[{"issue":"6","publication_status":"published","month":"12","abstract":[{"lang":"eng","text":"Let Q = (Q1, . . . , Qn) be a random vector drawn from the uniform distribution on the set of all n! permutations of {1, 2, . . . , n}. Let Z = (Z1, . . . , Zn), where Zj is the mean zero variance one random variable obtained by centralizing and normalizing Qj , j = 1, . . . , n. Assume that Xi , i = 1, . . . ,p are i.i.d. copies of 1/√ p Z and X = Xp,n is the p × n random matrix with Xi as its ith row. Then Sn = XX is called the p × n Spearman's rank correlation matrix which can be regarded as a high dimensional extension of the classical nonparametric statistic Spearman's rank correlation coefficient between two independent random variables. In this paper, we establish a CLT for the linear spectral statistics of this nonparametric random matrix model in the scenario of high dimension, namely, p = p(n) and p/n→c ∈ (0,∞) as n→∞.We propose a novel evaluation scheme to estimate the core quantity in Anderson and Zeitouni's cumulant method in [Ann. Statist. 36 (2008) 2553-2576] to bypass the so-called joint cumulant summability. In addition, we raise a two-step comparison approach to obtain the explicit formulae for the mean and covariance functions in the CLT. Relying on this CLT, we then construct a distribution-free statistic to test complete independence for components of random vectors. Owing to the nonparametric property, we can use this test on generally distributed random variables including the heavy-tailed ones."}],"title":"Spectral statistics of large dimensional spearman s rank correlation matrix and its application","volume":43,"date_published":"2015-12-01T00:00:00Z","language":[{"iso":"eng"}],"publisher":"Institute of Mathematical Statistics","oa_version":"Published Version","citation":{"ista":"Bao Z, Lin L, Pan G, Zhou W. 2015. Spectral statistics of large dimensional spearman s rank correlation matrix and its application. Annals of Statistics. 43(6), 2588–2623.","ama":"Bao Z, Lin L, Pan G, Zhou W. Spectral statistics of large dimensional spearman s rank correlation matrix and its application. <i>Annals of Statistics</i>. 2015;43(6):2588-2623. doi:<a href=\"https://doi.org/10.1214/15-AOS1353\">10.1214/15-AOS1353</a>","chicago":"Bao, Zhigang, Liang Lin, Guangming Pan, and Wang Zhou. “Spectral Statistics of Large Dimensional Spearman s Rank Correlation Matrix and Its Application.” <i>Annals of Statistics</i>. Institute of Mathematical Statistics, 2015. <a href=\"https://doi.org/10.1214/15-AOS1353\">https://doi.org/10.1214/15-AOS1353</a>.","apa":"Bao, Z., Lin, L., Pan, G., &#38; Zhou, W. (2015). Spectral statistics of large dimensional spearman s rank correlation matrix and its application. <i>Annals of Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/15-AOS1353\">https://doi.org/10.1214/15-AOS1353</a>","ieee":"Z. Bao, L. Lin, G. Pan, and W. Zhou, “Spectral statistics of large dimensional spearman s rank correlation matrix and its application,” <i>Annals of Statistics</i>, vol. 43, no. 6. Institute of Mathematical Statistics, pp. 2588–2623, 2015.","short":"Z. Bao, L. Lin, G. Pan, W. Zhou, Annals of Statistics 43 (2015) 2588–2623.","mla":"Bao, Zhigang, et al. “Spectral Statistics of Large Dimensional Spearman s Rank Correlation Matrix and Its Application.” <i>Annals of Statistics</i>, vol. 43, no. 6, Institute of Mathematical Statistics, 2015, pp. 2588–623, doi:<a href=\"https://doi.org/10.1214/15-AOS1353\">10.1214/15-AOS1353</a>."},"extern":"1","quality_controlled":"1","date_updated":"2021-01-12T06:51:14Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0003-3036-1475","first_name":"Zhigang","last_name":"Bao","full_name":"Bao, Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lin, Liang","first_name":"Liang","last_name":"Lin"},{"full_name":"Pan, Guangming","last_name":"Pan","first_name":"Guangming"},{"last_name":"Zhou","first_name":"Wang","full_name":"Zhou, Wang"}],"publication":"Annals of Statistics","publist_id":"5674","intvolume":"        43","type":"journal_article","_id":"1504","oa":1,"date_created":"2018-12-11T11:52:24Z","page":"2588 - 2623","status":"public","doi":"10.1214/15-AOS1353","main_file_link":[{"url":"https://arxiv.org/abs/1312.5119","open_access":"1"}],"day":"01","year":"2015"},{"acknowledgement":"B.Z. was supported  in  part  by  NSFC  Grant  11071213,  ZJNSF  Grant  R6090034  and  SRFDP  Grant 20100101110001. P.G. was supported in part by the Ministry of Education, Singapore, under Grant ARC 14/11. Z.W. was supported  in  part  by  the  Ministry  of  Education,  Singapore,  under  Grant  ARC  14/11,  and  by a Grant R-155-000-131-112 at the National University of Singapore\r\n","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1304.5690"}],"doi":"10.1214/14-AOS1281","page":"382 - 421","year":"2015","status":"public","day":"01","oa":1,"date_created":"2018-12-11T11:52:25Z","type":"journal_article","_id":"1505","publist_id":"5672","intvolume":"        43","publication":"Annals of Statistics","author":[{"first_name":"Zhigang","last_name":"Bao","orcid":"0000-0003-3036-1475","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","full_name":"Bao, Zhigang"},{"first_name":"Guangming","last_name":"Pan","full_name":"Pan, Guangming"},{"first_name":"Wang","last_name":"Zhou","full_name":"Zhou, Wang"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"LaEr"}],"quality_controlled":"1","date_updated":"2021-01-12T06:51:14Z","oa_version":"Preprint","citation":{"mla":"Bao, Zhigang, et al. “Universality for the Largest Eigenvalue of Sample Covariance Matrices with General Population.” <i>Annals of Statistics</i>, vol. 43, no. 1, Institute of Mathematical Statistics, 2015, pp. 382–421, doi:<a href=\"https://doi.org/10.1214/14-AOS1281\">10.1214/14-AOS1281</a>.","short":"Z. Bao, G. Pan, W. Zhou, Annals of Statistics 43 (2015) 382–421.","ama":"Bao Z, Pan G, Zhou W. Universality for the largest eigenvalue of sample covariance matrices with general population. <i>Annals of Statistics</i>. 2015;43(1):382-421. doi:<a href=\"https://doi.org/10.1214/14-AOS1281\">10.1214/14-AOS1281</a>","ista":"Bao Z, Pan G, Zhou W. 2015. Universality for the largest eigenvalue of sample covariance matrices with general population. Annals of Statistics. 43(1), 382–421.","chicago":"Bao, Zhigang, Guangming Pan, and Wang Zhou. “Universality for the Largest Eigenvalue of Sample Covariance Matrices with General Population.” <i>Annals of Statistics</i>. Institute of Mathematical Statistics, 2015. <a href=\"https://doi.org/10.1214/14-AOS1281\">https://doi.org/10.1214/14-AOS1281</a>.","apa":"Bao, Z., Pan, G., &#38; Zhou, W. (2015). Universality for the largest eigenvalue of sample covariance matrices with general population. <i>Annals of Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/14-AOS1281\">https://doi.org/10.1214/14-AOS1281</a>","ieee":"Z. Bao, G. Pan, and W. Zhou, “Universality for the largest eigenvalue of sample covariance matrices with general population,” <i>Annals of Statistics</i>, vol. 43, no. 1. Institute of Mathematical Statistics, pp. 382–421, 2015."},"date_published":"2015-02-01T00:00:00Z","publisher":"Institute of Mathematical Statistics","language":[{"iso":"eng"}],"volume":43,"title":"Universality for the largest eigenvalue of sample covariance matrices with general population","month":"02","publication_status":"published","abstract":[{"text":"This paper is aimed at deriving the universality of the largest eigenvalue of a class of high-dimensional real or complex sample covariance matrices of the form W N =Σ 1/2XX∗Σ 1/2 . Here, X = (xij )M,N is an M× N random matrix with independent entries xij , 1 ≤ i M,≤ 1 ≤ j ≤ N such that Exij = 0, E|xij |2 = 1/N . On dimensionality, we assume that M = M(N) and N/M → d ε (0, ∞) as N ∞→. For a class of general deterministic positive-definite M × M matrices Σ , under some additional assumptions on the distribution of xij 's, we show that the limiting behavior of the largest eigenvalue of W N is universal, via pursuing a Green function comparison strategy raised in [Probab. Theory Related Fields 154 (2012) 341-407, Adv. Math. 229 (2012) 1435-1515] by Erd″os, Yau and Yin for Wigner matrices and extended by Pillai and Yin [Ann. Appl. Probab. 24 (2014) 935-1001] to sample covariance matrices in the null case (&amp;Epsi = I ). Consequently, in the standard complex case (Ex2 ij = 0), combing this universality property and the results known for Gaussian matrices obtained by El Karoui in [Ann. Probab. 35 (2007) 663-714] (nonsingular case) and Onatski in [Ann. Appl. Probab. 18 (2008) 470-490] (singular case), we show that after an appropriate normalization the largest eigenvalue of W N converges weakly to the type 2 Tracy-Widom distribution TW2 . Moreover, in the real case, we show that whenΣ is spiked with a fixed number of subcritical spikes, the type 1 Tracy-Widom limit TW1 holds for the normalized largest eigenvalue of W N , which extends a result of Féral and Péché in [J. Math. Phys. 50 (2009) 073302] to the scenario of nondiagonal Σ and more generally distributed X . In summary, we establish the Tracy-Widom type universality for the largest eigenvalue of generally distributed sample covariance matrices under quite light assumptions on &amp;Sigma . Applications of these limiting results to statistical signal detection and structure recognition of separable covariance matrices are also discussed.","lang":"eng"}],"issue":"1"},{"volume":21,"title":"The logarithmic law of random determinant","publisher":"Bernoulli Society for Mathematical Statistics and Probability","date_published":"2015-08-01T00:00:00Z","language":[{"iso":"eng"}],"issue":"3","abstract":[{"text":"Consider the square random matrix An = (aij)n,n, where {aij:= a(n)ij , i, j = 1, . . . , n} is a collection of independent real random variables with means zero and variances one. Under the additional moment condition supn max1≤i,j ≤n Ea4ij &lt;∞, we prove Girko's logarithmic law of det An in the sense that as n→∞ log | detAn| ? (1/2) log(n-1)! d/→√(1/2) log n N(0, 1).","lang":"eng"}],"publication_status":"published","month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0003-3036-1475","first_name":"Zhigang","last_name":"Bao","full_name":"Bao, Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pan, Guangming","last_name":"Pan","first_name":"Guangming"},{"full_name":"Zhou, Wang","last_name":"Zhou","first_name":"Wang"}],"oa_version":"Preprint","citation":{"ieee":"Z. Bao, G. Pan, and W. Zhou, “The logarithmic law of random determinant,” <i>Bernoulli</i>, vol. 21, no. 3. Bernoulli Society for Mathematical Statistics and Probability, pp. 1600–1628, 2015.","apa":"Bao, Z., Pan, G., &#38; Zhou, W. (2015). The logarithmic law of random determinant. <i>Bernoulli</i>. Bernoulli Society for Mathematical Statistics and Probability. <a href=\"https://doi.org/10.3150/14-BEJ615\">https://doi.org/10.3150/14-BEJ615</a>","ista":"Bao Z, Pan G, Zhou W. 2015. The logarithmic law of random determinant. Bernoulli. 