[{"page":"77:1-77:12","ec_funded":1,"type":"conference","oa":1,"year":"2019","article_processing_charge":"No","publication_status":"published","file":[{"date_created":"2019-07-31T07:01:45Z","relation":"main_file","creator":"dernst","file_name":"2019_LIPICS_Kolmogorov.pdf","checksum":"f5ebee8eec6ae09e30365578ee63a492","file_size":575475,"access_level":"open_access","content_type":"application/pdf","file_id":"6738","date_updated":"2020-07-14T12:47:38Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2019-07-01T00:00:00Z","alternative_title":["LIPIcs"],"date_created":"2019-07-29T12:23:29Z","has_accepted_license":"1","abstract":[{"text":"A Valued Constraint Satisfaction Problem (VCSP) provides a common framework that can express a wide range of discrete optimization problems. A VCSP instance is given by a finite set of variables, a finite domain of labels, and an objective function to be minimized. This function is represented as a sum of terms where each term depends on a subset of the variables. To obtain different classes of optimization problems, one can restrict all terms to come from a fixed set Γ of cost functions, called a language. \r\nRecent breakthrough results have established a complete complexity classification of such classes with respect to language Γ: if all cost functions in Γ satisfy a certain algebraic condition then all Γ-instances can be solved in polynomial time, otherwise the problem is NP-hard. Unfortunately, testing this condition for a given language Γ is known to be NP-hard. We thus study exponential algorithms for this meta-problem. We show that the tractability condition of a finite-valued language Γ can be tested in O(3‾√3|D|⋅poly(size(Γ))) time, where D is the domain of Γ and poly(⋅) is some fixed polynomial. We also obtain a matching lower bound under the Strong Exponential Time Hypothesis (SETH). More precisely, we prove that for any constant δ<1 there is no O(3‾√3δ|D|) algorithm, assuming that SETH holds.","lang":"eng"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","language":[{"iso":"eng"}],"intvolume":" 132","status":"public","month":"07","ddc":["000"],"publication":"46th International Colloquium on Automata, Languages and Programming","publication_identifier":{"isbn":["978-3-95977-109-2"],"issn":["1868-8969"]},"file_date_updated":"2020-07-14T12:47:38Z","day":"01","arxiv":1,"license":"https://creativecommons.org/licenses/by/4.0/","conference":{"start_date":"2019-07-08","location":"Patras, Greece","name":"ICALP: Automata, Languages and Programming","end_date":"2019-07-12"},"external_id":{"arxiv":["1803.02289"]},"author":[{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir"}],"date_updated":"2025-07-10T11:53:47Z","title":"Testing the complexity of a valued CSP language","scopus_import":"1","department":[{"_id":"VlKo"}],"volume":132,"project":[{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"doi":"10.4230/LIPICS.ICALP.2019.77","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"V. Kolmogorov, in:, 46th International Colloquium on Automata, Languages and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 77:1-77:12.","chicago":"Kolmogorov, Vladimir. “Testing the Complexity of a Valued CSP Language.” In 46th International Colloquium on Automata, Languages and Programming, 132:77:1-77:12. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.ICALP.2019.77.","ama":"Kolmogorov V. Testing the complexity of a valued CSP language. In: 46th International Colloquium on Automata, Languages and Programming. Vol 132. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:77:1-77:12. doi:10.4230/LIPICS.ICALP.2019.77","apa":"Kolmogorov, V. (2019). Testing the complexity of a valued CSP language. In 46th International Colloquium on Automata, Languages and Programming (Vol. 132, p. 77:1-77:12). Patras, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ICALP.2019.77","ista":"Kolmogorov V. 2019. Testing the complexity of a valued CSP language. 46th International Colloquium on Automata, Languages and Programming. ICALP: Automata, Languages and Programming, LIPIcs, vol. 132, 77:1-77:12.","ieee":"V. Kolmogorov, “Testing the complexity of a valued CSP language,” in 46th International Colloquium on Automata, Languages and Programming, Patras, Greece, 2019, vol. 132, p. 77:1-77:12.","mla":"Kolmogorov, Vladimir. “Testing the Complexity of a Valued CSP Language.” 46th International Colloquium on Automata, Languages and Programming, vol. 132, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 77:1-77:12, doi:10.4230/LIPICS.ICALP.2019.77."},"_id":"6725","oa_version":"Published Version","quality_controlled":"1"},{"intvolume":" 11627","language":[{"iso":"eng"}],"publisher":"Springer Nature","date_created":"2019-07-29T12:25:31Z","abstract":[{"lang":"eng","text":"Randomness is an essential part of any secure cryptosystem, but many constructions rely on distributions that are not uniform. This is particularly true for lattice based cryptosystems, which more often than not make use of discrete Gaussian distributions over the integers. For practical purposes it is crucial to evaluate the impact that approximation errors have on the security of a scheme to provide the best possible trade-off between security and performance. Recent years have seen surprising results allowing to use relatively low precision while maintaining high levels of security. A key insight in these results is that sampling a distribution with low relative error can provide very strong security guarantees. Since floating point numbers provide guarantees on the relative approximation error, they seem a suitable tool in this setting, but it is not obvious which sampling algorithms can actually profit from them. While previous works have shown that inversion sampling can be adapted to provide a low relative error (Pöppelmann et al., CHES 2014; Prest, ASIACRYPT 2017), other works have called into question if this is possible for other sampling techniques (Zheng et al., Eprint report 2018/309). In this work, we consider all sampling algorithms that are popular in the cryptographic setting and analyze the relationship of floating point precision and the resulting relative error. We show that all of the algorithms either natively achieve a low relative error or can be adapted to do so."}],"month":"06","status":"public","publication":"Progress in Cryptology – AFRICACRYPT 2019","oa":1,"ec_funded":1,"type":"book_chapter","isi":1,"editor":[{"full_name":"Buchmann, J","last_name":"Buchmann","first_name":"J"},{"last_name":"Nitaj","first_name":"A","full_name":"Nitaj, A"},{"first_name":"T","last_name":"Rachidi","full_name":"Rachidi, T"}],"page":"157-180","date_published":"2019-06-29T00:00:00Z","place":"Cham","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","series_title":"LNCS","publication_status":"published","year":"2019","article_processing_charge":"No","citation":{"short":"M. Walter, in:, J. Buchmann, A. Nitaj, T. Rachidi (Eds.), Progress in Cryptology – AFRICACRYPT 2019, Springer Nature, Cham, 2019, pp. 157–180.","chicago":"Walter, Michael. “Sampling the Integers with Low Relative Error.” In Progress in Cryptology – AFRICACRYPT 2019, edited by J Buchmann, A Nitaj, and T Rachidi, 11627:157–80. LNCS. Cham: Springer Nature, 2019. https://doi.org/10.1007/978-3-030-23696-0_9.","apa":"Walter, M. (2019). Sampling the integers with low relative error. In J. Buchmann, A. Nitaj, & T. Rachidi (Eds.), Progress in Cryptology – AFRICACRYPT 2019 (Vol. 11627, pp. 157–180). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-23696-0_9","ista":"Walter M. 2019.Sampling the integers with low relative error. In: Progress in Cryptology – AFRICACRYPT 2019. vol. 11627, 157–180.","ama":"Walter M. Sampling the integers with low relative error. In: Buchmann J, Nitaj A, Rachidi T, eds. Progress in Cryptology – AFRICACRYPT 2019. Vol 11627. LNCS. Cham: Springer Nature; 2019:157-180. doi:10.1007/978-3-030-23696-0_9","ieee":"M. Walter, “Sampling the integers with low relative error,” in Progress in Cryptology – AFRICACRYPT 2019, vol. 11627, J. Buchmann, A. Nitaj, and T. Rachidi, Eds. Cham: Springer Nature, 2019, pp. 157–180.","mla":"Walter, Michael. “Sampling the Integers with Low Relative Error.” Progress in Cryptology – AFRICACRYPT 2019, edited by J Buchmann et al., vol. 11627, Springer Nature, 2019, pp. 157–80, doi:10.1007/978-3-030-23696-0_9."},"doi":"10.1007/978-3-030-23696-0_9","project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}],"volume":11627,"department":[{"_id":"KrPi"}],"scopus_import":"1","quality_controlled":"1","oa_version":"Preprint","main_file_link":[{"url":"https://eprint.iacr.org/2019/068","open_access":"1"}],"_id":"6726","external_id":{"isi":["001299240700009"]},"conference":{"start_date":"2019-07-09","location":"Rabat, Morocco","name":"AFRICACRYPT: International Conference on Cryptology in Africa","end_date":"2019-07-11"},"day":"29","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["978-3-0302-3695-3"],"eisbn":["978-3-0302-3696-0"]},"title":"Sampling the integers with low relative error","date_updated":"2025-09-10T10:38:28Z","author":[{"first_name":"Michael","orcid":"0000-0003-3186-2482","last_name":"Walter","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","full_name":"Walter, Michael"}]},{"day":"01","page":"1051-1060","arxiv":1,"conference":{"end_date":"2019-04-18","location":"Naha, Okinawa, Japan","name":"AISTATS: Artificial Intelligence and Statistics","start_date":"2019-04-16"},"type":"conference","oa":1,"external_id":{"arxiv":["1802.07301"]},"publication_status":"published","article_processing_charge":"No","year":"2019","author":[{"first_name":"Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco"},{"first_name":"Andrea","last_name":"Montanari","full_name":"Montanari, Andrea"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"On the connection between learning two-layers neural networks and tensor decomposition","date_updated":"2025-06-26T09:41:13Z","date_published":"2019-04-01T00:00:00Z","abstract":[{"lang":"eng","text":"We establish connections between the problem of learning a two-layer neural network and