[{"day":"01","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"doi":"10.12688/f1000research.7143.1","department":[{"_id":"JiFr"},{"_id":"ToBo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","oa":1,"file_date_updated":"2020-07-14T12:44:59Z","pubrep_id":"497","intvolume":"         4","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1","abstract":[{"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.","lang":"eng"}],"volume":4,"date_created":"2018-12-11T11:52:26Z","oa_version":"Published Version","file":[{"content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:44:59Z","access_level":"open_access","file_name":"IST-2016-497-v1+1_10.12688_f1000research.7143.1_20151102.pdf","date_created":"2018-12-12T10:16:12Z","checksum":"8beae5cbe988e1060265ae7de2ee8306","file_size":4414248,"file_id":"5198","creator":"system"}],"month":"10","citation":{"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>.","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.","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>","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>.","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.","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>","short":"J. Michalko, M. Lukacisinova, M.T. Bollenbach, J. Friml, F1000 Research  4 (2015)."},"_id":"1509","date_updated":"2025-04-15T07:48:03Z","corr_author":"1","publisher":"F1000 Research","language":[{"iso":"eng"}],"year":"2015","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","quality_controlled":"1","article_processing_charge":"No","ddc":["570"],"publication":"F1000 Research ","type":"journal_article","has_accepted_license":"1","date_published":"2015-10-01T00:00:00Z","title":"Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene","author":[{"full_name":"Michalko, Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87","first_name":"Jaroslav","last_name":"Michalko"},{"orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87","first_name":"Marta","last_name":"Dravecka","full_name":"Dravecka, Marta"},{"orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","last_name":"Bollenbach"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"}],"ec_funded":1,"publist_id":"5668"},{"oa_version":"Published Version","date_created":"2018-12-11T11:52:26Z","volume":34,"related_material":{"record":[{"id":"1408","relation":"later_version","status":"public"}]},"abstract":[{"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. ","lang":"eng"}],"scopus_import":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"intvolume":"        34","pubrep_id":"503","oa":1,"file_date_updated":"2020-07-14T12:44:59Z","publication_status":"published","status":"public","doi":"10.4230/LIPIcs.SOCG.2015.842","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"day":"11","ec_funded":1,"publist_id":"5667","alternative_title":["LIPIcs"],"title":"On computability and triviality of well groups","author":[{"orcid":"0000-0001-8878-8397","full_name":"Franek, Peter","first_name":"Peter","id":"473294AE-F248-11E8-B48F-1D18A9856A87","last_name":"Franek"},{"full_name":"Krcál, Marek","last_name":"Krcál","first_name":"Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2015-06-11T00:00:00Z","has_accepted_license":"1","type":"conference","ddc":["510"],"quality_controlled":"1","conference":{"end_date":"2015-06-25","start_date":"2015-06-22","location":"Eindhoven, Netherlands","name":"SoCG: Symposium on Computational Geometry"},"year":"2015","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","language":[{"iso":"eng"}],"month":"06","_id":"1510","citation":{"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>","short":"P. Franek, M. Krcál, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 842–856.","ista":"Franek P, Krcál M. 2015. On computability and triviality of well groups. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 842–856.","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>","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>.","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.","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>."},"date_updated":"2025-09-18T14:30:52Z","page":"842 - 856","file":[{"creator":"system","file_id":"5001","date_created":"2018-12-12T10:13:19Z","file_size":623563,"checksum":"49eb5021caafaabe5356c65b9c5f8c9c","file_name":"IST-2016-503-v1+1_32.pdf","date_updated":"2020-07-14T12:44:59Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}]},{"publication_status":"published","status":"public","doi":"10.4230/LIPIcs.SOCG.2015.476","department":[{"_id":"UlWa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"day":"11","pubrep_id":"502","oa":1,"file_date_updated":"2020-07-14T12:44:59Z","scopus_import":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa_version":"Published Version","date_created":"2018-12-11T11:52:27Z","volume":"34 ","related_material":{"record":[{"status":"public","relation":"later_version","id":"610"}]},"abstract":[{"lang":"eng","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."}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","language":[{"iso":"eng"}],"month":"06","_id":"1511","date_updated":"2025-09-11T07:35:35Z","page":"476 - 490","citation":{"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>.","short":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 476–490.","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>","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>.","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."},"file":[{"creator":"system","file_id":"4871","checksum":"0945811875351796324189312ca29e9e","file_size":636735,"date_created":"2018-12-12T10:11:18Z","file_name":"IST-2016-502-v1+1_42.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:59Z","relation":"main_file","content_type":"application/pdf"}],"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).","conference":{"end_date":"2015-06-25","start_date":"2015-06-22","location":"Eindhoven, Netherlands","name":"SoCG: Symposium on Computational Geometry"},"year":"2015","ddc":["510"],"quality_controlled":"1","publist_id":"5666","ec_funded":1,"alternative_title":["LIPIcs"],"title":"On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result","author":[{"last_name":"Goaoc","first_name":"Xavier","full_name":"Goaoc, Xavier"},{"first_name":"Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","last_name":"Mabillard","full_name":"Mabillard, Isaac"},{"last_name":"Paták","first_name":"Pavel","full_name":"Paták, Pavel"},{"orcid":"0000-0002-3975-1683","first_name":"Zuzana","id":"48B57058-F248-11E8-B48F-1D18A9856A87","last_name":"Patakova","full_name":"Patakova, Zuzana"},{"orcid":"0000-0002-1191-6714","last_name":"Tancer","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Tancer, Martin"},{"full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568"}],"date_published":"2015-06-11T00:00:00Z","has_accepted_license":"1","type":"conference"},{"department":[{"_id":"BeVi"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1093/gbe/evv215","day":"01","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication_status":"published","status":"public","pubrep_id":"496","file_date_updated":"2020-07-14T12:45:00Z","oa":1,"issue":"12","intvolume":"         7","scopus_import":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"isi":["000366498700008"]},"date_created":"2018-12-11T11:52:27Z","volume":7,"abstract":[{"lang":"eng","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. "}],"oa_version":"Published Version","file":[{"file_name":"IST-2016-496-v1+1_Genome_Biol_Evol-2015-Pal-3259-68.pdf","date_created":"2018-12-12T10:17:29Z","file_size":858027,"checksum":"2b56b8c2e2a1d4cc3c9cb8daba26dd9b","file_id":"5284","creator":"system","content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:45:00Z","access_level":"open_access"}],"language":[{"iso":"eng"}],"publisher":"Oxford University Press","corr_author":"1","page":"3259 - 3268","_id":"1513","citation":{"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>.","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>","short":"A. Pal, B. Vicoso, Genome Biology and Evolution 7 (2015) 3259–3268.","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.","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>.","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."