":"Lukacisin, Martin. “Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory.” IST Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6392\">https://doi.org/10.15479/AT:ISTA:6392</a>.","ista":"Lukacisin M. 2019. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. IST Austria.","mla":"Lukacisin, Martin. <i>Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory</i>. IST Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6392\">10.15479/AT:ISTA:6392</a>.","short":"M. Lukacisin, Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory, IST Austria, 2019."},"abstract":[{"lang":"eng","text":"The regulation of gene expression is one of the most fundamental processes in living systems. In recent years, thanks to advances in sequencing technology and automation, it has become possible to study gene expression quantitatively, genome-wide and in high-throughput. This leads to the possibility of exploring changes in gene expression in the context of many external perturbations and their combinations, and thus of characterising the basic principles governing gene regulation. In this thesis, I present quantitative experimental approaches to studying transcriptional and protein level changes in response to combinatorial drug treatment, as well as a theoretical data-driven approach to analysing thermodynamic principles guiding transcription of protein coding genes.  \r\nIn the first part of this work, I present a novel methodological framework for quantifying gene expression changes in drug combinations, termed isogrowth profiling. External perturbations through small molecule drugs influence the growth rate of the cell, leading to wide-ranging changes in cellular physiology and gene expression. This confounds the gene expression changes specifically elicited by the particular drug. Combinatorial perturbations, owing to the increased stress they exert, influence the growth rate even more strongly and hence suffer the convolution problem to a greater extent when measuring gene expression changes. Isogrowth profiling is a way to experimentally abstract non-specific, growth rate related changes, by performing the measurement using varying ratios of two drugs at such concentrations that the overall inhibition rate is constant. Using a robotic setup for automated high-throughput re-dilution culture of Saccharomyces cerevisiae, the budding yeast, I investigate all pairwise interactions of four small molecule drugs through sequencing RNA along a growth isobole. Through principal component analysis, I demonstrate here that isogrowth profiling can uncover drug-specific as well as drug-interaction-specific gene expression changes. I show that drug-interaction-specific gene expression changes can be used for prediction of higher-order drug interactions. I propose a simplified generalised framework of isogrowth profiling, with few measurements needed for each drug pair, enabling the broad application of isogrowth profiling to high-throughput screening of inhibitors of cellular growth and beyond. Such high-throughput screenings of gene expression changes specific to pairwise drug interactions will be instrumental for predicting the higher-order interactions of the drugs.\r\n\r\nIn the second part of this work, I extend isogrowth profiling to single-cell measurements of gene expression, characterising population heterogeneity in the budding yeast in response to combinatorial drug perturbation while controlling for non-specific growth rate effects. Through flow cytometry of strains with protein products fused to green fluorescent protein, I discover multiple proteins with bi-modally distributed expression levels in the population in response to drug treatment. I characterize more closely the effect of an ionic stressor, lithium chloride, and find that it inhibits the splicing of mRNA, most strongly affecting ribosomal protein transcripts and leading to a bi-stable behaviour of a small ribosomal subunit protein Rps22B. Time-lapse microscopy of a microfluidic culture system revealed that the induced Rps22B heterogeneity leads to preferential survival of Rps22B-low cells after long starvation, but to preferential proliferation of Rps22B-high cells after short starvation. Overall, this suggests that yeast cells might use splicing of ribosomal genes for bet-hedging in fluctuating environments. I give specific examples of how further exploration of cellular heterogeneity in yeast in response to external perturbation has the potential to reveal yet-undiscovered gene regulation circuitry.