tensor decomposition. We consider a model with feature vectors x∈ℝd, r hidden units with weights {wi}1≤i≤r and output y∈ℝ, i.e., y=∑ri=1σ(w𝖳ix), with activation functions given by low-degree polynomials. In particular, if σ(x)=a0+a1x+a3x3, we prove that no polynomial-time learning algorithm can outperform the trivial predictor that assigns to each example the response variable 𝔼(y), when d3/2≪r≪d2. Our conclusion holds for a `natural data distribution', namely standard Gaussian feature vectors x, and output distributed according to a two-layer neural network with random isotropic weights, and under a certain complexity-theoretic assumption on tensor decomposition. Roughly speaking, we assume that no polynomial-time algorithm can substantially outperform current methods for tensor decomposition based on the sum-of-squares hierarchy. We also prove generalizations of this statement for higher degree polynomial activations, and non-random weight vectors. Remarkably, several existing algorithms for learning two-layer networks with rigorous guarantees are based on tensor decomposition. Our results support the idea that this is indeed the core computational difficulty in learning such networks, under the stated generative model for the data. As a side result, we show that under this model learning the network requires accurate learning of its weights, a property that does not hold in a more general setting. "}],"date_created":"2019-07-31T09:31:26Z","publisher":"Proceedings of Machine Learning Research","volume":89,"language":[{"iso":"eng"}],"intvolume":" 89","citation":{"ama":"Mondelli M, Montanari A. On the connection between learning two-layers neural networks and tensor  decomposition. In: Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics. Vol 89. Proceedings of Machine Learning Research; 2019:1051-1060.","apa":"Mondelli, M., & Montanari, A. (2019). On the connection between learning two-layers neural networks and tensor  decomposition. In Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics (Vol. 89, pp. 1051–1060). Naha, Okinawa, Japan: Proceedings of Machine Learning Research.","ista":"Mondelli M, Montanari A. 2019. On the connection between learning two-layers neural networks and tensor  decomposition. Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics. AISTATS: Artificial Intelligence and Statistics vol. 89, 1051–1060.","mla":"Mondelli, Marco, and Andrea Montanari. “On the Connection between Learning Two-Layers Neural Networks and Tensor  Decomposition.” Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics, vol. 89, Proceedings of Machine Learning Research, 2019, pp. 1051–60.","ieee":"M. Mondelli and A. Montanari, “On the connection between learning two-layers neural networks and tensor  decomposition,” in Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics, Naha, Okinawa, Japan, 2019, vol. 89, pp. 1051–1060.","short":"M. Mondelli, A. Montanari, in:, Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics, Proceedings of Machine Learning Research, 2019, pp. 1051–1060.","chicago":"Mondelli, Marco, and Andrea Montanari. “On the Connection between Learning Two-Layers Neural Networks and Tensor  Decomposition.” In Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics, 89:1051–60. Proceedings of Machine Learning Research, 2019."},"extern":"1","_id":"6747","month":"04","publication":"Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics","oa_version":"Preprint","status":"public","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.07301"}]},{"status":"public","month":"11","publication":"IEEE Transactions on Signal Processing","issue":"22","language":[{"iso":"eng"}],"intvolume":" 67","date_created":"2019-07-31T09:51:14Z","abstract":[{"text":"Polar codes have gained extensive attention during the past few years and recently they have been selected for the next generation of wireless communications standards (5G). Successive-cancellation-based (SC-based) decoders, such as SC list (SCL) and SC flip (SCF), provide a reasonable error performance for polar codes at the cost of low decoding speed. Fast SC-based decoders, such as Fast-SSC, Fast-SSCL, and Fast-SSCF, identify the special constituent codes in a polar code graph off-line, produce a list of operations, store the list in memory, and feed the list to the decoder to decode the constituent codes in order efficiently, thus increasing the decoding speed. However, the list of operations is dependent on the code rate and as the rate changes, a new list is produced, making fast SC-based decoders not rate-flexible. In this paper, we propose a completely rate-flexible fast SC-based decoder by creating the list of operations directly in hardware, with low implementation complexity. We further propose a hardware architecture implementing the proposed method and show that the area occupation of the rate-flexible fast SC-based decoder in this paper is only 38% of the total area of the memory-based base-line decoder when 5G code rates are supported. ","lang":"eng"}],"publisher":"IEEE","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2019-11-15T00:00:00Z","article_number":"8854897","article_processing_charge":"No","year":"2019","publication_status":"published","type":"journal_article","oa":1,"_id":"6750","main_file_link":[{"url":"https://arxiv.org/abs/1903.09203","open_access":"1"}],"quality_controlled":"1","oa_version":"Preprint","citation":{"mla":"Hashemi, Seyyed Ali, et al. “Rate-Flexible Fast Polar Decoders.” IEEE Transactions on Signal Processing, vol. 67, no. 22, 8854897, IEEE, 2019, doi:10.1109/TSP.2019.2944738.","ieee":"S. A. Hashemi, C. Condo, M. Mondelli, and W. J. Gross, “Rate-flexible fast polar decoders,” IEEE Transactions on Signal Processing, vol. 67, no. 22. IEEE, 2019.","apa":"Hashemi, S. A., Condo, C., Mondelli, M., & Gross, W. J. (2019). Rate-flexible fast polar decoders. IEEE Transactions on Signal Processing. IEEE. https://doi.org/10.1109/TSP.2019.2944738","ista":"Hashemi SA, Condo C, Mondelli M, Gross WJ. 2019. Rate-flexible fast polar decoders. IEEE Transactions on Signal Processing. 67(22), 8854897.","ama":"Hashemi SA, Condo C, Mondelli M, Gross WJ. Rate-flexible fast polar decoders. IEEE Transactions on Signal Processing. 2019;67(22). doi:10.1109/TSP.2019.2944738","chicago":"Hashemi, Seyyed Ali, Carlo Condo, Marco Mondelli, and Warren J Gross. “Rate-Flexible Fast Polar Decoders.” IEEE Transactions on Signal Processing. IEEE, 2019. https://doi.org/10.1109/TSP.2019.2944738.","short":"S.A. Hashemi, C. Condo, M. Mondelli, W.J. Gross, IEEE Transactions on Signal Processing 67 (2019)."},"doi":"10.1109/TSP.2019.2944738","scopus_import":"1","department":[{"_id":"MaMo"}],"volume":67,"date_updated":"2025-01-14T14:34:26Z","title":"Rate-flexible fast polar decoders","author":[{"full_name":"Hashemi, Seyyed Ali","last_name":"Hashemi","first_name":"Seyyed Ali"},{"last_name":"Condo","first_name":"Carlo","full_name":"Condo, Carlo"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli","first_name":"Marco"},{"last_name":"Gross","first_name":"Warren J","full_name":"Gross, Warren J"}],"external_id":{"arxiv":["1903.09203"]},"publication_identifier":{"issn":["1053-587X"]},"article_type":"original","day":"15","arxiv":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"},{"_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23","name":"Rigorous Systems Engineering"},{"_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02369","name":"Formal Methods meets Algorithmic Game Theory"}],"citation":{"chicago":"Avni, Guy, Thomas A Henzinger, and Ventsislav K Chonev. “Infinite-Duration Bidding Games.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3340295.","short":"G. Avni, T.A. Henzinger, V.K. Chonev, Journal of the ACM 66 (2019).","mla":"Avni, Guy, et al. “Infinite-Duration Bidding Games.” Journal of the ACM, vol. 66, no. 4, 31, ACM, 2019, doi:10.1145/3340295.","ieee":"G. Avni, T. A. Henzinger, and V. K. Chonev, “Infinite-duration bidding games,” Journal of the ACM, vol. 66, no. 4. ACM, 2019.","ama":"Avni G, Henzinger TA, Chonev VK. Infinite-duration bidding games. Journal of the ACM. 2019;66(4). doi:10.1145/3340295","ista":"Avni G, Henzinger TA, Chonev VK. 2019. Infinite-duration bidding games. Journal of the ACM. 66(4), 31.","apa":"Avni, G., Henzinger, T. A., & Chonev, V. K. (2019). Infinite-duration bidding games. Journal of the ACM. ACM. https://doi.org/10.1145/3340295"},"doi":"10.1145/3340295","scopus_import":"1","department":[{"_id":"ToHe"}],"volume":66,"_id":"6752","oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.01433"}],"external_id":{"arxiv":["1705.01433"],"isi":["000487714900008"]},"day":"16","publication_identifier":{"issn":["0004-5411"],"eissn":["1557-735X"]},"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"950"}]},"arxiv":1,"title":"Infinite-duration bidding games","date_updated":"2025-07-10T11:53:47Z","author":[{"id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","last_name":"Avni","first_name":"Guy"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A"},{"first_name":"Ventsislav K","last_name":"Chonev","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","full_name":"Chonev, Ventsislav K"}],"language":[{"iso":"eng"}],"intvolume":" 66","date_created":"2019-08-04T21:59:16Z","abstract":[{"text":"Two-player games on graphs are widely studied in formal methods, as they model the interaction between a system and its environment. The game is played by moving a token throughout a graph to produce an infinite path. There are several common modes to determine how the players move the token through the graph; e.g., in turn-based games the players alternate turns in moving the token. We study the bidding mode of moving the token, which, to the best of our knowledge, has never been studied in infinite-duration games. The following bidding rule was previously defined and called Richman bidding. Both players have separate budgets, which sum up to 1. In each turn, a bidding takes place: Both players submit bids simultaneously, where a bid is legal if it does not exceed the available budget, and the higher bidder pays his bid