21(3), 1600–1628.","chicago":"Bao, Zhigang, Guangming Pan, and Wang Zhou. “The Logarithmic Law of Random Determinant.” <i>Bernoulli</i>. Bernoulli Society for Mathematical Statistics and Probability, 2015. <a href=\"https://doi.org/10.3150/14-BEJ615\">https://doi.org/10.3150/14-BEJ615</a>.","ama":"Bao Z, Pan G, Zhou W. The logarithmic law of random determinant. <i>Bernoulli</i>. 2015;21(3):1600-1628. doi:<a href=\"https://doi.org/10.3150/14-BEJ615\">10.3150/14-BEJ615</a>","short":"Z. Bao, G. Pan, W. Zhou, Bernoulli 21 (2015) 1600–1628.","mla":"Bao, Zhigang, et al. “The Logarithmic Law of Random Determinant.” <i>Bernoulli</i>, vol. 21, no. 3, Bernoulli Society for Mathematical Statistics and Probability, 2015, pp. 1600–28, doi:<a href=\"https://doi.org/10.3150/14-BEJ615\">10.3150/14-BEJ615</a>."},"date_updated":"2021-01-12T06:51:14Z","department":[{"_id":"LaEr"}],"quality_controlled":"1","publication":"Bernoulli","intvolume":"        21","publist_id":"5671","page":"1600 - 1628","doi":"10.3150/14-BEJ615","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1208.5823"}],"year":"2015","status":"public","day":"01","type":"journal_article","_id":"1506","date_created":"2018-12-11T11:52:25Z","oa":1},{"publisher":"European Mathematical Society","language":[{"iso":"eng"}],"date_published":"2015-08-01T00:00:00Z","title":"Gap universality of generalized Wigner and β ensembles","volume":17,"publication_status":"published","month":"08","abstract":[{"lang":"eng","text":"We consider generalized Wigner ensembles and general β-ensembles with analytic potentials for any β ≥ 1. The recent universality results in particular assert that the local averages of consecutive eigenvalue gaps in the bulk of the spectrum are universal in the sense that they coincide with those of the corresponding Gaussian β-ensembles. In this article, we show that local averaging is not necessary for this result, i.e. we prove that the single gap distributions in the bulk are universal. In fact, with an additional step, our result can be extended to any C4(ℝ) potential."}],"issue":"8","author":[{"orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Horng","last_name":"Yau","full_name":"Yau, Horng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"LaEr"}],"quality_controlled":"1","date_updated":"2021-01-12T06:51:15Z","oa_version":"Preprint","citation":{"ieee":"L. Erdös and H. Yau, “Gap universality of generalized Wigner and β ensembles,” <i>Journal of the European Mathematical Society</i>, vol. 17, no. 8. European Mathematical Society, pp. 1927–2036, 2015.","apa":"Erdös, L., &#38; Yau, H. (2015). Gap universality of generalized Wigner and β ensembles. <i>Journal of the European Mathematical Society</i>. European Mathematical Society. <a href=\"https://doi.org/10.4171/JEMS/548\">https://doi.org/10.4171/JEMS/548</a>","ista":"Erdös L, Yau H. 2015. Gap universality of generalized Wigner and β ensembles. Journal of the European Mathematical Society. 17(8), 1927–2036.","chicago":"Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and β Ensembles.” <i>Journal of the European Mathematical Society</i>. European Mathematical Society, 2015. <a href=\"https://doi.org/10.4171/JEMS/548\">https://doi.org/10.4171/JEMS/548</a>.","ama":"Erdös L, Yau H. Gap universality of generalized Wigner and β ensembles. <i>Journal of the European Mathematical Society</i>. 2015;17(8):1927-2036. doi:<a href=\"https://doi.org/10.4171/JEMS/548\">10.4171/JEMS/548</a>","mla":"Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and β Ensembles.” <i>Journal of the European Mathematical Society</i>, vol. 17, no. 8, European Mathematical Society, 2015, pp. 1927–2036, doi:<a href=\"https://doi.org/10.4171/JEMS/548\">10.4171/JEMS/548</a>.","short":"L. Erdös, H. Yau, Journal of the European Mathematical Society 17 (2015) 1927–2036."},"publist_id":"5669","intvolume":"        17","publication":"Journal of the European Mathematical Society","scopus_import":1,"page":"1927 - 2036","doi":"10.4171/JEMS/548","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1211.3786"}],"year":"2015","day":"01","status":"public","oa":1,"date_created":"2018-12-11T11:52:26Z","type":"journal_article","_id":"1508"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"citation":{"apa":"Michalko, J., Lukacisinova, M., Bollenbach, M. T., &#38; Friml, J. (2015). Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. <i>F1000 Research </i>. F1000 Research. <a href=\"https://doi.org/10.12688/f1000research.7143.1\">https://doi.org/10.12688/f1000research.7143.1</a>","ista":"Michalko J, Lukacisinova M, Bollenbach MT, Friml J. 2015. Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . 4.","chicago":"Michalko, Jaroslav, Marta Lukacisinova, Mark Tobias Bollenbach, and Jiří Friml. “Embryo-Lethal Phenotypes in Early Abp1 Mutants Are Due to Disruption of the Neighboring BSM Gene.” <i>F1000 Research </i>. F1000 Research, 2015. <a href=\"https://doi.org/10.12688/f1000research.7143.1\">https://doi.org/10.12688/f1000research.7143.1</a>.","ama":"Michalko J, Lukacisinova M, Bollenbach MT, Friml J. Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. <i>F1000 Research </i>. 2015;4. doi:<a href=\"https://doi.org/10.12688/f1000research.7143.1\">10.12688/f1000research.7143.1</a>","ieee":"J. Michalko, M. Lukacisinova, M. T. Bollenbach, and J. Friml, “Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene,” <i>F1000 Research </i>, vol. 4. F1000 Research, 2015.","short":"J. Michalko, M. Lukacisinova, M.T. Bollenbach, J. Friml, F1000 Research  4 (2015).","mla":"Michalko, Jaroslav, et al. “Embryo-Lethal Phenotypes in Early Abp1 Mutants Are Due to Disruption of the Neighboring BSM Gene.” <i>F1000 Research </i>, vol. 4, F1000 Research, 2015, doi:<a href=\"https://doi.org/10.12688/f1000research.7143.1\">10.12688/f1000research.7143.1</a>."},"department":[{"_id":"JiFr"},{"_id":"ToBo"}],"date_updated":"2025-05-07T11:12:30Z","title":"Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene","file_date_updated":"2020-07-14T12:44:59Z","publisher":"F1000 Research","date_published":"2015-10-01T00:00:00Z","ddc":["570"],"publication_status":"published","abstract":[{"lang":"eng","text":"The Auxin Binding Protein1 (ABP1) has been identified based on its ability to bind auxin with high affinity and studied for a long time as a prime candidate for the extracellular auxin receptor responsible for mediating in particular the fast non-transcriptional auxin responses. However, the contradiction between the embryo-lethal phenotypes of the originally described Arabidopsis T-DNA insertional knock-out alleles (abp1-1 and abp1-1s) and the wild type-like phenotypes of other recently described loss-of-function alleles (abp1-c1 and abp1-TD1) questions the biological importance of ABP1 and relevance of the previous genetic studies. Here we show that there is no hidden copy of the ABP1 gene in the Arabidopsis genome but the embryo-lethal phenotypes of abp1-1 and abp1-1s alleles are very similar to the knock-out phenotypes of the neighboring gene, BELAYA SMERT (BSM). Furthermore, the allelic complementation test between bsm and abp1 alleles shows that the embryo-lethality in the abp1-1 and abp1-1s alleles is caused by the off-target disruption of the BSM locus by the T-DNA insertions. This clarifies the controversy of different phenotypes among published abp1 knock-out alleles and asks for reflections on the developmental role of ABP1."}],"doi":"10.12688/f1000research.7143.1","year":"2015","day":"01","acknowledgement":"This work was supported by ERC Independent Research grant (ERC-2011-StG-20101109-PSDP to JF). JM internship was supported by the grant “Action Austria – Slovakia”.\r\nData associated with the article are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication). \r\n\r\nData availability: \r\nF1000Research: Dataset 1. Dataset 1, 10.5256/f1000research.7143.d104552\r\n\r\nF1000Research: Dataset 2. Dataset 2, 10.5256/f1000research.7143.d104553\r\n\r\nF1000Research: Dataset 3. Dataset 3, 10.5256/f1000research.7143.d104554","oa":1,"publication":"F1000 Research ","publist_id":"5668","intvolume":"         4","scopus_import":"1","author":[{"id":"483727CA-F248-11E8-B48F-1D18A9856A87","full_name":"Michalko, Jaroslav","first_name":"Jaroslav","last_name":"Michalko"},{"orcid":"0000-0002-2519-8004","first_name":"Marta","last_name":"Dravecka","full_name":"Dravecka, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bollenbach","first_name":"Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Tobias"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"oa_version":"Published Version","quality_controlled":"1","project":[{"call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants"}],"volume":4,"article_processing_charge":"No","language":[{"iso":"eng"}],"file":[{"creator":"system","file_id":"5198","checksum":"8beae5cbe988e1060265ae7de2ee8306","file_size":4414248,"access_level":"open_access","relation":"main_file","file_name":"IST-2016-497-v1+1_10.12688_f1000research.7143.1_20151102.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:59Z","date_created":"2018-12-12T10:16:12Z"}],"has_accepted_license":"1","month":"10","status":"public","license":"https://creativecommons.org/licenses/by/4.0/","_id":"1509","type":"journal_article","date_created":"2018-12-11T11:52:26Z","ec_funded":1,"pubrep_id":"497"},{"citation":{"mla":"Franek, Peter, and Marek Krcál. <i>On Computability and Triviality of Well Groups</i>. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 842–56, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.842\">10.4230/LIPIcs.SOCG.2015.842</a>.","short":"P. Franek, M. Krcál, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 842–856.","apa":"Franek, P., &#38; Krcál, M. (2015). On computability and triviality of well groups (Vol. 34, pp. 842–856). Presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.842\">https://doi.org/10.4230/LIPIcs.SOCG.2015.842</a>","ama":"Franek P, Krcál M. On computability and triviality of well groups. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:842-856. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.842\">10.4230/LIPIcs.SOCG.2015.842</a>","ista":"Franek P, Krcál M. 2015. On computability and triviality of well groups. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 842–856.","chicago":"Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well Groups,” 34:842–56. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. <a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.842\">https://doi.org/10.4230/LIPIcs.SOCG.2015.842</a>.","ieee":"P. Franek and M. Krcál, “On computability and triviality of well groups,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 842–856."