},"date_updated":"2025-09-23T14:18:15Z","month":"12","year":"2015","article_processing_charge":"No","quality_controlled":"1","publication":"Genome Biology and Evolution","ddc":["570"],"date_published":"2015-12-01T00:00:00Z","type":"journal_article","has_accepted_license":"1","publist_id":"5664","ec_funded":1,"isi":1,"author":[{"orcid":"0000-0002-4530-8469","full_name":"Pal, Arka","last_name":"Pal","first_name":"Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"}],"title":"The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression"},{"oa_version":"Published Version","date_created":"2018-12-11T11:52:29Z","volume":20,"article_number":"89","abstract":[{"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","lang":"eng"}],"scopus_import":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"isi":["000365470700001"]},"intvolume":"        20","pubrep_id":"494","oa":1,"file_date_updated":"2020-07-14T12:45:00Z","publication_status":"published","status":"public","doi":"10.1214/ECP.v20-4315","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"JaMa"}],"day":"29","isi":1,"publist_id":"5660","title":"From large deviations to Wasserstein gradient flows in multiple dimensions","author":[{"last_name":"Erbar","first_name":"Matthias","full_name":"Erbar, Matthias"},{"full_name":"Maas, Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","orcid":"0000-0002-0845-1338"},{"last_name":"Renger","first_name":"Michiel","full_name":"Renger, Michiel"}],"date_published":"2015-11-29T00:00:00Z","has_accepted_license":"1","type":"journal_article","publication":"Electronic Communications in Probability","ddc":["519"],"article_processing_charge":"No","quality_controlled":"1","year":"2015","publisher":"Institute of Mathematical Statistics","language":[{"iso":"eng"}],"month":"11","date_updated":"2025-09-23T08:53:14Z","_id":"1517","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>.","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>","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.","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>","short":"M. Erbar, J. Maas, M. Renger, Electronic Communications in Probability 20 (2015).","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>."},"file":[{"file_id":"4828","creator":"system","file_name":"IST-2016-494-v1+1_4315-23820-1-PB.pdf","checksum":"135741c17d3e1547ca696b6fbdcd559c","file_size":230525,"date_created":"2018-12-12T10:10:39Z","date_updated":"2020-07-14T12:45:00Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file"}]},{"year":"2015","corr_author":"1","publisher":"Wiley","language":[{"iso":"eng"}],"month":"03","date_updated":"2025-09-23T13:53:01Z","_id":"1519","citation":{"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>.","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>","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>.","ieee":"N. H. Barton and M. Servedio, “The interpretation of selection coefficients,” <i>Evolution</i>, vol. 69, no. 5. Wiley, pp. 1101–1112, 2015.","short":"N.H. Barton, M. Servedio, Evolution 69 (2015) 1101–1112.","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>","ista":"Barton NH, Servedio M. 2015. The interpretation of selection coefficients. Evolution. 69(5), 1101–1112."},"page":"1101 - 1112","file":[{"relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:45:00Z","access_level":"open_access","date_created":"2018-12-12T10:10:34Z","file_size":188872,"checksum":"fd8d23f476bc194419929b72ca265c02","file_name":"IST-2016-560-v1+1_Interpreting_ML_coefficients_11.2.15_App.pdf","creator":"system","file_id":"4822"},{"date_created":"2018-12-12T10:10:35Z","checksum":"b774911e70044641d556e258efcb52ef","file_size":577415,"file_name":"IST-2016-560-v1+2_Interpreting_ML_coefficients_11.2.15_mainText.pdf","creator":"system","file_id":"4823","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:45:00Z","access_level":"open_access"}],"isi":1,"publist_id":"5656","ec_funded":1,"title":"The interpretation of selection coefficients","author":[{"orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"full_name":"Servedio, Maria","first_name":"Maria","last_name":"Servedio"}],"date_published":"2015-03-19T00:00:00Z","type":"journal_article","has_accepted_license":"1","publication":"Evolution","ddc":["570"],"article_processing_charge":"No","quality_controlled":"1","issue":"5","pubrep_id":"560","oa":1,"file_date_updated":"2020-07-14T12:45:00Z","publication_status":"published","status":"public","doi":"10.1111/evo.12641","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"NiBa"}],"day":"19","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"oa_version":"Submitted Version","date_created":"2018-12-11T11:52:29Z","volume":69,"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"}],"scopus_import":"1","external_id":{"isi":["000354561600001"]},"intvolume":"        69"},{"year":"2015","conference":{"name":"SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation","end_date":"2015-08-09","start_date":"2015-08-07","location":"Los Angeles, CA, United States"},"language":[{"iso":"eng"}],"publication_status":"published","publisher":"ACM","citation":{"chicago":"Bharaj, Gaurav, Stelian Coros, Bernhard Thomaszewski, James Tompkin, Bernd Bickel, and Hanspeter Pfister. “Computational Design of Walking Automata,” 93–100. ACM, 2015. <a href=\"https://doi.org/10.1145/2786784.2786803\">https://doi.org/10.1145/2786784.2786803</a>.","short":"G. Bharaj, S. Coros, B. Thomaszewski, J. Tompkin, B. Bickel, H. Pfister, in:, ACM, 2015, pp. 93–100.","apa":"Bharaj, G., Coros, S., Thomaszewski, B., Tompkin, J., Bickel, B., &#38; Pfister, H. (2015). Computational design of walking automata (pp. 93–100). Presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Los Angeles, CA, United States: ACM. <a href=\"https://doi.org/10.1145/2786784.2786803\">https://doi.org/10.1145/2786784.2786803</a>","ista":"Bharaj G, Coros S, Thomaszewski B, Tompkin J, Bickel B, Pfister H. 2015. Computational design of walking automata. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 93–100.","ama":"Bharaj G, Coros S, Thomaszewski B, Tompkin J, Bickel B, Pfister H. Computational design of walking automata. In: ACM; 2015:93-100. doi:<a href=\"https://doi.org/10.1145/2786784.2786803\">10.1145/2786784.2786803</a>","mla":"Bharaj, Gaurav, et al. <i>Computational Design of Walking Automata</i>. ACM, 2015, pp. 93–100, doi:<a href=\"https://doi.org/10.1145/2786784.2786803\">10.1145/2786784.2786803</a>.","ieee":"G. Bharaj, S. Coros, B. Thomaszewski, J. Tompkin, B. Bickel, and H. Pfister, “Computational design of walking automata,” presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Los Angeles, CA, United States, 2015, pp. 93–100."