\r\n\r\nIn the last part of this thesis, a re-analysis of a published sequencing dataset of nascent elongating transcripts is used to characterise the thermodynamic constraints for RNA polymerase II (RNAP) elongation. Population-level data on RNAP position throughout the transcribed genome with single nucleotide resolution are used to infer the sequence specific thermodynamic determinants of RNAP pausing and backtracking. This analysis reveals that the basepairing strength of the eight nucleotide-long RNA:DNA duplex relative to the basepairing strength of the same sequence when in DNA:DNA duplex, and the change in this quantity during RNA polymerase movement, is the key determinant of RNAP pausing. This is true for RNAP pausing while elongating, but also of RNAP pausing while backtracking and of the backtracking length. The quantitative dependence of RNAP pausing on basepairing energetics is used to infer the increase in pausing due to transcriptional mismatches, leading to a hypothesis that pervasive RNA polymerase II pausing is due to basepairing energetics, as an evolutionary cost for increased RNA polymerase II fidelity.\r\n\r\nThis work advances our understanding of the general principles governing gene expression, with the goal of making computational predictions of single-cell gene expression responses to combinatorial perturbations based on the individual perturbations possible. This ability would substantially facilitate the design of drug combination treatments and, in the long term, lead to our increased ability to more generally design targeted manipulations to any biological system. "}],"type":"dissertation","extern":"1","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","file_date_updated":"2021-02-11T11:17:16Z","title":"Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory","author":[{"first_name":"Martin","orcid":"0000-0001-6549-4177","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisin","full_name":"Lukacisin, Martin"}],"date_updated":"2025-07-10T11:49:51Z","page":"103","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1029"}]},"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"supervisor":[{"first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"year":"2019","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-001-5"]},"file":[{"file_size":43740796,"creator":"mlukacisin","file_name":"Thesis_Draft_v3.4Final.docx","date_created":"2019-05-10T13:51:49Z","access_level":"closed","embargo_to":"open_access","file_id":"6409","date_updated":"2020-07-14T12:47:29Z","relation":"hidden","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"829bda074444857c7935171237bb7c0c"},{"access_level":"open_access","date_created":"2019-05-10T14:13:42Z","file_name":"Thesis_Draft_v3.4FinalA.pdf","file_size":35228388,"creator":"mlukacisin","embargo":"2020-04-17","relation":"main_file","content_type":"application/pdf","checksum":"56cb5e97f5f8fc41692401b53832d8e0","file_id":"6410","date_updated":"2021-02-11T11:17:16Z"}],"oa":1,"doi":"10.15479/AT:ISTA:6392","day":"09","date_published":"2019-05-09T00:00:00Z"},{"intvolume":"        38","date_published":"2019-11-06T00:00:00Z","doi":"10.1145/3355089.3356576","day":"06","oa":1,"file":[{"access_level":"open_access","file_name":"xcad_sup_mat_siga19.pdf","date_created":"2019-11-26T14:24:26Z","file_size":1673176,"creator":"bbickel","relation":"supplementary_material","checksum":"56a2fb019adcb556d2b022f5e5acb68c","content_type":"application/pdf","file_id":"7119","date_updated":"2020-07-14T12:47:49Z","title":"X-CAD Supplemental Material"},{"creator":"bbickel","file_size":14563618,"date_created":"2019-11-26T14:24:27Z","description":"This is the author's version of the work.","file_name":"XCAD_authors_version.pdf","access_level":"open_access","title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","date_updated":"2020-07-14T12:47:49Z","file_id":"7120","content_type":"application/pdf","checksum":"5f29d76aceb5102e766cbab9b17d776e","relation":"main_file"},{"access_level":"open_access","creator":"bbickel","file_size":259979129,"file_name":"XCAD_video.mp4","date_created":"2019-11-26T14:27:37Z","checksum":"0d31e123286cbec9e28b2001c2bb0d55","content_type":"video/mp4","relation":"main_file","date_updated":"2020-07-14T12:47:49Z","file_id":"7121"}],"ec_funded":1,"publication_identifier":{"issn":["0730-0301"]},"year":"2019","article_type":"original","article_number":"157","publication":"ACM Transactions on Graphics","isi":1,"ddc":["000"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"H2020","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"oa_version":"Submitted