},"department":[{"_id":"UlWa"},{"_id":"HeEd"}],"date_updated":"2023-02-21T17:02:57Z","alternative_title":["LIPIcs"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["510"],"publication_status":"published","abstract":[{"lang":"eng","text":"The concept of well group in a special but important case captures homological properties of the zero set of a continuous map f from K to R^n on a compact space K that are invariant with respect to perturbations of f. The perturbations are arbitrary continuous maps within L_infty distance r from f for a given r &gt; 0. The main drawback of the approach is that the computability of well groups was shown only when dim K = n or n = 1. Our contribution to the theory of well groups is twofold: on the one hand we improve on the computability issue, but on the other hand we present a range of examples where the well groups are incomplete invariants, that is, fail to capture certain important robust properties of the zero set. For the first part, we identify a computable subgroup of the well group that is obtained by cap product with the pullback of the orientation of R^n by f. In other words, well groups can be algorithmically approximated from below. When f is smooth and dim K &lt; 2n-2, our approximation of the (dim K-n)th well group is exact. For the second part, we find examples of maps f, f' from K to R^n with all well groups isomorphic but whose perturbations have different zero sets. We discuss on a possible replacement of the well groups of vector valued maps by an invariant of a better descriptive power and computability status. "}],"title":"On computability and triviality of well groups","date_published":"2015-06-11T00:00:00Z","file_date_updated":"2020-07-14T12:44:59Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"year":"2015","page":"842 - 856","doi":"10.4230/LIPIcs.SOCG.2015.842","day":"11","scopus_import":1,"related_material":{"record":[{"status":"public","id":"1408","relation":"later_version"}]},"publist_id":"5667","intvolume":"        34","oa_version":"Published Version","quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"author":[{"last_name":"Franek","first_name":"Peter","id":"473294AE-F248-11E8-B48F-1D18A9856A87","full_name":"Franek, Peter"},{"last_name":"Krcál","first_name":"Marek","full_name":"Krcál, Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87"}],"file":[{"file_name":"IST-2016-503-v1+1_32.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:13:19Z","date_updated":"2020-07-14T12:44:59Z","checksum":"49eb5021caafaabe5356c65b9c5f8c9c","file_id":"5001","creator":"system","access_level":"open_access","file_size":623563,"relation":"main_file"}],"month":"06","has_accepted_license":"1","volume":34,"language":[{"iso":"eng"}],"_id":"1510","type":"conference","date_created":"2018-12-11T11:52:26Z","status":"public","pubrep_id":"503","conference":{"name":"SoCG: Symposium on Computational Geometry","location":"Eindhoven, Netherlands","start_date":"2015-06-22","end_date":"2015-06-25"},"ec_funded":1},{"language":[{"iso":"eng"}],"volume":"34 ","month":"06","has_accepted_license":"1","file":[{"checksum":"0945811875351796324189312ca29e9e","file_id":"4871","creator":"system","access_level":"open_access","file_size":636735,"relation":"main_file","file_name":"IST-2016-502-v1+1_42.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:11:18Z","date_updated":"2020-07-14T12:44:59Z"}],"author":[{"last_name":"Goaoc","first_name":"Xavier","full_name":"Goaoc, Xavier"},{"last_name":"Mabillard","first_name":"Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","full_name":"Mabillard, Isaac"},{"full_name":"Paták, Pavel","last_name":"Paták","first_name":"Pavel"},{"first_name":"Zuzana","last_name":"Patakova","orcid":"0000-0002-3975-1683","id":"48B57058-F248-11E8-B48F-1D18A9856A87","full_name":"Patakova, Zuzana"},{"id":"38AC689C-F248-11E8-B48F-1D18A9856A87","full_name":"Tancer, Martin","first_name":"Martin","last_name":"Tancer","orcid":"0000-0002-1191-6714"},{"orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"oa_version":"Published Version","conference":{"start_date":"2015-06-22","end_date":"2015-06-25","location":"Eindhoven, Netherlands","name":"SoCG: Symposium on Computational Geometry"},"ec_funded":1,"pubrep_id":"502","status":"public","date_created":"2018-12-11T11:52:27Z","type":"conference","_id":"1511","file_date_updated":"2020-07-14T12:44:59Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_published":"2015-06-11T00:00:00Z","title":"On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result","publication_status":"published","abstract":[{"text":"The fact that the complete graph K_5 does not embed in the plane has been generalized in two independent directions. On the one hand, the solution of the classical Heawood problem for graphs on surfaces established that the complete graph K_n embeds in a closed surface M if and only if (n-3)(n-4) is at most 6b_1(M), where b_1(M) is the first Z_2-Betti number of M. On the other hand, Van Kampen and Flores proved that the k-skeleton of the n-dimensional simplex (the higher-dimensional analogue of K_{n+1}) embeds in R^{2k} if and only if n is less or equal to 2k+2. Two decades ago, Kuhnel conjectured that the k-skeleton of the n-simplex embeds in a compact, (k-1)-connected 2k-manifold with kth Z_2-Betti number b_k only if the following generalized Heawood inequality holds: binom{n-k-1}{k+1} is at most binom{2k+1}{k+1} b_k. This is a common generalization of the case of graphs on surfaces as well as the Van Kampen--Flores theorem. In the spirit of Kuhnel's conjecture, we prove that if the k-skeleton of the n-simplex embeds in a 2k-manifold with kth Z_2-Betti number b_k, then n is at most 2b_k binom{2k+2}{k} + 2k + 5. This bound is weaker than the generalized Heawood inequality, but does not require the assumption that M is (k-1)-connected. Our proof uses a result of Volovikov about maps that satisfy a certain homological triviality condition.","lang":"eng"}],"ddc":["510"],"alternative_title":["LIPIcs"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"UlWa"}],"date_updated":"2023-02-23T12:38:00Z","citation":{"apa":"Goaoc, X., Mabillard, I., Paták, P., Patakova, Z., Tancer, M., &#38; Wagner, U. (2015). On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result (Vol. 34, pp. 476–490). Presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.476\">https://doi.org/10.4230/LIPIcs.SOCG.2015.476</a>","ista":"Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. 2015. On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 476–490.","ama":"Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:476-490. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.476\">10.4230/LIPIcs.SOCG.2015.476</a>","chicago":"Goaoc, Xavier, Isaac Mabillard, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “On Generalized Heawood Inequalities for Manifolds: A Van Kampen–Flores-Type Nonembeddability Result,” 34:476–90. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. <a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.476\">https://doi.org/10.4230/LIPIcs.SOCG.2015.476</a>.","ieee":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 476–490.","mla":"Goaoc, Xavier, et al. <i>On Generalized Heawood Inequalities for Manifolds: A Van Kampen–Flores-Type Nonembeddability Result</i>. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 476–90, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.476\">10.4230/LIPIcs.SOCG.2015.476</a>.","short":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 476–490."},"publist_id":"5666","scopus_import":1,"related_material":{"record":[{"status":"public","relation":"later_version","id":"610"}]},"acknowledgement":"The work by Z. P. was partially supported by the Charles University Grant SVV-2014-260103. The\r\nwork by Z. P. and M. T. was partially supported by the project CE-ITI (GACR P202/12/G061) of\r\nthe Czech Science Foundation and by the ERC Advanced Grant No. 267165. Part of the research\r\nwork of M. T. was conducted at IST Austria, supported by an IST Fellowship. The work by U.W.\r\nwas partially supported by the Swiss National Science Foundation (grants SNSF-200020-138230 and\r\nSNSF-PP00P2-138948).","page":"476 - 490","day":"11","doi":"10.4230/LIPIcs.SOCG.2015.476","year":"2015","oa":1},{"alternative_title":["LIPIcs"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"UlWa"}],"date_updated":"2024-02-28T12:59:37Z","citation":{"apa":"Goaoc, X., Paták, P., Patakova, Z., Tancer, M., &#38; Wagner, U. (2015). Bounding Helly numbers via Betti numbers (Vol. 34, pp. 507–521). Presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.507\">https://doi.org/10.4230/LIPIcs.SOCG.2015.507</a>","ama":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Bounding Helly numbers via Betti numbers. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:507-521. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.507\">10.4230/LIPIcs.SOCG.2015.507</a>","ista":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2015. Bounding Helly numbers via Betti numbers. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 507–521.","chicago":"Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Bounding Helly Numbers via Betti Numbers,” 34:507–21. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. <a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.507\">https://doi.org/10.4230/LIPIcs.SOCG.2015.507</a>.","ieee":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Bounding Helly numbers via Betti numbers,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 507–521.","mla":"Goaoc, Xavier, et al. <i>Bounding Helly Numbers via Betti Numbers</i>. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 507–21, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.507\">10.4230/LIPIcs.SOCG.2015.507</a>.","short":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 507–521."