to the other player and moves the token. The central question studied in bidding games is a necessary and sufficient initial budget for winning the game: a threshold budget in a vertex is a value t ∈ [0, 1] such that if Player 1’s budget exceeds t, he can win the game; and if Player 2’s budget exceeds 1 − t, he can win the game. Threshold budgets were previously shown to exist in every vertex of a reachability game, which have an interesting connection with random-turn games—a sub-class of simple stochastic games in which the player who moves is chosen randomly. We show the existence of threshold budgets for a qualitative class of infinite-duration games, namely parity games, and a quantitative class, namely mean-payoff games. The key component of the proof is a quantitative solution to strongly connected mean-payoff bidding games in which we extend the connection with random-turn games to these games, and construct explicit optimal strategies for both players.","lang":"eng"}],"publisher":"ACM","publication":"Journal of the ACM","status":"public","month":"07","issue":"4","isi":1,"type":"journal_article","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"31","date_published":"2019-07-16T00:00:00Z","publication_status":"published","year":"2019","article_processing_charge":"No"},{"publication_identifier":{"eissn":["1759-6653"]},"file_date_updated":"2020-07-14T12:47:39Z","article_type":"original","day":"01","external_id":{"pmid":["31273378"],"isi":["000484039500018"]},"author":[{"id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","full_name":"Picard, Marion A L","orcid":"0000-0002-8101-2518","last_name":"Picard","first_name":"Marion A L"},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","last_name":"Roquis","full_name":"Roquis, David"},{"full_name":"Bulla, Ingo","first_name":"Ingo","last_name":"Bulla"},{"last_name":"Augusto","first_name":"Ronaldo C.","full_name":"Augusto, Ronaldo C."},{"last_name":"Arancibia","first_name":"Nathalie","full_name":"Arancibia, Nathalie"},{"full_name":"Grunau, Christoph","last_name":"Grunau","first_name":"Christoph"},{"full_name":"Boissier, Jérôme","first_name":"Jérôme","last_name":"Boissier"},{"full_name":"Cosseau, Céline","last_name":"Cosseau","first_name":"Céline"}],"date_updated":"2025-05-14T11:08:50Z","title":"Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome","volume":11,"department":[{"_id":"BeVi"}],"scopus_import":"1","citation":{"ama":"Picard MAL, Vicoso B, Roquis D, et al. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome biology and evolution. 2019;11(7):1909-1922. doi:10.1093/gbe/evz133","ista":"Picard MAL, Vicoso B, Roquis D, Bulla I, Augusto RC, Arancibia N, Grunau C, Boissier J, Cosseau C. 2019. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome biology and evolution. 11(7), 1909–1922.","apa":"Picard, M. A. L., Vicoso, B., Roquis, D., Bulla, I., Augusto, R. C., Arancibia, N., … Cosseau, C. (2019). Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evz133","mla":"Picard, Marion A. L., et al. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” Genome Biology and Evolution, vol. 11, no. 7, Oxford University Press, 2019, pp. 1909–22, doi:10.1093/gbe/evz133.","ieee":"M. A. L. Picard et al., “Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome,” Genome biology and evolution, vol. 11, no. 7. Oxford University Press, pp. 1909–1922, 2019.","short":"M.A.L. Picard, B. Vicoso, D. Roquis, I. Bulla, R.C. Augusto, N. Arancibia, C. Grunau, J. Boissier, C. Cosseau, Genome Biology and Evolution 11 (2019) 1909–1922.","chicago":"Picard, Marion A L, Beatriz Vicoso, David Roquis, Ingo Bulla, Ronaldo C. Augusto, Nathalie Arancibia, Christoph Grunau, Jérôme Boissier, and Céline Cosseau. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” Genome Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/gbe/evz133."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1093/gbe/evz133","quality_controlled":"1","oa_version":"Published Version","_id":"6755","page":"1909-1922","oa":1,"isi":1,"type":"journal_article","file":[{"file_size":580205,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-08-05T07:55:02Z","creator":"dernst","checksum":"f9e8f6863a406dcc5a36b2be001c138c","file_name":"2019_GenomeBiology_Picard.pdf","date_updated":"2020-07-14T12:47:39Z","file_id":"6765"}],"year":"2019","article_processing_charge":"No","publication_status":"published","date_published":"2019-07-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","abstract":[{"lang":"eng","text":"Differentiated sex chromosomes are accompanied by a difference in gene dose between X/Z-specific and autosomal genes. At the transcriptomic level, these sex-linked genes can lead to expression imbalance, or gene dosage can be compensated by epigenetic mechanisms and results into expression level equalization. Schistosoma mansoni has been previously described as a ZW species (i.e., female heterogamety, in opposition to XY male heterogametic species) with a partial dosage compensation, but underlying mechanisms are still unexplored. Here, we combine transcriptomic (RNA-Seq) and epigenetic data (ChIP-Seq against H3K4me3, H3K27me3,andH4K20me1histonemarks) in free larval cercariae and intravertebrate parasitic stages. For the first time, we describe differences in dosage compensation status in ZW females, depending on the parasitic status: free cercariae display global dosage compensation, whereas intravertebrate stages show a partial dosage compensation. We also highlight regional differences of gene expression along the Z chromosome in cercariae, but not in the intravertebrate stages. Finally, we feature a consistent permissive chromatin landscape of the Z chromosome in both sexes and stages. We argue that dosage compensation in schistosomes is characterized by chromatin remodeling mechanisms in the Z-specific region."}],"has_accepted_license":"1","pmid":1,"date_created":"2019-08-04T21:59:18Z","intvolume":" 11","language":[{"iso":"eng"}],"issue":"7","acknowledged_ssus":[{"_id":"CampIT"}],"ddc":["570"],"status":"public","month":"07","publication":"Genome biology and evolution"},{"title":"On grounded L-graphs and their relatives","date_updated":"2025-06-26T12:25:39Z","author":[{"full_name":"Jelínek, Vít","last_name":"Jelínek","first_name":"Vít"},{"last_name":"Töpfer","first_name":"Martin","full_name":"Töpfer, Martin","id":"4B865388-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["1808.04148"]},"OA_place":"publisher","DOAJ_listed":"1","arxiv":1,"day":"19","file_date_updated":"2020-07-14T12:47:39Z","article_type":"original","publication_identifier":{"eissn":["1077-8926"]},"oa_version":"Published Version","quality_controlled":"1","_id":"6759","citation":{"short":"V. Jelínek, M. Töpfer, Electronic Journal of Combinatorics 26 (2019).","chicago":"Jelínek, Vít, and Martin Töpfer. “On Grounded L-Graphs and Their Relatives.” Electronic Journal of Combinatorics. Electronic Journal of Combinatorics, 2019. https://doi.org/10.37236/8096.","apa":"Jelínek, V., & Töpfer, M. (2019). On grounded L-graphs and their relatives. Electronic Journal of Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/8096","ista":"Jelínek V, Töpfer M. 2019. On grounded L-graphs and their relatives. Electronic Journal of Combinatorics. 26(3), P3.17.","ama":"Jelínek V, Töpfer M. On grounded L-graphs and their relatives. Electronic Journal of Combinatorics. 2019;26(3). doi:10.37236/8096","mla":"Jelínek, Vít, and Martin Töpfer. “On Grounded L-Graphs and Their Relatives.” Electronic Journal of Combinatorics, vol. 26, no. 3, P3.17, Electronic Journal of Combinatorics, 2019, doi:10.37236/8096.","ieee":"V. Jelínek and M. Töpfer, “On grounded L-graphs and their relatives,” Electronic Journal of Combinatorics, vol. 26, no. 3. Electronic Journal of Combinatorics, 2019."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.37236/8096","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"volume":26,"scopus_import":"1","department":[{"_id":"DaAl"}],"article_number":"P3.17","date_published":"2019-07-19T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"6764","date_updated":"2020-07-14T12:47:39Z","file_name":"2019_eJourCombinatorics_Jelinek.pdf","checksum":"20fc366fc6683ef0b074a019b73a663a","creator":"dernst","date_created":"2019-08-05T06:46:55Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":533697}],"publication_status":"published","article_processing_charge":"Yes","year":"2019","oa":1,"ec_funded":1,"type":"journal_article","corr_author":"1","publication":"Electronic Journal of Combinatorics","status":"public","ddc":["510"],"month":"07","issue":"3","intvolume":" 26","language":[{"iso":"eng"}],"OA_type":"gold","publisher":"Electronic Journal of Combinatorics","has_accepted_license":"1","abstract":[{"text":"We consider the graph class Grounded-L corresponding to graphs that admit an intersection representation by L-shaped curves, where additionally the topmost points of each curve are assumed to belong to a common horizontal line. We prove that Grounded-L graphs admit an equivalent characterisation in terms of vertex ordering with forbidden patterns. \r\nWe also compare this class to related intersection classes, such as the grounded segment graphs, the monotone L-graphs (a.k.a. max point-tolerance graphs), or the outer-1-string graphs. We give constructions showing that these classes are all distinct and satisfy only trivial or previously known inclusions.","lang":"eng"}],"date_created":"2019-08-04T21:59:20Z"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.04200"}],"oa_version":"Preprint","quality_controlled":"1","_id":"6762","volume":17,"department":[{"_id":"JuFi"}],"scopus_import":"1","doi":"10.1137/18M1207272","citation":{"chicago":"Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density Functional Theory Motivated by Photovoltaics.” Multiscale Modeling and Simulation. SIAM, 2019. https://doi.org/10.1137/18M1207272.","short":"G. Friesecke, M. Kniely, Multiscale Modeling and Simulation 17 (2019) 926–947.","ieee":"G. Friesecke and M. Kniely, “New optimal control problems in density functional theory motivated by photovoltaics,” Multiscale Modeling and Simulation, vol. 17, no. 3. SIAM, pp. 926–947, 2019.","mla":"Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density Functional Theory Motivated by Photovoltaics.” Multiscale Modeling and Simulation, vol. 17, no. 3, SIAM, 2019, pp. 926–47, doi:10.1137/18M1207272.","ama":"Friesecke G, Kniely M. New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. 