Version","related_material":{"record":[{"relation":"dissertation_contains","id":"12897","status":"public"}]},"date_updated":"2026-05-14T22:30:07Z","author":[{"first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","full_name":"Hafner, Christian","last_name":"Hafner"},{"first_name":"Christian","last_name":"Schumacher","full_name":"Schumacher, Christian"},{"first_name":"Espen","last_name":"Knoop","full_name":"Knoop, Espen"},{"orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas","last_name":"Auzinger","id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd"},{"first_name":"Moritz","full_name":"Bächer, Moritz","last_name":"Bächer"}],"title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","file_date_updated":"2020-07-14T12:47:49Z","article_processing_charge":"No","has_accepted_license":"1","language":[{"iso":"eng"}],"status":"public","quality_controlled":"1","abstract":[{"text":"We propose a novel generic shape optimization method for CAD models based on the eXtended Finite Element Method (XFEM). Our method works directly on the intersection between the model and a regular simulation grid, without the need to mesh or remesh, thus removing a bottleneck of classical shape optimization strategies. This is made possible by a novel hierarchical integration scheme that accurately integrates finite element quantities with sub-element precision. For optimization, we efficiently compute analytical shape derivatives of the entire framework, from model intersection to integration rule generation and XFEM simulation. Moreover, we describe a differentiable projection of shape parameters onto a constraint manifold spanned by user-specified shape preservation, consistency, and manufacturability constraints. We demonstrate the utility of our approach by optimizing mass distribution, strength-to-weight ratio, and inverse elastic shape design objectives directly on parameterized 3D CAD models.","lang":"eng"}],"type":"journal_article","citation":{"ieee":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, and M. Bächer, “X-CAD: Optimizing CAD Models with Extended Finite Elements,” <i>ACM Transactions on Graphics</i>, vol. 38, no. 6. ACM, 2019.","apa":"Hafner, C., Schumacher, C., Knoop, E., Auzinger, T., Bickel, B., &#38; Bächer, M. (2019). X-CAD: Optimizing CAD Models with Extended Finite Elements. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3355089.3356576\">https://doi.org/10.1145/3355089.3356576</a>","ama":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. X-CAD: Optimizing CAD Models with Extended Finite Elements. <i>ACM Transactions on Graphics</i>. 2019;38(6). doi:<a href=\"https://doi.org/10.1145/3355089.3356576\">10.1145/3355089.3356576</a>","mla":"Hafner, Christian, et al. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” <i>ACM Transactions on Graphics</i>, vol. 38, no. 6, 157, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3355089.3356576\">10.1145/3355089.3356576</a>.","ista":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. 2019. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 38(6), 157.","chicago":"Hafner, Christian, Christian Schumacher, Espen Knoop, Thomas Auzinger, Bernd Bickel, and Moritz Bächer. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” <i>ACM Transactions on Graphics</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3355089.3356576\">https://doi.org/10.1145/3355089.3356576</a>.","short":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, M. Bächer, ACM Transactions on Graphics 38 (2019)."},"department":[{"_id":"BeBi"}],"volume":38,"publisher":"ACM","date_created":"2019-11-26T14:22:09Z","publication_status":"published","external_id":{"isi":["000498397300007"]},"_id":"7117","issue":"6","scopus_import":"1","month":"11"},{"quality_controlled":"1","citation":{"short":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E.B. Hannezo, C.-P.J. Heisenberg, Cell 177 (2019) 1463–1479.e18.","ista":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. 2019. Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. 177(6), 1463–1479.e18.","chicago":"Shamipour, Shayan, Roland Kardos, Shi-lei Xue, Björn Hof, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” <i>Cell</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">https://doi.org/10.1016/j.cell.2019.04.030</a>.","mla":"Shamipour, Shayan, et al. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” <i>Cell</i>, vol. 177, no. 6, Elsevier, 2019, p. 1463–1479.