},"_id":"1520","date_updated":"2021-01-12T06:51:21Z","status":"public","page":"93 - 100","month":"08","department":[{"_id":"BeBi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1145/2786784.2786803","day":"01","publist_id":"5655","oa_version":"None","author":[{"last_name":"Bharaj","first_name":"Gaurav","full_name":"Bharaj, Gaurav"},{"full_name":"Coros, Stelian","last_name":"Coros","first_name":"Stelian"},{"first_name":"Bernhard","last_name":"Thomaszewski","full_name":"Thomaszewski, Bernhard"},{"last_name":"Tompkin","first_name":"James","full_name":"Tompkin, James"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385"},{"last_name":"Pfister","first_name":"Hanspeter","full_name":"Pfister, Hanspeter"}],"title":"Computational design of walking automata","date_created":"2018-12-11T11:52:30Z","date_published":"2015-08-01T00:00:00Z","abstract":[{"text":"Creating mechanical automata that can walk in stable and pleasing manners is a challenging task that requires both skill and expertise. We propose to use computational design to offset the technical difficulties of this process. A simple drag-and-drop interface allows casual users to create personalized walking toys from a library of pre-defined template mechanisms. Provided with this input, our method leverages physical simulation and evolutionary optimization to refine the mechanical designs such that the resulting toys are able to walk. The optimization process is guided by an intuitive set of objectives that measure the quality of the walking motions. We demonstrate our approach on a set of simulated mechanical toys with different numbers of legs and various distinct gaits. Two fabricated prototypes showcase the feasibility of our designs.","lang":"eng"}],"type":"conference","scopus_import":1,"quality_controlled":"1","publication_identifier":{"isbn":["978-1-4503-3496-9"]}},{"oa_version":"None","date_created":"2018-12-11T11:52:33Z","volume":12,"abstract":[{"lang":"eng","text":"In growing cells, protein synthesis and cell growth are typically not synchronous, and, thus, protein concentrations vary over the cell division cycle. We have developed a theoretical description of genetic regulatory systems in bacteria that explicitly considers the cell division cycle to investigate its impact on gene expression. We calculate the cell-to-cell variations arising from cells being at different stages in the division cycle for unregulated genes and for basic regulatory mechanisms. These variations contribute to the extrinsic noise observed in single-cell experiments, and are most significant for proteins with short lifetimes. Negative autoregulation buffers against variation of protein concentration over the division cycle, but the effect is found to be relatively weak. Stronger buffering is achieved by an increased protein lifetime. Positive autoregulation can strongly amplify such variation if the parameters are set to values that lead to resonance-like behaviour. For cooperative positive autoregulation, the concentration variation over the division cycle diminishes the parameter region of bistability and modulates the switching times between the two stable states. The same effects are seen for a two-gene mutual-repression toggle switch. By contrast, an oscillatory circuit, the repressilator, is only weakly affected by the division cycle."}],"article_number":"066003","scopus_import":"1","external_id":{"isi":["000368186300009"]},"intvolume":"        12","issue":"6","publication_status":"published","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"MiSi"}],"doi":"10.1088/1478-3975/12/6/066003","day":"25","publist_id":"5641","isi":1,"author":[{"full_name":"Bierbaum, Veronika","first_name":"Veronika","id":"3FD04378-F248-11E8-B48F-1D18A9856A87","last_name":"Bierbaum"},{"full_name":"Klumpp, Stefan","first_name":"Stefan","last_name":"Klumpp"}],"title":"Impact of the cell division cycle on gene circuits","date_published":"2015-09-25T00:00:00Z","type":"journal_article","publication":"Physical Biology","article_processing_charge":"No","quality_controlled":"1","year":"2015","language":[{"iso":"eng"}],"publisher":"IOP Publishing","corr_author":"1","date_updated":"2025-09-23T09:19:53Z","_id":"1530","citation":{"chicago":"Bierbaum, Veronika, and Stefan Klumpp. “Impact of the Cell Division Cycle on Gene Circuits.” <i>Physical Biology</i>. IOP Publishing, 2015. <a href=\"https://doi.org/10.1088/1478-3975/12/6/066003\">https://doi.org/10.1088/1478-3975/12/6/066003</a>.","apa":"Bierbaum, V., &#38; Klumpp, S. (2015). Impact of the cell division cycle on gene circuits. <i>Physical Biology</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1478-3975/12/6/066003\">https://doi.org/10.1088/1478-3975/12/6/066003</a>","short":"V. Bierbaum, S. Klumpp, Physical Biology 12 (2015).","ista":"Bierbaum V, Klumpp S. 2015. Impact of the cell division cycle on gene circuits. Physical Biology. 12(6), 066003.","ama":"Bierbaum V, Klumpp S. Impact of the cell division cycle on gene circuits. <i>Physical Biology</i>. 2015;12(6). doi:<a href=\"https://doi.org/10.1088/1478-3975/12/6/066003\">10.1088/1478-3975/12/6/066003</a>","mla":"Bierbaum, Veronika, and Stefan Klumpp. “Impact of the Cell Division Cycle on Gene Circuits.” <i>Physical Biology</i>, vol. 12, no. 6, 066003, IOP Publishing, 2015, doi:<a href=\"https://doi.org/10.1088/1478-3975/12/6/066003\">10.1088/1478-3975/12/6/066003</a>.","ieee":"V. Bierbaum and S. Klumpp, “Impact of the cell division cycle on gene circuits,” <i>Physical Biology</i>, vol. 12, no. 6. IOP Publishing, 2015."},"month":"09"},{"edition":"1","status":"public","publication_status":"published","day":"01","department":[{"_id":"HeEd"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-319-15090-1_13","oa_version":"None","abstract":[{"text":"The Heat Kernel Signature (HKS) is a scalar quantity which is derived from the heat kernel of a given shape. Due to its robustness, isometry invariance, and multiscale nature, it has been successfully applied in many geometric applications. From a more general point of view, the HKS can be considered as a descriptor of the metric of a Riemannian manifold. Given a symmetric positive definite tensor field we may interpret it as the metric of some Riemannian manifold and thereby apply the HKS to visualize and analyze the given tensor data. In this paper, we propose a generalization of this approach that enables the treatment of indefinite tensor fields, like the stress tensor, by interpreting them as a generator of a positive definite tensor field. To investigate the usefulness of this approach we consider the stress tensor from the two-point-load model example and from a mechanical work piece.","lang":"eng"}],"date_created":"2018-12-11T11:52:33Z","volume":40,"scopus_import":"1","intvolume":"        40","year":"2015","citation":{"ista":"Zobel V, Reininghaus J, Hotz I. 2015.Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In: Visualization and Processing of Higher Order Descriptors for Multi-Valued Data. Mathematics and Visualization, vol. 40, 257–267.","apa":"Zobel, V., Reininghaus, J., &#38; Hotz, I. (2015). Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In I. Hotz &#38; T. Schultz (Eds.), <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i> (1st ed., Vol. 40, pp. 257–267). Springer. <a href=\"https://doi.org/10.1007/978-3-319-15090-1_13\">https://doi.org/10.1007/978-3-319-15090-1_13</a>","short":"V. Zobel, J. Reininghaus, I. Hotz, in:, I. Hotz, T. Schultz (Eds.), Visualization and Processing of Higher Order Descriptors for Multi-Valued Data, 1st ed., Springer, 2015, pp. 257–267.","ieee":"V. Zobel, J. Reininghaus, and I. Hotz, “Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature,” in <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i>, 1st ed., vol. 40, I. Hotz and T. Schultz, Eds. Springer, 2015, pp. 257–267.","mla":"Zobel, Valentin, et al. “Visualizing Symmetric Indefinite 2D Tensor Fields Using The Heat Kernel Signature.” <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i>, edited by Ingrid Hotz and Thomas Schultz, 1st ed., vol. 40, Springer, 2015, pp. 257–67, doi:<a href=\"https://doi.org/10.1007/978-3-319-15090-1_13\">10.1007/978-3-319-15090-1_13</a>.","ama":"Zobel V, Reininghaus J, Hotz I. Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In: Hotz I, Schultz T, eds. <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i>. Vol 40. 1st ed. Springer; 2015:257-267. doi:<a href=\"https://doi.org/10.1007/978-3-319-15090-1_13\">10.1007/978-3-319-15090-1_13</a>","chicago":"Zobel, Valentin, Jan Reininghaus, and Ingrid Hotz. “Visualizing Symmetric Indefinite 2D Tensor Fields Using The Heat Kernel Signature.” In <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i>, edited by Ingrid Hotz and Thomas Schultz, 1st ed., 40:257–67. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-319-15090-1_13\">https://doi.org/10.1007/978-3-319-15090-1_13</a>."