[{"title":"Purification of ovine respiratory complex i results in a highly active and stable preparation","page":"24657 - 24675","project":[{"_id":"2593EBD6-B435-11E9-9278-68D0E5697425","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (FEBS)"},{"grant_number":"701309","_id":"2590DB08-B435-11E9-9278-68D0E5697425","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)","call_identifier":"H2020"}],"department":[{"_id":"LeSa"}],"ec_funded":1,"_id":"1209","publisher":"American Society for Biochemistry and Molecular Biology","publist_id":"6139","publication_status":"published","author":[{"orcid":"0000-0002-9864-3586","last_name":"Letts","full_name":"Letts, James A","id":"322DA418-F248-11E8-B48F-1D18A9856A87","first_name":"James A"},{"first_name":"Gianluca","last_name":"Degliesposti","full_name":"Degliesposti, Gianluca"},{"id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","full_name":"Fiedorczuk, Karol","last_name":"Fiedorczuk","first_name":"Karol"},{"last_name":"Skehel","full_name":"Skehel, Mark","first_name":"Mark"},{"last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","first_name":"Leonid A","orcid":"0000-0002-0977-7989"}],"language":[{"iso":"eng"}],"abstract":[{"text":"NADH-ubiquinone oxidoreductase (complex I) is the largest (∼1 MDa) and the least characterized complex of the mitochondrial electron transport chain. Because of the ease of sample availability, previous work has focused almost exclusively on bovine complex I. However, only medium resolution structural analyses of this complex have been reported. Working with other mammalian complex I homologues is a potential approach for overcoming these limitations. Due to the inherent difficulty of expressing large membrane protein complexes, screening of complex I homologues is limited to large mammals reared for human consumption. The high sequence identity among these available sources may preclude the benefits of screening. Here, we report the characterization of complex I purified from Ovis aries (ovine) heart mitochondria. All 44 unique subunits of the intact complex were identified by mass spectrometry. We identified differences in the subunit composition of subcomplexes of ovine complex I as compared with bovine, suggesting differential stability of inter-subunit interactions within the complex. Furthermore, the 42-kDa subunit, which is easily lost from the bovine enzyme, remains tightly bound to ovine complex I. Additionally, we developed a novel purification protocol for highly active and stable mitochondrial complex I using the branched-chain detergent lauryl maltose neopentyl glycol. Our data demonstrate that, although closely related, significant differences exist between the biochemical properties of complex I prepared from ovine and bovine mitochondria and that ovine complex I represents a suitable alternative target for further structural studies. ","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:49:06Z","volume":291,"scopus_import":1,"issue":"47","year":"2016","oa":1,"day":"18","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5114416/"}],"date_published":"2016-11-18T00:00:00Z","doi":"10.1074/jbc.M116.735142","intvolume":"       291","status":"public","month":"11","acknowledgement":"J.A.S supported in part by a Medical Research D.G.Council UK Ph.D. fellowship.\r\nThis work was supported in part by European Union's 2020 Research and Innovation Program under Grant 701309. \r\n","quality_controlled":"1","type":"journal_article","oa_version":"Submitted Version","citation":{"chicago":"Letts, James A, Gianluca Degliesposti, Karol Fiedorczuk, Mark Skehel, and Leonid A Sazanov. “Purification of Ovine Respiratory Complex i Results in a Highly Active and Stable Preparation.” <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology, 2016. <a href=\"https://doi.org/10.1074/jbc.M116.735142\">https://doi.org/10.1074/jbc.M116.735142</a>.","ista":"Letts JA, Degliesposti G, Fiedorczuk K, Skehel M, Sazanov LA. 2016. Purification of ovine respiratory complex i results in a highly active and stable preparation. Journal of Biological Chemistry. 291(47), 24657–24675.","ieee":"J. A. Letts, G. Degliesposti, K. Fiedorczuk, M. Skehel, and L. A. Sazanov, “Purification of ovine respiratory complex i results in a highly active and stable preparation,” <i>Journal of Biological Chemistry</i>, vol. 291, no. 47. American Society for Biochemistry and Molecular Biology, pp. 24657–24675, 2016.","short":"J.A. Letts, G. Degliesposti, K. Fiedorczuk, M. Skehel, L.A. Sazanov, Journal of Biological Chemistry 291 (2016) 24657–24675.","mla":"Letts, James A., et al. “Purification of Ovine Respiratory Complex i Results in a Highly Active and Stable Preparation.” <i>Journal of Biological Chemistry</i>, vol. 291, no. 47, American Society for Biochemistry and Molecular Biology, 2016, pp. 24657–75, doi:<a href=\"https://doi.org/10.1074/jbc.M116.735142\">10.1074/jbc.M116.735142</a>.","apa":"Letts, J. A., Degliesposti, G., Fiedorczuk, K., Skehel, M., &#38; Sazanov, L. A. (2016). Purification of ovine respiratory complex i results in a highly active and stable preparation. <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology. <a href=\"https://doi.org/10.1074/jbc.M116.735142\">https://doi.org/10.1074/jbc.M116.735142</a>","ama":"Letts JA, Degliesposti G, Fiedorczuk K, Skehel M, Sazanov LA. Purification of ovine respiratory complex i results in a highly active and stable preparation. <i>Journal of Biological Chemistry</i>. 2016;291(47):24657-24675. doi:<a href=\"https://doi.org/10.1074/jbc.M116.735142\">10.1074/jbc.M116.735142</a>"},"date_created":"2018-12-11T11:50:44Z","publication":"Journal of Biological Chemistry"},{"abstract":[{"lang":"eng","text":"Mechanisms for cell protection are essential for survival of multicellular organisms. In plants, the apical hook, which is transiently formed in darkness when the germinating seedling penetrates towards the soil surface, plays such protective role and shields the vitally important shoot apical meristem and cotyledons from damage. The apical hook is formed by bending of the upper hypocotyl soon after germination, and it is maintained in a closed stage while the hypocotyl continues to penetrate through the soil and rapidly opens when exposed to light in proximity of the soil surface. To uncover the complex molecular network orchestrating this spatiotemporally tightly coordinated process, monitoring of the apical hook development in real time is indispensable. Here we describe an imaging platform that enables high-resolution kinetic analysis of this dynamic developmental process. © Springer Science+Business Media New York 2017."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank Herman  \r\nHöfte \r\n, Todor Asenov, Robert Hauschield, and \r\nMarcal  Gallemi  for  help  with  the  establishment  of  the  real-time  \r\nimaging platform and technical support. This work was supported \r\nby the Czech Science Foundation (GA13-39982S) to Eva Benková. \r\nDominique   Van   Der   Straeten   acknowledges   the   Research   \r\nFoundation  Flanders  for  fi\r\n  nancial  support  (G.0656.13N).  Dajo  \r\nSmet holds a PhD fellowship of the Research Foundation Flanders. ","date_updated":"2021-01-12T06:49:07Z","quality_controlled":"1","month":"11","author":[{"first_name":"Qiang","full_name":"Zhu, Qiang","last_name":"Zhu","id":"40A4B9E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Žádníková","full_name":"Žádníková, Petra","first_name":"Petra"},{"last_name":"Smet","full_name":"Smet, Dajo","first_name":"Dajo"},{"last_name":"Van Der Straeten","full_name":"Van Der Straeten, Dominique","first_name":"Dominique"},{"orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"citation":{"apa":"Zhu, Q., Žádníková, P., Smet, D., Van Der Straeten, D., &#38; Benková, E. (2016). Real time analysis of the apical hook development. In <i>Plant Hormones</i> (Vol. 1497, pp. 1–8). Humana Press. <a href=\"https://doi.org/10.1007/978-1-4939-6469-7_1\">https://doi.org/10.1007/978-1-4939-6469-7_1</a>","mla":"Zhu, Qiang, et al. “Real Time Analysis of the Apical Hook Development.” <i>Plant Hormones</i>, vol. 1497, Humana Press, 2016, pp. 1–8, doi:<a href=\"https://doi.org/10.1007/978-1-4939-6469-7_1\">10.1007/978-1-4939-6469-7_1</a>.","ama":"Zhu Q, Žádníková P, Smet D, Van Der Straeten D, Benková E. Real time analysis of the apical hook development. In: <i>Plant Hormones</i>. Vol 1497. Humana Press; 2016:1-8. doi:<a href=\"https://doi.org/10.1007/978-1-4939-6469-7_1\">10.1007/978-1-4939-6469-7_1</a>","ista":"Zhu Q, Žádníková P, Smet D, Van Der Straeten D, Benková E. 2016.Real time analysis of the apical hook development. In: Plant Hormones. Methods in Molecular Biology, vol. 1497, 1–8.","chicago":"Zhu, Qiang, Petra Žádníková, Dajo Smet, Dominique Van Der Straeten, and Eva Benková. “Real Time Analysis of the Apical Hook Development.” In <i>Plant Hormones</i>, 1497:1–8. Humana Press, 2016. <a href=\"https://doi.org/10.1007/978-1-4939-6469-7_1\">https://doi.org/10.1007/978-1-4939-6469-7_1</a>.","short":"Q. Zhu, P. Žádníková, D. Smet, D. Van Der Straeten, E. Benková, in:, Plant Hormones, Humana Press, 2016, pp. 1–8.","ieee":"Q. Zhu, P. Žádníková, D. Smet, D. Van Der Straeten, and E. Benková, “Real time analysis of the apical hook development,” in <i>Plant Hormones</i>, vol. 1497, Humana Press, 2016, pp. 1–8."