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">10.1016/j.cell.2019.04.030</a>.","apa":"Shamipour, S., Kardos, R., Xue, S., Hof, B., Hannezo, E. B., &#38; Heisenberg, C.-P. J. (2019). Bulk actin dynamics drive phase segregation in zebrafish oocytes. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">https://doi.org/10.1016/j.cell.2019.04.030</a>","ama":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. Bulk actin dynamics drive phase segregation in zebrafish oocytes. <i>Cell</i>. 2019;177(6):1463-1479.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">10.1016/j.cell.2019.04.030</a>","ieee":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E. B. Hannezo, and C.-P. J. Heisenberg, “Bulk actin dynamics drive phase segregation in zebrafish oocytes,” <i>Cell</i>, vol. 177, no. 6. Elsevier, p. 1463–1479.e18, 2019."},"pmid":1,"abstract":[{"lang":"eng","text":"Segregation of maternal determinants within the oocyte constitutes the first step in embryo patterning. In zebrafish oocytes, extensive ooplasmic streaming leads to the segregation of ooplasm from yolk granules along the animal-vegetal axis of the oocyte. Here, we show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the oocyte. This wave functions in segregation by both pulling ooplasm animally and pushing yolk granules vegetally. Using biophysical experimentation and theory, we show that ooplasm pulling is mediated by bulk actin network flows exerting friction forces on the ooplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. Our study defines a novel role of cell-cycle-controlled bulk actin polymerization waves in oocyte polarization via ooplasmic segregation."}],"type":"journal_article","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"BjHo"}],"volume":177,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2019.04.030"}],"publisher":"Elsevier","date_created":"2019-06-02T21:59:12Z","publication_status":"published","external_id":{"isi":["000469415100013"],"pmid":["31080065"]},"_id":"6508","scopus_import":"1","issue":"6","month":"05","date_published":"2019-05-30T00:00:00Z","intvolume":"       177","file":[{"access_level":"open_access","date_created":"2020-10-21T07:22:34Z","file_name":"2019_Cell_Shamipour_accepted.pdf","success":1,"creator":"dernst","file_size":3356292,"content_type":"application/pdf","checksum":"aea43726d80e35ce3885073a5f05c3e3","relation":"main_file","date_updated":"2020-10-21T07:22:34Z","file_id":"8686"}],"oa":1,"day":"30","doi":"10.1016/j.cell.2019.04.030","acknowledgement":"We would like to thank Pierre Recho, Guillaume Salbreux, and Silvia Grigolon for advice on the theory, Lila Solnica-Krezel for kindly providing us with zebrafish dachsous mutants, members of the Heisenberg and Hannezo groups for fruitful discussions, and the Bioimaging and zebrafish facilities at IST Austria for their continuous support. This project has received funding from the European Union (European Research Council Advanced Grant 742573 to C.P.H.) and from the Austrian Science Fund (FWF) (P 31639 to E.H.).","year":"2019","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"article_type":"original","ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"isi":1,"publication":"Cell","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"},{"_id":"268294B6-B435-11E9-9278-68D0E5697425","name":"Active mechano-chemical description of the cell cytoskeleton","grant_number":"P31639","call_identifier":"FWF"}],"oa_version":"Published Version","date_updated":"2026-05-14T22:30:09Z","related_material":{"record":[{"relation":"dissertation_contains","id":"8350","status":"public"}],"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-the-cytoplasm-separates-from-the-yolk/"}]},"page":"1463-1479.e18","title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes","author":[{"first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour","full_name":"Shamipour, Shayan"},{"id":"4039350E-F248-11E8-B48F-1D18A9856A87","full_name":"Kardos, Roland","last_name":"Kardos","first_name":"Roland"},{"first_name":"Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87","last_name":"Xue","full_name":"Xue, Shi-lei"},{"orcid":"0000-0003-2057-2754","last_name":"Hof","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2020-10-21T07:22:34Z","language":[{"iso":"eng"}],"status":"public"},{"external_id":{"isi":["000493898000012"],"pmid":["31675500"]},"publication_status":"published","date_created":"2019-11-12T12:51:06Z","month":"10","issue":"4","scopus_import":"1","_id":"7001","citation":{"apa":"Schwayer, C., Shamipour, S., Pranjic-Ferscha, K., Schauer, A., Balda, M., Tada, M., … Heisenberg, C.