[{"_id":"9356","external_id":{"arxiv":["2105.08353"],"isi":["000947350400021"]},"doi":"10.1109/LICS52264.2021.9470547","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"quality_controlled":"1","acknowledgement":"We thank the anonymous reviewers for their helpful comments. This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","isi":1,"article_processing_charge":"No","citation":{"ama":"Henzinger TA, Sarac NE. Quantitative and approximate monitoring. In: <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>. Institute of Electrical and Electronics Engineers; 2021. doi:<a href=\"https://doi.org/10.1109/LICS52264.2021.9470547\">10.1109/LICS52264.2021.9470547</a>","short":"T.A. Henzinger, N.E. Sarac, in:, Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2021.","chicago":"Henzinger, Thomas A, and Naci E Sarac. “Quantitative and Approximate Monitoring.” In <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>. Institute of Electrical and Electronics Engineers, 2021. <a href=\"https://doi.org/10.1109/LICS52264.2021.9470547\">https://doi.org/10.1109/LICS52264.2021.9470547</a>.","apa":"Henzinger, T. A., &#38; Sarac, N. E. (2021). Quantitative and approximate monitoring. In <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>. Online: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/LICS52264.2021.9470547\">https://doi.org/10.1109/LICS52264.2021.9470547</a>","mla":"Henzinger, Thomas A., and Naci E. Sarac. “Quantitative and Approximate Monitoring.” <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, 9470547, Institute of Electrical and Electronics Engineers, 2021, doi:<a href=\"https://doi.org/10.1109/LICS52264.2021.9470547\">10.1109/LICS52264.2021.9470547</a>.","ista":"Henzinger TA, Sarac NE. 2021. Quantitative and approximate monitoring. Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science, 9470547.","ieee":"T. A. Henzinger and N. E. Sarac, “Quantitative and approximate monitoring,” in <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, Online, 2021."},"type":"conference","status":"public","title":"Quantitative and approximate monitoring","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"06","oa_version":"Published Version","date_updated":"2023-08-08T13:52:56Z","ddc":["000"],"conference":{"location":"Online","start_date":"2021-06-29","end_date":"2021-07-02","name":"LICS: Symposium on Logic in Computer Science"},"oa":1,"publication_status":"published","arxiv":1,"has_accepted_license":"1","article_number":"9470547","date_created":"2021-04-30T17:30:47Z","project":[{"call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"}],"publisher":"Institute of Electrical and Electronics Engineers","file":[{"file_id":"9557","creator":"esarac","date_created":"2021-06-16T08:23:54Z","relation":"main_file","checksum":"6e4cba3f72775f479c5b1b75d1a4a0c4","date_updated":"2021-06-16T08:23:54Z","content_type":"application/pdf","file_name":"qam.pdf","file_size":641990,"access_level":"open_access","success":1}],"scopus_import":"1","language":[{"iso":"eng"}],"year":"2021","day":"29","publication":"Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science","file_date_updated":"2021-06-16T08:23:54Z","date_published":"2021-06-29T00:00:00Z","abstract":[{"lang":"eng","text":"In runtime verification, a monitor watches a trace of a system and, if possible, decides after observing each finite prefix whether or not the unknown infinite trace satisfies a given specification. We generalize the theory of runtime verification to monitors that attempt to estimate numerical values of quantitative trace properties (instead of attempting to conclude boolean values of trace specifications), such as maximal or average response time along a trace. Quantitative monitors are approximate: with every finite prefix, they can improve their estimate of the infinite trace's unknown property value. Consequently, quantitative monitors can be compared with regard to a precision-cost trade-off: better approximations of the property value require more monitor resources, such as states (in the case of finite-state monitors) or registers, and additional resources yield better approximations. We introduce a formal framework for quantitative and approximate monitoring, show how it conservatively generalizes the classical boolean setting for monitoring, and give several precision-cost trade-offs for monitors. For example, we prove that there are quantitative properties for which every additional register improves monitoring precision."