},"oa_version":"None","date_created":"2018-12-11T11:50:44Z","scopus_import":1,"publication":"Plant Hormones","year":"2016","type":"book_chapter","volume":1497,"alternative_title":["Methods in Molecular Biology"],"department":[{"_id":"EvBe"}],"title":"Real time analysis of the apical hook development","page":"1 - 8","day":"19","publication_status":"published","status":"public","_id":"1210","date_published":"2016-11-19T00:00:00Z","publisher":"Humana Press","doi":"10.1007/978-1-4939-6469-7_1","intvolume":"      1497","publist_id":"6135"},{"abstract":[{"text":"Plants adjust their growth according to gravity. Gravitropism involves gravity perception, signal transduction, and asymmetric growth response, with organ bending as a consequence [1]. Asymmetric growth results from the asymmetric distribution of the plant-specific signaling molecule auxin [2] that is generated by lateral transport, mediated in the hypocotyl predominantly by the auxin transporter PIN-FORMED3 (PIN3) [3–5]. Gravity stimulation polarizes PIN3 to the bottom sides of endodermal cells, correlating with increased auxin accumulation in adjacent tissues at the lower side of the stimulated organ, where auxin induces cell elongation and, hence, organ bending. A curvature response allows the hypocotyl to resume straight growth at a defined angle [6], implying that at some point auxin symmetry is restored to prevent overbending. Here, we present initial insights into cellular and molecular mechanisms that lead to the termination of the tropic response. We identified an auxin feedback on PIN3 polarization as underlying mechanism that restores symmetry of the PIN3-dependent auxin flow. Thus, two mechanistically distinct PIN3 polarization events redirect auxin fluxes at different time points of the gravity response: first, gravity-mediated redirection of PIN3-mediated auxin flow toward the lower hypocotyl side, where auxin gradually accumulates and promotes growth, and later PIN3 polarization to the opposite cell side, depleting this auxin maximum to end the bending. Accordingly, genetic or pharmacological interference with the late PIN3 polarization prevents termination of the response and leads to hypocotyl overbending. This observation reveals a role of auxin feedback on PIN polarity in the termination of the tropic response. © 2016 Elsevier Ltd","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-07-14T12:44:39Z","file_name":"IST-2018-1008-v1+1_Rakusova_CurrBiol_2016_proof.pdf","checksum":"79ed2498185a027cf51a8f88100379e6","creator":"system","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"4757","date_created":"2018-12-12T10:09:33Z","file_size":5391923}],"date_updated":"2021-01-12T06:49:08Z","author":[{"first_name":"Hana","last_name":"Rakusová","full_name":"Rakusová, Hana"},{"full_name":"Abbas, Mohamad","id":"47E8FC1C-F248-11E8-B48F-1D18A9856A87","last_name":"Abbas","first_name":"Mohamad"},{"last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin","first_name":"Huibin"},{"full_name":"Song, Siyuan","last_name":"Song","first_name":"Siyuan"},{"first_name":"Hélène","last_name":"Robert","full_name":"Robert, Hélène"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596"}],"language":[{"iso":"eng"}],"issue":"22","scopus_import":1,"year":"2016","has_accepted_license":"1","volume":26,"department":[{"_id":"JiFr"}],"title":"Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity","page":"3026 - 3032","project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"ddc":["581"],"publication_status":"published","file_date_updated":"2020-07-14T12:44:39Z","ec_funded":1,"_id":"1212","publisher":"Cell Press","publist_id":"6138","acknowledgement":"We thank Dr. Jie Li (Key Laboratory of Plant Molecular Physiology, Chinese Academy of Science, China) for the pPIN3::PIN3-GFP/DII::VENUS line and Martine De Cock for help in preparing the manuscript. This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP), by the Czech Science Foundation GAČR (GA13-40637S) to J.F., and by the Ministry of Education, Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) to H.S.R. H.R. is indebted to the Agency for Innovation by Science and Technology (IWT) for a predoctoral fellowship.\r\n","quality_controlled":"1","pubrep_id":"1008","month":"11","citation":{"apa":"Rakusová, H., Abbas, M., Han, H., Song, S., Robert, H., &#38; Friml, J. (2016). Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2016.08.067\">https://doi.org/10.1016/j.cub.2016.08.067</a>","mla":"Rakusová, Hana, et al. “Termination of Shoot Gravitropic Responses by Auxin Feedback on PIN3 Polarity.” <i>Current Biology</i>, vol. 26, no. 22, Cell Press, 2016, pp. 3026–32, doi:<a href=\"https://doi.org/10.1016/j.cub.2016.08.067\">10.1016/j.cub.2016.08.067</a>.","ama":"Rakusová H, Abbas M, Han H, Song S, Robert H, Friml J. Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity. <i>Current Biology</i>. 2016;26(22):3026-3032. doi:<a href=\"https://doi.org/10.1016/j.cub.2016.08.067\">10.1016/j.cub.2016.08.067</a>","ista":"Rakusová H, Abbas M, Han H, Song S, Robert H, Friml J. 2016. Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity. Current Biology. 26(22), 3026–3032.","chicago":"Rakusová, Hana, Mohamad Abbas, Huibin Han, Siyuan Song, Hélène Robert, and Jiří Friml. “Termination of Shoot Gravitropic Responses by Auxin Feedback on PIN3 Polarity.” <i>Current Biology</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.cub.2016.08.067\">https://doi.org/10.1016/j.cub.2016.08.067</a>.","short":"H. Rakusová, M. Abbas, H. Han, S. Song, H. Robert, J. Friml, Current Biology 26 (2016) 3026–3032.","ieee":"H. Rakusová, M. Abbas, H. Han, S. Song, H. Robert, and J. Friml, “Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity,” <i>Current Biology</i>, vol. 26, no. 22. Cell Press, pp. 3026–3032, 2016."},"oa_version":"Submitted Version","date_created":"2018-12-11T11:50:44Z","publication":"Current Biology","type":"journal_article","oa":1,"day":"21","status":"public","doi":"10.1016/j.cub.2016.08.067","date_published":"2016-11-21T00:00:00Z","intvolume":"        26"},{"department":[{"_id":"ChLa"},{"_id":"GaTk"}],"title":"Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm","day":"28","publication_status":"published","status":"public","_id":"1214","article_number":"7759138","publisher":"IEEE","date_published":"2016-11-28T00:00:00Z","doi":"10.1109/IROS.2016.7759138","publist_id":"6121","abstract":[{"text":"With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. While very successful with classical robots, these methods run into severe difficulties when applied to soft robots, a new field of robotics with large interest for human-robot interaction. We claim that a novel controller paradigm opens new perspective for this field. This paper applies a recently developed neuro controller with differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object's internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently develops to rotate it. In this way, the robot discovers affordances of objects its body is interacting with.","lang":"eng"}],"acknowledgement":"RD thanks for the hospitality at the Max-Planck-Institute and for helpful discussions with Nihat Ay and Keyan Zahedi.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:49:08Z","quality_controlled":"1","month":"11","author":[{"first_name":"Georg S","last_name":"Martius","full_name":"Martius, Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hostettler","full_name":"Hostettler, Raphael","first_name":"Raphael"},{"first_name":"Alois","last_name":"Knoll","full_name":"Knoll, Alois"},{"full_name":"Der, Ralf","last_name":"Der","first_name":"Ralf"}],"conference":{"name":"IEEE RSJ International Conference on Intelligent Robots and Systems IROS ","start_date":"2016-09-09","location":"Daejeon, Korea","end_date":"2016-09-14"},"language":[{"iso":"eng"}],"citation":{"ama":"Martius GS, Hostettler R, Knoll A, Der R. Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm. In: Vol 2016-November. IEEE; 2016. doi:<a href=\"https://doi.org/10.1109/IROS.2016.7759138\">10.1109/IROS.2016.7759138</a>","apa":"Martius, G. S., Hostettler, R., Knoll, A., &#38; Der, R. (2016). Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm (Vol. 2016–November). Presented at the IEEE RSJ International Conference on Intelligent Robots and Systems IROS , Daejeon, Korea: IEEE. <a href=\"https://doi.org/10.1109/IROS.2016.7759138\">https://doi.org/10.1109/IROS.2016.7759138</a>","mla":"Martius, Georg S., et al. <i>Compliant Control for Soft Robots: Emergent Behavior of a Tendon Driven Anthropomorphic Arm</i>. Vol. 2016–November, 7759138, IEEE, 2016, doi:<a href=\"https://doi.org/10.1109/IROS.2016.7759138\">10.1109/IROS.2016.7759138</a>.","ieee":"G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm,” presented at the IEEE RSJ International Conference on Intelligent Robots and Systems IROS , Daejeon, Korea, 2016, vol. 2016–November.","short":"G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, IEEE, 2016.","chicago":"Martius, Georg S, Raphael Hostettler, Alois Knoll, and Ralf Der. “Compliant Control for Soft Robots: Emergent Behavior of a Tendon Driven Anthropomorphic Arm,” Vol. 2016–November. IEEE, 2016. <a href=\"https://doi.org/10.1109/IROS.2016.7759138\">https://doi.org/10.1109/IROS.2016.7759138</a>.","ista":"Martius GS, Hostettler R, Knoll A, Der R. 2016. Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm. IEEE RSJ International Conference on Intelligent Robots and Systems IROS  vol. 2016–November, 7759138."},"oa_version":"None","date_created":"2018-12-11T11:50:45Z","scopus_import":1,"year":"2016","type":"conference","volume":"2016-November"},{"abstract":[{"lang":"eng","text":"How likely is it that a population escapes extinction through adaptive evolution? The answer to this question is of great relevance in conservation biology, where we aim at species’ rescue and the maintenance of biodiversity, and in agriculture and medicine, where we seek to hamper the emergence of pesticide or drug resistance. By reshuffling the genome, recombination has two antagonistic effects on the probability of evolutionary rescue: It generates and it breaks up favorable gene combinations. Which of the two effects prevails depends on the fitness effects of mutations and on the impact of stochasticity on the allele frequencies. In this article, we analyze a mathematical model for rescue after a sudden environmental change when adaptation is contingent on mutations at two loci. The analysis reveals a complex nonlinear dependence of population survival on recombination. We moreover find that, counterintuitively, a fast eradication of the wild type can promote rescue in the presence of recombination. The model also shows that two-step rescue is not unlikely to happen and can even be more likely than single-step rescue (where adaptation relies on a single mutation), depending on the circumstances."