2019;17(3):926-947. doi:10.1137/18M1207272","apa":"Friesecke, G., & Kniely, M. (2019). New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. SIAM. https://doi.org/10.1137/18M1207272","ista":"Friesecke G, Kniely M. 2019. New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. 17(3), 926–947."},"author":[{"last_name":"Friesecke","first_name":"Gero","full_name":"Friesecke, Gero"},{"orcid":"0000-0001-5645-4333","last_name":"Kniely","first_name":"Michael","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","full_name":"Kniely, Michael"}],"date_updated":"2025-07-10T11:53:49Z","title":"New optimal control problems in density functional theory motivated by photovoltaics","arxiv":1,"publication_identifier":{"eissn":["1540-3467"],"issn":["1540-3459"]},"day":"16","external_id":{"arxiv":["1808.04200"],"isi":["000487931800002"]},"issue":"3","month":"07","status":"public","publication":"Multiscale Modeling and Simulation","publisher":"SIAM","date_created":"2019-08-04T21:59:21Z","abstract":[{"text":"We present and study novel optimal control problems motivated by the search for photovoltaic materials with high power-conversion efficiency. The material must perform the first step: convert light (photons) into electronic excitations. We formulate various desirable properties of the excitations as mathematical control goals at the Kohn-Sham-DFT level\r\nof theory, with the control being given by the nuclear charge distribution. We prove that nuclear distributions exist which give rise to optimal HOMO-LUMO excitations, and present illustrative numerical simulations for 1D finite nanocrystals. We observe pronounced goal-dependent features such as large electron-hole separation, and a hierarchy of length scales: internal HOMO and LUMO wavelengths < atomic spacings < (irregular) fluctuations of the doping profiles < system size.","lang":"eng"}],"intvolume":" 17","language":[{"iso":"eng"}],"article_processing_charge":"No","year":"2019","publication_status":"published","date_published":"2019-07-16T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"926-947","oa":1,"isi":1,"type":"journal_article"},{"file":[{"creator":"dernst","file_name":"2019_NatureComm_Zhang.pdf","checksum":"d2c654fdb97f33078f606fe0c298bf6e","relation":"main_file","date_created":"2019-08-12T07:09:20Z","content_type":"application/pdf","access_level":"open_access","file_size":6406141,"file_id":"6798","date_updated":"2020-07-14T12:47:40Z"}],"publication_status":"published","article_processing_charge":"No","year":"2019","date_published":"2019-08-02T00:00:00Z","article_number":"3480","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"ec_funded":1,"type":"journal_article","isi":1,"ddc":["580"],"month":"08","publication":"Nature Communications","status":"public","publisher":"Springer Nature","has_accepted_license":"1","date_created":"2019-08-09T08:46:26Z","pmid":1,"abstract":[{"text":"An important adaptation during colonization of land by plants is gravitropic growth of roots, which enabled roots to reach water and nutrients, and firmly anchor plants in the ground. Here we provide insights into the evolution of an efficient root gravitropic mechanism in the seed plants. Architectural innovation, with gravity perception constrained in the root tips\r\nalong with a shootward transport route for the phytohormone auxin, appeared only upon the emergence of seed plants. Interspecies complementation and protein domain swapping revealed functional innovations within the PIN family of auxin transporters leading to the evolution of gravitropism-specific PINs. The unique apical/shootward subcellular localization of PIN proteins is the major evolutionary innovation that connected the anatomically separated sites of gravity perception and growth response via the mobile auxin signal. We conclude that the crucial anatomical and functional components emerged hand-in-hand to facilitate the evolution of fast gravitropic response, which is one of the major adaptations of seed plants to dry land.","lang":"eng"}],"intvolume":" 10","language":[{"iso":"eng"}],"author":[{"id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956","last_name":"Zhang","first_name":"Yuzhou"},{"full_name":"Xiao, G","last_name":"Xiao","first_name":"G"},{"full_name":"Wang, X","first_name":"X","last_name":"Wang"},{"id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","last_name":"Zhang","first_name":"Xixi"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"title":"Evolution of fast root gravitropism in seed plants","date_updated":"2025-04-14T07:45:04Z","day":"02","file_date_updated":"2020-07-14T12:47:40Z","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/when-plant-roots-learned-to-follow-gravity/"}]},"article_type":"original","publication_identifier":{"issn":["2041-1723"]},"external_id":{"pmid":["31375675"],"isi":["000478576500012"]},"quality_controlled":"1","oa_version":"Published Version","_id":"6778","volume":10,"department":[{"_id":"JiFr"}],"scopus_import":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"Y. Zhang, G. Xiao, X. Wang, X. Zhang, J. Friml, Nature Communications 10 (2019).","chicago":"Zhang, Yuzhou, G Xiao, X Wang, Xixi Zhang, and Jiří Friml. “Evolution of Fast Root Gravitropism in Seed Plants.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-11471-8.","apa":"Zhang, Y., Xiao, G., Wang, X., Zhang, X., & Friml, J. (2019). Evolution of fast root gravitropism in seed plants. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-11471-8","ista":"Zhang Y, Xiao G, Wang X, Zhang X, Friml J. 2019. Evolution of fast root gravitropism in seed plants. Nature Communications. 10, 3480.","ama":"Zhang Y, Xiao G, Wang X, Zhang X, Friml J. Evolution of fast root gravitropism in seed plants. Nature Communications. 2019;10. doi:10.1038/s41467-019-11471-8","mla":"Zhang, Yuzhou, et al. “Evolution of Fast Root Gravitropism in Seed Plants.” Nature Communications, vol. 10, 3480, Springer Nature, 2019, doi:10.1038/s41467-019-11471-8.","ieee":"Y. Zhang, G. Xiao, X. Wang, X. Zhang, and J. Friml, “Evolution of fast root gravitropism in seed plants,” Nature Communications, vol. 10. Springer Nature, 2019."},"doi":"10.1038/s41467-019-11471-8","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"issue":"1","status":"public","ddc":["532"],"month":"07","publication":"Physical Review E","date_created":"2019-08-09T09:40:41Z","abstract":[{"text":"Recent studies suggest that unstable recurrent solutions of the Navier-Stokes equation provide new insights\r\ninto dynamics of turbulent flows. In this study, we compute an extensive network of dynamical connections\r\nbetween such solutions in a weakly turbulent quasi-two-dimensional Kolmogorov flow that lies in the inversion symmetric subspace. In particular, we find numerous isolated heteroclinic connections between different\r\ntypes of solutions—equilibria, periodic, and quasiperiodic orbits—as well as continua of connections forming\r\nhigher-dimensional connecting manifolds. We also compute a homoclinic connection of a periodic orbit and\r\nprovide strong evidence that the associated homoclinic tangle forms the chaotic repeller that underpins transient\r\nturbulence in the symmetric subspace.","lang":"eng"}],"publisher":"American Physical Society","language":[{"iso":"eng"}],"intvolume":" 100","publication_status":"published","article_processing_charge":"No","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2019-07-25T00:00:00Z","article_number":"013112","type":"journal_article","ec_funded":1,"isi":1,"oa":1,"_id":"6779","oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1907.05860","open_access":"1"}],"department":[{"_id":"BjHo"}],"scopus_import":"1","volume":100,"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"doi":"10.1103/physreve.100.013112","citation":{"ieee":"B. Suri, R. K. Pallantla, M. F. Schatz, and R. O. Grigoriev, “Heteroclinic and homoclinic connections in a Kolmogorov-like flow,” Physical Review E, vol. 100, no. 1. American Physical Society, 2019.","mla":"Suri, Balachandra, et al. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.” Physical Review E, vol. 100, no. 1, 013112, American Physical Society, 2019, doi:10.1103/physreve.100.013112.","apa":"Suri, B., Pallantla, R. K., Schatz, M. F., & Grigoriev, R. O. (2019). Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.100.013112","ama":"Suri B, Pallantla RK, Schatz MF, Grigoriev RO. Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. 2019;100(1). doi:10.1103/physreve.100.013112","ista":"Suri B, Pallantla RK, Schatz MF, Grigoriev RO. 2019. Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. 100(1), 013112.","chicago":"Suri, Balachandra, Ravi Kumar Pallantla, Michael F. Schatz, and Roman O. Grigoriev. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.” Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/physreve.100.013112.","short":"B. Suri, R.K. Pallantla, M.F. Schatz, R.O. Grigoriev, Physical Review E 100 (2019)."},"author":[{"id":"47A5E706-F248-11E8-B48F-1D18A9856A87","full_name":"Suri, Balachandra","last_name":"Suri","first_name":"Balachandra"},{"full_name":"Pallantla, Ravi Kumar","first_name":"Ravi Kumar","last_name":"Pallantla"},{"full_name":"Schatz, Michael F.","last_name":"Schatz","first_name":"Michael F."},{"last_name":"Grigoriev","first_name":"Roman O.","full_name":"Grigoriev, Roman O."