},"file_date_updated":"2020-07-14T12:45:00Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_published":"2015-01-01T00:00:00Z","title":"Bounding Helly numbers via Betti numbers","publication_status":"published","abstract":[{"text":"We show that very weak topological assumptions are enough to ensure the existence of a Helly-type theorem. More precisely, we show that for any non-negative integers b and d there exists an integer h(b,d) such that the following holds. If F is a finite family of subsets of R^d such that the ith reduced Betti number (with Z_2 coefficients in singular homology) of the intersection of any proper subfamily G of F is at most b for every non-negative integer i less or equal to (d-1)/2, then F has Helly number at most h(b,d). These topological conditions are sharp: not controlling any of these first Betti numbers allow for families with unbounded Helly number. Our proofs combine homological non-embeddability results with a Ramsey-based approach to build, given an arbitrary simplicial complex K, some well-behaved chain map from C_*(K) to C_*(R^d). Both techniques are of independent interest.","lang":"eng"}],"ddc":["510"],"acknowledgement":"PP, ZP and MT were partially supported by the Charles University Grant GAUK 421511. ZP was\r\npartially supported by the Charles University Grant SVV-2014-260103. ZP and MT were partially\r\nsupported by the ERC Advanced Grant No. 267165 and by the project CE-ITI (GACR P202/12/G061)\r\nof the Czech Science Foundation. UW was partially supported by the Swiss National Science Foundation\r\n(grants SNSF-200020-138230 and SNSF-PP00P2-138948). Part of this work was done when XG was affiliated with INRIA Nancy Grand-Est and when MT was affiliated with Institutionen för matematik, Kungliga Tekniska Högskolan, then IST Austria.","day":"01","page":"507 - 521","year":"2015","doi":"10.4230/LIPIcs.SOCG.2015.507","oa":1,"publist_id":"5665","intvolume":"        34","scopus_import":"1","related_material":{"record":[{"id":"424","relation":"later_version","status":"public"}]},"author":[{"last_name":"Goaoc","first_name":"Xavier","full_name":"Goaoc, Xavier"},{"first_name":"Pavel","last_name":"Paták","full_name":"Paták, Pavel"},{"full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683","last_name":"Patakova","first_name":"Zuzana"},{"orcid":"0000-0002-1191-6714","last_name":"Tancer","first_name":"Martin","full_name":"Tancer, Martin"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","first_name":"Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568"}],"quality_controlled":"1","oa_version":"Submitted Version","language":[{"iso":"eng"}],"volume":34,"article_processing_charge":"No","has_accepted_license":"1","month":"01","file":[{"date_created":"2018-12-12T10:10:09Z","date_updated":"2020-07-14T12:45:00Z","content_type":"application/pdf","file_name":"IST-2016-501-v1+1_46.pdf","relation":"main_file","access_level":"open_access","file_size":633712,"file_id":"4794","checksum":"e6881df44d87fe0c2529c9f7b2724614","creator":"system"}],"status":"public","date_created":"2018-12-11T11:52:27Z","_id":"1512","type":"conference","conference":{"location":"Eindhoven, Netherlands","name":"SoCG: Symposium on Computational Geometry","end_date":"2015-06-25","start_date":"2015-06-22"},"pubrep_id":"501"},{"oa":1,"year":"2015","page":"3259 - 3268","day":"01","doi":"10.1093/gbe/evv215","scopus_import":1,"publication":"Genome Biology and Evolution","publist_id":"5664","intvolume":"         7","citation":{"mla":"Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression.” <i>Genome Biology and Evolution</i>, vol. 7, no. 12, Oxford University Press, 2015, pp. 3259–68, doi:<a href=\"https://doi.org/10.1093/gbe/evv215\">10.1093/gbe/evv215</a>.","short":"A. Pal, B. Vicoso, Genome Biology and Evolution 7 (2015) 3259–3268.","apa":"Pal, A., &#38; Vicoso, B. (2015). The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evv215\">https://doi.org/10.1093/gbe/evv215</a>","ista":"Pal A, Vicoso B. 2015. The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. Genome Biology and Evolution. 7(12), 3259–3268.","chicago":"Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/gbe/evv215\">https://doi.org/10.1093/gbe/evv215</a>.","ama":"Pal A, Vicoso B. The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. <i>Genome Biology and Evolution</i>. 2015;7(12):3259-3268. doi:<a href=\"https://doi.org/10.1093/gbe/evv215\">10.1093/gbe/evv215</a>","ieee":"A. Pal and B. Vicoso, “The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression,” <i>Genome Biology and Evolution</i>, vol. 7, no. 12. Oxford University Press, pp. 3259–3268, 2015."},"department":[{"_id":"BeVi"}],"date_updated":"2021-01-12T06:51:18Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"publication_status":"published","abstract":[{"text":"Insects of the order Hemiptera (true bugs) use a wide range of mechanisms of sex determination, including genetic sex determination, paternal genome elimination, and haplodiploidy. Genetic sex determination, the prevalent mode, is generally controlled by a pair of XY sex chromosomes or by an XX/X0 system, but different configurations that include additional sex chromosomes are also present. Although this diversity of sex determining systems has been extensively studied at the cytogenetic level, only the X chromosome of the model pea aphid Acyrthosiphon pisum has been analyzed at the genomic level, and little is known about X chromosome biology in the rest of the order.\r\n\r\nIn this study, we take advantage of published DNA- and RNA-seq data from three additional Hemiptera species to perform a comparative analysis of the gene content and expression of the X chromosome throughout this clade. We find that, despite showing evidence of dosage compensation, the X chromosomes of these species show female-biased expression, and a deficit of male-biased genes, in direct contrast to the pea aphid X. We further detect an excess of shared gene content between these very distant species, suggesting that despite the diversity of sex determining systems, the same chromosomal element is used as the X throughout a large portion of the order. ","lang":"eng"}],"title":"The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression","file_date_updated":"2020-07-14T12:45:00Z","publisher":"Oxford University Press","date_published":"2015-12-01T00:00:00Z","type":"journal_article","_id":"1513","date_created":"2018-12-11T11:52:27Z","status":"public","pubrep_id":"496","ec_funded":1,"oa_version":"Published Version","quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"author":[{"first_name":"Arka","last_name":"Pal","full_name":"Pal, Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425"},{"last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"file":[{"access_level":"open_access","file_size":858027,"checksum":"2b56b8c2e2a1d4cc3c9cb8daba26dd9b","file_id":"5284","creator":"system","relation":"main_file","file_name":"IST-2016-496-v1+1_Genome_Biol_Evol-2015-Pal-3259-68.pdf","date_created":"2018-12-12T10:17:29Z","date_updated":"2020-07-14T12:45:00Z","content_type":"application/pdf"}],"issue":"12","month":"12","has_accepted_license":"1","volume":7,"article_processing_charge":"No","language":[{"iso":"eng"}]},{"oa":1,"year":"2015","doi":"10.1214/ECP.v20-4315","day":"29","scopus_import":1,"publist_id":"5660","intvolume":"        20","publication":"Electronic Communications in Probability","department":[{"_id":"JaMa"}],"date_updated":"2021-01-12T06:51:19Z","citation":{"mla":"Erbar, Matthias, et al. “From Large Deviations to Wasserstein Gradient Flows in Multiple Dimensions.” <i>Electronic Communications in Probability</i>, vol. 20, 89, Institute of Mathematical Statistics, 2015, doi:<a href=\"https://doi.org/10.1214/ECP.v20-4315\">10.1214/ECP.v20-4315</a>.","short":"M. Erbar, J. Maas, M. Renger, Electronic Communications in Probability 20 (2015).","apa":"Erbar, M., Maas, J., &#38; Renger, M. (2015). From large deviations to Wasserstein gradient flows in multiple dimensions. <i>Electronic Communications in Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/ECP.v20-4315\">https://doi.org/10.1214/ECP.v20-4315</a>","ama":"Erbar M, Maas J, Renger M. From large deviations to Wasserstein gradient flows in multiple dimensions. <i>Electronic Communications in Probability</i>. 2015;20. doi:<a href=\"https://doi.org/10.1214/ECP.v20-4315\">10.1214/ECP.v20-4315</a>","ista":"Erbar M, Maas J, Renger M. 2015. From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability. 20, 89.","chicago":"Erbar, Matthias, Jan Maas, and Michiel Renger. “From Large Deviations to Wasserstein Gradient Flows in Multiple Dimensions.” <i>Electronic Communications in Probability</i>. Institute of Mathematical Statistics, 2015. <a href=\"https://doi.org/10.1214/ECP.v20-4315\">https://doi.org/10.1214/ECP.v20-4315</a>.","ieee":"M. Erbar, J. Maas, and M. Renger, “From large deviations to Wasserstein gradient flows in multiple dimensions,” <i>Electronic Communications in Probability</i>, vol. 20. Institute of Mathematical Statistics, 2015."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","abstract":[{"lang":"eng","text":"We study the large deviation rate functional for the empirical distribution of independent Brownian particles with drift. In one dimension, it has been shown by Adams, Dirr, Peletier and Zimmer that this functional is asymptotically equivalent (in the sense of Γ-convergence) to the Jordan-Kinderlehrer-Otto functional arising in the Wasserstein gradient flow structure of the Fokker-Planck equation. In higher dimensions, part of this statement (the lower bound) has been recently proved by Duong, Laschos and Renger, but the upper bound remained open, since the proof of Duong et al relies on regularity properties of optimal transport maps that are restricted to one dimension. In this note we present a new proof of the upper bound, thereby generalising the result of Adams et al to arbitrary dimensions.\r\n"}],"ddc":["519"],"publisher":"Institute of Mathematical Statistics","file_date_updated":"2020-07-14T12:45:00Z","date_published":"2015-11-29T00:00:00Z","title":"From large deviations to Wasserstein gradient flows in multiple dimensions","date_created":"2018-12-11T11:52:29Z","type":"journal_article","_id":"1517","status":"public","pubrep_id":"494","quality_controlled":"1","oa_version":"Published Version","author":[{"full_name":"Erbar, Matthias","last_name":"Erbar","first_name":"Matthias"},{"full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","last_name":"Maas","first_name":"Jan"},{"first_name":"Michiel","last_name":"Renger","full_name":"Renger, Michiel"}],"has_accepted_license":"1","month":"11","article_number":"89","file":[{"relation":"main_file","creator":"system","checksum":"135741c17d3e1547ca696b6fbdcd559c","file_id":"4828","file_size":230525,"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:00Z","date_created":"2018-12-12T10:10:39Z","file_name":"IST-2016-494-v1+1_4315-23820-1-PB.pdf"}],"language":[{"iso":"eng"}],"volume":20},{"oa":1,"doi":"10.1111/evo.12641","page":"1101 - 1112","year":"2015","day":"19","scopus_import":1,"publist_id":"5656","intvolume":"        69","publication":"Evolution","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T06:51:20Z","citation":{"ieee":"N. H. Barton and M. Servedio, “The interpretation of selection coefficients,” <i>Evolution</i>, vol. 69, no. 5. Wiley, pp. 1101–1112, 2015.","ama":"Barton NH, Servedio M. The interpretation of selection coefficients. <i>Evolution</i>. 2015;69(5):1101-1112. doi:<a href=\"https://doi.org/10.1111/evo.12641\">10.1111/evo.12641</a>","ista":"Barton NH, Servedio M. 2015. The interpretation of selection coefficients. Evolution. 69(5), 1101–1112.","chicago":"Barton, Nicholas H, and Maria Servedio. “The Interpretation of Selection Coefficients.” <i>Evolution</i>. Wiley, 2015. <a href=\"https://doi.org/10.1111/evo.12641\">https://doi.org/10.1111/evo.12641</a>.","apa":"Barton, N. H., &#38; Servedio, M. (2015). The interpretation of selection coefficients. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.12641\">https://doi.org/10.1111/evo.12641</a>","mla":"Barton, Nicholas H., and Maria Servedio. “The Interpretation of Selection Coefficients.” <i>Evolution</i>, vol. 69, no. 5, Wiley, 2015, pp. 1101–12, doi:<a href=\"https://doi.org/10.1111/evo.12641\">10.1111/evo.12641</a>.","short":"N.H. Barton, M. Servedio, Evolution 69 (2015) 1101–1112."