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_updated":"2026-06-18T07:59:00Z","author":[{"full_name":"Uecker, Hildegard","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","last_name":"Uecker","first_name":"Hildegard","orcid":"0000-0001-9435-2813"},{"first_name":"Joachim","full_name":"Hermisson, Joachim","last_name":"Hermisson"}],"language":[{"iso":"eng"}],"issue":"2","scopus_import":"1","year":"2016","volume":202,"department":[{"_id":"NiBa"}],"title":"The role of recombination in evolutionary rescue","page":"721 - 732","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"},{"name":"L'OREAL Fellowship","_id":"25B67606-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","ddc":["570"],"das_tickbox":"1","ec_funded":1,"_id":"1241","publisher":"Genetics Society of America","publist_id":"6091","acknowledgement":"This work was made possible by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with the Austrian Commission for the United Nations Educational, Scientific, and Cultural Organization and the Austrian Academy of Sciences with financial support from the Federal Ministry for Science and Research Austria) and European Research Council grant 250152 (to Nick Barton).","quality_controlled":"1","month":"02","oa_version":"Preprint","citation":{"chicago":"Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.115.180299\">https://doi.org/10.1534/genetics.115.180299</a>.","ista":"Uecker H, Hermisson J. 2016. The role of recombination in evolutionary rescue. Genetics. 202(2), 721–732.","ieee":"H. Uecker and J. Hermisson, “The role of recombination in evolutionary rescue,” <i>Genetics</i>, vol. 202, no. 2. Genetics Society of America, pp. 721–732, 2016.","short":"H. Uecker, J. Hermisson, Genetics 202 (2016) 721–732.","mla":"Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” <i>Genetics</i>, vol. 202, no. 2, Genetics Society of America, 2016, pp. 721–32, doi:<a href=\"https://doi.org/10.1534/genetics.115.180299\">10.1534/genetics.115.180299</a>.","apa":"Uecker, H., &#38; Hermisson, J. (2016). The role of recombination in evolutionary rescue. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.115.180299\">https://doi.org/10.1534/genetics.115.180299</a>","ama":"Uecker H, Hermisson J. The role of recombination in evolutionary rescue. <i>Genetics</i>. 2016;202(2):721-732. doi:<a href=\"https://doi.org/10.1534/genetics.115.180299\">10.1534/genetics.115.180299</a>"},"date_created":"2018-12-11T11:50:54Z","publication":"Genetics","type":"journal_article","oa":1,"main_file_link":[{"url":"http://biorxiv.org/content/early/2015/07/06/022020.abstract","open_access":"1"}],"day":"01","status":"public","date_published":"2016-02-01T00:00:00Z","doi":"10.1534/genetics.115.180299","intvolume":"       202"},{"department":[{"_id":"ChLa"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"title":"Quantifying self-organizing behavior of autonomous robots","page":"78","publication_status":"published","ddc":["000"],"file_date_updated":"2023-05-02T07:02:59Z","publisher":"MIT Press","_id":"12881","ec_funded":1,"date_updated":"2023-05-02T07:06:21Z","file":[{"file_name":"2015_ECAL_Martius.pdf","date_updated":"2023-05-02T07:02:59Z","checksum":"880eabe59c9df12f06a882aa1bc4e600","success":1,"file_size":1674241,"date_created":"2023-05-02T07:02:59Z","access_level":"open_access","content_type":"application/pdf","creator":"dernst","file_id":"12882","relation":"main_file"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9780262330275"]},"conference":{"end_date":"2015-07-24","location":"York, United Kingdom","start_date":"2015-07-20","name":"ECAL: European Conference on Artificial Life"},"author":[{"first_name":"Georg S","full_name":"Martius, Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","last_name":"Martius"},{"first_name":"Eckehard","last_name":"Olbrich","full_name":"Olbrich, Eckehard"}],"year":"2015","scopus_import":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","day":"01","oa":1,"status":"public","doi":"10.7551/978-0-262-33027-5-ch018","date_published":"2015-07-01T00:00:00Z","quality_controlled":"1","acknowledgement":"This work was supported by the DFG (SPP 1527) and the EU (FP7, REA grant no 291734).","license":"https://creativecommons.org/licenses/by/4.0/","month":"07","publication":"Proceedings of the 13th European Conference on Artificial Life","date_created":"2023-04-30T22:01:07Z","oa_version":"Published Version","citation":{"ieee":"G. S. Martius and E. Olbrich, “Quantifying self-organizing behavior of autonomous robots,” in <i>Proceedings of the 13th European Conference on Artificial Life</i>, York, United Kingdom, 2015, p. 78.","short":"G.S. Martius, E. Olbrich, in:, Proceedings of the 13th European Conference on Artificial Life, MIT Press, 2015, p. 78.","chicago":"Martius, Georg S, and Eckehard Olbrich. “Quantifying Self-Organizing Behavior of Autonomous Robots.” In <i>Proceedings of the 13th European Conference on Artificial Life</i>, 78. MIT Press, 2015. <a href=\"https://doi.org/10.7551/978-0-262-33027-5-ch018\">https://doi.org/10.7551/978-0-262-33027-5-ch018</a>.","ista":"Martius GS, Olbrich E. 2015. Quantifying self-organizing behavior of autonomous robots. Proceedings of the 13th European Conference on Artificial Life. ECAL: European Conference on Artificial Life, 78.","ama":"Martius GS, Olbrich E. Quantifying self-organizing behavior of autonomous robots. In: <i>Proceedings of the 13th European Conference on Artificial Life</i>. MIT Press; 2015:78. doi:<a href=\"https://doi.org/10.7551/978-0-262-33027-5-ch018\">10.7551/978-0-262-33027-5-ch018</a>","mla":"Martius, Georg S., and Eckehard Olbrich. “Quantifying Self-Organizing Behavior of Autonomous Robots.” <i>Proceedings of the 13th European Conference on Artificial Life</i>, MIT Press, 2015, p. 78, doi:<a href=\"https://doi.org/10.7551/978-0-262-33027-5-ch018\">10.7551/978-0-262-33027-5-ch018</a>.","apa":"Martius, G. S., &#38; Olbrich, E. (2015). Quantifying self-organizing behavior of autonomous robots. In <i>Proceedings of the 13th European Conference on Artificial Life</i> (p. 78). York, United Kingdom: MIT Press. <a href=\"https://doi.org/10.7551/978-0-262-33027-5-ch018\">https://doi.org/10.7551/978-0-262-33027-5-ch018</a>"},"type":"conference"},{"publication":"Glycobiology","year":"2015","scopus_import":1,"issue":"12","date_created":"2018-12-11T11:48:35Z","citation":{"ama":"Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. <i>Glycobiology</i>. 2015;25(12):1423-1430. doi:<a href=\"https://doi.org/10.1093/glycob/cwv059\">10.1093/glycob/cwv059</a>","apa":"Engel, J., Schmalhorst, P. S., Kruger, A., Muller, C., Buettner, F., &#38; Routier, F. (2015). Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. <i>Glycobiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/glycob/cwv059\">https://doi.org/10.1093/glycob/cwv059</a>","mla":"Engel, Jakob, et al. “Characterization of an N-Acetylglucosaminyltransferase Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.” <i>Glycobiology</i>, vol. 25, no. 12, Oxford University Press, 2015, pp. 1423–30, doi:<a href=\"https://doi.org/10.1093/glycob/cwv059\">10.1093/glycob/cwv059</a>.","short":"J. Engel, P.S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, F. Routier, Glycobiology 25 (2015) 1423–1430.","ieee":"J. Engel, P. S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, and F. Routier, “Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis,” <i>Glycobiology</i>, vol. 25, no. 12. Oxford University Press, pp. 1423–1430, 2015.","ista":"Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. 2015. Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. Glycobiology. 25(12), 1423–1430.","chicago":"Engel, Jakob, Philipp S Schmalhorst, Anke Kruger, Christina Muller, Falk Buettner, and Françoise Routier. “Characterization of an N-Acetylglucosaminyltransferase Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.” <i>Glycobiology</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/glycob/cwv059\">https://doi.org/10.1093/glycob/cwv059</a>."},"oa_version":"None","volume":25,"type":"journal_article","date_updated":"2021-01-12T08:16:33Z","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Glycoinositolphosphoceramides (GIPCs) are complex sphingolipids present at the plasma membrane of various eukaryotes with the important exception of mammals. In fungi, these glycosphingolipids commonly contain an alpha-mannose residue (Man) linked at position 2 of the inositol. However, several pathogenic fungi additionally synthesize zwitterionic GIPCs carrying an alpha-glucosamine residue (GlcN) at this position. In the human pathogen Aspergillus fumigatus, the GlcNalpha1,2IPC core (where IPC is inositolphosphoceramide) is elongated to Manalpha1,3Manalpha1,6GlcNalpha1,2IPC, which is the most abundant GIPC synthesized by this fungus. In this study, we identified an A. fumigatus N-acetylglucosaminyltransferase, named GntA, and demonstrate its involvement in the initiation of zwitterionic GIPC biosynthesis. Targeted deletion of the gene encoding GntA in A. fumigatus resulted in complete absence of zwitterionic GIPC; a phenotype that could be reverted by episomal expression of GntA in the mutant. The N-acetylhexosaminyltransferase activity of GntA was substantiated by production of N-acetylhexosamine-IPC in the yeast Saccharomyces cerevisiae upon GntA expression. Using an in vitro assay, GntA was furthermore shown to use UDP-N-acetylglucosamine as donor substrate to generate a glycolipid product resistant to saponification and to digestion by phosphatidylinositol-phospholipase C as expected for GlcNAcalpha1,2IPC. Finally, as the enzymes involved in mannosylation of IPC, GntA was localized to the Golgi apparatus, the site of IPC synthesis.","lang":"eng"}],"language":[{"iso":"eng"}],"pmid":1,"author":[{"full_name":"Engel, Jakob","last_name":"Engel","first_name":"Jakob"},{"id":"309D50DA-F248-11E8-B48F-1D18A9856A87","last_name":"Schmalhorst","full_name":"Schmalhorst, Philipp S","first_name":"Philipp