},"_id":"1531","date_updated":"2022-06-10T09:50:14Z","page":"257 - 267","month":"01","language":[{"iso":"eng"}],"publisher":"Springer","editor":[{"full_name":"Hotz, Ingrid","last_name":"Hotz","first_name":"Ingrid"},{"full_name":"Schultz, Thomas","last_name":"Schultz","first_name":"Thomas"}],"author":[{"full_name":"Zobel, Valentin","first_name":"Valentin","last_name":"Zobel"},{"last_name":"Reininghaus","id":"4505473A-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Reininghaus, Jan"},{"first_name":"Ingrid","last_name":"Hotz","full_name":"Hotz, Ingrid"}],"title":"Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature","alternative_title":["Mathematics and Visualization"],"publist_id":"5640","type":"book_chapter","date_published":"2015-01-01T00:00:00Z","publication":"Visualization and Processing of Higher Order Descriptors for Multi-Valued Data","quality_controlled":"1","publication_identifier":{"isbn":["978-3-319-15089-5"]},"article_processing_charge":"No"},{"title":"Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source","author":[{"full_name":"Yang, Huaiyu","last_name":"Yang","first_name":"Huaiyu"},{"last_name":"Von Der Fecht Bartenbach","first_name":"Jenny","full_name":"Von Der Fecht Bartenbach, Jenny"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"full_name":"Lohmann, Jan","last_name":"Lohmann","first_name":"Jan"},{"first_name":"Benjamin","last_name":"Neuhäuser","full_name":"Neuhäuser, Benjamin"},{"full_name":"Ludewig, Uwe","last_name":"Ludewig","first_name":"Uwe"}],"isi":1,"publist_id":"5639","type":"journal_article","date_published":"2015-03-01T00:00:00Z","publication":"Functional Plant Biology","publication_identifier":{"issn":["1445-4408"]},"quality_controlled":"1","article_processing_charge":"No","year":"2015","month":"03","_id":"1532","date_updated":"2025-09-23T07:59:44Z","page":"239 - 251","citation":{"ama":"Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig U. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. <i>Functional Plant Biology</i>. 2015;42(3):239-251. doi:<a href=\"https://doi.org/10.1071/FP14171\">10.1071/FP14171</a>","mla":"Yang, Huaiyu, et al. “Auxin-Modulated Root Growth Inhibition in Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” <i>Functional Plant Biology</i>, vol. 42, no. 3, CSIRO, 2015, pp. 239–51, doi:<a href=\"https://doi.org/10.1071/FP14171\">10.1071/FP14171</a>.","ieee":"H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, and U. Ludewig, “Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source,” <i>Functional Plant Biology</i>, vol. 42, no. 3. CSIRO, pp. 239–251, 2015.","apa":"Yang, H., Von Der Fecht Bartenbach, J., Friml, J., Lohmann, J., Neuhäuser, B., &#38; Ludewig, U. (2015). Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. <i>Functional Plant Biology</i>. CSIRO. <a href=\"https://doi.org/10.1071/FP14171\">https://doi.org/10.1071/FP14171</a>","short":"H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, U. Ludewig, Functional Plant Biology 42 (2015) 239–251.","ista":"Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig U. 2015. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology. 42(3), 239–251.","chicago":"Yang, Huaiyu, Jenny Von Der Fecht Bartenbach, Jiří Friml, Jan Lohmann, Benjamin Neuhäuser, and Uwe Ludewig. “Auxin-Modulated Root Growth Inhibition in Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” <i>Functional Plant Biology</i>. CSIRO, 2015. <a href=\"https://doi.org/10.1071/FP14171\">https://doi.org/10.1071/FP14171</a>."},"publisher":"CSIRO","language":[{"iso":"eng"}],"pmid":1,"oa_version":"None","abstract":[{"text":"Ammonium is the major nitrogen source in some plant ecosystems but is toxic at high concentrations, especially when available as the exclusive nitrogen source. Ammonium stress rapidly leads to various metabolic and hormonal imbalances that ultimately inhibit root and shoot growth in many plant species, including Arabidopsis thaliana (L.) Heynh. To identify molecular and genetic factors involved in seedling survival with prolonged exclusive NH4+ nutrition, a transcriptomic analysis with microarrays was used. Substantial transcriptional differences were most pronounced in (NH4)2SO4-grown seedlings, compared with plants grown on KNO3 or NH4NO3. Consistent with previous physiological analyses, major differences in the expression modules of photosynthesis-related genes, an altered mitochondrial metabolism, differential expression of the primary NH4+ assimilation, alteration of transporter gene expression and crucial changes in cell wall biosynthesis were found. A major difference in plant hormone responses, particularly of auxin but not cytokinin, was striking. The activity of the DR5::GUS reporter revealed a dramatically decreased auxin response in (NH4)2SO4-grown primary roots. The impaired root growth on (NH4)2SO4 was partially rescued by exogenous auxin or in specific mutants in the auxin pathway. The data suggest that NH4+-induced nutritional and metabolic imbalances can be partially overcome by elevated auxin levels.","lang":"eng"}],"volume":42,"date_created":"2018-12-11T11:52:34Z","article_type":"original","external_id":{"isi":["000349635900003"],"pmid":["32480670"]},"scopus_import":"1","intvolume":"        42","issue":"3","status":"public","publication_status":"published","day":"01","doi":"10.1071/FP14171","department":[{"_id":"JiFr"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"ChLa"}],"doi":"10.1109/TCSVT.2014.2379972","day":"01","publication_status":"published","status":"public","issue":"8","intvolume":"        25","scopus_import":"1","external_id":{"isi":["000359213400004"]},"volume":25,"date_created":"2018-12-11T11:52:34Z","abstract":[{"text":"This paper addresses the problem of semantic segmentation, where the possible class labels are from a predefined set. We exploit top-down guidance, i.e., the coarse localization of the objects and their class labels provided by object detectors. For each detected bounding box, figure-ground segmentation is performed and the final result is achieved by merging the figure-ground segmentations. The main idea of the proposed approach, which is presented in our preliminary work, is to reformulate the figure-ground segmentation problem as sparse reconstruction pursuing the object mask in a nonparametric manner. The latent segmentation mask should be coherent subject to sparse error caused by intra-category diversity; thus, the object mask is inferred by making use of sparse representations over the training set. To handle local spatial deformations, local patch-level masks are also considered and inferred by sparse representations over the spatially nearby patches. The sparse reconstruction coefficients and the latent mask are alternately optimized by applying the Lasso algorithm and the accelerated proximal gradient method. The proposed formulation results in a convex optimization problem; thus, the global optimal solution is achieved. In this paper, we provide theoretical analysis of the convergence and optimality. We also give an extended numerical analysis of the proposed algorithm and a comprehensive comparison with the related semantic segmentation methods on the challenging PASCAL visual object class object segmentation datasets and the Weizmann horse dataset. The experimental results demonstrate that the proposed algorithm achieves a competitive performance when compared with the state of the arts.","lang":"eng"}],"oa_version":"None","language":[{"iso":"eng"}],"publisher":"IEEE","citation":{"chicago":"Xia, Wei, Csaba Domokos, Junjun Xiong, Loongfah Cheong, and Shuicheng Yan. “Segmentation over Detection via Optimal Sparse Reconstructions.” <i>IEEE Transactions on Circuits and Systems for Video Technology</i>. IEEE, 2015. <a href=\"https://doi.org/10.1109/TCSVT.2014.2379972\">https://doi.org/10.1109/TCSVT.2014.2379972</a>.","mla":"Xia, Wei, et al. “Segmentation over Detection via Optimal Sparse Reconstructions.” <i>IEEE Transactions on Circuits and Systems for Video Technology</i>, vol. 25, no. 8, IEEE, 2015, pp. 1295–308, doi:<a href=\"https://doi.org/10.1109/TCSVT.2014.2379972\">10.1109/TCSVT.2014.2379972</a>.","ama":"Xia W, Domokos C, Xiong J, Cheong L, Yan S. Segmentation over detection via optimal sparse reconstructions. <i>IEEE Transactions on Circuits and Systems for Video Technology</i>. 