}],"author":[{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","last_name":"Sarac"}]},{"day":"27","language":[{"iso":"eng"}],"year":"2021","publication":"Geometry & Topology","keyword":["Generalized configuration spaces","homological stability","homological densities","chiral algebras","chiral homology","factorization algebras","Koszul duality","Ran space"],"ec_funded":1,"issue":"2","file_date_updated":"2021-05-03T06:54:06Z","abstract":[{"text":"We prove that the factorization homologies of a scheme with coefficients in truncated polynomial algebras compute the cohomologies of its generalized configuration spaces. Using Koszul duality between commutative algebras and Lie algebras, we obtain new expressions for the cohomologies of the latter. As a consequence, we obtain a uniform and conceptual approach for treating homological stability, homological densities, and arithmetic densities of generalized configuration spaces. Our results categorify, generalize, and in fact provide a conceptual understanding of the coincidences appearing in the work of Farb--Wolfson--Wood. Our computation of the stable homological densities also yields rational homotopy types, answering a question posed by Vakil--Wood. Our approach hinges on the study of homological stability of cohomological Chevalley complexes, which is of independent interest.\r\n","lang":"eng"}],"volume":25,"date_published":"2021-04-27T00:00:00Z","author":[{"last_name":"Ho","first_name":"Quoc P","id":"3DD82E3C-F248-11E8-B48F-1D18A9856A87","full_name":"Ho, Quoc P"}],"article_type":"original","project":[{"grant_number":"320593","call_identifier":"FP7","_id":"25E549F4-B435-11E9-9278-68D0E5697425","name":"Arithmetic and physics of Higgs moduli spaces"},{"name":"Algebro-Geometric Applications of Factorization Homology","_id":"26B96266-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02751"}],"date_created":"2021-05-02T06:59:33Z","file":[{"date_updated":"2021-05-03T06:54:06Z","content_type":"application/pdf","file_name":"densities.pdf","file_size":479268,"access_level":"open_access","file_id":"9366","date_created":"2021-05-03T06:54:06Z","creator":"qho","checksum":"643a8d2d6f06f0888dcd7503f55d0920","relation":"main_file","success":1}],"publisher":"Mathematical Sciences Publishers","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"04","oa_version":"Submitted Version","ddc":["514","516","512"],"date_updated":"2023-08-08T13:28:59Z","publication_identifier":{"issn":["1364-0380"]},"oa":1,"publication_status":"published","arxiv":1,"has_accepted_license":"1","_id":"9359","page":"813-912","intvolume":"        25","doi":"10.2140/gt.2021.25.813","external_id":{"isi":["000682738600005"],"arxiv":["1802.07948"]},"department":[{"_id":"TaHa"}],"acknowledgement":"This paper owes an obvious intellectual debt to the illuminating treatments of factorization homology by J.\r\nFrancis, D. Gaitsgory, and J. Lurie in [GL,G1, FG]. The author would like to thank B. Farb and J. Wolfson for\r\nbringing the question of explaining coincidences in homological densities to his attention. Moreover, the author\r\nthanks J. Wolfson for many helpful conversations on the subject, O. Randal-Williams for many comments which\r\ngreatly help improve the exposition, and G. C. Drummond-Cole for many useful conversations on L∞-algebras.\r\nFinally, the author is grateful to the anonymous referee for carefully reading the manuscript and for providing\r\nnumerous comments which greatly helped improve the clarity and precision of the exposition.\r\nThis work is supported by the Advanced Grant “Arithmetic and Physics of Higgs moduli spaces” No. 320593 of\r\nthe European Research Council and the Lise Meitner fellowship “Algebro-Geometric Applications of Factorization\r\nHomology,” Austrian Science Fund (FWF): M 2751.","quality_controlled":"1","isi":1,"citation":{"short":"Q.P. Ho, Geometry &#38; Topology 25 (2021) 813–912.","chicago":"Ho, Quoc P. “Homological Stability and Densities of Generalized Configuration Spaces.” <i>Geometry &#38; Topology</i>. Mathematical Sciences Publishers, 2021. <a href=\"https://doi.org/10.2140/gt.2021.25.813\">https://doi.org/10.2140/gt.2021.25.813</a>.","ama":"Ho QP. Homological stability and densities of generalized configuration spaces. <i>Geometry &#38; Topology</i>. 