S","orcid":"0000-0002-5795-0133"},{"last_name":"Kruger","full_name":"Kruger, Anke","first_name":"Anke"},{"first_name":"Christina","full_name":"Muller, Christina","last_name":"Muller"},{"first_name":"Falk","full_name":"Buettner, Falk","last_name":"Buettner"},{"first_name":"Françoise","full_name":"Routier, Françoise","last_name":"Routier"}],"month":"12","status":"public","publication_status":"published","publist_id":"6851","intvolume":"        25","publisher":"Oxford University Press","doi":"10.1093/glycob/cwv059","date_published":"2015-12-01T00:00:00Z","_id":"802","department":[{"_id":"CaHe"}],"day":"01","external_id":{"pmid":["26306635"]},"title":"Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis","page":"1423 - 1430"},{"language":[{"iso":"eng"}],"arxiv":1,"month":"11","author":[{"first_name":"Sergey","full_name":"Avvakumov, Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","last_name":"Avvakumov"},{"first_name":"Isaac","last_name":"Mabillard","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","full_name":"Mabillard, Isaac"},{"first_name":"A.","full_name":"Skopenkov, A.","last_name":"Skopenkov"},{"first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568"}],"date_updated":"2023-09-07T13:12:17Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We would like to thank A. Klyachko, V. Krushkal, S. Melikhov, M. Tancer, P. Teichner and anonymous referees for helpful discussions.","abstract":[{"lang":"eng","text":"We study conditions under which a finite simplicial complex $K$ can be mapped to $\\mathbb R^d$ without higher-multiplicity intersections. An almost $r$-embedding is a map $f: K\\to \\mathbb R^d$ such that the images of any $r$\r\npairwise disjoint simplices of $K$ do not have a common point. We show that if $r$ is not a prime power and $d\\geq 2r+1$, then there is a counterexample to the topological Tverberg conjecture, i.e., there is an almost $r$-embedding of\r\nthe $(d+1)(r-1)$-simplex in $\\mathbb R^d$. This improves on previous constructions of counterexamples (for $d\\geq 3r$) based on a series of papers by M. \\\"Ozaydin, M. Gromov, P. Blagojevi\\'c, F. Frick, G. Ziegler, and the second and fourth present authors. The counterexamples are obtained by proving the following algebraic criterion in codimension 2: If $r\\ge3$ and if $K$ is a finite $2(r-1)$-complex then there exists an almost $r$-embedding $K\\to \\mathbb R^{2r}$ if and only if there exists a general position PL map $f:K\\to \\mathbb R^{2r}$ such that the algebraic intersection number of the $f$-images of any $r$ pairwise disjoint simplices of $K$ is zero. This result can be restated in terms of cohomological obstructions or equivariant maps, and extends an analogous codimension 3 criterion by the second and fourth authors. As another application we classify ornaments $f:S^3 \\sqcup S^3\\sqcup S^3\\to \\mathbb R^5$ up to ornament\r\nconcordance. It follows from work of M. Freedman, V. Krushkal and P. Teichner that the analogous criterion for $r=2$ is false. We prove a lemma on singular higher-dimensional Borromean rings, yielding an elementary proof of the counterexample."}],"type":"preprint","year":"2015","publication":"arXiv","date_created":"2020-07-30T10:45:19Z","oa_version":"Preprint","citation":{"short":"S. Avvakumov, I. Mabillard, A. Skopenkov, U. Wagner, ArXiv (n.d.).","ieee":"S. Avvakumov, I. Mabillard, A. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity intersections, III. Codimension 2,” <i>arXiv</i>. .","ista":"Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity intersections, III. Codimension 2. arXiv, 1511.03501.","chicago":"Avvakumov, Sergey, Isaac Mabillard, A. Skopenkov, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections, III. Codimension 2.” <i>ArXiv</i>, n.d.","ama":"Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity intersections, III. Codimension 2. <i>arXiv</i>.","apa":"Avvakumov, S., Mabillard, I., Skopenkov, A., &#38; Wagner, U. (n.d.). Eliminating higher-multiplicity intersections, III. Codimension 2. <i>arXiv</i>.","mla":"Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections, III. Codimension 2.” <i>ArXiv</i>, 1511.03501."},"day":"15","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.03501"}],"external_id":{"arxiv":["1511.03501"]},"oa":1,"title":"Eliminating higher-multiplicity intersections, III. Codimension 2","department":[{"_id":"UlWa"}],"date_published":"2015-11-15T00:00:00Z","article_number":"1511.03501","_id":"8183","status":"public","related_material":{"record":[{"relation":"later_version","id":"9308","status":"public"},{"id":"10220","relation":"later_version","status":"public"},{"status":"public","id":"8156","relation":"dissertation_contains"}]},"publication_status":"submitted"},{"month":"01","acknowledgement":"A Technical Report of this paper is available at: \r\nhttps://repository.ist.ac.at/id/eprint/146.\r\n","quality_controlled":"1","type":"conference","date_created":"2018-12-11T11:52:16Z","citation":{"short":"U. Ahmed, K. Chatterjee, S. Gulwani, in:, Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence, AAAI Press, 2015, pp. 745–752.","ieee":"U. Ahmed, K. Chatterjee, and S. Gulwani, “Automatic generation of alternative starting positions for simple traditional board games,” in <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence</i>, Austin, TX, USA, 2015, vol. 2, pp. 745–752.","chicago":"Ahmed, Umair, Krishnendu Chatterjee, and Sumit Gulwani. “Automatic Generation of Alternative Starting Positions for Simple Traditional Board Games.” In <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence</i>, 2:745–52. AAAI Press, 2015.","ista":"Ahmed U, Chatterjee K, Gulwani S. 2015. Automatic generation of alternative starting positions for simple traditional board games. Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 2, 745–752.","ama":"Ahmed U, Chatterjee K, Gulwani S. Automatic generation of alternative starting positions for simple traditional board games. In: <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence</i>. Vol 2. AAAI Press; 2015:745-752.","mla":"Ahmed, Umair, et al. “Automatic Generation of Alternative Starting Positions for Simple Traditional Board Games.” <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence</i>, vol. 2, AAAI Press, 2015, pp. 745–52.","apa":"Ahmed, U., Chatterjee, K., &#38; Gulwani, S. (2015). Automatic generation of alternative starting positions for simple traditional board games. In <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence</i> (Vol. 2, pp. 745–752). Austin, TX, USA: AAAI Press."},"oa_version":"None","publication":"Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence","oa":1,"day":"01","main_file_link":[{"url":"https://www.aaai.org/ocs/index.php/AAAI/AAAI15/paper/download/9523/9300","open_access":"1"}],"intvolume":"         2","date_published":"2015-01-01T00:00:00Z","related_material":{"record":[{"relation":"earlier_version","id":"5410","status":"public"}]},"status":"public","author":[{"last_name":"Ahmed","full_name":"Ahmed, Umair","first_name":"Umair"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Sumit","last_name":"Gulwani","full_name":"Gulwani, Sumit"}],"conference":{"start_date":"2015-01-25","location":"Austin, TX, USA","name":"AAAI: Conference on Artificial Intelligence","end_date":"2015-01-30"},"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Simple board games, like Tic-Tac-Toe and CONNECT-4, play an important role not only in the development of mathematical and logical skills, but also in the emotional and social development. In this paper, we address the problem of generating targeted starting positions for such games. This can facilitate new approaches for bringing novice players to mastery, and also leads to discovery of interesting game variants. We present an approach that generates starting states of varying hardness levels for player 1 in a two-player board game, given rules of the board game, the desired number of steps required for player 1 to win, and the expertise levels of the two players. Our approach leverages symbolic methods and iterative simulation to efficiently search the extremely large state space. We present experimental results that include discovery of states of varying hardness levels for several simple grid-based board games. The presence of such states for standard game variants like 4×4 Tic-Tac-Toe opens up new games to be played that have never been played as the default start state is heavily biased. "}],"date_updated":"2023-02-23T12:25:07Z","article_processing_charge":"No","volume":2,"year":"2015","scopus_import":1,"page":"745 - 752","title":"Automatic generation of alternative starting positions for simple traditional board games","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"department":[{"_id":"KrCh"}],"_id":"1481","ec_funded":1,"publist_id":"5713","publisher":"AAAI Press","publication_status":"published"},{"type":"conference","scopus_import":1,"year":"2015","oa_version":"Preprint","citation":{"chicago":"Reininghaus, Jan, Stefan Huber, Ulrich Bauer, and Roland Kwitt. “A Stable Multi-Scale Kernel for Topological Machine Learning,” 4741–48. IEEE, 2015. <a href=\"https://doi.org/10.1109/CVPR.2015.7299106\">https://doi.org/10.1109/CVPR.2015.7299106</a>.","ista":"Reininghaus J, Huber S, Bauer U, Kwitt R. 2015. A stable multi-scale kernel for topological machine learning. CVPR: Computer Vision and Pattern Recognition, 4741–4748.","ieee":"J. Reininghaus, S. Huber, U. Bauer, and R. Kwitt, “A stable multi-scale kernel for topological machine learning,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA, 2015, pp. 4741–4748.","short":"J. Reininghaus, S. Huber, U. Bauer, R. Kwitt, in:, IEEE, 2015, pp. 4741–4748.","mla":"Reininghaus, Jan, et al. <i>A Stable Multi-Scale Kernel for Topological Machine Learning</i>. IEEE, 2015, pp. 4741–48, doi:<a href=\"https://doi.org/10.1109/CVPR.2015.7299106\">10.1109/CVPR.2015.7299106</a>.","apa":"Reininghaus, J., Huber, S., Bauer, U., &#38; Kwitt, R. (2015). A stable multi-scale kernel for topological machine learning (pp. 4741–4748). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA: IEEE. <a href=\"https://doi.org/10.1109/CVPR.2015.7299106\">https://doi.org/10.1109/CVPR.2015.7299106</a>","ama":"Reininghaus J, Huber S, Bauer U, Kwitt R. A stable multi-scale kernel for topological machine learning. In: IEEE; 2015:4741-4748. doi:<a href=\"https://doi.org/10.1109/CVPR.2015.7299106\">10.1109/CVPR.2015.7299106</a>"},"date_created":"2018-12-11T11:52:17Z","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"eisbn":["978-1-4673-6964-0 "]},"author":[{"full_name":"Reininghaus, Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","last_name":"Reininghaus","first_name":"Jan"},{"orcid":"0000-0002-8871-5814","first_name":"Stefan","last_name":"Huber","id":"4700A070-F248-11E8-B48F-1D18A9856A87","full_name":"Huber, Stefan"},{"orcid":"0000-0002-9683-0724","last_name":"Bauer","full_name":"Bauer, Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich"},{"first_name":"Roland","full_name":"Kwitt, Roland","last_name":"Kwitt"}],"conference":{"location":"Boston, MA, USA","name":"CVPR: Computer Vision and Pattern Recognition","start_date":"2015-06-07","end_date":"2015-06-12"},"date_updated":"2021-01-12T06:51:03Z","abstract":[{"text":"Topological data analysis offers a rich source of valuable information to study vision problems. Yet, so far we lack a theoretically sound connection to popular kernel-based learning techniques, such as kernel SVMs or kernel PCA. In this work, we establish such a connection by designing a multi-scale kernel for persistence diagrams, a stable summary representation of topological features in data. We show that this kernel is positive definite and prove its stability with respect to the 1-Wasserstein distance. Experiments on two benchmark datasets for 3D shape classification/retrieval and texture recognition show considerable performance gains of the proposed method compared to an alternative approach that is based on the recently introduced persistence landscapes.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IEEE","doi":"10.1109/CVPR.2015.7299106","date_published":"2015-10-14T00:00:00Z","publist_id":"5709","_id":"1483","status":"public","publication_status":"published","main_file_link":[{"url":"http://arxiv.org/abs/1412.6821","open_access":"1"}],"day":"14","title":"A stable multi-scale kernel for topological machine learning","oa":1,"page":"4741 - 4748","department":[{"_id":"HeEd"}]},{"publication_status":"published","status":"public","_id":"1495","ec_funded":1,"publist_id":"5684","publisher":"Queen's University","date_published":"2015-08-01T00:00:00Z","department":[{"_id":"HeEd"}],"page":"128-135","title":"Relaxed disk packing","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1505.03402","open_access":"1"}],"day":"01","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Topological Complex Systems","grant_number":"318493"}],"date_created":"2018-12-11T11:52:21Z","citation":{"ama":"Edelsbrunner H, Iglesias Ham M, Kurlin V. Relaxed disk packing. In: <i>Proceedings of the 27th Canadian Conference on Computational Geometry</i>. Vol 2015-August. Queen’s University; 2015:128-135.","apa":"Edelsbrunner, H., Iglesias Ham, M., &#38; Kurlin, V. (2015). Relaxed disk packing. In <i>Proceedings of the 27th Canadian Conference on Computational Geometry</i> (Vol. 2015–August, pp. 128–135). Ontario, Canada: Queen’s University.","mla":"Edelsbrunner, Herbert, et al. “Relaxed Disk Packing.” <i>Proceedings of the 27th Canadian Conference on Computational Geometry</i>, vol. 2015–August, Queen’s University, 2015, pp. 128–35.","short":"H. Edelsbrunner, M. Iglesias Ham, V. Kurlin, in:, Proceedings of the 27th Canadian Conference on Computational Geometry, Queen’s University, 2015, pp. 128–135.","ieee":"H. Edelsbrunner, M. Iglesias Ham, and V. Kurlin, “Relaxed disk packing,” in <i>Proceedings of the 27th Canadian Conference on Computational Geometry</i>, Ontario, Canada, 2015, vol. 2015–August, pp. 128–135.","ista":"Edelsbrunner H, Iglesias Ham M, Kurlin V. 2015. Relaxed disk packing. Proceedings of the 27th Canadian Conference on Computational Geometry. CCCG: Canadian Conference on Computational Geometry vol. 2015–August, 128–135.","chicago":"Edelsbrunner, Herbert, Mabel Iglesias Ham, and Vitaliy Kurlin. “Relaxed Disk Packing.” In <i>Proceedings of the 27th Canadian Conference on Computational Geometry</i>, 2015–August:128–35. Queen’s University, 2015."},"oa_version":"Submitted Version","year":"2015","publication":"Proceedings of the 27th Canadian Conference on Computational Geometry","scopus_import":1,"volume":"2015-August","type":"conference","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Motivated by biological questions, we study configurations of equal-sized disks in the Euclidean plane that neither pack nor cover. Measuring the quality by the probability that a random point lies in exactly one disk, we show that the regular hexagonal grid gives the maximum among lattice configurations. ","lang":"eng"}],"quality_controlled":"1","date_updated":"2021-01-12T06:51:09Z","month":"08","conference":{"end_date":"2015-08-12","start_date":"2015-08-10","name":"CCCG: Canadian Conference on Computational Geometry","location":"Ontario, Canada"},"author":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert"},{"first_name":"Mabel","full_name":"Iglesias Ham, Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","last_name":"Iglesias Ham"},{"first_name":"Vitaliy","last_name":"Kurlin","full_name":"Kurlin, Vitaliy"}],"language":[{"iso":"eng"}]},{"doi":"10.1093/nar/gkv727","date_published":"2015-07-21T00:00:00Z","intvolume":"        43","article_number":"e146","status":"public","day":"21","oa":1,"type":"journal_article","publication":"Nucleic Acids Research","oa_version":"Published Version","citation":{"ama":"Andergassen D, Dotter C, Kulinski T, et al. Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. <i>Nucleic Acids Research</i>. 2015;43(21). doi:<a href=\"https://doi.org/10.1093/nar/gkv727\">10.1093/nar/gkv727</a>","mla":"Andergassen, Daniel, et al. “Allelome.PRO, a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing Data.” <i>Nucleic Acids Research</i>, vol. 43, no. 21, e146, Oxford University Press, 2015, doi:<a href=\"https://doi.org/10.1093/nar/gkv727\">10.1093/nar/gkv727</a>.","apa":"Andergassen, D., Dotter, C., Kulinski, T., Guenzl, P., Bammer, P., Barlow, D., … Hudson, Q. (2015). Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. <i>Nucleic Acids Research</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nar/gkv727\">https://doi.org/10.1093/nar/gkv727</a>","ieee":"D. Andergassen <i>et al.</i>, “Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data,” <i>Nucleic Acids Research</i>, vol. 43, no. 21. Oxford University Press, 2015.","short":"D. Andergassen, C. Dotter, T. Kulinski, P. Guenzl, P. Bammer, D. Barlow, F. Pauler, Q. Hudson, Nucleic Acids Research 43 (2015).","ista":"Andergassen D, Dotter C, Kulinski T, Guenzl P, Bammer P, Barlow D, Pauler F, Hudson Q. 2015. Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. 43(21), e146.","chicago":"Andergassen, Daniel, Christoph Dotter, Tomasz Kulinski, Philipp Guenzl, Philipp Bammer, Denise Barlow, Florian Pauler, and Quanah Hudson. “Allelome.PRO, a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing Data.” <i>Nucleic Acids Research</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/nar/gkv727\">https://doi.org/10.1093/nar/gkv727</a>."},"date_created":"2018-12-11T11:52:22Z","month":"07","quality_controlled":"1","acknowledgement":"Austrian Science Fund [FWF P25185-B22, FWF F4302- B09, FWFW1207-B09]. Funding for open access charge: Austrian Science Fund.\r\nWe thank Florian Breitwieser for advice during the early stages of this project. High-throughput sequencing was conducted by the Biomedical Sequencing Facility (BSF) at CeMM in Vienna.","publisher":"Oxford University Press","publist_id":"5682","_id":"1497","ddc":["570"],"file_date_updated":"2020-07-14T12:44:58Z","publication_status":"published","title":"Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data","department":[{"_id":"GaNo"}],"volume":43,"has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"issue":"21","scopus_import":1,"year":"2015","language":[{"iso":"eng"}],"author":[{"first_name":"Daniel","full_name":"Andergassen, Daniel","last_name":"Andergassen"},{"first_name":"Christoph","last_name":"Dotter","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","full_name":"Dotter, Christoph"},{"first_name":"Tomasz","last_name":"Kulinski","full_name":"Kulinski, Tomasz"},{"first_name":"Philipp","full_name":"Guenzl, Philipp","last_name":"Guenzl"},{"full_name":"Bammer, Philipp","last_name":"Bammer","first_name":"Philipp"},{"first_name":"Denise","last_name":"Barlow","full_name":"Barlow, Denise"},{"first_name":"Florian","last_name":"Pauler","full_name":"Pauler, Florian"},{"first_name":"Quanah","last_name":"Hudson","full_name":"Hudson, Quanah"}],"file":[{"file_name":"2015_NucleicAcidsRes_Andergassen.pdf","date_updated":"2020-07-14T12:44:58Z","checksum":"385b83854fd0eb2e4f386867da2823e2","file_size":6863297,"date_created":"2018-12-20T14:18:57Z","access_level":"open_access","content_type":"application/pdf","creator":"dernst","file_id":"5768","relation":"main_file"}],"date_updated":"2021-01-12T06:51:09Z","abstract":[{"lang":"eng","text":"Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here, we present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analyzed imprinted expression to give a complete picture of the ‘allelome’ by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity to analyze lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data. We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This approach can be easily extended to analyze histone marks of active enhancers, or transcription factor binding sites and therefore provides a powerful tool to identify candidate cis regulatory elements genome wide."