2015;25(8):1295-1308. doi:<a href=\"https://doi.org/10.1109/TCSVT.2014.2379972\">10.1109/TCSVT.2014.2379972</a>","ieee":"W. Xia, C. Domokos, J. Xiong, L. Cheong, and S. Yan, “Segmentation over detection via optimal sparse reconstructions,” <i>IEEE Transactions on Circuits and Systems for Video Technology</i>, vol. 25, no. 8. IEEE, pp. 1295–1308, 2015.","short":"W. Xia, C. Domokos, J. Xiong, L. Cheong, S. Yan, IEEE Transactions on Circuits and Systems for Video Technology 25 (2015) 1295–1308.","apa":"Xia, W., Domokos, C., Xiong, J., Cheong, L., &#38; Yan, S. (2015). Segmentation over detection via optimal sparse reconstructions. <i>IEEE Transactions on Circuits and Systems for Video Technology</i>. IEEE. <a href=\"https://doi.org/10.1109/TCSVT.2014.2379972\">https://doi.org/10.1109/TCSVT.2014.2379972</a>","ista":"Xia W, Domokos C, Xiong J, Cheong L, Yan S. 2015. Segmentation over detection via optimal sparse reconstructions. IEEE Transactions on Circuits and Systems for Video Technology. 25(8), 1295–1308."},"_id":"1533","date_updated":"2025-09-23T10:44:22Z","page":"1295 - 1308","month":"08","year":"2015","article_processing_charge":"No","quality_controlled":"1","publication":"IEEE Transactions on Circuits and Systems for Video Technology","date_published":"2015-08-01T00:00:00Z","type":"journal_article","publist_id":"5638","isi":1,"author":[{"last_name":"Xia","first_name":"Wei","full_name":"Xia, Wei"},{"last_name":"Domokos","first_name":"Csaba","id":"492DACF8-F248-11E8-B48F-1D18A9856A87","full_name":"Domokos, Csaba"},{"full_name":"Xiong, Junjun","first_name":"Junjun","last_name":"Xiong"},{"full_name":"Cheong, Loongfah","first_name":"Loongfah","last_name":"Cheong"},{"full_name":"Yan, Shuicheng","first_name":"Shuicheng","last_name":"Yan"}],"title":"Segmentation over detection via optimal sparse reconstructions"},{"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."}],"article_number":"8822","date_created":"2018-12-11T11:52:34Z","volume":6,"oa_version":"Published Version","intvolume":"         6","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"isi":["000366295500008"]},"scopus_import":"1","oa":1,"file_date_updated":"2020-07-14T12:45:01Z","pubrep_id":"485","day":"18","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"JiFr"}],"doi":"10.1038/ncomms9822","status":"public","publication_status":"published","type":"journal_article","has_accepted_license":"1","date_published":"2015-11-18T00:00:00Z","author":[{"last_name":"Wang","first_name":"Hongzhe","full_name":"Wang, Hongzhe"},{"first_name":"Kezhen","last_name":"Yang","full_name":"Yang, Kezhen"},{"full_name":"Zou, Junjie","first_name":"Junjie","last_name":"Zou"},{"first_name":"Lingling","last_name":"Zhu","full_name":"Zhu, Lingling"},{"first_name":"Zidian","last_name":"Xie","full_name":"Xie, Zidian"},{"last_name":"Morita","first_name":"Miyoterao","full_name":"Morita, Miyoterao"},{"full_name":"Tasaka, Masao","last_name":"Tasaka","first_name":"Masao"},{"last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"first_name":"Erich","last_name":"Grotewold","full_name":"Grotewold, Erich"},{"full_name":"Beeckman, Tom","first_name":"Tom","last_name":"Beeckman"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"full_name":"Sack, Fred","first_name":"Fred","last_name":"Sack"},{"full_name":"Le, Jie","first_name":"Jie","last_name":"Le"}],"title":"Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism","ec_funded":1,"publist_id":"5637","isi":1,"quality_controlled":"1","article_processing_charge":"No","ddc":["570"],"publication":"Nature Communications","year":"2015","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:45:01Z","relation":"main_file","content_type":"application/pdf","creator":"system","file_id":"5259","date_created":"2018-12-12T10:17:07Z","file_size":1852268,"checksum":"3c06735fc7cd7e482ca830cbd26001bf","file_name":"IST-2016-485-v1+1_ncomms9822.pdf"}],"date_updated":"2025-09-23T14:55:59Z","_id":"1534","citation":{"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>.","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>","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>.","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.","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>","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."},"month":"11","language":[{"iso":"eng"}],"publisher":"Nature Publishing Group"},{"publication":"Current Molecular Pharmacology","article_processing_charge":"No","quality_controlled":"1","isi":1,"publist_id":"5636","title":"Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells","author":[{"orcid":"0000-0001-7577-1676","full_name":"Vandael, David H","first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","last_name":"Vandael"},{"full_name":"Marcantoni, Andrea","first_name":"Andrea","last_name":"Marcantoni"},{"last_name":"Carbone","first_name":"Emilio","full_name":"Carbone, Emilio"}],"date_published":"2015-10-01T00:00:00Z","type":"journal_article","publisher":"Bentham Science Publishers","language":[{"iso":"eng"}],"month":"10","_id":"1535","date_updated":"2025-09-23T08:12:18Z","citation":{"short":"D.H. Vandael, A. Marcantoni, E. Carbone, Current Molecular Pharmacology 8 (2015) 149–161.","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>","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.","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>.","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>","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.","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>."},"page":"149 - 161","acknowledgement":"This work was supported by the Italian MIUR (PRIN 2010/2011 project 2010JFYFY2) and the University of Torino.","year":"2015","scopus_import":"1","external_id":{"pmid":["25966692"],"isi":["000217186100005"]},"intvolume":"         8","pmid":1,"oa_version":"Submitted Version","volume":8,"date_created":"2018-12-11T11:52:35Z","article_type":"original","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","status":"public","doi":"10.2174/1874467208666150507105443","department":[{"_id":"PeJo"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","issue":"2","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384372/"}]},{"publication_status":"published","status":"public","doi":"10.1016/j.cub.2015.01.015","department":[{"_id":"JiFr"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"12","issue":"5","scopus_import":"1","external_id":{"isi":["000350708800029"]},"intvolume":"        25","oa_version":"None","date_created":"2018-12-11T11:52:35Z","volume":25,"abstract":[{"lang":"eng","text":"Strigolactones, first discovered as germination stimulants for parasitic weeds [1], are carotenoid-derived phytohormones that play major roles in inhibiting lateral bud outgrowth and promoting plant-mycorrhizal symbiosis [2-4]. Furthermore, strigolactones are involved in the regulation of lateral and adventitious root development, root cell division [5, 6], secondary growth [7], and leaf senescence [8]. Recently, we discovered the strigolactone transporter Petunia axillaris PLEIOTROPIC DRUG RESISTANCE 1 (PaPDR1), which is required for efficient mycorrhizal colonization and inhibition of lateral bud outgrowth [9]. However, how strigolactones are transported through the plant remained unknown. Here we show that PaPDR1 exhibits a cell-type-specific asymmetric localization in different root tissues. In root tips, PaPDR1 is co-expressed with the strigolactone biosynthetic gene DAD1 (CCD8), and it is localized at the apical membrane of root hypodermal cells, presumably mediating the shootward transport of strigolactone. Above the root tip, in the hypodermal passage cells that form gates for the entry of mycorrhizal fungi, PaPDR1 is present in the outer-lateral membrane, compatible with its postulated function as strigolactone exporter from root to soil. Transport studies are in line with our localization studies since (1) a papdr1 mutant displays impaired transport of strigolactones out of the root tip to the shoot as well as into the rhizosphere and (2) DAD1 expression and PIN1/PIN2 levels change in plants deregulated for PDR1 expression, suggestive of variations in endogenous strigolactone contents. In conclusion, our results indicate that the polar localizations of PaPDR1 mediate directional shootward strigolactone transport as well as localized exudation into the soil."