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"text":"Evolutionary biologists have an array of powerful theoretical techniques that can accurately predict changes in the genetic composition of populations. Changes in gene frequencies and genetic associations between loci can be tracked as they respond to a wide variety of evolutionary forces. However, it is often less clear how to decompose these various forces into components that accurately reflect the underlying biology. Here, we present several issues that arise in the definition and interpretation of selection and selection coefficients, focusing on insights gained through the examination of selection coefficients in multilocus notation. Using this notation, we discuss how its flexibility-which allows different biological units to be identified as targets of selection-is reflected in the interpretation of the coefficients that the notation generates. In many situations, it can be difficult to agree on whether loci can be considered to be under &quot;direct&quot; versus &quot;indirect&quot; selection, or to quantify this selection. We present arguments for what the terms direct and indirect selection might best encompass, considering a range of issues, from viability and sexual selection to kin selection. We show how multilocus notation can discriminate between direct and indirect selection, and describe when it can do so.","lang":"eng"}],"ddc":["570"],"publisher":"Wiley","date_published":"2015-03-19T00:00:00Z","file_date_updated":"2020-07-14T12:45:00Z","title":"The interpretation of selection coefficients","date_created":"2018-12-11T11:52:29Z","_id":"1519","type":"journal_article","status":"public","pubrep_id":"560","ec_funded":1,"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"quality_controlled":"1","oa_version":"Submitted Version","author":[{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maria","last_name":"Servedio","full_name":"Servedio, Maria"}],"month":"03","has_accepted_license":"1","file":[{"date_created":"2018-12-12T10:10:34Z","date_updated":"2020-07-14T12:45:00Z","content_type":"application/pdf","file_name":"IST-2016-560-v1+1_Interpreting_ML_coefficients_11.2.15_App.pdf","relation":"main_file","access_level":"open_access","file_size":188872,"checksum":"fd8d23f476bc194419929b72ca265c02","file_id":"4822","creator":"system"},{"relation":"main_file","file_size":577415,"access_level":"open_access","creator":"system","checksum":"b774911e70044641d556e258efcb52ef","file_id":"4823","date_updated":"2020-07-14T12:45:00Z","date_created":"2018-12-12T10:10:35Z","content_type":"application/pdf","file_name":"IST-2016-560-v1+2_Interpreting_ML_coefficients_11.2.15_mainText.pdf"}],"issue":"5","language":[{"iso":"eng"}],"volume":69},{"oa":1,"doi":"10.5281/zenodo.33178","year":"2015","page":"580 - 607","day":"12","scopus_import":1,"intvolume":"        68","publist_id":"5648","publication":"VÖB Mitteilungen","date_updated":"2021-01-12T06:51:22Z","department":[{"_id":"E-Lib"}],"citation":{"ieee":"B. Bauer <i>et al.</i>, “Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA,” <i>VÖB Mitteilungen</i>, vol. 68, no. 3. Verein Österreichischer Bibliothekare, pp. 580–607, 2015.","ista":"Bauer B, Blechl G, Bock C, Danowski P, Ferus A, Graschopf A, König T, Mayer K, Reckling F, Rieck K, Seitz P, Stöger H, Welzig E. 2015. Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. VÖB Mitteilungen. 68(3), 580–607.","ama":"Bauer B, Blechl G, Bock C, et al. Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. <i>VÖB Mitteilungen</i>. 2015;68(3):580-607. doi:<a href=\"https://doi.org/10.5281/zenodo.33178\">10.5281/zenodo.33178</a>","chicago":"Bauer, Bruno, Guido Blechl, Christoph Bock, Patrick Danowski, Andreas Ferus, Anton Graschopf, Thomas König, et al. “Arbeitsgruppe „Nationale Strategie“ Des Open Access Network Austria OANA.” <i>VÖB Mitteilungen</i>. Verein Österreichischer Bibliothekare, 2015. <a href=\"https://doi.org/10.5281/zenodo.33178\">https://doi.org/10.5281/zenodo.33178</a>.","apa":"Bauer, B., Blechl, G., Bock, C., Danowski, P., Ferus, A., Graschopf, A., … Welzig, E. (2015). Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. <i>VÖB Mitteilungen</i>. Verein Österreichischer Bibliothekare. <a href=\"https://doi.org/10.5281/zenodo.33178\">https://doi.org/10.5281/zenodo.33178</a>","short":"B. Bauer, G. Blechl, C. Bock, P. Danowski, A. Ferus, A. Graschopf, T. König, K. Mayer, F. Reckling, K. Rieck, P. Seitz, H. Stöger, E. Welzig, VÖB Mitteilungen 68 (2015) 580–607.","mla":"Bauer, Bruno, et al. “Arbeitsgruppe „Nationale Strategie“ Des Open Access Network Austria OANA.” <i>VÖB Mitteilungen</i>, vol. 68, no. 3, Verein Österreichischer Bibliothekare, 2015, pp. 580–607, doi:<a href=\"https://doi.org/10.5281/zenodo.33178\">10.5281/zenodo.33178</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Based on 16 recommendations, efforts should be made to achieve the following goal: By 2025, all scholarly publication activity in Austria should be Open Access. In other words, the final versions of all scholarly publications resulting from the support of public resources must be freely accessible on the Internet without delay (Gold Open Access). The resources required to meet this obligation shall be provided to the authors, or the cost of the publication venues shall be borne directly by the research organisations."}],"publication_status":"published","ddc":["020"],"publisher":"Verein Österreichischer Bibliothekare","file_date_updated":"2020-07-14T12:45:00Z","date_published":"2015-11-12T00:00:00Z","title":"Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA","date_created":"2018-12-11T11:52:31Z","type":"journal_article","_id":"1525","article_type":"original","status":"public","pubrep_id":"720","quality_controlled":"1","oa_version":"Published Version","author":[{"full_name":"Bauer, Bruno","last_name":"Bauer","first_name":"Bruno"},{"full_name":"Blechl, Guido","last_name":"Blechl","first_name":"Guido"},{"full_name":"Bock, Christoph","first_name":"Christoph","last_name":"Bock"},{"full_name":"Danowski, Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6026-4409","first_name":"Patrick","last_name":"Danowski"},{"first_name":"Andreas","last_name":"Ferus","full_name":"Ferus, Andreas"},{"full_name":"Graschopf, Anton","last_name":"Graschopf","first_name":"Anton"},{"first_name":"Thomas","last_name":"König","full_name":"König, Thomas"},{"last_name":"Mayer","first_name":"Katja","full_name":"Mayer, Katja"},{"last_name":"Reckling","first_name":"Falk","full_name":"Reckling, Falk"},{"first_name":"Katharina","last_name":"Rieck","full_name":"Rieck, Katharina"},{"first_name":"Peter","last_name":"Seitz","full_name":"Seitz, Peter"},{"full_name":"Stöger, Herwig","first_name":"Herwig","last_name":"Stöger"},{"last_name":"Welzig","first_name":"Elvira","full_name":"Welzig, Elvira"}],"month":"11","has_accepted_license":"1","issue":"3","file":[{"creator":"system","file_id":"5317","checksum":"a495fe253bbc7615b1d60e9e85c94408","file_size":931707,"access_level":"open_access","relation":"main_file","file_name":"IST-2016-720-v1+1_OANA_OA-Empfehlungen_12-11-2015.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:45:00Z","date_created":"2018-12-12T10:17:59Z"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","volume":68},{"date_created":"2018-12-11T11:52:34Z","_id":"1534","type":"journal_article","status":"public","pubrep_id":"485","ec_funded":1,"project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"quality_controlled":"1","oa_version":"Published Version","author":[{"full_name":"Wang, Hongzhe","last_name":"Wang","first_name":"Hongzhe"},{"full_name":"Yang, Kezhen","first_name":"Kezhen","last_name":"Yang"},{"full_name":"Zou, Junjie","last_name":"Zou","first_name":"Junjie"},{"first_name":"Lingling","last_name":"Zhu","full_name":"Zhu, Lingling"},{"full_name":"Xie, Zidian","first_name":"Zidian","last_name":"Xie"},{"full_name":"Morita, Miyoterao","last_name":"Morita","first_name":"Miyoterao"},{"full_name":"Tasaka, Masao","last_name":"Tasaka","first_name":"Masao"},{"first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"full_name":"Grotewold, Erich","first_name":"Erich","last_name":"Grotewold"},{"first_name":"Tom","last_name":"Beeckman","full_name":"Beeckman, Tom"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"last_name":"Sack","first_name":"Fred","full_name":"Sack, Fred"},{"last_name":"Le","first_name":"Jie","full_name":"Le, Jie"}],"has_accepted_license":"1","month":"11","article_number":"8822","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:45:01Z","date_created":"2018-12-12T10:17:07Z","file_name":"IST-2016-485-v1+1_ncomms9822.pdf","relation":"main_file","creator":"system","checksum":"3c06735fc7cd7e482ca830cbd26001bf","file_id":"5259","file_size":1852268,"access_level":"open_access"}],"language":[{"iso":"eng"}],"volume":6,"oa":1,"doi":"10.1038/ncomms9822","year":"2015","day":"18","scopus_import":1,"publist_id":"5637","intvolume":"         6","publication":"Nature Communications","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:51:26Z","citation":{"mla":"Wang, Hongzhe, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” <i>Nature Communications</i>, vol. 6, 8822, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/ncomms9822\">10.1038/ncomms9822</a>.","short":"H. Wang, K. Yang, J. Zou, L. Zhu, Z. Xie, M. Morita, M. Tasaka, J. Friml, E. Grotewold, T. Beeckman, S. Vanneste, F. Sack, J. Le, Nature Communications 6 (2015).","apa":"Wang, H., Yang, K., Zou, J., Zhu, L., Xie, Z., Morita, M., … Le, J. (2015). Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms9822\">https://doi.org/10.1038/ncomms9822</a>","ama":"Wang H, Yang K, Zou J, et al. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. <i>Nature Communications</i>. 2015;6. doi:<a href=\"https://doi.org/10.1038/ncomms9822\">10.1038/ncomms9822</a>","ista":"Wang H, Yang K, Zou J, Zhu L, Xie Z, Morita M, Tasaka M, Friml J, Grotewold E, Beeckman T, Vanneste S, Sack F, Le J. 2015. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. 6, 8822.","chicago":"Wang, Hongzhe, Kezhen Yang, Junjie Zou, Lingling Zhu, Zidian Xie, Miyoterao Morita, Masao Tasaka, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” <i>Nature Communications</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/ncomms9822\">https://doi.org/10.1038/ncomms9822</a>.","ieee":"H. Wang <i>et al.</i>, “Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism,” <i>Nature Communications</i>, vol. 6. Nature Publishing Group, 2015."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","abstract":[{"lang":"eng","text":"PIN proteins are auxin export carriers that direct intercellular auxin flow and in turn regulate many aspects of plant growth and development including responses to environmental changes. The Arabidopsis R2R3-MYB transcription factor FOUR LIPS (FLP) and its paralogue MYB88 regulate terminal divisions during stomatal development, as well as female reproductive development and stress responses. Here we show that FLP and MYB88 act redundantly but differentially in regulating the transcription of PIN3 and PIN7 in gravity-sensing cells of primary and lateral roots. On the one hand, FLP is involved in responses to gravity stimulation in primary roots, whereas on the other, FLP and MYB88 function complementarily in establishing the gravitropic set-point angles of lateral roots. Our results support a model in which FLP and MYB88 expression specifically determines the temporal-spatial patterns of PIN3 and PIN7 transcription that are closely associated with their preferential functions during root responses to gravity."