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"alternative_title":["LIPIcs"],"department":[{"_id":"ToHe"}],"page":"90 - 102","title":"The need for language support for fault-tolerant distributed systems","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","call_identifier":"FWF","grant_number":"S11402-N23"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"file_date_updated":"2020-07-14T12:44:58Z","series_title":"Leibniz International Proceedings in Informatics","ddc":["005"],"publication_status":"published","ec_funded":1,"_id":"1498","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publist_id":"5681","abstract":[{"text":"Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. Nonetheless there is surprisingly little language and verification support to build distributed systems based on fault-tolerant algorithms. In this paper, we present some of the challenges that a designer has to overcome to implement a fault-tolerant distributed system. Then we review different models that have been proposed to reason about distributed algorithms and sketch how such a model can form the basis for a domain-specific programming language. Adopting a high-level programming model can simplify the programmer's life and make the code amenable to automated verification, while still compiling to efficiently executable code. We conclude by summarizing the current status of an ongoing language design and implementation project that is based on this idea.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-07-14T12:44:58Z","file_name":"IST-2016-499-v1+1_9.pdf","checksum":"cf5e94baa89a2dc4c5de01abc676eda8","date_created":"2018-12-12T10:14:02Z","file_size":489362,"creator":"system","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"5050"}],"date_updated":"2020-08-11T10:09:14Z","conference":{"end_date":"2015-05-06","start_date":"2015-05-03","location":"Asilomar, CA, United States","name":"SNAPL: Summit oN Advances in Programming Languages"},"author":[{"id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","last_name":"Dragoi","full_name":"Dragoi, Cezara","first_name":"Cezara"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724"},{"id":"4397AC76-F248-11E8-B48F-1D18A9856A87","full_name":"Zufferey, Damien","last_name":"Zufferey","first_name":"Damien","orcid":"0000-0002-3197-8736"}],"publication_identifier":{"isbn":["978-3-939897-80-4 "]},"language":[{"iso":"eng"}],"scopus_import":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2015","has_accepted_license":"1","volume":32,"oa":1,"day":"01","status":"public","date_published":"2015-01-01T00:00:00Z","doi":"10.4230/LIPIcs.SNAPL.2015.90","intvolume":"        32","quality_controlled":"1","pubrep_id":"499","month":"01","oa_version":"Published Version","citation":{"chicago":"Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “The Need for Language Support for Fault-Tolerant Distributed Systems.” Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. <a href=\"https://doi.org/10.4230/LIPIcs.SNAPL.2015.90\">https://doi.org/10.4230/LIPIcs.SNAPL.2015.90</a>.","ista":"Dragoi C, Henzinger TA, Zufferey D. 2015. The need for language support for fault-tolerant distributed systems. 32, 90–102.","short":"C. Dragoi, T.A. Henzinger, D. Zufferey, 32 (2015) 90–102.","ieee":"C. Dragoi, T. A. Henzinger, and D. Zufferey, “The need for language support for fault-tolerant distributed systems,” vol. 32. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 90–102, 2015.","mla":"Dragoi, Cezara, et al. <i>The Need for Language Support for Fault-Tolerant Distributed Systems</i>. Vol. 32, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 90–102, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SNAPL.2015.90\">10.4230/LIPIcs.SNAPL.2015.90</a>.","apa":"Dragoi, C., Henzinger, T. A., &#38; Zufferey, D. (2015). The need for language support for fault-tolerant distributed systems. Presented at the SNAPL: Summit oN Advances in Programming Languages, Asilomar, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SNAPL.2015.90\">https://doi.org/10.4230/LIPIcs.SNAPL.2015.90</a>","ama":"Dragoi C, Henzinger TA, Zufferey D. The need for language support for fault-tolerant distributed systems. 2015;32:90-102. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SNAPL.2015.90\">10.4230/LIPIcs.SNAPL.2015.90</a>"},"date_created":"2018-12-11T11:52:22Z","type":"conference"},{"publication_status":"published","file_date_updated":"2020-07-14T12:44:58Z","ddc":["000","003"],"ec_funded":1,"_id":"1499","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publist_id":"5680","alternative_title":["LIPIcs"],"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"page":"142 - 154","title":"Polynomial time decidability of weighted synchronization under partial observability","project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":1,"year":"2015","has_accepted_license":"1","volume":42,"abstract":[{"lang":"eng","text":"We consider weighted automata with both positive and negative integer weights on edges and\r\nstudy the problem of synchronization using adaptive strategies that may only observe whether\r\nthe current weight-level is negative or nonnegative. We show that the synchronization problem is decidable in polynomial time for deterministic weighted automata."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:10Z","file":[{"file_id":"4672","relation":"main_file","access_level":"open_access","content_type":"application/pdf","creator":"system","file_size":623563,"date_created":"2018-12-12T10:08:12Z","checksum":"49eb5021caafaabe5356c65b9c5f8c9c","file_name":"IST-2016-498-v1+1_32.pdf","date_updated":"2020-07-14T12:44:58Z"}],"conference":{"name":"CONCUR: Concurrency Theory","location":"Madrid, Spain","start_date":"2015-09-01","end_date":"2015-09-04"},"author":[{"orcid":"0000-0002-8122-2881","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","full_name":"Kretinsky, Jan","last_name":"Kretinsky"},{"last_name":"Larsen","full_name":"Larsen, Kim","first_name":"Kim"},{"first_name":"Simon","last_name":"Laursen","full_name":"Laursen, Simon"},{"first_name":"Jiří","full_name":"Srba, Jiří","last_name":"Srba"}],"language":[{"iso":"eng"}],"status":"public","date_published":"2015-01-01T00:00:00Z","doi":"10.4230/LIPIcs.CONCUR.2015.142","intvolume":"        42","oa":1,"day":"01","oa_version":"Published Version","citation":{"ama":"Kretinsky J, Larsen K, Laursen S, Srba J. Polynomial time decidability of weighted synchronization under partial observability. In: Vol 42. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:142-154. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2015.142\">10.4230/LIPIcs.CONCUR.2015.142</a>","apa":"Kretinsky, J., Larsen, K., Laursen, S., &#38; Srba, J. (2015). Polynomial time decidability of weighted synchronization under partial observability (Vol. 42, pp. 142–154). Presented at the CONCUR: Concurrency Theory, Madrid, Spain: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2015.142\">https://doi.org/10.4230/LIPIcs.CONCUR.2015.142</a>","mla":"Kretinsky, Jan, et al. <i>Polynomial Time Decidability of Weighted Synchronization under Partial Observability</i>. Vol. 42, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 142–54, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2015.142\">10.4230/LIPIcs.CONCUR.2015.142</a>.","short":"J. Kretinsky, K. Larsen, S. Laursen, J. Srba, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 142–154.","ieee":"J. Kretinsky, K. Larsen, S. Laursen, and J. Srba, “Polynomial time decidability of weighted synchronization under partial observability,” presented at the CONCUR: Concurrency Theory, Madrid, Spain, 2015, vol. 42, pp. 142–154.","chicago":"Kretinsky, Jan, Kim Larsen, Simon Laursen, and Jiří Srba. “Polynomial Time Decidability of Weighted Synchronization under Partial Observability,” 42:142–54. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2015.142\">https://doi.org/10.4230/LIPIcs.CONCUR.2015.142</a>.","ista":"Kretinsky J, Larsen K, Laursen S, Srba J. 2015. Polynomial time decidability of weighted synchronization under partial observability. CONCUR: Concurrency Theory, LIPIcs, vol. 42, 142–154."},"date_created":"2018-12-11T11:52:22Z","type":"conference","acknowledgement":"The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement 601148 (CASSTING), EU FP7 FET project SENSATION, Sino-Danish Basic Research Center IDAE4CPS, the European Research Council (ERC) under grant agreement 267989 (QUAREM), the Austrian Science Fund (FWF) project S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), the Czech Science Foundation under grant agreement P202/12/G061, and People Programme (Marie Curie Actions) of the European Union’s Seventh Framework\r\nProgramme (FP7/2007-2013) REA Grant No 291734.","quality_controlled":"1","pubrep_id":"498","month":"01"},{"volume":47,"issue":"2","scopus_import":1,"year":"2015","language":[{"iso":"eng"}],"author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Martin","full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik"},{"full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","last_name":"Daca","first_name":"Przemyslaw"}],"date_updated":"2023-09-07T11:58:33Z","abstract":[{"lang":"eng","text":"We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability. We introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph algorithms with quadratic complexity to compute the simulation relation. We present an automated technique for assume-guarantee style reasoning for compositional analysis of two-player games by giving a counterexample guided abstraction-refinement approach to compute our new simulation relation. We show a tight link between two-player games and MDPs, and as a consequence the results for games are lifted to MDPs with qualitative properties. We have implemented our algorithms and show that the compositional analysis leads to significant improvements. "}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","publist_id":"5677","ec_funded":1,"_id":"1501","publication_status":"published","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989"}],"page":"230 - 264","title":"CEGAR for compositional analysis of qualitative properties in Markov decision processes","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"type":"journal_article","publication":"Formal Methods in System Design","citation":{"ista":"Chatterjee K, Chmelik M, Daca P. 2015. CEGAR for compositional analysis of qualitative properties in Markov decision processes. Formal Methods in System Design. 47(2), 230–264.