}],"publisher":"Cell Press","language":[{"iso":"eng"}],"month":"02","_id":"1536","page":"647 - 655","date_updated":"2025-09-23T07:57:02Z","citation":{"ieee":"J. Sasse <i>et al.</i>, “Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport,” <i>Current Biology</i>, vol. 25, no. 5. Cell Press, pp. 647–655, 2015.","ama":"Sasse J, Simon S, Gübeli C, et al. Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. <i>Current Biology</i>. 2015;25(5):647-655. doi:<a href=\"https://doi.org/10.1016/j.cub.2015.01.015\">10.1016/j.cub.2015.01.015</a>","mla":"Sasse, Joëlle, et al. “Asymmetric Localizations of the ABC Transporter PaPDR1 Trace Paths of Directional Strigolactone Transport.” <i>Current Biology</i>, vol. 25, no. 5, Cell Press, 2015, pp. 647–55, doi:<a href=\"https://doi.org/10.1016/j.cub.2015.01.015\">10.1016/j.cub.2015.01.015</a>.","ista":"Sasse J, Simon S, Gübeli C, Liu G, Cheng X, Friml J, Bouwmeester H, Martinoia E, Borghi L. 2015. Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. 25(5), 647–655.","short":"J. Sasse, S. Simon, C. Gübeli, G. Liu, X. Cheng, J. Friml, H. Bouwmeester, E. Martinoia, L. Borghi, Current Biology 25 (2015) 647–655.","apa":"Sasse, J., Simon, S., Gübeli, C., Liu, G., Cheng, X., Friml, J., … Borghi, L. (2015). Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2015.01.015\">https://doi.org/10.1016/j.cub.2015.01.015</a>","chicago":"Sasse, Joëlle, Sibu Simon, Christian Gübeli, Guowei Liu, Xi Cheng, Jiří Friml, Harro Bouwmeester, Enrico Martinoia, and Lorenzo Borghi. “Asymmetric Localizations of the ABC Transporter PaPDR1 Trace Paths of Directional Strigolactone Transport.” <i>Current Biology</i>. Cell Press, 2015. <a href=\"https://doi.org/10.1016/j.cub.2015.01.015\">https://doi.org/10.1016/j.cub.2015.01.015</a>."},"acknowledgement":"This work was funded by a grant of the Swiss National Foundation to E.M.\r\nWe thank Dr. José María Mateos (University of Zurich) for providing us with the vibratome, Prof. Dolf Weijers (Wageningen University, the Netherlands) for shipping us his set of ligation-independent cloning vectors, Prof. Bruno Humbel (University of Lausanne) for suggestions on GFP-PDR1 detection, and Dr. Undine Krügel (University of Zurich) and Prof. Michal Jasinski (Polish Academy of Science) for hints on protein quantification.","year":"2015","publication":"Current Biology","article_processing_charge":"No","quality_controlled":"1","isi":1,"publist_id":"5635","title":"Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport","author":[{"last_name":"Sasse","first_name":"Joëlle","full_name":"Sasse, Joëlle"},{"orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu","last_name":"Simon","first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gübeli","first_name":"Christian","full_name":"Gübeli, Christian"},{"full_name":"Liu, Guowei","last_name":"Liu","first_name":"Guowei"},{"full_name":"Cheng, Xi","last_name":"Cheng","first_name":"Xi"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"full_name":"Bouwmeester, Harro","last_name":"Bouwmeester","first_name":"Harro"},{"first_name":"Enrico","last_name":"Martinoia","full_name":"Martinoia, Enrico"},{"last_name":"Borghi","first_name":"Lorenzo","full_name":"Borghi, Lorenzo"}],"date_published":"2015-02-12T00:00:00Z","type":"journal_article"},{"publication_status":"published","status":"public","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1073/pnas.1423947112","day":"30","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"issue":"26","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4491780/","open_access":"1"}],"oa":1,"scopus_import":"1","external_id":{"isi":["000357079400070"],"pmid":["26085136"]},"intvolume":"       112","oa_version":"Submitted Version","pmid":1,"volume":112,"date_created":"2018-12-11T11:52:36Z","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"}],"language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","_id":"1538","page":"8148 - 8153","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.","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>","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>.","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.","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>","short":"J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, J. Lygeros, PNAS 112 (2015) 8148–8153.","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>."},"date_updated":"2025-09-23T09:24:24Z","month":"06","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). ","year":"2015","publication":"PNAS","article_processing_charge":"No","quality_controlled":"1","ec_funded":1,"publist_id":"5633","isi":1,"author":[{"orcid":"0000-0003-1615-3282","last_name":"Ruess","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","first_name":"Jakob","full_name":"Ruess, Jakob"},{"full_name":"Parise, Francesca","last_name":"Parise","first_name":"Francesca"},{"last_name":"Milias Argeitis","first_name":"Andreas","full_name":"Milias Argeitis, Andreas"},{"full_name":"Khammash, Mustafa","first_name":"Mustafa","last_name":"Khammash"},{"last_name":"Lygeros","first_name":"John","full_name":"Lygeros, John"}],"title":"Iterative experiment design guides the characterization of a light-inducible gene expression circuit","date_published":"2015-06-30T00:00:00Z","type":"journal_article"},{"author":[{"last_name":"Ruess","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","first_name":"Jakob","full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282"}],"title":"Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space","publist_id":"5632","ec_funded":1,"isi":1,"type":"journal_article","has_accepted_license":"1","date_published":"2015-12-22T00:00:00Z","ddc":["000"],"publication":"Journal of Chemical Physics","quality_controlled":"1","article_processing_charge":"No","year":"2015","citation":{"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.","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>","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>.","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.","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>","short":"J. Ruess, Journal of Chemical Physics 143 (2015).","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>."},"_id":"1539","date_updated":"2025-09-23T09:34:48Z","month":"12","language":[{"iso":"eng"}],"corr_author":"1","publisher":"American Institute of Physics","file":[{"file_id":"4641","creator":"system","file_name":"IST-2016-593-v1+1_Minimal_moment_equations.pdf","date_created":"2018-12-12T10:07:43Z","checksum":"838657118ae286463a2b7737319f35ce","file_size":605355,"access_level":"open_access","date_updated":"2020-07-14T12:45:01Z","content_type":"application/pdf","relation":"main_file"}],"oa_version":"Published Version","abstract":[{"lang":"eng","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. "}],"article_number":"244103","date_created":"2018-12-11T11:52:36Z","volume":143,"external_id":{"isi":["000370412900068"]},"scopus_import":"1","intvolume":"       143","issue":"24","file_date_updated":"2020-07-14T12:45:01Z","oa":1,"pubrep_id":"593","status":"public","publication_status":"published","day":"22","project":[{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7"},{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems"},{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"doi":"10.1063/1.4937937"},{"quality_controlled":"1","article_processing_charge":"No","publication":"Journal of Experimental Botany","type":"journal_article","date_published":"2015-05-05T00:00:00Z","author":[{"full_name":"Robert, Hélène","last_name":"Robert","first_name":"Hélène"},{"full_name":"Crhák Khaitová, Lucie","last_name":"Crhák Khaitová","first_name":"Lucie"},{"full_name":"Mroue, Souad","last_name":"Mroue","first_name":"Souad"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"}],"title":"The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis","publist_id":"5631","isi":1,"page":"5029 - 5042","_id":"1540","citation":{"chicago":"Robert, Hélène, Lucie Crhák Khaitová, Souad Mroue, and Eva Benková. “The Importance of Localized Auxin Production for Morphogenesis of Reproductive Organs and Embryos in Arabidopsis.