2021;25(2):813-912. doi:<a href=\"https://doi.org/10.2140/gt.2021.25.813\">10.2140/gt.2021.25.813</a>","mla":"Ho, Quoc P. “Homological Stability and Densities of Generalized Configuration Spaces.” <i>Geometry &#38; Topology</i>, vol. 25, no. 2, Mathematical Sciences Publishers, 2021, pp. 813–912, doi:<a href=\"https://doi.org/10.2140/gt.2021.25.813\">10.2140/gt.2021.25.813</a>.","apa":"Ho, Q. P. (2021). Homological stability and densities of generalized configuration spaces. <i>Geometry &#38; Topology</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/gt.2021.25.813\">https://doi.org/10.2140/gt.2021.25.813</a>","ieee":"Q. P. Ho, “Homological stability and densities of generalized configuration spaces,” <i>Geometry &#38; Topology</i>, vol. 25, no. 2. Mathematical Sciences Publishers, pp. 813–912, 2021.","ista":"Ho QP. 2021. Homological stability and densities of generalized configuration spaces. Geometry &#38; Topology. 25(2), 813–912."},"article_processing_charge":"No","status":"public","type":"journal_article","title":"Homological stability and densities of generalized configuration spaces"},{"department":[{"_id":"Bio"}],"quality_controlled":"1","acknowledgement":"This work was supported by the Swiss National Science Foundation (referencenumber 310030_173185 to P. P.).","intvolume":"         6","_id":"9361","external_id":{"pmid":["33853875"],"isi":["000663823400025"]},"doi":"10.1128/mSphere.01024-20","type":"journal_article","status":"public","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)"},"title":"Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein","isi":1,"article_processing_charge":"No","citation":{"ieee":"M. Gast, N. P. Kadzioch, D. Milius, F. Origgi, and P. Plattet, “Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein,” <i>mSphere</i>, vol. 6, no. 2. American Society for Microbiology, 2021.","ista":"Gast M, Kadzioch NP, Milius D, Origgi F, Plattet P. 2021. Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. mSphere. 6(2), e01024-20.","apa":"Gast, M., Kadzioch, N. P., Milius, D., Origgi, F., &#38; Plattet, P. (2021). Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. <i>MSphere</i>. American Society for Microbiology. <a href=\"https://doi.org/10.1128/mSphere.01024-20\">https://doi.org/10.1128/mSphere.01024-20</a>","mla":"Gast, Matthieu, et al. “Oligomerization and Cell Egress Controlled by Two Microdomains of Canine Distemper Virus Matrix Protein.” <i>MSphere</i>, vol. 6, no. 2, e01024-20, American Society for Microbiology, 2021, doi:<a href=\"https://doi.org/10.1128/mSphere.01024-20\">10.1128/mSphere.01024-20</a>.","short":"M. Gast, N.P. Kadzioch, D. Milius, F. Origgi, P. Plattet, MSphere 6 (2021).","ama":"Gast M, Kadzioch NP, Milius D, Origgi F, Plattet P. Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. <i>mSphere</i>. 2021;6(2). doi:<a href=\"https://doi.org/10.1128/mSphere.01024-20\">10.1128/mSphere.01024-20</a>","chicago":"Gast, Matthieu, Nicole P. Kadzioch, Doreen Milius, Francesco Origgi, and Philippe Plattet. “Oligomerization and Cell Egress Controlled by Two Microdomains of Canine Distemper Virus Matrix Protein.” <i>MSphere</i>. American Society for Microbiology, 2021. <a href=\"https://doi.org/10.1128/mSphere.01024-20\">https://doi.org/10.1128/mSphere.01024-20</a>."},"publication_identifier":{"eissn":["23795042"]},"ddc":["570"],"date_updated":"2023-08-08T13:26:12Z","publication_status":"published","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"04","oa_version":"Published Version","article_number":"e01024-20","has_accepted_license":"1","date_created":"2021-05-02T22:01:28Z","scopus_import":"1","pmid":1,"file":[{"file_id":"9370","checksum":"310748d140c8838335c1314431095898","relation":"main_file","creator":"kschuh","date_created":"2021-05-04T12:41:38Z","content_type":"application/pdf","date_updated":"2021-05-04T12:41:38Z","file_size":3379349,"access_level":"open_access","file_name":"2021_mSphere_Gast.pdf","success":1}],"publisher":"American Society for Microbiology","language":[{"iso":"eng"}],"year":"2021","day":"14","publication":"mSphere","date_published":"2021-04-14T00:00:00Z","volume":6,"abstract":[{"lang":"eng","text":"The multimeric matrix (M) protein of clinically relevant paramyxoviruses orchestrates assembly and budding activity of viral particles at the plasma membrane (PM). We identified within the canine