}],"title":"Heteroclinic and homoclinic connections in a Kolmogorov-like flow","date_updated":"2025-04-15T06:50:28Z","day":"25","article_type":"original","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"arxiv":1,"external_id":{"arxiv":["1907.05860"],"isi":["000477911800012"]}},{"date_updated":"2025-04-14T13:46:26Z","title":"Molecular noise of innate immunity shapes bacteria-phage ecologies","author":[{"last_name":"Ruess","orcid":"0000-0003-1615-3282","first_name":"Jakob","full_name":"Ruess, Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maros","orcid":"0000-0001-7460-7479","last_name":"Pleska","id":"4569785E-F248-11E8-B48F-1D18A9856A87","full_name":"Pleska, Maros"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","first_name":"Calin C","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"external_id":{"isi":["000481577700032"]},"article_type":"original","file_date_updated":"2020-07-14T12:47:40Z","related_material":{"record":[{"relation":"research_data","id":"9786","status":"public"}]},"publication_identifier":{"eissn":["1553-7358"]},"day":"02","_id":"6784","quality_controlled":"1","oa_version":"Published Version","project":[{"_id":"251D65D8-B435-11E9-9278-68D0E5697425","grant_number":"24210","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level"},{"_id":"251BCBEC-B435-11E9-9278-68D0E5697425","grant_number":"RGY0079/2011","name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ieee":"J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Molecular noise of innate immunity shapes bacteria-phage ecologies,” PLoS Computational Biology, vol. 15, no. 7. Public Library of Science, 2019.","mla":"Ruess, Jakob, et al. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” PLoS Computational Biology, vol. 15, no. 7, e1007168, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007168.","apa":"Ruess, J., Pleska, M., Guet, C. C., & Tkačik, G. (2019). Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007168","ama":"Ruess J, Pleska M, Guet CC, Tkačik G. Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. 2019;15(7). doi:10.1371/journal.pcbi.1007168","ista":"Ruess J, Pleska M, Guet CC, Tkačik G. 2019. Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. 15(7), e1007168.","chicago":"Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” PLoS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007168.","short":"J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, PLoS Computational Biology 15 (2019)."},"doi":"10.1371/journal.pcbi.1007168","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"scopus_import":"1","volume":15,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"e1007168","date_published":"2019-07-02T00:00:00Z","year":"2019","article_processing_charge":"No","publication_status":"published","file":[{"date_created":"2019-08-12T12:27:26Z","relation":"main_file","checksum":"7ded4721b41c2a0fc66a1c634540416a","creator":"dernst","file_name":"2019_PlosComputBiology_Ruess.pdf","file_size":2200003,"access_level":"open_access","content_type":"application/pdf","file_id":"6803","date_updated":"2020-07-14T12:47:40Z"}],"type":"journal_article","isi":1,"oa":1,"month":"07","publication":"PLoS Computational Biology","status":"public","ddc":["570"],"issue":"7","language":[{"iso":"eng"}],"intvolume":" 15","date_created":"2019-08-11T21:59:19Z","abstract":[{"text":"Mathematical models have been used successfully at diverse scales of biological organization, ranging from ecology and population dynamics to stochastic reaction events occurring between individual molecules in single cells. Generally, many biological processes unfold across multiple scales, with mutations being the best studied example of how stochasticity at the molecular scale can influence outcomes at the population scale. In many other contexts, however, an analogous link between micro- and macro-scale remains elusive, primarily due to the challenges involved in setting up and analyzing multi-scale models. Here, we employ such a model to investigate how stochasticity propagates from individual biochemical reaction events in the bacterial innate immune system to the ecology of bacteria and bacterial viruses. We show analytically how the dynamics of bacterial populations are shaped by the activities of immunity-conferring enzymes in single cells and how the ecological consequences imply optimal bacterial defense strategies against viruses. Our results suggest that bacterial populations in the presence of viruses can either optimize their initial growth rate or their population size, with the first strategy favoring simple immunity featuring a single restriction modification system and the second strategy favoring complex bacterial innate immunity featuring several simultaneously active restriction modification systems.","lang":"eng"}],"has_accepted_license":"1","publisher":"Public Library of Science"},{"arxiv":1,"file_date_updated":"2020-07-14T12:47:40Z","publication_identifier":{"eissn":["2160-3308"]},"article_type":"original","day":"08","external_id":{"isi":["000467402900001"],"arxiv":["1807.11238"]},"author":[{"full_name":"Hubert, Colin","first_name":"Colin","last_name":"Hubert"},{"full_name":"Baruchi, Yifat","last_name":"Baruchi","first_name":"Yifat"},{"first_name":"Yotam","last_name":"Mazuz-Harpaz","full_name":"Mazuz-Harpaz, Yotam"},{"last_name":"Cohen","first_name":"Kobi","full_name":"Cohen, Kobi"},{"first_name":"Klaus","last_name":"Biermann","full_name":"Biermann, Klaus"},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802"},{"full_name":"West, Ken","first_name":"Ken","last_name":"West"},{"full_name":"Pfeiffer, Loren","last_name":"Pfeiffer","first_name":"Loren"},{"first_name":"Ronen","last_name":"Rapaport","full_name":"Rapaport, Ronen"},{"last_name":"Santos","first_name":"Paulo","full_name":"Santos, Paulo"}],"date_updated":"2025-04-15T07:59:29Z","title":"Attractive dipolar coupling between stacked exciton fluids","volume":9,"department":[{"_id":"MiLe"}],"scopus_import":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1103/PhysRevX.9.021026","citation":{"short":"C. Hubert, Y. Baruchi, Y. Mazuz-Harpaz, K. Cohen, K. Biermann, M. Lemeshko, K. West, L. Pfeiffer, R. Rapaport, P. Santos, Physical Review X 9 (2019).","chicago":"Hubert, Colin, Yifat Baruchi, Yotam Mazuz-Harpaz, Kobi Cohen, Klaus Biermann, Mikhail Lemeshko, Ken West, Loren Pfeiffer, Ronen Rapaport, and Paulo Santos. “Attractive Dipolar Coupling between Stacked Exciton Fluids.” Physical Review X. American Physical Society, 2019. https://doi.org/10.1103/PhysRevX.9.021026.","ama":"Hubert C, Baruchi Y, Mazuz-Harpaz Y, et al. Attractive dipolar coupling between stacked exciton fluids. Physical Review X. 2019;9(2). doi:10.1103/PhysRevX.9.021026","apa":"Hubert, C., Baruchi, Y., Mazuz-Harpaz, Y., Cohen, K., Biermann, K., Lemeshko, M., … Santos, P. (2019). Attractive dipolar coupling between stacked exciton fluids. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.9.021026","ista":"Hubert C, Baruchi Y, Mazuz-Harpaz Y, Cohen K, Biermann K, Lemeshko M, West K, Pfeiffer L, Rapaport R, Santos P. 2019. Attractive dipolar coupling between stacked exciton fluids. Physical Review X. 9(2), 021026.","ieee":"C. Hubert et al., “Attractive dipolar coupling between stacked exciton fluids,” Physical Review X, vol. 9, no. 2. American Physical Society, 2019.","mla":"Hubert, Colin, et al. “Attractive Dipolar Coupling between Stacked Exciton Fluids.” Physical Review X, vol. 9, no. 2, 021026, American Physical Society, 2019, doi:10.1103/PhysRevX.9.021026."},"project":[{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa_version":"Published Version","_id":"6786","oa":1,"type":"journal_article","isi":1,"file":[{"date_updated":"2020-07-14T12:47:40Z","file_id":"6802","content_type":"application/pdf","access_level":"open_access","file_size":1193550,"creator":"dernst","checksum":"065ff82ee4a1d2c3773ce4b76ff4213c","file_name":"2019_PhysReviewX_Hubert.pdf","relation":"main_file","date_created":"2019-08-12T12:14:18Z"}],"year":"2019","article_processing_charge":"No","publication_status":"published","article_number":"021026","date_published":"2019-05-08T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","abstract":[{"lang":"eng","text":"Dipolar coupling plays a fundamental role in the interaction between electrically or magnetically polarized species such as magnetic atoms and dipolar molecules in a gas or dipolar excitons in the solid state. Unlike Coulomb or contactlike interactions found in many atomic, molecular, and condensed-matter systems, this interaction is long-ranged and highly anisotropic, as it changes from repulsive to attractive depending on the relative positions and orientation of the dipoles. Because of this unique property, many exotic, symmetry-breaking collective states have been recently predicted for cold dipolar gases, but only a few have been experimentally detected and only in dilute atomic dipolar Bose-Einstein condensates. Here, we report on the first observation of attractive dipolar coupling between excitonic dipoles using a new design of stacked semiconductor bilayers. We show that the presence of a dipolar exciton fluid in one bilayer modifies the spatial distribution and increases the binding energy of excitonic dipoles in a vertically remote layer. The binding energy changes are explained using a many-body polaron model describing the deformation of the exciton cloud due to its interaction with a remote dipolar exciton. The surprising nonmonotonic dependence on the cloud density indicates the important role of dipolar correlations, which is unique to dense, strongly interacting dipolar solid-state systems. Our concept provides a route for the realization of dipolar lattices with strong anisotropic interactions in semiconductor systems, which open the way for the observation of theoretically predicted new and exotic collective phases, as well as for engineering and sensing their collective excitations."}],"has_accepted_license":"1","date_created":"2019-08-11T21:59:20Z","intvolume":" 9","language":[{"iso":"eng"}],"issue":"2","status":"public","month":"05","ddc":["530"],"publication":"Physical Review X"},{"page":"765-775","ec_funded":1,"isi":1,"type":"journal_article","oa":1,"publication_status":"published","year":"2019","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2019-10-01T00:00:00Z","date_created":"2019-08-11T21:59:23Z","abstract":[{"lang":"eng","text":"The Regge symmetry is a set of remarkable relations between two tetrahedra whose edge lengths are related in a simple fashion. It was first discovered as a consequence of an asymptotic formula in mathematical physics. Here, we give a simple geometric proof of Regge symmetries in Euclidean, spherical, and hyperbolic geometry."