-P. J. (2019). Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">https://doi.org/10.1016/j.cell.2019.10.006</a>","ieee":"C. Schwayer <i>et al.</i>, “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” <i>Cell</i>, vol. 179, no. 4. Cell Press, p. 937–952.e18, 2019.","ama":"Schwayer C, Shamipour S, Pranjic-Ferscha K, et al. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. <i>Cell</i>. 2019;179(4):937-952.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">10.1016/j.cell.2019.10.006</a>","chicago":"Schwayer, Cornelia, Shayan Shamipour, Kornelija Pranjic-Ferscha, Alexandra Schauer, M Balda, M Tada, K Matter, and Carl-Philipp J Heisenberg. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” <i>Cell</i>. Cell Press, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">https://doi.org/10.1016/j.cell.2019.10.006</a>.","ista":"Schwayer C, Shamipour S, Pranjic-Ferscha K, Schauer A, Balda M, Tada M, Matter K, Heisenberg C-PJ. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 179(4), 937–952.e18.","mla":"Schwayer, Cornelia, et al. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” <i>Cell</i>, vol. 179, no. 4, Cell Press, 2019, p. 937–952.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">10.1016/j.cell.2019.10.006</a>.","short":"C. Schwayer, S. Shamipour, K. Pranjic-Ferscha, A. Schauer, M. Balda, M. Tada, K. Matter, C.-P.J. Heisenberg, Cell 179 (2019) 937–952.e18."},"type":"journal_article","pmid":1,"quality_controlled":"1","publisher":"Cell Press","volume":179,"department":[{"_id":"CaHe"},{"_id":"BjHo"}],"oa_version":"Submitted Version","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2020-10-21T07:09:45Z","author":[{"first_name":"Cornelia","id":"3436488C-F248-11E8-B48F-1D18A9856A87","last_name":"Schwayer","full_name":"Schwayer, Cornelia","orcid":"0000-0001-5130-2226"},{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour","full_name":"Shamipour, Shayan","first_name":"Shayan"},{"id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","last_name":"Pranjic-Ferscha","full_name":"Pranjic-Ferscha, Kornelija","first_name":"Kornelija"},{"last_name":"Schauer","full_name":"Schauer, Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7659-9142","first_name":"Alexandra"},{"last_name":"Balda","full_name":"Balda, M","first_name":"M"},{"last_name":"Tada","full_name":"Tada, M","first_name":"M"},{"last_name":"Matter","full_name":"Matter, K","first_name":"K"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow","related_material":{"record":[{"status":"public","id":"7186","relation":"dissertation_contains"},{"status":"public","id":"8350","relation":"dissertation_contains"}],"link":[{"relation":"press_release","description":"News auf IST Website","url":"https://ist.ac.at/en/news/biochemistry-meets-mechanics-the-sensitive-nature-of-cell-cell-contact-formation-in-embryo-development/"}]},"date_updated":"2026-05-14T22:30:09Z","page":"937-952.e18","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"article_type":"original","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"year":"2019","ec_funded":1,"oa":1,"file":[{"file_name":"2019_Cell_Schwayer_accepted.pdf","success":1,"date_created":"2020-10-21T07:09:45Z","file_size":8805878,"creator":"dernst","access_level":"open_access","file_id":"8684","date_updated":"2020-10-21T07:09:45Z","relation":"main_file","checksum":"33dac4bb77ee630e2666e936b4d57980","content_type":"application/pdf"}],"doi":"10.1016/j.cell.2019.10.006","day":"31","date_published":"2019-10-31T00:00:00Z","intvolume":"       179","project":[{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"isi":1,"publication":"Cell"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020"},{"grant_number":"708497","_id":"25BAF7B2-B435-11E9-9278-68D0E5697425","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse","call_identifier":"H2020"},{"grant_number":"W01205","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","name":"Zellkommunikation in Gesundheit und Krankheit","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312"}],"publication":"Intrinsic Activity","article_number":"A3.27","acknowledgement":"This work was supported by the ERC and EU Horizon 2020 (ERC 692692; MSC-IF 708497) and FWF Z 312-B27 Wittgenstein award; W 1205-B09).","publication_identifier":{"issn":["2309-8503"]},"year":"2019","ec_funded":1,"oa":1,"day":"11","doi":"10.25006/ia.7.s1-a3.27","date_published":"2019-09-11T00:00:00Z","intvolume":"         7","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","author":[{"first_name":"Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","last_name":"Kim","full_name":"Kim, Olena","orcid":"0000-0003-2344-1039"},{"full_name":"Borges