}],"ddc":["570"],"publisher":"Nature Publishing Group","date_published":"2015-11-18T00:00:00Z","file_date_updated":"2020-07-14T12:45:01Z","title":"Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism"},{"issue":"2","month":"10","article_processing_charge":"No","volume":8,"language":[{"iso":"eng"}],"oa_version":"Submitted Version","quality_controlled":"1","author":[{"orcid":"0000-0001-7577-1676","first_name":"David H","last_name":"Vandael","full_name":"Vandael, David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andrea","last_name":"Marcantoni","full_name":"Marcantoni, Andrea"},{"last_name":"Carbone","first_name":"Emilio","full_name":"Carbone, Emilio"}],"type":"journal_article","_id":"1535","article_type":"original","date_created":"2018-12-11T11:52:35Z","status":"public","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384372/","open_access":"1"}],"abstract":[{"text":"Neuronal and neuroendocrine L-type calcium channels (Cav1.2, Cav1.3) open readily at relatively low membrane potentials and allow Ca2+ to enter the cells near resting potentials. In this way, Cav1.2 and Cav1.3 shape the action potential waveform, contribute to gene expression, synaptic plasticity, neuronal differentiation, hormone secretion and pacemaker activity. In the chromaffin cells (CCs) of the adrenal medulla, Cav1.3 is highly expressed and is shown to support most of the pacemaking current that sustains action potential (AP) firings and part of the catecholamine secretion. Cav1.3 forms Ca2+-nanodomains with the fast inactivating BK channels and drives the resting SK currents. These latter set the inter-spike interval duration between consecutive spikes during spontaneous firing and the rate of spike adaptation during sustained depolarizations. Cav1.3 plays also a primary role in the switch from “tonic” to “burst” firing that occurs in mouse CCs when either the availability of voltage-gated Na channels (Nav) is reduced or the β2 subunit featuring the fast inactivating BK channels is deleted. Here, we discuss the functional role of these “neuronlike” firing modes in CCs and how Cav1.3 contributes to them. The open issue is to understand how these novel firing patterns are adapted to regulate the quantity of circulating catecholamines during resting condition or in response to acute and chronic stress.","lang":"eng"}],"publication_status":"published","title":"Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells","date_published":"2015-10-01T00:00:00Z","publisher":"Bentham Science Publishers","pmid":1,"citation":{"ieee":"D. H. Vandael, A. Marcantoni, and E. Carbone, “Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells,” <i>Current Molecular Pharmacology</i>, vol. 8, no. 2. Bentham Science Publishers, pp. 149–161, 2015.","ista":"Vandael DH, Marcantoni A, Carbone E. 2015. Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology. 8(2), 149–161.","chicago":"Vandael, David H, Andrea Marcantoni, and Emilio Carbone. “Cav1.3 Channels as Key Regulators of Neuron-like Firings and Catecholamine Release in Chromaffin Cells.” <i>Current Molecular Pharmacology</i>. Bentham Science Publishers, 2015. <a href=\"https://doi.org/10.2174/1874467208666150507105443\">https://doi.org/10.2174/1874467208666150507105443</a>.","ama":"Vandael DH, Marcantoni A, Carbone E. Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. <i>Current Molecular Pharmacology</i>. 2015;8(2):149-161. doi:<a href=\"https://doi.org/10.2174/1874467208666150507105443\">10.2174/1874467208666150507105443</a>","apa":"Vandael, D. H., Marcantoni, A., &#38; Carbone, E. (2015). Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. <i>Current Molecular Pharmacology</i>. Bentham Science Publishers. <a href=\"https://doi.org/10.2174/1874467208666150507105443\">https://doi.org/10.2174/1874467208666150507105443</a>","mla":"Vandael, David H., et al. “Cav1.3 Channels as Key Regulators of Neuron-like Firings and Catecholamine Release in Chromaffin Cells.” <i>Current Molecular Pharmacology</i>, vol. 8, no. 2, Bentham Science Publishers, 2015, pp. 149–61, doi:<a href=\"https://doi.org/10.2174/1874467208666150507105443\">10.2174/1874467208666150507105443</a>.","short":"D.H. Vandael, A. Marcantoni, E. Carbone, Current Molecular Pharmacology 8 (2015) 149–161."},"date_updated":"2021-01-12T06:51:26Z","department":[{"_id":"PeJo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["25966692"]},"scopus_import":1,"publication":"Current Molecular Pharmacology","intvolume":"         8","publist_id":"5636","oa":1,"page":"149 - 161","doi":"10.2174/1874467208666150507105443","year":"2015","day":"01","acknowledgement":"This work was supported by the Italian MIUR (PRIN 2010/2011 project 2010JFYFY2) and the University of Torino."},{"acknowledged_ssus":[{"_id":"SSU"}],"volume":160,"language":[{"iso":"eng"}],"issue":"4","file":[{"relation":"main_file","access_level":"open_access","file_size":4362653,"file_id":"5003","checksum":"228d3edf40627d897b3875088a0ac51f","creator":"system","date_created":"2018-12-12T10:13:21Z","date_updated":"2020-07-14T12:45:01Z","content_type":"application/pdf","file_name":"IST-2016-484-v1+1_1-s2.0-S0092867415000094-main.pdf"}],"has_accepted_license":"1","month":"02","author":[{"full_name":"Ruprecht, Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4088-8633","last_name":"Ruprecht","first_name":"Verena"},{"first_name":"Stefan","last_name":"Wieser","orcid":"0000-0002-2670-2217","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","full_name":"Wieser, Stefan"},{"full_name":"Callan Jones, Andrew","first_name":"Andrew","last_name":"Callan Jones"},{"id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","full_name":"Smutny, Michael","last_name":"Smutny","first_name":"Michael","orcid":"0000-0002-5920-9090"},{"first_name":"Hitoshi","last_name":"Morita","full_name":"Morita, Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Keisuke","last_name":"Sako","orcid":"0000-0002-6453-8075","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","full_name":"Sako, Keisuke"},{"full_name":"Barone, Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367","last_name":"Barone","first_name":"Vanessa"},{"full_name":"Ritsch Marte, Monika","last_name":"Ritsch Marte","first_name":"Monika"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"full_name":"Voituriez, Raphaël","first_name":"Raphaël","last_name":"Voituriez"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"oa_version":"Published Version","quality_controlled":"1","project":[{"call_identifier":"FWF","grant_number":"T 560-B17","_id":"2529486C-B435-11E9-9278-68D0E5697425","name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation"},{"name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","_id":"2527D5CC-B435-11E9-9278-68D0E5697425","grant_number":"I 812-B12","call_identifier":"FWF"}],"pubrep_id":"484","status":"public","_id":"1537","type":"journal_article","date_created":"2018-12-11T11:52:35Z","title":"Cortical contractility triggers a stochastic switch to fast amoeboid cell motility","date_published":"2015-02-12T00:00:00Z","publisher":"Cell Press","file_date_updated":"2020-07-14T12:45:01Z","ddc":["570"],"abstract":[{"lang":"eng","text":"3D amoeboid cell migration is central to many developmental and disease-related processes such as cancer metastasis. Here, we identify a unique prototypic amoeboid cell migration mode in early zebrafish embryos, termed stable-bleb migration. Stable-bleb cells display an invariant polarized balloon-like shape with exceptional migration speed and persistence. Progenitor cells can be reversibly transformed into stable-bleb cells irrespective of their primary fate and motile characteristics by increasing myosin II activity through biochemical or mechanical stimuli. Using a combination of theory and experiments, we show that, in stable-bleb cells, cortical contractility fluctuations trigger a stochastic switch into amoeboid motility, and a positive feedback between cortical flows and gradients in contractility maintains stable-bleb cell polarization. We further show that rearward cortical flows drive stable-bleb cell migration in various adhesive and non-adhesive environments, unraveling a highly versatile amoeboid migration phenotype."}],"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"short":"V. Ruprecht, S. Wieser, A. Callan Jones, M. Smutny, H. Morita, K. Sako, V. Barone, M. Ritsch Marte, M.K. Sixt, R. Voituriez, C.-P.J. Heisenberg, Cell 160 (2015) 673–685.","mla":"Ruprecht, Verena, et al. “Cortical Contractility Triggers a Stochastic Switch to Fast Amoeboid Cell Motility.” <i>Cell</i>, vol. 160, no. 4, Cell Press, 2015, pp. 673–85, doi:<a href=\"https://doi.org/10.1016/j.cell.2015.01.008\">10.1016/j.cell.2015.01.008</a>.","ieee":"V. Ruprecht <i>et al.</i>, “Cortical contractility triggers a stochastic switch to fast amoeboid cell motility,” <i>Cell</i>, vol. 160, no. 4. Cell Press, pp. 673–685, 2015.","apa":"Ruprecht, V., Wieser, S., Callan Jones, A., Smutny, M., Morita, H., Sako, K., … Heisenberg, C.-P. J. (2015). Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2015.01.008\">https://doi.org/10.1016/j.cell.2015.01.008</a>","chicago":"Ruprecht, Verena, Stefan Wieser, Andrew Callan Jones, Michael Smutny, Hitoshi Morita, Keisuke Sako, Vanessa Barone, et al. “Cortical Contractility Triggers a Stochastic Switch to Fast Amoeboid Cell Motility.” <i>Cell</i>. Cell Press, 2015. <a href=\"https://doi.org/10.1016/j.cell.2015.01.008\">https://doi.org/10.1016/j.cell.2015.01.008</a>.","ama":"Ruprecht V, Wieser S, Callan Jones A, et al. Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. <i>Cell</i>. 2015;160(4):673-685. doi:<a href=\"https://doi.org/10.1016/j.cell.2015.01.008\">10.1016/j.cell.2015.01.008</a>","ista":"Ruprecht V, Wieser S, Callan Jones A, Smutny M, Morita H, Sako K, Barone V, Ritsch Marte M, Sixt MK, Voituriez R, Heisenberg C-PJ. 2015. Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. Cell. 160(4), 673–685."