}],"publisher":"London Mathematical Society","language":[{"iso":"eng"}],"intvolume":" 51","issue":"5","month":"10","publication":"Bulletin of the London Mathematical Society","status":"public","day":"01","publication_identifier":{"issn":["0024-6093"],"eissn":["1469-2120"]},"article_type":"original","arxiv":1,"external_id":{"isi":["000478560200001"],"arxiv":["1903.04929"]},"author":[{"full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","last_name":"Akopyan","orcid":"0000-0002-2548-617X"},{"full_name":"Izmestiev, Ivan","first_name":"Ivan","last_name":"Izmestiev"}],"title":"The Regge symmetry, confocal conics, and the Schläfli formula","date_updated":"2025-07-10T11:53:52Z","scopus_import":"1","department":[{"_id":"HeEd"}],"volume":51,"project":[{"grant_number":"788183","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"doi":"10.1112/blms.12276","citation":{"ieee":"A. Akopyan and I. Izmestiev, “The Regge symmetry, confocal conics, and the Schläfli formula,” Bulletin of the London Mathematical Society, vol. 51, no. 5. London Mathematical Society, pp. 765–775, 2019.","mla":"Akopyan, Arseniy, and Ivan Izmestiev. “The Regge Symmetry, Confocal Conics, and the Schläfli Formula.” Bulletin of the London Mathematical Society, vol. 51, no. 5, London Mathematical Society, 2019, pp. 765–75, doi:10.1112/blms.12276.","ama":"Akopyan A, Izmestiev I. The Regge symmetry, confocal conics, and the Schläfli formula. Bulletin of the London Mathematical Society. 2019;51(5):765-775. doi:10.1112/blms.12276","ista":"Akopyan A, Izmestiev I. 2019. The Regge symmetry, confocal conics, and the Schläfli formula. Bulletin of the London Mathematical Society. 51(5), 765–775.","apa":"Akopyan, A., & Izmestiev, I. (2019). The Regge symmetry, confocal conics, and the Schläfli formula. Bulletin of the London Mathematical Society. London Mathematical Society. https://doi.org/10.1112/blms.12276","chicago":"Akopyan, Arseniy, and Ivan Izmestiev. “The Regge Symmetry, Confocal Conics, and the Schläfli Formula.” Bulletin of the London Mathematical Society. London Mathematical Society, 2019. https://doi.org/10.1112/blms.12276.","short":"A. Akopyan, I. Izmestiev, Bulletin of the London Mathematical Society 51 (2019) 765–775."},"_id":"6793","oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.04929"}]},{"author":[{"first_name":"Barbora","last_name":"Trubenova","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hager, Reinmar","first_name":"Reinmar","last_name":"Hager"}],"date_updated":"2026-04-03T09:50:31Z","title":"Green beards in the light of indirect genetic effects","article_type":"original","file_date_updated":"2020-07-14T12:47:40Z","publication_identifier":{"eissn":["2045-7758"]},"day":"01","external_id":{"isi":["000479973400001"]},"_id":"6795","oa_version":"Published Version","quality_controlled":"1","scopus_import":"1","department":[{"_id":"NiBa"}],"volume":9,"project":[{"name":"Rate of Adaptation in Changing Environment","grant_number":"704172","call_identifier":"H2020","_id":"25AEDD42-B435-11E9-9278-68D0E5697425"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect Genetic Effects.” Ecology and Evolution. Wiley, 2019. https://doi.org/10.1002/ece3.5484.","short":"B. Trubenova, R. Hager, Ecology and Evolution 9 (2019) 9597–9608.","mla":"Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect Genetic Effects.” Ecology and Evolution, vol. 9, no. 17, Wiley, 2019, pp. 9597–608, doi:10.1002/ece3.5484.","ieee":"B. Trubenova and R. Hager, “Green beards in the light of indirect genetic effects,” Ecology and Evolution, vol. 9, no. 17. Wiley, pp. 9597–9608, 2019.","ista":"Trubenova B, Hager R. 2019. Green beards in the light of indirect genetic effects. Ecology and Evolution. 9(17), 9597–9608.","apa":"Trubenova, B., & Hager, R. (2019). Green beards in the light of indirect genetic effects. Ecology and Evolution. Wiley. https://doi.org/10.1002/ece3.5484","ama":"Trubenova B, Hager R. Green beards in the light of indirect genetic effects. Ecology and Evolution. 2019;9(17):9597-9608. doi:10.1002/ece3.5484"},"doi":"10.1002/ece3.5484","year":"2019","article_processing_charge":"No","publication_status":"published","file":[{"file_size":2839636,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-08-12T07:30:30Z","creator":"dernst","file_name":"2019_EcologyEvolution_Trubenova.pdf","checksum":"adcb70af4901977d95b8747eeee01bd7","date_updated":"2020-07-14T12:47:40Z","file_id":"6799"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2019-09-01T00:00:00Z","page":"9597-9608","type":"journal_article","ec_funded":1,"isi":1,"oa":1,"issue":"17","publication":"Ecology and Evolution","month":"09","status":"public","ddc":["576"],"abstract":[{"lang":"eng","text":"The green‐beard effect is one proposed mechanism predicted to underpin the evolu‐tion of altruistic behavior. It relies on the recognition and the selective help of altruists to each other in order to promote and sustain altruistic behavior. However, this mechanism has often been dismissed as unlikely or uncommon, as it is assumed that both the signaling trait and altruistic trait need to be encoded by the same gene or through tightly linked genes. Here, we use models of indirect genetic effects (IGEs) to find the minimum correlation between the signaling and altruistic trait required for the evolution of the latter. We show that this correlation threshold depends on the strength of the interaction (influence of the green beard on the expression of the altruistic trait), as well as the costs and benefits of the altruistic behavior. We further show that this correlation does not necessarily have to be high and support our analytical results by simulations."}],"date_created":"2019-08-11T21:59:24Z","has_accepted_license":"1","publisher":"Wiley","language":[{"iso":"eng"}],"intvolume":" 9"},{"volume":12,"department":[{"_id":"LifeSc"}],"scopus_import":1,"citation":{"ama":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. 2019;12. doi:10.1186/s13104-019-4534-3","ista":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. 12, 494.","apa":"Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin, C. V. (2019). Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. BioMed Central. https://doi.org/10.1186/s13104-019-4534-3","mla":"Antoniou, Michael N., et al. “Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes, vol. 12, 494, BioMed Central, 2019, doi:10.1186/s13104-019-4534-3.","ieee":"M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells,” BMC Research Notes, vol. 12. BioMed Central, 2019.","short":"M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, BMC Research Notes 12 (2019).","chicago":"Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes. BioMed Central, 2019. https://doi.org/10.1186/s13104-019-4534-3."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1186/s13104-019-4534-3","quality_controlled":"1","oa_version":"Published Version","_id":"6819","file_date_updated":"2020-07-14T12:47:40Z","related_material":{"record":[{"relation":"research_data","id":"9784","status":"public"}]},"publication_identifier":{"eissn":["1756-0500"]},"day":"08","external_id":{"pmid":["31395095"]},"author":[{"last_name":"Antoniou","first_name":"Michael N.","full_name":"Antoniou, Michael N."},{"id":"2A103192-F248-11E8-B48F-1D18A9856A87","full_name":"Nicolas, Armel","last_name":"Nicolas","first_name":"Armel"},{"last_name":"Mesnage","first_name":"Robin","full_name":"Mesnage, Robin"},{"first_name":"Martina","last_name":"Biserni","full_name":"Biserni, Martina"},{"full_name":"Rao, Francesco V.","first_name":"Francesco V.","last_name":"Rao"},{"full_name":"Martin, Cristina Vazquez","last_name":"Martin","first_name":"Cristina Vazquez"}],"date_updated":"2023-02-23T14:08:14Z","title":"Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells","publisher":"BioMed Central","pmid":1,"abstract":[{"text":"Glyphosate (N-phosphonomethyl glycine) and its commercial herbicide formulations have been shown to exert toxicity via various mechanisms. It has been asserted that glyphosate substitutes for glycine in polypeptide chains leading to protein misfolding and toxicity. However, as no direct evidence exists for glycine to glyphosate substitution in proteins, including in mammalian organisms, we tested this claim by conducting a proteomics analysis of MDA-MB-231 human breast cancer cells grown in the presence of 100 mg/L glyphosate for 6 days. Protein extracts from three treated and three untreated cell cultures were analysed as one TMT-6plex labelled sample, to highlight a specific pattern (+/+/+/−/−/−) of reporter intensities for peptides bearing true glyphosate treatment induced-post translational modifications as well as allowing an investigation of the total proteome.","lang":"eng"}],"date_created":"2019-08-18T22:00:39Z","has_accepted_license":"1","intvolume":" 12","language":[{"iso":"eng"}],"publication":"BMC Research Notes","month":"08","status":"public","ddc":["570"],"oa":1,"type":"journal_article","file":[{"file_size":1177482,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-08-23T11:10:35Z","file_name":"2019_BMC_Antoniou.pdf","creator":"dernst","checksum":"4a2bb7994b7f2c432bf44f5127ea3102","date_updated":"2020-07-14T12:47:40Z","file_id":"6829"}],"year":"2019","article_processing_charge":"No","publication_status":"published","article_number":"494","date_published":"2019-08-08T00:00:00Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"author":[{"last_name":"Yourick","first_name":"Miranda R.","full_name":"Yourick, Miranda R."},{"first_name":"Benjamin A.","last_name":"Sandkam","full_name":"Sandkam, Benjamin A."},{"last_name":"Gammerdinger","orcid":"0000-0001-9638-1220","first_name":"William J","full_name":"Gammerdinger, William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Escobar-Camacho, Daniel","last_name":"Escobar-Camacho","first_name":"Daniel"},{"first_name":"Sri Pratima","last_name":"Nandamuri","full_name":"Nandamuri, Sri Pratima"},{"last_name":"Clark","first_name":"Frances E.","full_name":"Clark, Frances E."