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Przemyslaw Daca. “CEGAR for Compositional Analysis of Qualitative Properties in Markov Decision Processes.” <i>Formal Methods in System Design</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s10703-015-0235-2\">https://doi.org/10.1007/s10703-015-0235-2</a>.","short":"K. Chatterjee, M. Chmelik, P. Daca, Formal Methods in System Design 47 (2015) 230–264.","ieee":"K. Chatterjee, M. Chmelik, and P. Daca, “CEGAR for compositional analysis of qualitative properties in Markov decision processes,” <i>Formal Methods in System Design</i>, vol. 47, no. 2. Springer, pp. 230–264, 2015.","mla":"Chatterjee, Krishnendu, et al. “CEGAR for Compositional Analysis of Qualitative Properties in Markov Decision Processes.” <i>Formal Methods in System Design</i>, vol. 47, no. 2, Springer, 2015, pp. 230–64, doi:<a href=\"https://doi.org/10.1007/s10703-015-0235-2\">10.1007/s10703-015-0235-2</a>.","apa":"Chatterjee, K., Chmelik, M., &#38; Daca, P. (2015). CEGAR for compositional analysis of qualitative properties in Markov decision processes. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-015-0235-2\">https://doi.org/10.1007/s10703-015-0235-2</a>","ama":"Chatterjee K, Chmelik M, Daca P. CEGAR for compositional analysis of qualitative properties in Markov decision processes. <i>Formal Methods in System Design</i>. 2015;47(2):230-264. doi:<a href=\"https://doi.org/10.1007/s10703-015-0235-2\">10.1007/s10703-015-0235-2</a>"},"oa_version":"Preprint","date_created":"2018-12-11T11:52:23Z","month":"10","quality_controlled":"1","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No. P23499- N23, FWF NFN Grant No. S11407-N23, FWF Grant S11403-N23 (RiSE), and FWF Grant Z211-N23 (Wittgenstein Award), ERC Start Grant (279307: Graph Games), Microsoft faculty fellows award, the ERC Advanced Grant QUAREM (Quantitative Reactive Modeling).","date_published":"2015-10-01T00:00:00Z","doi":"10.1007/s10703-015-0235-2","intvolume":"        47","status":"public","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1155"}]},"day":"01","main_file_link":[{"url":"https://arxiv.org/abs/1405.0835","open_access":"1"}],"oa":1},{"publication_identifier":{"isbn":["978-1-4503-3471-6"]},"conference":{"end_date":"2015-05-08","location":"Montreal, QC, Canada","name":"CBSE: Component-Based Software Engineering ","start_date":"2015-05-04"},"author":[{"full_name":"Beneš, Nikola","last_name":"Beneš","first_name":"Nikola"},{"full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","last_name":"Daca","first_name":"Przemyslaw"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724"},{"first_name":"Jan","last_name":"Kretinsky","full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881"},{"first_name":"Dejan","last_name":"Nickovic","full_name":"Nickovic, Dejan"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We extend the theory of input-output conformance with operators for merge and quotient. The former is useful when testing against multiple requirements or views. The latter can be used to generate tests for patches of an already tested system. Both operators can combine systems with different action alphabets, which is usually the case when constructing complex systems and specifications from parts, for instance different views as well as newly defined functionality of a~previous version of the system.","lang":"eng"}],"file":[{"checksum":"c6ce681035c163a158751f240cb7d389","file_name":"IST-2016-625-v1+1_conf-cbse-BenesDHKN15.pdf","date_updated":"2020-07-14T12:44:59Z","file_size":467561,"date_created":"2018-12-12T10:17:46Z","file_id":"5303","relation":"main_file","access_level":"open_access","content_type":"application/pdf","creator":"system"}],"date_updated":"2023-09-07T11:58:33Z","has_accepted_license":"1","year":"2015","scopus_import":1,"title":"Complete composition operators for IOCO-testing theory","page":"101 - 110","project":[{"grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"alternative_title":["Proceedings of the 18th International ACM SIGSOFT Symposium on Component-Based Software Engineering "],"_id":"1502","ec_funded":1,"publist_id":"5676","publisher":"ACM","ddc":["000"],"file_date_updated":"2020-07-14T12:44:59Z","publication_status":"published","month":"05","pubrep_id":"625","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) projects S11402-N23(RiSE) and Z211-N23 (Wittgestein Award), by People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 291734, and by the ARTEMIS JU under grant agreement 295373 (nSafeCer).  Jan Křetínský has been partially supported by the Czech Science Foundation, grant No.  P202/12/G061.  Nikola Beneš has been supported by the\r\nMEYS project No. CZ.1.07/2.3.00/30.0009 Employment of Newly Graduated Doctors of Science for Scientific Excellence.","quality_controlled":"1","type":"conference","date_created":"2018-12-11T11:52:24Z","oa_version":"Submitted Version","citation":{"short":"N. Beneš, P. Daca, T.A. Henzinger, J. Kretinsky, D. Nickovic, in:, ACM, 2015, pp. 101–110.","ieee":"N. Beneš, P. Daca, T. A. Henzinger, J. Kretinsky, and D. Nickovic, “Complete composition operators for IOCO-testing theory,” presented at the CBSE: Component-Based Software Engineering , Montreal, QC, Canada, 2015, pp. 101–110.","chicago":"Beneš, Nikola, Przemyslaw Daca, Thomas A Henzinger, Jan Kretinsky, and Dejan Nickovic. “Complete Composition Operators for IOCO-Testing Theory,” 101–10. ACM, 2015. <a href=\"https://doi.org/10.1145/2737166.2737175\">https://doi.org/10.1145/2737166.2737175</a>.","ista":"Beneš N, Daca P, Henzinger TA, Kretinsky J, Nickovic D. 2015. Complete composition operators for IOCO-testing theory. CBSE: Component-Based Software Engineering , Proceedings of the 18th International ACM SIGSOFT Symposium on Component-Based Software Engineering , , 101–110.","ama":"Beneš N, Daca P, Henzinger TA, Kretinsky J, Nickovic D. Complete composition operators for IOCO-testing theory. In: ACM; 2015:101-110. doi:<a href=\"https://doi.org/10.1145/2737166.2737175\">10.1145/2737166.2737175</a>","apa":"Beneš, N., Daca, P., Henzinger, T. A., Kretinsky, J., &#38; Nickovic, D. (2015). Complete composition operators for IOCO-testing theory (pp. 101–110). Presented at the CBSE: Component-Based Software Engineering , Montreal, QC, Canada: ACM. <a href=\"https://doi.org/10.1145/2737166.2737175\">https://doi.org/10.1145/2737166.2737175</a>","mla":"Beneš, Nikola, et al. <i>Complete Composition Operators for IOCO-Testing Theory</i>. ACM, 2015, pp. 101–10, doi:<a href=\"https://doi.org/10.1145/2737166.2737175\">10.1145/2737166.2737175</a>."},"oa":1,"day":"01","doi":"10.1145/2737166.2737175","date_published":"2015-05-01T00:00:00Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1155"}]},"status":"public"},{"quality_controlled":"1","date_updated":"2021-01-12T06:51:14Z","abstract":[{"text":"This paper is aimed at deriving the universality of the largest eigenvalue of a class of high-dimensional real or complex sample covariance matrices of the form W N =Σ 1/2XX∗Σ 1/2 . Here, X = (xij )M,N is an M× N random matrix with independent entries xij , 1 ≤ i M,≤ 1 ≤ j ≤ N such that Exij = 0, E|xij |2 = 1/N . On dimensionality, we assume that M = M(N) and N/M → d ε (0, ∞) as N ∞→. For a class of general deterministic positive-definite M × M matrices Σ , under some additional assumptions on the distribution of xij 's, we show that the limiting behavior of the largest eigenvalue of W N is universal, via pursuing a Green function comparison strategy raised in [Probab. Theory Related Fields 154 (2012) 341-407, Adv. Math. 229 (2012) 1435-1515] by Erd″os, Yau and Yin for Wigner matrices and extended by Pillai and Yin [Ann. Appl. Probab. 24 (2014) 935-1001] to sample covariance matrices in the null case (&amp;Epsi = I ). Consequently, in the standard complex case (Ex2 ij = 0), combing this universality property and the results known for Gaussian matrices obtained by El Karoui in [Ann. Probab. 35 (2007) 663-714] (nonsingular case) and Onatski in [Ann. Appl. Probab. 18 (2008) 470-490] (singular case), we show that after an appropriate normalization the largest eigenvalue of W N converges weakly to the type 2 Tracy-Widom distribution TW2 . Moreover, in the real case, we show that whenΣ is spiked with a fixed number of subcritical spikes, the type 1 Tracy-Widom limit TW1 holds for the normalized largest eigenvalue of W N , which extends a result of Féral and Péché in [J. Math. Phys. 50 (2009) 073302] to the scenario of nondiagonal Σ and more generally distributed X . In summary, we establish the Tracy-Widom type universality for the largest eigenvalue of generally distributed sample covariance matrices under quite light assumptions on &amp;Sigma . Applications of these limiting results to statistical signal detection and structure recognition of separable covariance matrices are also discussed.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"B.Z. was supported  in  part  by  NSFC  Grant  11071213,  ZJNSF  Grant  R6090034  and  SRFDP  Grant 20100101110001. P.G. was supported in part by the Ministry of Education, Singapore, under Grant ARC 14/11. Z.W. was supported  in  part  by  the  Ministry  of  Education,  Singapore,  under  Grant  ARC  14/11,  and  by a Grant R-155-000-131-112 at the National University of Singapore\r\n","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0003-3036-1475","last_name":"Bao","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","full_name":"Bao, Zhigang","first_name":"Zhigang"},{"first_name":"Guangming","full_name":"Pan, Guangming","last_name":"Pan"},{"first_name":"Wang","last_name":"Zhou","full_name":"Zhou, Wang"}],"month":"02","issue":"1","publication":"Annals of Statistics","year":"2015","citation":{"chicago":"Bao, Zhigang, Guangming Pan, and Wang Zhou. “Universality for the Largest Eigenvalue of Sample Covariance Matrices with General Population.” <i>Annals of Statistics</i>. Institute of Mathematical Statistics, 2015. <a href=\"https://doi.org/10.1214/14-AOS1281\">https://doi.org/10.1214/14-AOS1281</a>.","ista":"Bao Z, Pan G, Zhou W. 2015. Universality for the largest eigenvalue of sample covariance matrices with general population. Annals of Statistics. 