},"date_updated":"2023-09-07T12:05:08Z","department":[{"_id":"CaHe"},{"_id":"MiSi"}],"publication":"Cell","intvolume":"       160","publist_id":"5634","related_material":{"record":[{"status":"public","id":"961","relation":"dissertation_contains"}]},"scopus_import":1,"day":"12","doi":"10.1016/j.cell.2015.01.008","page":"673 - 685","year":"2015","acknowledgement":"We would like to thank R. Hausschild and E. Papusheva for technical assistance and the service facilities at the IST Austria for continuous support. The caRhoA plasmid was a kind gift of T. Kudoh and A. Takesono. We thank M. Piel and E. Paluch for exchanging unpublished data. ","oa":1},{"title":"Iterative experiment design guides the characterization of a light-inducible gene expression circuit","pmid":1,"date_published":"2015-06-30T00:00:00Z","publisher":"National Academy of Sciences","publication_status":"published","abstract":[{"text":"Systems biology rests on the idea that biological complexity can be better unraveled through the interplay of modeling and experimentation. However, the success of this approach depends critically on the informativeness of the chosen experiments, which is usually unknown a priori. Here, we propose a systematic scheme based on iterations of optimal experiment design, flow cytometry experiments, and Bayesian parameter inference to guide the discovery process in the case of stochastic biochemical reaction networks. To illustrate the benefit of our methodology, we apply it to the characterization of an engineered light-inducible gene expression circuit in yeast and compare the performance of the resulting model with models identified from nonoptimal experiments. In particular, we compare the parameter posterior distributions and the precision to which the outcome of future experiments can be predicted. Moreover, we illustrate how the identified stochastic model can be used to determine light induction patterns that make either the average amount of protein or the variability in a population of cells follow a desired profile. Our results show that optimal experiment design allows one to derive models that are accurate enough to precisely predict and regulate the protein expression in heterogeneous cell populations over extended periods of time.","lang":"eng"}],"external_id":{"pmid":["26085136"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, and J. Lygeros, “Iterative experiment design guides the characterization of a light-inducible gene expression circuit,” <i>PNAS</i>, vol. 112, no. 26. National Academy of Sciences, pp. 8148–8153, 2015.","apa":"Ruess, J., Parise, F., Milias Argeitis, A., Khammash, M., &#38; Lygeros, J. (2015). Iterative experiment design guides the characterization of a light-inducible gene expression circuit. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1423947112\">https://doi.org/10.1073/pnas.1423947112</a>","chicago":"Ruess, Jakob, Francesca Parise, Andreas Milias Argeitis, Mustafa Khammash, and John Lygeros. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1423947112\">https://doi.org/10.1073/pnas.1423947112</a>.","ista":"Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. 2015. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. 112(26), 8148–8153.","ama":"Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. <i>PNAS</i>. 2015;112(26):8148-8153. doi:<a href=\"https://doi.org/10.1073/pnas.1423947112\">10.1073/pnas.1423947112</a>","short":"J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, J. Lygeros, PNAS 112 (2015) 8148–8153.","mla":"Ruess, Jakob, et al. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” <i>PNAS</i>, vol. 112, no. 26, National Academy of Sciences, 2015, pp. 8148–53, doi:<a href=\"https://doi.org/10.1073/pnas.1423947112\">10.1073/pnas.1423947112</a>."},"department":[{"_id":"ToHe"},{"_id":"GaTk"}],"date_updated":"2021-01-12T06:51:27Z","publication":"PNAS","publist_id":"5633","intvolume":"       112","scopus_import":1,"page":"8148 - 8153","doi":"10.1073/pnas.1423947112","year":"2015","day":"30","acknowledgement":"J.R., F.P., and J.L. acknowledge support from the European Commission under the Network of Excellence HYCON2 (highly-complex and networked control systems) and SystemsX.ch under the SignalX Project. J.R. acknowledges support from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme FP7/2007-2013 under REA (Research Executive Agency) Grant 291734. M.K. acknowledges support from Human Frontier Science Program Grant RP0061/2011 (www.hfsp.org). ","oa":1,"volume":112,"language":[{"iso":"eng"}],"issue":"26","month":"06","author":[{"first_name":"Jakob","last_name":"Ruess","orcid":"0000-0003-1615-3282","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","full_name":"Ruess, Jakob"},{"first_name":"Francesca","last_name":"Parise","full_name":"Parise, Francesca"},{"first_name":"Andreas","last_name":"Milias Argeitis","full_name":"Milias Argeitis, Andreas"},{"full_name":"Khammash, Mustafa","last_name":"Khammash","first_name":"Mustafa"},{"last_name":"Lygeros","first_name":"John","full_name":"Lygeros, John"}],"oa_version":"Submitted Version","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"quality_controlled":"1","ec_funded":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4491780/"}],"status":"public","type":"journal_article","_id":"1538","date_created":"2018-12-11T11:52:36Z"},{"pubrep_id":"593","ec_funded":1,"_id":"1539","type":"journal_article","date_created":"2018-12-11T11:52:36Z","status":"public","file":[{"relation":"main_file","creator":"system","file_id":"4641","checksum":"838657118ae286463a2b7737319f35ce","file_size":605355,"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:01Z","date_created":"2018-12-12T10:07:43Z","file_name":"IST-2016-593-v1+1_Minimal_moment_equations.pdf"}],"article_number":"244103","issue":"24","month":"12","has_accepted_license":"1","volume":143,"language":[{"iso":"eng"}],"oa_version":"Published Version","project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","author":[{"last_name":"Ruess","first_name":"Jakob","orcid":"0000-0003-1615-3282","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","full_name":"Ruess, Jakob"}],"scopus_import":1,"publication":"Journal of Chemical Physics","publist_id":"5632","intvolume":"       143","oa":1,"doi":"10.1063/1.4937937","year":"2015","day":"22","ddc":["000"],"publication_status":"published","abstract":[{"text":"Many stochastic models of biochemical reaction networks contain some chemical species for which the number of molecules that are present in the system can only be finite (for instance due to conservation laws), but also other species that can be present in arbitrarily large amounts. The prime example of such networks are models of gene expression, which typically contain a small and finite number of possible states for the promoter but an infinite number of possible states for the amount of mRNA and protein. One of the main approaches to analyze such models is through the use of equations for the time evolution of moments of the chemical species. Recently, a new approach based on conditional moments of the species with infinite state space given all the different possible states of the finite species has been proposed. It was argued that this approach allows one to capture more details about the full underlying probability distribution with a smaller number of equations. Here, I show that the result that less moments provide more information can only stem from an unnecessarily complicated description of the system in the classical formulation. The foundation of this argument will be the derivation of moment equations that describe the complete probability distribution over the finite state space but only low-order moments over the infinite state space. I will show that the number of equations that is needed is always less than what was previously claimed and always less than the number of conditional moment equations up to the same order. To support these arguments, a symbolic algorithm is provided that can be used to derive minimal systems of unconditional moment equations for models with partially finite state space. ","lang":"eng"}],"title":"Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space","file_date_updated":"2020-07-14T12:45:01Z","publisher":"American Institute of Physics","date_published":"2015-12-22T00:00:00Z","citation":{"mla":"Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.” <i>Journal of Chemical Physics</i>, vol. 143, no. 24, 244103, American Institute of Physics, 2015, doi:<a href=\"https://doi.org/10.1063/1.4937937\">10.1063/1.4937937</a>.","short":"J. Ruess, Journal of Chemical Physics 143 (2015).","apa":"Ruess, J. (2015). Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. <i>Journal of Chemical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4937937\">https://doi.org/10.1063/1.4937937</a>","chicago":"Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.” <i>Journal of Chemical Physics</i>. American Institute of Physics, 2015. <a href=\"https://doi.org/10.1063/1.4937937\">https://doi.org/10.1063/1.4937937</a>.","ista":"Ruess J. 2015. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. 143(24), 244103.","ama":"Ruess J. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. <i>Journal of Chemical Physics</i>. 2015;143(24). doi:<a href=\"https://doi.org/10.1063/1.4937937\">10.1063/1.4937937</a>","ieee":"J. Ruess, “Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space,” <i>Journal of Chemical Physics</i>, vol. 143, no. 24. American Institute of Physics, 2015."},"department":[{"_id":"ToHe"},{"_id":"GaTk"}],"date_updated":"2021-01-12T06:51:28Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","status":"public","date_created":"2018-12-11T11:52:37Z","_id":"1542","type":"journal_article","ec_funded":1,"pubrep_id":"483","author":[{"full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","last_name":"Paixao","first_name":"Tiago"},{"full_name":"Badkobeh, Golnaz","first_name":"Golnaz","last_name":"Badkobeh"},{"first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"first_name":"Doğan","last_name":"Çörüş","full_name":"Çörüş, Doğan"},{"first_name":"Duccuong","last_name":"Dang","full_name":"Dang, Duccuong"},{"full_name":"Friedrich, Tobias","first_name":"Tobias","last_name":"Friedrich"},{"last_name":"Lehre","first_name":"Per","full_name":"Lehre, Per"},{"first_name":"Dirk","last_name":"Sudholt","full_name":"Sudholt, Dirk"},{"full_name":"Sutton, Andrew","first_name":"Andrew","last_name":"Sutton"},{"last_name":"Trubenova","first_name":"Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora"}],"project":[{"grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"volume":383,"month":"10","has_accepted_license":"1","file":[{"access_level":"open_access","file_size":595307,"file_id":"5244","checksum":"33b60ecfea60764756a9ee9df5eb65ca","creator":"system","relation":"main_file","file_name":"IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf","date_created":"2018-12-12T10:16:53Z","date_updated":"2020-07-14T12:45:01Z","content_type":"application/pdf"}],"year":"2015","doi":"10.1016/j.jtbi.2015.07.011","page":"28 - 43","day":"21","oa":1,"intvolume":"       383","publist_id":"5629","publication":" Journal of Theoretical Biology","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"date_updated":"2021-01-12T06:51:29Z","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"citation":{"ista":"Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes.  Journal of Theoretical Biology. 383, 28–43.","chicago":"Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova. “Toward a Unifying Framework for Evolutionary Processes.” <i> Journal of Theoretical Biology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">https://doi.org/10.1016/j.jtbi.2015.07.011</a>.","ama":"Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary processes. <i> Journal of Theoretical Biology</i>. 