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/jxb/erv256\">https://doi.org/10.1093/jxb/erv256</a>.","short":"H. Robert, L. Crhák Khaitová, S. Mroue, E. Benková, Journal of Experimental Botany 66 (2015) 5029–5042.","apa":"Robert, H., Crhák Khaitová, L., Mroue, S., &#38; Benková, E. (2015). The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/erv256\">https://doi.org/10.1093/jxb/erv256</a>","ista":"Robert H, Crhák Khaitová L, Mroue S, Benková E. 2015. The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. Journal of Experimental Botany. 66(16), 5029–5042.","ama":"Robert H, Crhák Khaitová L, Mroue S, Benková E. The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. <i>Journal of Experimental Botany</i>. 2015;66(16):5029-5042. doi:<a href=\"https://doi.org/10.1093/jxb/erv256\">10.1093/jxb/erv256</a>","mla":"Robert, Hélène, et al. “The Importance of Localized Auxin Production for Morphogenesis of Reproductive Organs and Embryos in Arabidopsis.” <i>Journal of Experimental Botany</i>, vol. 66, no. 16, Oxford University Press, 2015, pp. 5029–42, doi:<a href=\"https://doi.org/10.1093/jxb/erv256\">10.1093/jxb/erv256</a>.","ieee":"H. Robert, L. Crhák Khaitová, S. Mroue, and E. Benková, “The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis,” <i>Journal of Experimental Botany</i>, vol. 66, no. 16. Oxford University Press, pp. 5029–5042, 2015."},"date_updated":"2025-09-23T13:51:25Z","month":"05","language":[{"iso":"eng"}],"publisher":"Oxford University Press","year":"2015","acknowledgement":"The work was supported by grants from: the Employment of Best Young Scientists for International Cooperation Empowerment/OPVKII programme (CZ.1.07/2.3.00/30.0037) to HSR and LCK; the Czech Science Foundation (GA13-39982S) to EB, LCK and SM; and the SoMoPro II programme (3SGA5602), cofinanced by the South-Moravian Region and the EU (FP7/2007–2013 People Programme), to HSR.","intvolume":"        66","external_id":{"isi":["000359688300015"]},"scopus_import":"1","abstract":[{"text":"Plant sexual reproduction involves highly structured and specialized organs: stamens (male) and gynoecia (female, containing ovules). These organs synchronously develop within protective flower buds, until anthesis, via tightly coordinated mechanisms that are essential for effective fertilization and production of viable seeds. The phytohormone auxin is one of the key endogenous signalling molecules controlling initiation and development of these, and other, plant organs. In particular, its uneven distribution, resulting from tightly controlled production, metabolism and directional transport, is an important morphogenic factor. In this review we discuss how developmentally controlled and localized auxin biosynthesis and transport contribute to the coordinated development of plants' reproductive organs, and their fertilized derivatives (embryos) via the regulation of auxin levels and distribution within and around them. Current understanding of the links between de novo local auxin biosynthesis, auxin transport and/or signalling is presented to highlight the importance of the non-cell autonomous action of auxin production on development and morphogenesis of reproductive organs and embryos. An overview of transcription factor families, which spatiotemporally define local auxin production by controlling key auxin biosynthetic enzymes, is also presented.","lang":"eng"}],"volume":66,"date_created":"2018-12-11T11:52:36Z","oa_version":"None","day":"05","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"EvBe"}],"doi":"10.1093/jxb/erv256","status":"public","publication_status":"published","issue":"16"},{"alternative_title":["LNCS"],"title":"XSpeed: Accelerating reachability analysis on multi-core processors","author":[{"full_name":"Ray, Rajarshi","first_name":"Rajarshi","last_name":"Ray"},{"first_name":"Amit","last_name":"Gurung","full_name":"Gurung, Amit"},{"full_name":"Das, Binayak","last_name":"Das","first_name":"Binayak"},{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"last_name":"Bogomolov","first_name":"Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365"},{"first_name":"Radu","last_name":"Grosu","full_name":"Grosu, Radu"}],"series_title":"Lecture Notes in Computer Science","publist_id":"5630","ec_funded":1,"type":"conference","date_published":"2015-11-28T00:00:00Z","quality_controlled":"1","acknowledgement":"This work was supported in part by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award).","conference":{"name":"HVC: Haifa Verification Conference","start_date":"2015-11-17","location":"Haifa, Israel","end_date":"2015-11-19"},"year":"2015","month":"11","page":"3 - 18","_id":"1541","date_updated":"2025-04-15T06:26:02Z","citation":{"ista":"Ray R, Gurung A, Das B, Bartocci E, Bogomolov S, Grosu R. 2015. XSpeed: Accelerating reachability analysis on multi-core processors. 9434, 3–18.","short":"R. Ray, A. Gurung, B. Das, E. Bartocci, S. Bogomolov, R. Grosu, 9434 (2015) 3–18.","apa":"Ray, R., Gurung, A., Das, B., Bartocci, E., Bogomolov, S., &#38; Grosu, R. (2015). XSpeed: Accelerating reachability analysis on multi-core processors. Presented at the HVC: Haifa Verification Conference, Haifa, Israel: Springer. <a href=\"https://doi.org/10.1007/978-3-319-26287-1_1\">https://doi.org/10.1007/978-3-319-26287-1_1</a>","ieee":"R. Ray, A. Gurung, B. Das, E. Bartocci, S. Bogomolov, and R. Grosu, “XSpeed: Accelerating reachability analysis on multi-core processors,” vol. 9434. Springer, pp. 3–18, 2015.","ama":"Ray R, Gurung A, Das B, Bartocci E, Bogomolov S, Grosu R. XSpeed: Accelerating reachability analysis on multi-core processors. 2015;9434:3-18. doi:<a href=\"https://doi.org/10.1007/978-3-319-26287-1_1\">10.1007/978-3-319-26287-1_1</a>","mla":"Ray, Rajarshi, et al. <i>XSpeed: Accelerating Reachability Analysis on Multi-Core Processors</i>. Vol. 9434, Springer, 2015, pp. 3–18, doi:<a href=\"https://doi.org/10.1007/978-3-319-26287-1_1\">10.1007/978-3-319-26287-1_1</a>.","chicago":"Ray, Rajarshi, Amit Gurung, Binayak Das, Ezio Bartocci, Sergiy Bogomolov, and Radu Grosu. “XSpeed: Accelerating Reachability Analysis on Multi-Core Processors.” Lecture Notes in Computer Science. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-319-26287-1_1\">https://doi.org/10.1007/978-3-319-26287-1_1</a>."},"publisher":"Springer","language":[{"iso":"eng"}],"oa_version":"None","abstract":[{"lang":"eng","text":"We present XSpeed a parallel state-space exploration algorithm for continuous systems with linear dynamics and nondeterministic inputs. The motivation of having parallel algorithms is to exploit the computational power of multi-core processors to speed-up performance. The parallelization is achieved on two fronts. First, we propose a parallel implementation of the support function algorithm by sampling functions in parallel. Second, we propose a parallel state-space exploration by slicing the time horizon and computing the reachable states in the time slices in parallel. The second method can be however applied only to a class of linear systems with invertible dynamics and fixed input. A GP-GPU implementation is also presented following a lazy evaluation strategy on support functions. The parallel algorithms are implemented in the tool XSpeed. We evaluated the performance on two benchmarks including an 28 dimension Helicopter model. Comparison with the sequential counterpart shows a maximum speed-up of almost 7× on a 6 core, 12 thread Intel Xeon CPU E5-2420 processor. Our GP-GPU implementation shows a maximum speed-up of 12× over the sequential implementation and 53× over SpaceEx (LGG scenario), the state of the art tool for reachability analysis of linear hybrid systems. Experiments illustrate that our parallel algorithm with time slicing not only speeds-up performance but also improves precision."