43(1), 382–421.","short":"Z. Bao, G. Pan, W. Zhou, Annals of Statistics 43 (2015) 382–421.","ieee":"Z. Bao, G. Pan, and W. Zhou, “Universality for the largest eigenvalue of sample covariance matrices with general population,” <i>Annals of Statistics</i>, vol. 43, no. 1. Institute of Mathematical Statistics, pp. 382–421, 2015.","apa":"Bao, Z., Pan, G., &#38; Zhou, W. (2015). Universality for the largest eigenvalue of sample covariance matrices with general population. <i>Annals of Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/14-AOS1281\">https://doi.org/10.1214/14-AOS1281</a>","mla":"Bao, Zhigang, et al. “Universality for the Largest Eigenvalue of Sample Covariance Matrices with General Population.” <i>Annals of Statistics</i>, vol. 43, no. 1, Institute of Mathematical Statistics, 2015, pp. 382–421, doi:<a href=\"https://doi.org/10.1214/14-AOS1281\">10.1214/14-AOS1281</a>.","ama":"Bao Z, Pan G, Zhou W. Universality for the largest eigenvalue of sample covariance matrices with general population. <i>Annals of Statistics</i>. 2015;43(1):382-421. doi:<a href=\"https://doi.org/10.1214/14-AOS1281\">10.1214/14-AOS1281</a>"},"oa_version":"Preprint","date_created":"2018-12-11T11:52:25Z","type":"journal_article","volume":43,"department":[{"_id":"LaEr"}],"main_file_link":[{"url":"https://arxiv.org/abs/1304.5690","open_access":"1"}],"day":"01","oa":1,"title":"Universality for the largest eigenvalue of sample covariance matrices with general population","page":"382 - 421","status":"public","publication_status":"published","publisher":"Institute of Mathematical Statistics","doi":"10.1214/14-AOS1281","date_published":"2015-02-01T00:00:00Z","publist_id":"5672","intvolume":"        43","_id":"1505"},{"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1208.5823"}],"day":"01","title":"The logarithmic law of random determinant","oa":1,"page":"1600 - 1628","department":[{"_id":"LaEr"}],"publist_id":"5671","intvolume":"        21","doi":"10.3150/14-BEJ615","date_published":"2015-08-01T00:00:00Z","publisher":"Bernoulli Society for Mathematical Statistics and Probability","_id":"1506","status":"public","publication_status":"published","language":[{"iso":"eng"}],"author":[{"id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","full_name":"Bao, Zhigang","last_name":"Bao","first_name":"Zhigang","orcid":"0000-0003-3036-1475"},{"first_name":"Guangming","full_name":"Pan, Guangming","last_name":"Pan"},{"first_name":"Wang","full_name":"Zhou, Wang","last_name":"Zhou"}],"month":"08","date_updated":"2021-01-12T06:51:14Z","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Consider the square random matrix An = (aij)n,n, where {aij:= a(n)ij , i, j = 1, . . . , n} is a collection of independent real random variables with means zero and variances one. Under the additional moment condition supn max1≤i,j ≤n Ea4ij &lt;∞, we prove Girko's logarithmic law of det An in the sense that as n→∞ log | detAn| ? (1/2) log(n-1)! d/→√(1/2) log n N(0, 1)."}],"volume":21,"type":"journal_article","publication":"Bernoulli","year":"2015","issue":"3","date_created":"2018-12-11T11:52:25Z","citation":{"ista":"Bao Z, Pan G, Zhou W. 2015. The logarithmic law of random determinant. Bernoulli. 21(3), 1600–1628.","chicago":"Bao, Zhigang, Guangming Pan, and Wang Zhou. “The Logarithmic Law of Random Determinant.” <i>Bernoulli</i>. Bernoulli Society for Mathematical Statistics and Probability, 2015. <a href=\"https://doi.org/10.3150/14-BEJ615\">https://doi.org/10.3150/14-BEJ615</a>.","ieee":"Z. Bao, G. Pan, and W. Zhou, “The logarithmic law of random determinant,” <i>Bernoulli</i>, vol. 21, no. 3. Bernoulli Society for Mathematical Statistics and Probability, pp. 1600–1628, 2015.","short":"Z. Bao, G. Pan, W. Zhou, Bernoulli 21 (2015) 1600–1628.","mla":"Bao, Zhigang, et al. “The Logarithmic Law of Random Determinant.” <i>Bernoulli</i>, vol. 21, no. 3, Bernoulli Society for Mathematical Statistics and Probability, 2015, pp. 1600–28, doi:<a href=\"https://doi.org/10.3150/14-BEJ615\">10.3150/14-BEJ615</a>.","apa":"Bao, Z., Pan, G., &#38; Zhou, W. (2015). The logarithmic law of random determinant. <i>Bernoulli</i>. Bernoulli Society for Mathematical Statistics and Probability. <a href=\"https://doi.org/10.3150/14-BEJ615\">https://doi.org/10.3150/14-BEJ615</a>","ama":"Bao Z, Pan G, Zhou W. The logarithmic law of random determinant. <i>Bernoulli</i>. 2015;21(3):1600-1628. doi:<a href=\"https://doi.org/10.3150/14-BEJ615\">10.3150/14-BEJ615</a>"},"oa_version":"Preprint"},{"language":[{"iso":"eng"}],"author":[{"first_name":"László","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","orcid":"0000-0001-5366-9603"},{"first_name":"Horng","last_name":"Yau","full_name":"Yau, Horng"}],"month":"08","date_updated":"2021-01-12T06:51:15Z","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We consider generalized Wigner ensembles and general β-ensembles with analytic potentials for any β ≥ 1. The recent universality results in particular assert that the local averages of consecutive eigenvalue gaps in the bulk of the spectrum are universal in the sense that they coincide with those of the corresponding Gaussian β-ensembles. In this article, we show that local averaging is not necessary for this result, i.e. we prove that the single gap distributions in the bulk are universal. In fact, with an additional step, our result can be extended to any C4(ℝ) potential."}],"volume":17,"type":"journal_article","year":"2015","publication":"Journal of the European Mathematical Society","scopus_import":1,"issue":"8","date_created":"2018-12-11T11:52:26Z","oa_version":"Preprint","citation":{"ama":"Erdös L, Yau H. Gap universality of generalized Wigner and β ensembles. <i>Journal of the European Mathematical Society</i>. 2015;17(8):1927-2036. doi:<a href=\"https://doi.org/10.4171/JEMS/548\">10.4171/JEMS/548</a>","apa":"Erdös, L., &#38; Yau, H. (2015). Gap universality of generalized Wigner and β ensembles. <i>Journal of the European Mathematical Society</i>. European Mathematical Society. <a href=\"https://doi.org/10.4171/JEMS/548\">https://doi.org/10.4171/JEMS/548</a>","mla":"Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and β Ensembles.” <i>Journal of the European Mathematical Society</i>, vol. 17, no. 8, European Mathematical Society, 2015, pp. 1927–2036, doi:<a href=\"https://doi.org/10.4171/JEMS/548\">10.4171/JEMS/548</a>.","ieee":"L. Erdös and H. Yau, “Gap universality of generalized Wigner and β ensembles,” <i>Journal of the European Mathematical Society</i>, vol. 17, no. 8. European Mathematical Society, pp. 1927–2036, 2015.","short":"L. Erdös, H. Yau, Journal of the European Mathematical Society 17 (2015) 1927–2036.","ista":"Erdös L, Yau H. 2015. Gap universality of generalized Wigner and β ensembles. Journal of the European Mathematical Society. 17(8), 1927–2036.","chicago":"Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and β Ensembles.” <i>Journal of the European Mathematical Society</i>. European Mathematical Society, 2015. <a href=\"https://doi.org/10.4171/JEMS/548\">https://doi.org/10.4171/JEMS/548</a>."},"day":"01","main_file_link":[{"url":"http://arxiv.org/abs/1211.3786","open_access":"1"}],"page":"1927 - 2036","title":"Gap universality of generalized Wigner and β ensembles","oa":1,"department":[{"_id":"LaEr"}],"intvolume":"        17","publist_id":"5669","doi":"10.4171/JEMS/548","date_published":"2015-08-01T00:00:00Z","publisher":"European Mathematical Society","_id":"1508","status":"public","publication_status":"published"},{"status":"public","intvolume":"         4","doi":"10.12688/f1000research.7143.1","date_published":"2015-10-01T00:00:00Z","oa":1,"day":"01","date_created":"2018-12-11T11:52:26Z","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>.","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.","ieee":"J. Michalko, M. Lukacisinova, M. T. Bollenbach, and J. Friml, “Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene,” <i>F1000 Research </i>, vol. 4. F1000 Research, 2015.","short":"J. Michalko, M. Lukacisinova, M.T. Bollenbach, J. Friml, F1000 Research  4 (2015).","mla":"Michalko, Jaroslav, et al. “Embryo-Lethal Phenotypes in Early Abp1 Mutants Are Due to Disruption of the Neighboring BSM Gene.” <i>F1000 Research </i>, vol. 4, F1000 Research, 2015, doi:<a href=\"https://doi.org/10.12688/f1000research.7143.1\">10.12688/f1000research.7143.1</a>.","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>","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>"},"oa_version":"Published Version","publication":"F1000 Research ","type":"journal_article","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","pubrep_id":"497","month":"10","ddc":["570"],"file_date_updated":"2020-07-14T12:44:59Z","publication_status":"published","_id":"1509","ec_funded":1,"publist_id":"5668","publisher":"F1000 Research","department":[{"_id":"JiFr"},{"_id":"ToBo"}],"title":"Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene","project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"year":"2015","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1","has_accepted_license":"1","volume":4,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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"}],"date_updated":"2025-05-07T11:12:30Z","file":[{"file_id":"5198","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"system","file_size":4414248,"date_created":"2018-12-12T10:16:12Z","checksum":"8beae5cbe988e1060265ae7de2ee8306","file_name":"IST-2016-497-v1+1_10.12688_f1000research.7143.1_20151102.pdf","date_updated":"2020-07-14T12:44:59Z"}],"article_processing_charge":"No","author":[{"first_name":"Jaroslav","last_name":"Michalko","id":"483727CA-F248-11E8-B48F-1D18A9856A87","full_name":"Michalko, Jaroslav"},{"first_name":"Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Dravecka, Marta","last_name":"Dravecka","orcid":"0000-0002-2519-8004"},{"last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Tobias","first_name":"Tobias","orcid":"0000-0003-4398-476X"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"language":[{"iso":"eng"}]}]