distemper virus (CDV) M protein two microdomains, potentially assuming α-helix structures, which are essential for membrane budding activity. Remarkably, while two rationally designed microdomain M mutants (E89R, microdomain 1 and L239D, microdomain 2) preserved proper folding, dimerization, interaction with the nucleocapsid protein, localization at and deformation of the PM, the virus-like particle formation, as well as production of infectious virions (as monitored using a membrane budding-complementation system), were, in sharp contrast, strongly impaired. Of major importance, raster image correlation spectroscopy (RICS) revealed that both microdomains contributed to finely tune M protein mobility specifically at the PM. Collectively, our data highlighted the cornerstone membrane budding-priming activity of two spatially discrete M microdomains, potentially by coordinating the assembly of productive higher oligomers at the PM."}],"author":[{"full_name":"Gast, Matthieu","first_name":"Matthieu","last_name":"Gast"},{"first_name":"Nicole P.","last_name":"Kadzioch","full_name":"Kadzioch, Nicole P."},{"id":"384050BC-F248-11E8-B48F-1D18A9856A87","full_name":"Milius, Doreen","first_name":"Doreen","last_name":"Milius"},{"first_name":"Francesco","last_name":"Origgi","full_name":"Origgi, Francesco"},{"last_name":"Plattet","first_name":"Philippe","full_name":"Plattet, Philippe"}],"issue":"2","file_date_updated":"2021-05-04T12:41:38Z"},{"scopus_import":"1","file":[{"file_id":"9371","creator":"kschuh","date_created":"2021-05-04T13:22:19Z","checksum":"c52da133850307d2031f552d998f00e8","relation":"main_file","date_updated":"2021-05-04T13:22:19Z","content_type":"application/pdf","file_name":"2021_pone_Chalk.pdf","file_size":2768282,"access_level":"open_access","success":1}],"publisher":"Public Library of Science","pmid":1,"date_created":"2021-05-02T22:01:28Z","article_type":"original","author":[{"full_name":"Chalk, Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7782-4436","first_name":"Matthew J","last_name":"Chalk"},{"first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"}],"abstract":[{"lang":"eng","text":"A central goal in systems neuroscience is to understand the functions performed by neural circuits. Previous top-down models addressed this question by comparing the behaviour of an ideal model circuit, optimised to perform a given function, with neural recordings. However, this requires guessing in advance what function is being performed, which may not be possible for many neural systems. To address this, we propose an inverse reinforcement learning (RL) framework for inferring the function performed by a neural network from data. We assume that the responses of each neuron in a network are optimised so as to drive the network towards ‘rewarded’ states, that are desirable for performing a given function. We then show how one can use inverse RL to infer the reward function optimised by the network from observing its responses. This inferred reward function can be used to predict how the neural network should adapt its dynamics to perform the same function when the external environment or network structure changes. This could lead to theoretical predictions about how neural network dynamics adapt to deal with cell death and/or varying sensory stimulus statistics."}],"volume":16,"date_published":"2021-04-15T00:00:00Z","file_date_updated":"2021-05-04T13:22:19Z","issue":"4","publication":"PLoS ONE","day":"15","language":[{"iso":"eng"}],"year":"2021","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)"},"title":"Inferring the function performed by a recurrent neural network","type":"journal_article","status":"public","citation":{"ieee":"M. J. Chalk, G. Tkačik, and O. Marre, “Inferring the function performed by a recurrent neural network,” <i>PLoS ONE</i>, vol. 16, no. 4. Public Library of Science, 2021.","ista":"Chalk MJ, Tkačik G, Marre O. 2021. Inferring the function performed by a recurrent neural network. PLoS ONE. 16(4), e0248940.","ama":"Chalk MJ, Tkačik G, Marre O. Inferring the function performed by a recurrent neural network. <i>PLoS ONE</i>. 