},{"full_name":"Joyce, Brendan","last_name":"Joyce","first_name":"Brendan"},{"full_name":"Conte, Matthew A.","first_name":"Matthew A.","last_name":"Conte"},{"first_name":"Thomas D.","last_name":"Kocher","full_name":"Kocher, Thomas D."},{"full_name":"Carleton, Karen L.","last_name":"Carleton","first_name":"Karen L."}],"title":"Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses","date_updated":"2023-08-29T07:10:44Z","day":"01","article_type":"original","publication_identifier":{"eissn":["1755-0998"]},"external_id":{"pmid":["31325910"],"isi":["000480196800001"]},"_id":"6821","quality_controlled":"1","oa_version":"Submitted Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6995727","open_access":"1"}],"department":[{"_id":"BeVi"}],"scopus_import":"1","volume":19,"doi":"10.1111/1755-0998.13062","citation":{"ieee":"M. R. Yourick et al., “Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses,” Molecular Ecology Resources, vol. 19, no. 6. Wiley, pp. 1447–1460, 2019.","mla":"Yourick, Miranda R., et al. “Diurnal Variation in Opsin Expression and Common Housekeeping Genes Necessitates Comprehensive Normalization Methods for Quantitative Real-Time PCR Analyses.” Molecular Ecology Resources, vol. 19, no. 6, Wiley, 2019, pp. 1447–60, doi:10.1111/1755-0998.13062.","ista":"Yourick MR, Sandkam BA, Gammerdinger WJ, Escobar-Camacho D, Nandamuri SP, Clark FE, Joyce B, Conte MA, Kocher TD, Carleton KL. 2019. Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. Molecular Ecology Resources. 19(6), 1447–1460.","ama":"Yourick MR, Sandkam BA, Gammerdinger WJ, et al. Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. Molecular Ecology Resources. 2019;19(6):1447-1460. doi:10.1111/1755-0998.13062","apa":"Yourick, M. R., Sandkam, B. A., Gammerdinger, W. J., Escobar-Camacho, D., Nandamuri, S. P., Clark, F. E., … Carleton, K. L. (2019). Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13062","chicago":"Yourick, Miranda R., Benjamin A. Sandkam, William J Gammerdinger, Daniel Escobar-Camacho, Sri Pratima Nandamuri, Frances E. Clark, Brendan Joyce, Matthew A. Conte, Thomas D. Kocher, and Karen L. Carleton. “Diurnal Variation in Opsin Expression and Common Housekeeping Genes Necessitates Comprehensive Normalization Methods for Quantitative Real-Time PCR Analyses.” Molecular Ecology Resources. Wiley, 2019. https://doi.org/10.1111/1755-0998.13062.","short":"M.R. Yourick, B.A. Sandkam, W.J. Gammerdinger, D. Escobar-Camacho, S.P. Nandamuri, F.E. Clark, B. Joyce, M.A. Conte, T.D. Kocher, K.L. Carleton, Molecular Ecology Resources 19 (2019) 1447–1460."},"publication_status":"published","article_processing_charge":"No","year":"2019","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2019-11-01T00:00:00Z","page":"1447-1460","type":"journal_article","isi":1,"oa":1,"issue":"6","publication":"Molecular Ecology Resources","month":"11","status":"public","date_created":"2019-08-18T22:00:41Z","pmid":1,"abstract":[{"lang":"eng","text":"To determine the visual sensitivities of an organism of interest, quantitative reverse transcription–polymerase chain reaction (qRT–PCR) is often used to quantify expression of the light‐sensitive opsins in the retina. While qRT–PCR is an affordable, high‐throughput method for measuring expression, it comes with inherent normalization issues that affect the interpretation of results, especially as opsin expression can vary greatly based on developmental stage, light environment or diurnal cycles. We tested for diurnal cycles of opsin expression over a period of 24 hr at 1‐hr increments and examined how normalization affects a data set with fluctuating expression levels using qRT–PCR and transcriptome data from the retinae of the cichlid Pelmatolapia mariae. We compared five methods of normalizing opsin expression relative to (a) the average of three stably expressed housekeeping genes (Ube2z, EF1‐α and β‐actin), (b) total RNA concentration, (c) GNAT2, (the cone‐specific subunit of transducin), (d) total opsin expression and (e) only opsins expressed in the same cone type. Normalizing by proportion of cone type produced the least variation and would be best for removing time‐of‐day variation. In contrast, normalizing by housekeeping genes produced the highest daily variation in expression and demonstrated that the peak of cone opsin expression was in the late afternoon. A weighted correlation network analysis showed that the expression of different cone opsins follows a very similar daily cycle. With the knowledge of how these normalization methods affect opsin expression data, we make recommendations for designing sampling approaches and quantification methods based upon the scientific question being examined."}],"publisher":"Wiley","language":[{"iso":"eng"}],"intvolume":" 19"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2019-11-15T00:00:00Z","publication_status":"published","article_processing_charge":"No","year":"2019","type":"journal_article","isi":1,"oa":1,"page":"261-289","status":"public","month":"11","publication":"Journal of Algebra","language":[{"iso":"eng"}],"intvolume":" 538","abstract":[{"lang":"eng","text":"In this paper we construct a family of exact functors from the category of Whittaker modules of the simple complex Lie algebra of type to the category of finite-dimensional modules of the graded affine Hecke algebra of type . Using results of Backelin [2] and of Arakawa-Suzuki [1], we prove that these functors map standard modules to standard modules (or zero) and simple modules to simple modules (or zero). Moreover, we show that each simple module of the graded affine Hecke algebra appears as the image of a simple Whittaker module. Since the Whittaker category contains the BGG category as a full subcategory, our results generalize results of Arakawa-Suzuki [1], which in turn generalize Schur-Weyl duality between finite-dimensional representations of and representations of the symmetric group ."}],"date_created":"2019-08-22T07:54:13Z","publisher":"Elsevier","title":"Arakawa-Suzuki functors for Whittaker modules","date_updated":"2023-08-29T07:11:47Z","author":[{"id":"70B7FDF6-608D-11E9-9333-8535E6697425","full_name":"Brown, Adam","last_name":"Brown","first_name":"Adam"}],"external_id":{"arxiv":["1805.04676"],"isi":["000487176300011"]},"day":"15","article_type":"original","publication_identifier":{"issn":["0021-8693"]},"arxiv":1,"_id":"6828","quality_controlled":"1","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1805.04676"}],"doi":"10.1016/j.jalgebra.2019.07.027","citation":{"ieee":"A. Brown, “Arakawa-Suzuki functors for Whittaker modules,” Journal of Algebra, vol. 538. Elsevier, pp. 261–289, 2019.","mla":"Brown, Adam. “Arakawa-Suzuki Functors for Whittaker Modules.” Journal of Algebra, vol. 538, Elsevier, 2019, pp. 261–89, doi:10.1016/j.jalgebra.2019.07.027.","ama":"Brown A. Arakawa-Suzuki functors for Whittaker modules. Journal of Algebra. 2019;538:261-289. doi:10.1016/j.jalgebra.2019.07.027","apa":"Brown, A. (2019). Arakawa-Suzuki functors for Whittaker modules. Journal of Algebra. Elsevier. https://doi.org/10.1016/j.jalgebra.2019.07.027","ista":"Brown A. 2019. Arakawa-Suzuki functors for Whittaker modules. Journal of Algebra. 538, 261–289.","chicago":"Brown, Adam. “Arakawa-Suzuki Functors for Whittaker Modules.” Journal of Algebra. Elsevier, 2019. https://doi.org/10.1016/j.jalgebra.2019.07.027.","short":"A. Brown, Journal of Algebra 538 (2019) 261–289."},"department":[{"_id":"HeEd"}],"volume":538},{"publisher":"Wiley","abstract":[{"lang":"eng","text":"* Understanding the mechanisms causing phenotypic differences between females and males has long fascinated evolutionary biologists. An extensive literature exists on animal sexual dimorphism but less information is known about sex differences in plants, particularly the extent of geographical variation in sexual dimorphism and its life‐cycle dynamics.\r\n* Here, we investigated patterns of genetically based sexual dimorphism in vegetative and reproductive traits of a wind‐pollinated dioecious plant, Rumex hastatulus, across three life‐cycle stages using open‐pollinated families from 30 populations spanning the geographic range and chromosomal variation (XY and XY1Y2) of the species.\r\n* The direction and degree of sexual dimorphism was highly variable among populations and life‐cycle stages. Sex‐specific differences in reproductive function explained a significant amount of temporal change in sexual dimorphism. For several traits, geographical variation in sexual dimorphism was associated with bioclimatic parameters, likely due to the differential responses of the sexes to climate. We found no systematic differences in sexual dimorphism between chromosome races.\r\n* Sex‐specific trait differences in dioecious plants largely result from a balance between sexual and natural selection on resource allocation. Our results indicate that abiotic factors associated with geographical context also play a role in modifying sexual dimorphism during the plant life‐cycle."}],"date_created":"2019-08-25T22:00:51Z","has_accepted_license":"1","intvolume":" 224","language":[{"iso":"eng"}],"issue":"3","publication":"New Phytologist","ddc":["570"],"corr_author":"1","month":"11","status":"public","page":"1108-1120","oa":1,"type":"journal_article","ec_funded":1,"isi":1,"file":[{"date_updated":"2020-07-14T12:47:42Z","file_id":"6833","file_size":2314016,"access_level":"open_access","content_type":"application/pdf","date_created":"2019-08-27T12:44:54Z","relation":"main_file","checksum":"6370e7567d96b7b562e77d8b89653f80","creator":"apreinsp","file_name":"2019_NewPhytologist_Puixeu.pdf"}],"publication_status":"published","article_processing_charge":"Yes (via OA deal)","year":"2019","date_published":"2019-11-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":224,"department":[{"_id":"NiBa"},{"_id":"BeVi"}],"scopus_import":"1","citation":{"ista":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. 2019. Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. 