Merjane, Carolina","last_name":"Borges Merjane","id":"4305C450-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0005-401X","first_name":"Carolina"},{"orcid":"0000-0001-5001-4804","last_name":"Jonas","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"title":"Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy","related_material":{"record":[{"relation":"dissertation_contains","id":"11196","status":"public"}]},"date_updated":"2026-05-14T22:30:34Z","keyword":["hippocampus","mossy fibers","readily releasable pool","electron microscopy"],"oa_version":"Published Version","publisher":"Austrian Pharmacological Society","corr_author":"1","main_file_link":[{"url":"https://www.intrinsicactivity.org/2019/7/S1/A3.27/","open_access":"1"}],"volume":7,"department":[{"_id":"PeJo"}],"citation":{"short":"O. Kim, C. Borges Merjane, P.M. Jonas, in:, Intrinsic Activity, Austrian Pharmacological Society, 2019.","ieee":"O. Kim, C. Borges Merjane, and P. M. Jonas, “Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy,” in <i>Intrinsic Activity</i>, Innsbruck, Austria, 2019, vol. 7, no. Suppl. 1.","ama":"Kim O, Borges Merjane C, Jonas PM. Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy. In: <i>Intrinsic Activity</i>. Vol 7. Austrian Pharmacological Society; 2019. doi:<a href=\"https://doi.org/10.25006/ia.7.s1-a3.27\">10.25006/ia.7.s1-a3.27</a>","apa":"Kim, O., Borges Merjane, C., &#38; Jonas, P. M. (2019). Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy. In <i>Intrinsic Activity</i> (Vol. 7). Innsbruck, Austria: Austrian Pharmacological Society. <a href=\"https://doi.org/10.25006/ia.7.s1-a3.27\">https://doi.org/10.25006/ia.7.s1-a3.27</a>","mla":"Kim, Olena, et al. “Functional Analysis of the Docked Vesicle Pool in Hippocampal Mossy Fiber Terminals by Electron Microscopy.” <i>Intrinsic Activity</i>, vol. 7, no. Suppl. 1, A3.27, Austrian Pharmacological Society, 2019, doi:<a href=\"https://doi.org/10.25006/ia.7.s1-a3.27\">10.25006/ia.7.s1-a3.27</a>.","ista":"Kim O, Borges Merjane C, Jonas PM. 2019. Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy. Intrinsic Activity. ANA: Austrian Neuroscience Association ; APHAR: Austrian Pharmacological Society vol. 7, A3.27.","chicago":"Kim, Olena, Carolina Borges Merjane, and Peter M Jonas. “Functional Analysis of the Docked Vesicle Pool in Hippocampal Mossy Fiber Terminals by Electron Microscopy.” In <i>Intrinsic Activity</i>, Vol. 7. Austrian Pharmacological Society, 2019. <a href=\"https://doi.org/10.25006/ia.7.s1-a3.27\">https://doi.org/10.25006/ia.7.s1-a3.27</a>."},"type":"conference_abstract","quality_controlled":"1","month":"09","issue":"Suppl. 1","_id":"11222","conference":{"start_date":"2019-09-25","location":"Innsbruck, Austria","name":"ANA: Austrian Neuroscience Association ; APHAR: Austrian Pharmacological Society","end_date":"2019-09-27"},"publication_status":"published","date_created":"2022-04-20T15:06:05Z"},{"issue":"12","scopus_import":"1","month":"12","_id":"7391","external_id":{"pmid":["31786521"],"isi":["000504652000020"]},"date_created":"2020-01-29T15:56:56Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","corr_author":"1","publisher":"Elsevier","department":[{"_id":"RySh"}],"volume":22,"quality_controlled":"1","citation":{"ieee":"S. Tabata <i>et al.</i>, “Electron microscopic detection of single membrane proteins by a specific chemical labeling,” <i>iScience</i>, vol. 22, no. 12. Elsevier, pp. 256–268, 2019.","apa":"Tabata, S., Jevtic, M., Kurashige, N., Fuchida, H., Kido, M., Tani, K., … Ojida, A. (2019). Electron microscopic detection of single membrane proteins by a specific chemical labeling. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2019.11.025\">https://doi.org/10.1016/j.isci.2019.11.025</a>","ama":"Tabata S, Jevtic M, Kurashige N, et al. Electron microscopic detection of single membrane proteins by a specific chemical labeling. <i>iScience</i>. 2019;22(12):256-268. doi:<a href=\"https://doi.org/10.1016/j.isci.2019.11.025\">10.1016/j.isci.2019.11.025</a>","chicago":"Tabata, Shigekazu, Marijo Jevtic, Nobutaka Kurashige, Hirokazu Fuchida, Munetsugu Kido, Kazushi Tani, Naoki Zenmyo, et al. “Electron Microscopic Detection of Single Membrane Proteins by a Specific Chemical Labeling.” <i>IScience</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.isci.2019.11.025\">https://doi.org/10.1016/j.isci.2019.11.025</a>.","ista":"Tabata S, Jevtic M, Kurashige N, Fuchida H, Kido M, Tani K, Zenmyo N, Uchinomiya S, Harada H, Itakura M, Hamachi I, Shigemoto R, Ojida A. 2019. Electron microscopic detection of single membrane proteins by a specific chemical labeling. iScience. 