2021;16(4). doi:<a href=\"https://doi.org/10.1371/journal.pone.0248940\">10.1371/journal.pone.0248940</a>","short":"M.J. Chalk, G. Tkačik, O. Marre, PLoS ONE 16 (2021).","chicago":"Chalk, Matthew J, Gašper Tkačik, and Olivier Marre. “Inferring the Function Performed by a Recurrent Neural Network.” <i>PLoS ONE</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pone.0248940\">https://doi.org/10.1371/journal.pone.0248940</a>.","mla":"Chalk, Matthew J., et al. “Inferring the Function Performed by a Recurrent Neural Network.” <i>PLoS ONE</i>, vol. 16, no. 4, e0248940, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pone.0248940\">10.1371/journal.pone.0248940</a>.","apa":"Chalk, M. J., Tkačik, G., &#38; Marre, O. (2021). Inferring the function performed by a recurrent neural network. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0248940\">https://doi.org/10.1371/journal.pone.0248940</a>"},"article_processing_charge":"No","isi":1,"acknowledgement":"The authors would like to thank Ulisse Ferrari for useful discussions and feedback.","quality_controlled":"1","department":[{"_id":"GaTk"}],"doi":"10.1371/journal.pone.0248940","external_id":{"pmid":["33857170"],"isi":["000641474900072"]},"_id":"9362","intvolume":"        16","article_number":"e0248940","has_accepted_license":"1","publication_status":"published","oa":1,"ddc":["570"],"date_updated":"2023-10-18T08:17:42Z","publication_identifier":{"eissn":["19326203"]},"oa_version":"Published Version","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"scopus_import":"1","file":[{"file_id":"9369","relation":"main_file","checksum":"82a74668f863e8dfb22fdd4f845c92ce","creator":"kschuh","date_created":"2021-05-04T09:05:27Z","content_type":"application/pdf","date_updated":"2021-05-04T09:05:27Z","file_size":3072764,"access_level":"open_access","file_name":"2021_PLOS_Ingles-Prieto.pdf","success":1}],"publisher":"Public Library of Science","date_created":"2021-05-02T22:01:29Z","volume":17,"abstract":[{"lang":"eng","text":"Optogenetics has been harnessed to shed new mechanistic light on current and future therapeutic strategies. This has been to date achieved by the regulation of ion flow and electrical signals in neuronal cells and neural circuits that are known to be affected by disease. In contrast, the optogenetic delivery of trophic biochemical signals, which support cell survival and are implicated in degenerative disorders, has never been demonstrated in an animal model of disease. Here, we reengineered the human and Drosophila melanogaster REarranged during Transfection (hRET and dRET) receptors to be activated by light, creating one-component optogenetic tools termed Opto-hRET and Opto-dRET. Upon blue light stimulation, these receptors robustly induced the MAPK/ERK proliferative signaling pathway in cultured cells. In PINK1B9 flies that exhibit loss of PTEN-induced putative kinase 1 (PINK1), a kinase associated with familial Parkinson’s disease (PD), light activation of Opto-dRET suppressed mitochondrial defects, tissue degeneration and behavioral deficits. In human cells with PINK1 loss-of-function, mitochondrial fragmentation was rescued using Opto-dRET via the PI3K/NF-кB pathway. Our results demonstrate that a light-activated receptor can ameliorate disease hallmarks in a genetic model of PD. The optogenetic delivery of trophic signals is cell type-specific and reversible and thus has the potential to inspire novel strategies towards a spatio-temporal regulation of tissue repair."}],"date_published":"2021-04-01T00:00:00Z","author":[{"orcid":"0000-0002-5409-8571","last_name":"Inglés Prieto","first_name":"Álvaro","full_name":"Inglés Prieto, Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Furthmann","first_name":"Nikolas","full_name":"Furthmann, Nikolas"},{"last_name":"Crossman","first_name":"Samuel H.","full_name":"Crossman, Samuel H."},{"last_name":"Tichy","first_name":"Alexandra Madelaine","full_name":"Tichy, Alexandra Madelaine"},{"first_name":"Nina","last_name":"Hoyer","full_name":"Hoyer, Nina"},{"last_name":"Petersen","first_name":"Meike","full_name":"Petersen, Meike"},{"full_name":"Zheden, Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","last_name":"Zheden","first_name":"Vanessa"},{"full_name":"Bicher, Julia","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Bicher"},{"full_name":"Gschaider-Reichhart, Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7218-7738","first_name":"Eva","last_name":"Gschaider-Reichhart"},{"orcid":"0000-0002-1819-198X","first_name":"Attila","last_name":"György","full_name":"György, Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E","last_name":"Siekhaus","first_name":"Daria E","orcid":"0000-0001-8323-8353"},{"first_name":"Peter","last_name":"Soba","full_name":"Soba, Peter"},{"full_name":"Winklhofer, Konstanze F.","last_name":"Winklhofer","first_name":"Konstanze F."