2015;383:28-43. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">10.1016/j.jtbi.2015.07.011</a>","apa":"Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T., … Trubenova, B. (2015). Toward a unifying framework for evolutionary processes. <i> Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">https://doi.org/10.1016/j.jtbi.2015.07.011</a>","ieee":"T. Paixao <i>et al.</i>, “Toward a unifying framework for evolutionary processes,” <i> Journal of Theoretical Biology</i>, vol. 383. Elsevier, pp. 28–43, 2015.","mla":"Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.” <i> Journal of Theoretical Biology</i>, vol. 383, Elsevier, 2015, pp. 28–43, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">10.1016/j.jtbi.2015.07.011</a>.","short":"T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P. Lehre, D. Sudholt, A. Sutton, B. Trubenova,  Journal of Theoretical Biology 383 (2015) 28–43."},"file_date_updated":"2020-07-14T12:45:01Z","publisher":"Elsevier","date_published":"2015-10-21T00:00:00Z","title":"Toward a unifying framework for evolutionary processes","abstract":[{"text":"The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. ","lang":"eng"}],"publication_status":"published","ddc":["570"]},{"oa_version":"Submitted Version","quality_controlled":"1","author":[{"full_name":"Nguyen, Phuong","last_name":"Nguyen","first_name":"Phuong"},{"full_name":"Field, Christine","first_name":"Christine","last_name":"Field"},{"full_name":"Groen, Aaron","last_name":"Groen","first_name":"Aaron"},{"full_name":"Mitchison, Timothy","last_name":"Mitchison","first_name":"Timothy"},{"last_name":"Loose","first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin"}],"month":"04","volume":128,"language":[{"iso":"eng"}],"_id":"1544","type":"book_chapter","date_created":"2018-12-11T11:52:38Z","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578691/","open_access":"1"}],"status":"public","citation":{"mla":"Nguyen, Phuong, et al. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound Proteins.” <i>Building a Cell from Its Components Parts</i>, vol. 128, Academic Press, 2015, pp. 223–41, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2015.01.007\">10.1016/bs.mcb.2015.01.007</a>.","short":"P. Nguyen, C. Field, A. Groen, T. Mitchison, M. Loose, in:, Building a Cell from Its Components Parts, Academic Press, 2015, pp. 223–241.","ista":"Nguyen P, Field C, Groen A, Mitchison T, Loose M. 2015.Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In: Building a Cell from its Components Parts. vol. 128, 223–241.","ama":"Nguyen P, Field C, Groen A, Mitchison T, Loose M. Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In: <i>Building a Cell from Its Components Parts</i>. Vol 128. Academic Press; 2015:223-241. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2015.01.007\">10.1016/bs.mcb.2015.01.007</a>","chicago":"Nguyen, Phuong, Christine Field, Aaron Groen, Timothy Mitchison, and Martin Loose. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound Proteins.” In <i>Building a Cell from Its Components Parts</i>, 128:223–41. Academic Press, 2015. <a href=\"https://doi.org/10.1016/bs.mcb.2015.01.007\">https://doi.org/10.1016/bs.mcb.2015.01.007</a>.","apa":"Nguyen, P., Field, C., Groen, A., Mitchison, T., &#38; Loose, M. (2015). Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In <i>Building a Cell from its Components Parts</i> (Vol. 128, pp. 223–241). Academic Press. <a href=\"https://doi.org/10.1016/bs.mcb.2015.01.007\">https://doi.org/10.1016/bs.mcb.2015.01.007</a>","ieee":"P. Nguyen, C. Field, A. Groen, T. Mitchison, and M. Loose, “Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins,” in <i>Building a Cell from its Components Parts</i>, vol. 128, Academic Press, 2015, pp. 223–241."},"department":[{"_id":"MaLo"}],"date_updated":"2021-01-12T06:51:30Z","external_id":{"pmid":["25997350"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"text":"Cell division in prokaryotes and eukaryotes is commonly initiated by the well-controlled binding of proteins to the cytoplasmic side of the cell membrane. However, a precise characterization of the spatiotemporal dynamics of membrane-bound proteins is often difficult to achieve in vivo. Here, we present protocols for the use of supported lipid bilayers to rebuild the cytokinetic machineries of cells with greatly different dimensions: the bacterium Escherichia coli and eggs of the vertebrate Xenopus laevis. Combined with total internal reflection fluorescence microscopy, these experimental setups allow for precise quantitative analyses of membrane-bound proteins. The protocols described to obtain glass-supported membranes from bacterial and vertebrate lipids can be used as starting points for other reconstitution experiments. We believe that similar biochemical assays will be instrumental to study the biochemistry and biophysics underlying a variety of complex cellular tasks, such as signaling, vesicle trafficking, and cell motility.","lang":"eng"}],"title":"Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins","pmid":1,"publisher":"Academic Press","date_published":"2015-04-08T00:00:00Z","oa":1,"doi":"10.1016/bs.mcb.2015.01.007","year":"2015","page":"223 - 241","day":"08","scopus_import":1,"publication":"Building a Cell from its Components Parts","publist_id":"5627","intvolume":"       128"},{"acknowledgement":"This work was supported by the Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Agency to T.T. and R.S.; by the funding provided by Okinawa Institute of Science and Technology (OIST) to T.T. and Y.N.; by JSPS Core-to-Core Program, A. Advanced Networks to T.T.; by the Grant-in-Aid for Young Scientists from the Japanese Ministry of Education, Culture, Sports, Science and Technology (#23700474) to Y.N.; by the Centre National de la Recherche Scientifique through the Actions Thematiques et Initatives sur Programme, Fondation Fyssen, Fondation pour la Recherche Medicale, Federation pour la Recherche sur le Cerveau, Agence Nationale de la Recherche (ANR-2007-Neuro-008-01 and ANR-2010-BLAN-1411-01) to D.D. and Y.N.; and by the European Commission Coordination Action ENINET (LSHM-CT-2005-19063) to D.D. and R.A.S. R.A.S. and J.S.R. were funded by Wellcome Trust Senior (064413) and Principal (095667) Research Fellowship and an ERC advance grant (294667) to RAS.","day":"07","year":"2015","page":"145 - 158","doi":"10.1016/j.neuron.2014.11.019","oa":1,"intvolume":"        85","publist_id":"5625","publication":"Neuron","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2021-01-12T06:51:31Z","department":[{"_id":"RySh"}],"citation":{"chicago":"Nakamura, Yukihiro, Harumi Harada, Naomi Kamasawa, Ko Matsui, Jason Rothman, Ryuichi Shigemoto, R Angus Silver, David Digregorio, and Tomoyuki Takahashi. “Nanoscale Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release during Development.” <i>Neuron</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.neuron.2014.11.019\">https://doi.org/10.1016/j.neuron.2014.11.019</a>.","ama":"Nakamura Y, Harada H, Kamasawa N, et al. Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. <i>Neuron</i>. 2015;85(1):145-158. doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.11.019\">10.1016/j.neuron.2014.11.019</a>","ista":"Nakamura Y, Harada H, Kamasawa N, Matsui K, Rothman J, Shigemoto R, Silver RA, Digregorio D, Takahashi T. 2015. Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. Neuron. 85(1), 145–158.","apa":"Nakamura, Y., Harada, H., Kamasawa, N., Matsui, K., Rothman, J., Shigemoto, R., … Takahashi, T. (2015). Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2014.11.019\">https://doi.org/10.1016/j.neuron.2014.11.019</a>","ieee":"Y. Nakamura <i>et al.</i>, “Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development,” <i>Neuron</i>, vol. 85, no. 1. Elsevier, pp. 145–158, 2015.","mla":"Nakamura, Yukihiro, et al. “Nanoscale Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release during Development.” <i>Neuron</i>, vol. 85, no. 1, Elsevier, 2015, pp. 145–58, doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.11.019\">10.1016/j.neuron.2014.11.019</a>.","short":"Y. Nakamura, H. Harada, N. Kamasawa, K. Matsui, J. Rothman, R. Shigemoto, R.A. Silver, D. Digregorio, T. Takahashi, Neuron 85 (2015) 145–158."},"file_date_updated":"2020-07-14T12:45:01Z","date_published":"2015-01-07T00:00:00Z","publisher":"Elsevier","title":"Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development","abstract":[{"lang":"eng","text":"Synaptic efficacy and precision are influenced by the coupling of voltage-gated Ca2+ channels (VGCCs) to vesicles. But because the topography of VGCCs and their proximity to vesicles is unknown, a quantitative understanding of the determinants of vesicular release at nanometer scale is lacking. To investigate this, we combined freeze-fracture replica immunogold labeling of Cav2.1 channels, local [Ca2+] imaging, and patch pipette perfusion of EGTA at the calyx of Held. Between postnatal day 7 and 21, VGCCs formed variable sized clusters and vesicular release became less sensitive to EGTA, whereas fixed Ca2+ buffer properties remained constant. Experimentally constrained reaction-diffusion simulations suggest that Ca2+ sensors for vesicular release are located at the perimeter of VGCC clusters (&lt;30nm) and predict that VGCC number per cluster determines vesicular release probability without altering release time course. This &quot;perimeter release model&quot; provides a unifying framework accounting for developmental changes in both synaptic efficacy and time course."}],"publication_status":"published","ddc":["570"],"status":"public","date_created":"2018-12-11T11:52:39Z","_id":"1546","type":"journal_article","pubrep_id":"482","author":[{"full_name":"Nakamura, Yukihiro","last_name":"Nakamura","first_name":"Yukihiro"},{"orcid":"0000-0001-7429-7896","first_name":"Harumi","last_name":"Harada","full_name":"Harada, Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Naomi","last_name":"Kamasawa","full_name":"Kamasawa, Naomi"},{"first_name":"Ko","last_name":"Matsui","full_name":"Matsui, Ko"},{"full_name":"Rothman, Jason","last_name":"Rothman","first_name":"Jason"},{"first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"},{"full_name":"Silver, R Angus","last_name":"Silver","first_name":"R Angus"},{"last_name":"Digregorio","first_name":"David","full_name":"Digregorio, David"},{"full_name":"Takahashi, Tomoyuki","first_name":"Tomoyuki","last_name":"Takahashi"}],"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"volume":85,"has_accepted_license":"1","month":"01","issue":"1","file":[{"file_name":"IST-2016-482-v1+1_1-s2.0-S0896627314010472-main.pdf","date_updated":"2020-07-14T12:45:01Z","date_created":"2018-12-12T10:15:47Z","content_type":"application/pdf","file_size":3080111,"access_level":"open_access","creator":"system","checksum":"725f4d5be2dbb44b283ce722645ef37d","file_id":"5170","relation":"main_file"}]}]