22(12), 256–268.","mla":"Tabata, Shigekazu, et al. “Electron Microscopic Detection of Single Membrane Proteins by a Specific Chemical Labeling.” <i>IScience</i>, vol. 22, no. 12, Elsevier, 2019, pp. 256–68, doi:<a href=\"https://doi.org/10.1016/j.isci.2019.11.025\">10.1016/j.isci.2019.11.025</a>.","short":"S. Tabata, M. Jevtic, N. Kurashige, H. Fuchida, M. Kido, K. Tani, N. Zenmyo, S. Uchinomiya, H. Harada, M. Itakura, I. Hamachi, R. Shigemoto, A. Ojida, IScience 22 (2019) 256–268."},"abstract":[{"lang":"eng","text":"Electron microscopy (EM) is a technology that enables visualization of single proteins at a nanometer resolution. However, current protein analysis by EM mainly relies on immunolabeling with gold-particle-conjugated antibodies, which is compromised by large size of antibody, precluding precise detection of protein location in biological samples. Here, we develop a specific chemical labeling method for EM detection of proteins at single-molecular level. Rational design of α-helical peptide tag and probe structure provided a complementary reaction pair that enabled specific cysteine conjugation of the tag. The developed chemical labeling with gold-nanoparticle-conjugated probe showed significantly higher labeling efficiency and detectability of high-density clusters of tag-fused G protein-coupled receptors in freeze-fracture replicas compared with immunogold labeling. Furthermore, in ultrathin sections, the spatial resolution of the chemical labeling was significantly higher than that of antibody-mediated labeling. These results demonstrate substantial advantages of the chemical labeling approach for single protein visualization by EM."}],"type":"journal_article","pmid":1,"has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:57Z","language":[{"iso":"eng"}],"status":"public","related_material":{"record":[{"status":"public","id":"11393","relation":"dissertation_contains"}]},"date_updated":"2026-05-14T22:30:39Z","page":"256-268","title":"Electron microscopic detection of single membrane proteins by a specific chemical labeling","author":[{"last_name":"Tabata","full_name":"Tabata, Shigekazu","id":"4427179E-F248-11E8-B48F-1D18A9856A87","first_name":"Shigekazu"},{"full_name":"Jevtic, Marijo","last_name":"Jevtic","id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87","first_name":"Marijo"},{"first_name":"Nobutaka","full_name":"Kurashige, Nobutaka","last_name":"Kurashige"},{"first_name":"Hirokazu","full_name":"Fuchida, Hirokazu","last_name":"Fuchida"},{"full_name":"Kido, Munetsugu","last_name":"Kido","first_name":"Munetsugu"},{"first_name":"Kazushi","full_name":"Tani, Kazushi","last_name":"Tani"},{"first_name":"Naoki","last_name":"Zenmyo","full_name":"Zenmyo, Naoki"},{"full_name":"Uchinomiya, Shohei","last_name":"Uchinomiya","first_name":"Shohei"},{"orcid":"0000-0001-7429-7896","full_name":"Harada, Harumi","last_name":"Harada","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Harumi"},{"last_name":"Itakura","full_name":"Itakura, Makoto","first_name":"Makoto"},{"last_name":"Hamachi","full_name":"Hamachi, Itaru","first_name":"Itaru"},{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi"},{"first_name":"Akio","full_name":"Ojida, Akio","last_name":"Ojida"}],"oa_version":"Published Version","ddc":["570"],"project":[{"call_identifier":"H2020","grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"720270","name":"Human Brain Project Specific Grant Agreement 1","_id":"25CBA828-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"publication":"iScience","year":"2019","publication_identifier":{"issn":["2589-0042"]},"article_type":"original","ec_funded":1,"date_published":"2019-12-20T00:00:00Z","intvolume":"        22","file":[{"date_created":"2020-02-04T10:48:36Z","file_name":"2019_iScience_Tabata.pdf","file_size":7197776,"creator":"dernst","access_level":"open_access","file_id":"7448","date_updated":"2020-07-14T12:47:57Z","relation":"main_file","checksum":"f3e90056a49f09b205b1c4f8c739ffd1","content_type":"application/pdf"}],"oa":1,"doi":"10.1016/j.isci.2019.11.025","day":"20"},{"quality_controlled":"1","abstract":[{"text":"Grid cells with their rigid hexagonal firing fields are thought to provide an invariant metric to the hippocampal cognitive map, yet environmental geometrical features have recently been shown to distort the grid structure. Given that the hippocampal