},{"full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315"}],"issue":"4","file_date_updated":"2021-05-04T09:05:27Z","day":"01","year":"2021","language":[{"iso":"eng"}],"publication":"PLoS genetics","type":"journal_article","status":"public","title":"Optogenetic delivery of trophic signals in a genetic model of Parkinson's disease","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)"},"isi":1,"citation":{"ista":"Inglés Prieto Á, Furthmann N, Crossman SH, Tichy AM, Hoyer N, Petersen M, Zheden V, Bicher J, Gschaider-Reichhart E, György A, Siekhaus DE, Soba P, Winklhofer KF, Janovjak HL. 2021. Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. PLoS genetics. 17(4), e1009479.","ieee":"Á. Inglés Prieto <i>et al.</i>, “Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease,” <i>PLoS genetics</i>, vol. 17, no. 4. Public Library of Science, p. e1009479, 2021.","short":"Á. Inglés Prieto, N. Furthmann, S.H. Crossman, A.M. Tichy, N. Hoyer, M. Petersen, V. Zheden, J. Bicher, E. Gschaider-Reichhart, A. György, D.E. Siekhaus, P. Soba, K.F. Winklhofer, H.L. Janovjak, PLoS Genetics 17 (2021) e1009479.","chicago":"Inglés Prieto, Álvaro, Nikolas Furthmann, Samuel H. Crossman, Alexandra Madelaine Tichy, Nina Hoyer, Meike Petersen, Vanessa Zheden, et al. “Optogenetic Delivery of Trophic Signals in a Genetic Model of Parkinson’s Disease.” <i>PLoS Genetics</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pgen.1009479\">https://doi.org/10.1371/journal.pgen.1009479</a>.","ama":"Inglés Prieto Á, Furthmann N, Crossman SH, et al. Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. <i>PLoS genetics</i>. 2021;17(4):e1009479. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1009479\">10.1371/journal.pgen.1009479</a>","apa":"Inglés Prieto, Á., Furthmann, N., Crossman, S. H., Tichy, A. M., Hoyer, N., Petersen, M., … Janovjak, H. L. (2021). Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1009479\">https://doi.org/10.1371/journal.pgen.1009479</a>","mla":"Inglés Prieto, Álvaro, et al. “Optogenetic Delivery of Trophic Signals in a Genetic Model of Parkinson’s Disease.” <i>PLoS Genetics</i>, vol. 17, no. 4, Public Library of Science, 2021, p. e1009479, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1009479\">10.1371/journal.pgen.1009479</a>."},"article_processing_charge":"No","department":[{"_id":"EM-Fac"},{"_id":"LoSw"},{"_id":"DaSi"}],"acknowledgement":"We thank R. Cagan, A. Whitworth and J. Nagpal for fly lines and advice, S. Herlitze for provision of a tissue culture illuminator, and Verian Bader for help with statistical analysis.","quality_controlled":"1","_id":"9363","page":"e1009479","intvolume":"        17","doi":"10.1371/journal.pgen.1009479","external_id":{"isi":["000640606700001"]},"has_accepted_license":"1","date_updated":"2023-08-08T13:17:47Z","ddc":["570"],"publication_identifier":{"eissn":["15537404"]},"publication_status":"published","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"04","oa_version":"Published Version"},{"publisher":"Taylor and Francis","scopus_import":"1","article_type":"original","date_created":"2021-05-02T22:01:29Z","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","grant_number":"616160"}],"author":[{"first_name":"Ferdinard U.","last_name":"Ogbuisi","full_name":"Ogbuisi, Ferdinard U."},{"id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","full_name":"Shehu, Yekini","last_name":"Shehu","first_name":"Yekini","orcid":"0000-0001-9224-7139"},{"first_name":"Jen Chih","last_name":"Yao","full_name":"Yao, Jen Chih"}],"abstract":[{"lang":"eng","text":"In this paper, we propose a new iterative method with alternated inertial step for solving split common null point problem in real Hilbert spaces. We obtain weak convergence of the proposed iterative algorithm. Furthermore, we introduce the notion of bounded linear regularity property for the split common null point problem and obtain the linear convergence property for the new algorithm under some mild assumptions. Finally, we provide some numerical examples to demonstrate the performance and efficiency of the proposed method."