}],"volume":9434,"date_created":"2018-12-11T11:52:37Z","scopus_import":1,"intvolume":"      9434","status":"public","publication_status":"published","day":"28","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"doi":"10.1007/978-3-319-26287-1_1","department":[{"_id":"ToHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"file":[{"file_id":"5244","creator":"system","file_name":"IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf","date_created":"2018-12-12T10:16:53Z","file_size":595307,"checksum":"33b60ecfea60764756a9ee9df5eb65ca","date_updated":"2020-07-14T12:45:01Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file"}],"_id":"1542","page":"28 - 43","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.","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>","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.","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.","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>","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>.","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>."},"date_updated":"2025-09-23T14:55:02Z","month":"10","language":[{"iso":"eng"}],"publisher":"Elsevier","corr_author":"1","year":"2015","quality_controlled":"1","article_processing_charge":"No","ddc":["570"],"publication":" Journal of Theoretical Biology","type":"journal_article","has_accepted_license":"1","date_published":"2015-10-21T00:00:00Z","author":[{"orcid":"0000-0003-2361-3953","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","full_name":"Paixao, Tiago"},{"full_name":"Badkobeh, Golnaz","last_name":"Badkobeh","first_name":"Golnaz"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"full_name":"Çörüş, Doğan","last_name":"Çörüş","first_name":"Doğan"},{"full_name":"Dang, Duccuong","first_name":"Duccuong","last_name":"Dang"},{"full_name":"Friedrich, Tobias","last_name":"Friedrich","first_name":"Tobias"},{"last_name":"Lehre","first_name":"Per","full_name":"Lehre, Per"},{"full_name":"Sudholt, Dirk","first_name":"Dirk","last_name":"Sudholt"},{"full_name":"Sutton, Andrew","last_name":"Sutton","first_name":"Andrew"},{"orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora","last_name":"Trubenova"}],"title":"Toward a unifying framework for evolutionary processes","ec_funded":1,"publist_id":"5629","isi":1,"project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","call_identifier":"FP7"},{"name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7"}],"day":"21","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1016/j.jtbi.2015.07.011","status":"public","publication_status":"published","oa":1,"file_date_updated":"2020-07-14T12:45:01Z","pubrep_id":"483","intvolume":"       383","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"external_id":{"isi":["000362056300005"]},"scopus_import":"1","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"}],"volume":383,"date_created":"2018-12-11T11:52:37Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa_version":"Published Version"},{"abstract":[{"lang":"eng","text":"A plethora of diverse programmed cell death (PCD) processes has been described in living organisms. In animals and plants, different forms of PCD play crucial roles in development, immunity, and responses to the environment. While the molecular control of some animal PCD forms such as apoptosis is known in great detail, we still know comparatively little about the regulation of the diverse types of plant PCD. In part, this deficiency in molecular understanding is caused by the lack of reliable reporters to detect PCD processes. Here, we addressed this issue by using a combination of bioinformatics approaches to identify commonly regulated genes during diverse plant PCD processes in Arabidopsis (Arabidopsis thaliana). Our results indicate that the transcriptional signatures of developmentally controlled cell death are largely distinct from the ones associated with environmentally induced cell death. Moreover, different cases of developmental PCD share a set of cell death-associated genes. Most of these genes are evolutionary conserved within the green plant lineage, arguing for an evolutionary conserved core machinery of developmental PCD. Based on this information, we established an array of specific promoter-reporter lines for developmental PCD in Arabidopsis. These PCD indicators represent a powerful resource that can be used in addition to established morphological and biochemical methods to detect and analyze PCD processes in vivo and in planta."}],"type":"journal_article","date_created":"2018-12-11T11:52:38Z","volume":169,"date_published":"2015-12-01T00:00:00Z","author":[{"full_name":"Olvera Carrillo, Yadira","last_name":"Olvera Carrillo","first_name":"Yadira"},{"full_name":"Van Bel, Michiel","first_name":"Michiel","last_name":"Van Bel"},{"last_name":"Van Hautegem","first_name":"Tom","full_name":"Van Hautegem, Tom"},{"orcid":"0000-0002-9767-8699","first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","full_name":"Fendrych, Matyas"},{"full_name":"Huysmans, Marlies","first_name":"Marlies","last_name":"Huysmans"},{"full_name":"Šimášková, Mária","first_name":"Mária","last_name":"Šimášková"},{"last_name":"Van Durme","first_name":"Matthias","full_name":"Van Durme, Matthias"},{"full_name":"Buscaill, Pierre","last_name":"Buscaill","first_name":"Pierre"},{"full_name":"Rivas, Susana","last_name":"Rivas","first_name":"Susana"},{"full_name":"Coll, Núria","last_name":"Coll","first_name":"Núria"},{"full_name":"Coppens, Frederik","last_name":"Coppens","first_name":"Frederik"},{"full_name":"Maere, Steven","first_name":"Steven","last_name":"Maere"},{"last_name":"Nowack","first_name":"Moritz","full_name":"Nowack, Moritz"}],"oa_version":"None","title":"A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants","publist_id":"5628","isi":1,"intvolume":"       169","article_processing_charge":"No","external_id":{"isi":["000368472700025"]},"scopus_import":"1","publication":"Plant Physiology","year":"2015","issue":"4","day":"01","department":[{"_id":"JiFr"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1104/pp.15.00769","status":"public","_id":"1543","citation":{"chicago":"Olvera Carrillo, Yadira, Michiel Van Bel, Tom Van Hautegem, Matyas Fendrych, Marlies Huysmans, Mária Šimášková, Matthias Van Durme, et al. “A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2015. <a href=\"https://doi.org/10.1104/pp.15.00769\">https://doi.org/10.1104/pp.15.00769</a>.","short":"Y. Olvera Carrillo, M. Van Bel, T. Van Hautegem, M. Fendrych, M. Huysmans, M. Šimášková, M. Van Durme, P. Buscaill, S. Rivas, N. Coll, F. Coppens, S. Maere, M. Nowack, Plant Physiology 169 (2015) 2684–2699.","apa":"Olvera Carrillo, Y., Van Bel, M., Van Hautegem, T., Fendrych, M., Huysmans, M., Šimášková, M., … Nowack, M. (2015). A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1104/pp.15.00769\">https://doi.org/10.1104/pp.15.00769</a>","ista":"Olvera Carrillo Y, Van Bel M, Van Hautegem T, Fendrych M, Huysmans M, Šimášková M, Van Durme M, Buscaill P, Rivas S, Coll N, Coppens F, Maere S, Nowack M. 2015. A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. 169(4), 2684–2699.","ama":"Olvera Carrillo Y, Van Bel M, Van Hautegem T, et al. A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. <i>Plant Physiology</i>. 2015;169(4):2684-2699. doi:<a href=\"https://doi.org/10.1104/pp.15.00769\">10.1104/pp.15.00769</a>","mla":"Olvera Carrillo, Yadira, et al. “A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.” <i>Plant Physiology</i>, vol. 169, no. 4, American Society of Plant Biologists, 2015, pp. 2684–99, doi:<a href=\"https://doi.org/10.1104/pp.15.00769\">10.1104/pp.15.00769</a>.","ieee":"Y. Olvera Carrillo <i>et al.</i>, “A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants,” <i>Plant Physiology</i>, vol. 169, no. 4. American Society of Plant Biologists, pp. 2684–2699, 2015."},"page":"2684 - 2699","date_updated":"2025-09-22T14:28:43Z","month":"12","language":[{"iso":"eng"}],"publication_status":"published","publisher":"American Society of Plant Biologists"}]