role goes beyond space, we tested the influence of nonspatial information on the grid organization. We trained rats to daily learn three new reward locations on a cheeseboard maze while recording from the medial entorhinal cortex and the hippocampal CA1 region. Many grid fields moved toward goal location, leading to long-lasting deformations of the entorhinal map. Therefore, distortions in the grid structure contribute to goal representation during both learning and recall, which demonstrates that grid cells participate in mnemonic coding and do not merely provide a simple metric of space.","lang":"eng"}],"type":"journal_article","citation":{"apa":"Boccara, C. N., Nardin, M., Stella, F., O’Neill, J., &#38; Csicsvari, J. L. (2019). The entorhinal cognitive map is attracted to goals. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aav4837\">https://doi.org/10.1126/science.aav4837</a>","ieee":"C. N. Boccara, M. Nardin, F. Stella, J. O’Neill, and J. L. Csicsvari, “The entorhinal cognitive map is attracted to goals,” <i>Science</i>, vol. 363, no. 6434. American Association for the Advancement of Science, pp. 1443–1447, 2019.","ama":"Boccara CN, Nardin M, Stella F, O’Neill J, Csicsvari JL. The entorhinal cognitive map is attracted to goals. <i>Science</i>. 2019;363(6434):1443-1447. doi:<a href=\"https://doi.org/10.1126/science.aav4837\">10.1126/science.aav4837</a>","ista":"Boccara CN, Nardin M, Stella F, O’Neill J, Csicsvari JL. 2019. The entorhinal cognitive map is attracted to goals. Science. 363(6434), 1443–1447.","chicago":"Boccara, Charlotte N., Michele Nardin, Federico Stella, Joseph O’Neill, and Jozsef L Csicsvari. “The Entorhinal Cognitive Map Is Attracted to Goals.” <i>Science</i>. American Association for the Advancement of Science, 2019. <a href=\"https://doi.org/10.1126/science.aav4837\">https://doi.org/10.1126/science.aav4837</a>.","mla":"Boccara, Charlotte N., et al. “The Entorhinal Cognitive Map Is Attracted to Goals.” <i>Science</i>, vol. 363, no. 6434, American Association for the Advancement of Science, 2019, pp. 1443–47, doi:<a href=\"https://doi.org/10.1126/science.aav4837\">10.1126/science.aav4837</a>.","short":"C.N. Boccara, M. Nardin, F. Stella, J. O’Neill, J.L. Csicsvari, Science 363 (2019) 1443–1447."},"publisher":"American Association for the Advancement of Science","department":[{"_id":"JoCs"}],"volume":363,"external_id":{"isi":["000462738000034"]},"date_created":"2019-04-04T08:39:30Z","publication_status":"published","issue":"6434","scopus_import":"1","month":"03","_id":"6194","ec_funded":1,"year":"2019","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"article_type":"original","intvolume":"       363","date_published":"2019-03-29T00:00:00Z","day":"29","doi":"10.1126/science.aav4837","file":[{"relation":"main_file","content_type":"application/pdf","checksum":"5e6b16742cde10a560cfaf2130764da1","file_id":"7826","date_updated":"2020-07-14T12:47:23Z","access_level":"open_access","file_size":9045923,"creator":"dernst","file_name":"2019_Science_Boccara.pdf","date_created":"2020-05-14T09:11:10Z"}],"oa":1,"ddc":["570"],"project":[{"_id":"257A4776-B435-11E9-9278-68D0E5697425","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","grant_number":"281511","call_identifier":"FP7"},{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Science","isi":1,"oa_version":"Submitted Version","file_date_updated":"2020-07-14T12:47:23Z","has_accepted_license":"1","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"popular_science","id":"6062","status":"public"},{"relation":"dissertation_contains","id":"11932","status":"public"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/grid-cells-create-treasure-map-in-rat-brain/","description":"News on IST Homepage"}]},"page":"1443-1447","date_updated":"2026-05-14T22:30:42Z","author":[{"first_name":"Charlotte N.","full_name":"Boccara, Charlotte N.","last_name":"Boccara","id":"3FC06552-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7237-5109"},{"first_name":"Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","last_name":"Nardin","full_name":"Nardin, Michele","orcid":"0000-0001-8849-6570"},{"orcid":"0000-0001-9439-3148","last_name":"Stella","full_name":"Stella, Federico","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","first_name":"Federico"},{"last_name":"O'Neill","full_name":"O'Neill, Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87","first_name":"Joseph"},{"first_name":"Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L"}],"title":"The entorhinal cognitive map is attracted to goals"}]