224(3), 1108–1120.","apa":"Puixeu Sala, G., Pickup, M., Field, D., & Barrett, S. C. H. (2019). Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. Wiley. https://doi.org/10.1111/nph.16050","ama":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. 2019;224(3):1108-1120. doi:10.1111/nph.16050","ieee":"G. Puixeu Sala, M. Pickup, D. Field, and S. C. H. Barrett, “Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics,” New Phytologist, vol. 224, no. 3. Wiley, pp. 1108–1120, 2019.","mla":"Puixeu Sala, Gemma, et al. “Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” New Phytologist, vol. 224, no. 3, Wiley, 2019, pp. 1108–20, doi:10.1111/nph.16050.","short":"G. Puixeu Sala, M. Pickup, D. Field, S.C.H. Barrett, New Phytologist 224 (2019) 1108–1120.","chicago":"Puixeu Sala, Gemma, Melinda Pickup, David Field, and Spencer C.H. Barrett. “Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16050."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1111/nph.16050","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"quality_controlled":"1","oa_version":"Published Version","_id":"6831","day":"01","article_type":"original","related_material":{"record":[{"relation":"research_data","id":"9803","status":"public"},{"id":"14058","relation":"dissertation_contains","status":"public"}]},"publication_identifier":{"eissn":["1469-8137"]},"file_date_updated":"2020-07-14T12:47:42Z","external_id":{"isi":["000481376500001"]},"author":[{"orcid":"0000-0001-8330-1754","last_name":"Puixeu Sala","first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","full_name":"Puixeu Sala, Gemma"},{"orcid":"0000-0001-6118-0541","last_name":"Pickup","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda"},{"full_name":"Field, David","first_name":"David","orcid":"0000-0002-4014-8478","last_name":"Field"},{"full_name":"Barrett, Spencer C.H.","last_name":"Barrett","first_name":"Spencer C.H."}],"title":"Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics","date_updated":"2026-04-07T13:25:33Z"},{"_id":"6836","oa_version":"Submitted Version","quality_controlled":"1","scopus_import":"1","department":[{"_id":"KrCh"}],"volume":572,"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"doi":"10.1038/s41586-019-1488-5","citation":{"mla":"Hauser, Oliver P., et al. “Social Dilemmas among Unequals.” Nature, vol. 572, no. 7770, Springer Nature, 2019, pp. 524–27, doi:10.1038/s41586-019-1488-5.","ieee":"O. P. Hauser, C. Hilbe, K. Chatterjee, and M. A. Nowak, “Social dilemmas among unequals,” Nature, vol. 572, no. 7770. Springer Nature, pp. 524–527, 2019.","apa":"Hauser, O. P., Hilbe, C., Chatterjee, K., & Nowak, M. A. (2019). Social dilemmas among unequals. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1488-5","ista":"Hauser OP, Hilbe C, Chatterjee K, Nowak MA. 2019. Social dilemmas among unequals. Nature. 572(7770), 524–527.","ama":"Hauser OP, Hilbe C, Chatterjee K, Nowak MA. Social dilemmas among unequals. Nature. 2019;572(7770):524-527. doi:10.1038/s41586-019-1488-5","chicago":"Hauser, Oliver P., Christian Hilbe, Krishnendu Chatterjee, and Martin A. Nowak. “Social Dilemmas among Unequals.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1488-5.","short":"O.P. Hauser, C. Hilbe, K. Chatterjee, M.A. Nowak, Nature 572 (2019) 524–527."},"author":[{"full_name":"Hauser, Oliver P.","last_name":"Hauser","first_name":"Oliver P."},{"full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Hilbe","orcid":"0000-0001-5116-955X"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin A.","last_name":"Nowak","full_name":"Nowak, Martin A."}],"date_updated":"2025-07-10T11:53:55Z","title":"Social dilemmas among unequals","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/too-much-inequality-impedes-support-for-public-goods-according-to-research-published-in-nature/","description":"News on IST Homepage"}]},"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"file_date_updated":"2020-07-14T12:47:42Z","article_type":"letter_note","day":"22","external_id":{"isi":["000482219600045"]},"issue":"7770","status":"public","ddc":["000"],"month":"08","publication":"Nature","date_created":"2019-09-01T22:00:56Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Direct reciprocity is a powerful mechanism for the evolution of cooperation on the basis of repeated interactions1,2,3,4. It requires that interacting individuals are sufficiently equal, such that everyone faces similar consequences when they cooperate or defect. Yet inequality is ubiquitous among humans5,6 and is generally considered to undermine cooperation and welfare7,8,9,10. Most previous models of reciprocity do not include inequality11,12,13,14,15. These models assume that individuals are the same in all relevant aspects. Here we introduce a general framework to study direct reciprocity among unequal individuals. Our model allows for multiple sources of inequality. Subjects can differ in their endowments, their productivities and in how much they benefit from public goods. We find that extreme inequality prevents cooperation. But if subjects differ in productivity, some endowment inequality can be necessary for cooperation to prevail. Our mathematical predictions are supported by a behavioural experiment in which we vary the endowments and productivities of the subjects. We observe that overall welfare is maximized when the two sources of heterogeneity are aligned, such that more productive individuals receive higher endowments. By contrast, when endowments and productivities are misaligned, cooperation quickly breaks down. Our findings have implications for policy-makers concerned with equity, efficiency and the provisioning of public goods."}],"publisher":"Springer Nature","language":[{"iso":"eng"}],"intvolume":" 572","year":"2019","article_processing_charge":"No","publication_status":"published","file":[{"file_name":"2019_Nature_Hauser.pdf","creator":"dernst","checksum":"a6e0e3168bf62de624e7772cdfaeb26f","date_created":"2020-05-14T10:00:32Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":18577756,"file_id":"7828","date_updated":"2020-07-14T12:47:42Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2019-08-22T00:00:00Z","page":"524-527","isi":1,"ec_funded":1,"type":"journal_article","oa":1},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2019-06-13T00:00:00Z","article_number":"063101","publication_status":"published","year":"2019","article_processing_charge":"No","isi":1,"type":"journal_article","ec_funded":1,"oa":1,"publication":"Journal of Statistical Mechanics: Theory and Experiment","month":"06","status":"public","issue":"6","language":[{"iso":"eng"}],"intvolume":" 2019","date_created":"2019-09-01T22:00:59Z","abstract":[{"lang":"eng","text":"We discuss thermodynamic properties of harmonically trapped\r\nimperfect quantum gases. The spatial inhomogeneity of these systems imposes\r\na redefinition of the mean-field interparticle potential energy as compared\r\nto the homogeneous case. In our approach, it takes the form a\r\n2N2 ωd, where\r\nN is the number of particles, ω—the harmonic trap frequency, d—system’s\r\ndimensionality, and a is a parameter characterizing the interparticle interaction.\r\nWe provide arguments that this model corresponds to the limiting case of\r\na long-ranged interparticle potential of vanishingly small amplitude. This\r\nconclusion is drawn from a computation similar to the well-known Kac scaling\r\nprocedure, which is presented here in a form adapted to the case of an isotropic\r\nharmonic trap. We show that within the model, the imperfect gas of trapped\r\nrepulsive bosons undergoes the Bose–Einstein condensation provided d > 1.\r\nThe main result of our analysis is that in d = 1 the gas of attractive imperfect\r\nfermions with a = −aF < 0 is thermodynamically equivalent to the gas of\r\nrepulsive bosons with a = aB > 0 provided the parameters aF and aB fulfill\r\nthe relation aB + aF = \u001f. This result supplements similar recent conclusion\r\nabout thermodynamic equivalence of two-dimensional (2D) uniform imperfect\r\nrepulsive Bose and attractive Fermi gases."}],"publisher":"IOP Publishing","title":"Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps","date_updated":"2025-03-31T16:01:18Z","author":[{"last_name":"Mysliwy","first_name":"Krzysztof","full_name":"Mysliwy, Krzysztof","id":"316457FC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Napiórkowski, Marek","first_name":"Marek","last_name":"Napiórkowski"}],"external_id":{"isi":["000471650100001"],"arxiv":["1810.02209"]},"day":"13","publication_identifier":{"eissn":["1742-5468"]},"arxiv":1,"_id":"6840","quality_controlled":"1","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1810.02209","open_access":"1"}],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"doi":"10.1088/1742-5468/ab190d","citation":{"short":"K. Mysliwy, M. Napiórkowski, Journal of Statistical Mechanics: Theory and Experiment 2019 (2019).","chicago":"Mysliwy, Krzysztof, and Marek Napiórkowski. “Thermodynamics of Inhomogeneous Imperfect Quantum Gases in Harmonic Traps.” Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing, 2019. https://doi.org/10.1088/1742-5468/ab190d.","apa":"Mysliwy, K., & Napiórkowski, M. (2019). Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps. Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/ab190d","ista":"Mysliwy K, Napiórkowski M. 2019. Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps. Journal of Statistical Mechanics: Theory and Experiment. 2019(6), 063101.","ama":"Mysliwy K, Napiórkowski M. Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps. Journal of Statistical Mechanics: Theory and Experiment. 2019;2019(6). doi:10.1088/1742-5468/ab190d","mla":"Mysliwy, Krzysztof, and Marek Napiórkowski. “Thermodynamics of Inhomogeneous Imperfect Quantum Gases in Harmonic Traps.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2019, no. 6, 063101, IOP Publishing, 2019, doi:10.1088/1742-5468/ab190d.","ieee":"K. Mysliwy and M. Napiórkowski, “Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2019, no. 6. IOP Publishing, 2019."},"department":[{"_id":"RoSe"}],"scopus_import":"1","volume":2019}]