}],"date_published":"2021-04-14T00:00:00Z","publication":"Optimization","day":"14","year":"2021","language":[{"iso":"eng"}],"ec_funded":1,"article_processing_charge":"No","citation":{"ista":"Ogbuisi FU, Shehu Y, Yao JC. 2021. Convergence analysis of new inertial method for the split common null point problem. Optimization.","ieee":"F. U. Ogbuisi, Y. Shehu, and J. C. Yao, “Convergence analysis of new inertial method for the split common null point problem,” <i>Optimization</i>. Taylor and Francis, 2021.","short":"F.U. Ogbuisi, Y. Shehu, J.C. Yao, Optimization (2021).","chicago":"Ogbuisi, Ferdinard U., Yekini Shehu, and Jen Chih Yao. “Convergence Analysis of New Inertial Method for the Split Common Null Point Problem.” <i>Optimization</i>. Taylor and Francis, 2021. <a href=\"https://doi.org/10.1080/02331934.2021.1914035\">https://doi.org/10.1080/02331934.2021.1914035</a>.","ama":"Ogbuisi FU, Shehu Y, Yao JC. Convergence analysis of new inertial method for the split common null point problem. <i>Optimization</i>. 2021. doi:<a href=\"https://doi.org/10.1080/02331934.2021.1914035\">10.1080/02331934.2021.1914035</a>","mla":"Ogbuisi, Ferdinard U., et al. “Convergence Analysis of New Inertial Method for the Split Common Null Point Problem.” <i>Optimization</i>, Taylor and Francis, 2021, doi:<a href=\"https://doi.org/10.1080/02331934.2021.1914035\">10.1080/02331934.2021.1914035</a>.","apa":"Ogbuisi, F. U., Shehu, Y., &#38; Yao, J. C. (2021). Convergence analysis of new inertial method for the split common null point problem. <i>Optimization</i>. Taylor and Francis. <a href=\"https://doi.org/10.1080/02331934.2021.1914035\">https://doi.org/10.1080/02331934.2021.1914035</a>"},"isi":1,"title":"Convergence analysis of new inertial method for the split common null point problem","status":"public","type":"journal_article","doi":"10.1080/02331934.2021.1914035","external_id":{"isi":["000640109300001"]},"_id":"9365","acknowledgement":"The second author has received funding from the European Research Council (ERC) under the European Union's Seventh Framework Program (FP7-2007-2013) (Grant agreement No. 616160).","quality_controlled":"1","department":[{"_id":"VlKo"}],"oa_version":"None","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_updated":"2023-10-10T09:48:41Z","publication_identifier":{"eissn":["1029-4945"],"issn":["0233-1934"]}},{"date_created":"2021-05-03T13:28:20Z","article_type":"original","project":[{"_id":"256FEF10-B435-11E9-9278-68D0E5697425","name":"Long Term Fellowship","grant_number":"723-2015"},{"grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"publisher":"American Society of Plant Biologists","main_file_link":[{"url":"https://doi.org/10.1093/plphys/kiab199","open_access":"1"}],"pmid":1,"day":"30","year":"2021","language":[{"iso":"eng"}],"publication":"Plant Physiology","volume":186,"abstract":[{"lang":"eng","text":"The quality control system for messenger RNA (mRNA) is fundamental for cellular activities in eukaryotes. To elucidate the molecular mechanism of 3'-Phosphoinositide-Dependent Protein Kinase1 (PDK1), a master regulator that is essential throughout eukaryotic growth and development, we employed a forward genetic approach to screen for suppressors of the loss-of-function T-DNA insertion double mutant pdk1.1 pdk1.2 in Arabidopsis thaliana. Notably, the severe growth attenuation of pdk1.1 pdk1.2 was rescued by sop21 (suppressor of pdk1.1 pdk1.2), which harbours a loss-of-function mutation in PELOTA1 (PEL1). PEL1 is a homologue of mammalian PELOTA and yeast (Saccharomyces cerevisiae) DOM34p, which each form a heterodimeric complex with the GTPase HBS1 (HSP70 SUBFAMILY B SUPPRESSOR1, also called SUPERKILLER PROTEIN7, SKI7), a protein that is responsible for ribosomal rescue and thereby assures the quality and fidelity of mRNA molecules during translation. Genetic analysis further revealed that a dysfunctional PEL1-HBS1 complex failed to degrade the T-DNA-disrupted PDK1 transcripts, which were truncated but functional, and thus rescued the growth and developmental defects of pdk1.1 pdk1.2. Our studies demonstrated the functionality of a homologous PELOTA-HBS1 complex and identified its essential regulatory role in plants, providing insights into the mechanism of mRNA quality control."}],"date_published":"2021-04-30T00:00:00Z","author":[{"full_name":"Kong, W","last_name":"Kong","first_name":"W"},{"orcid":"0000-0002-0471-8285","first_name":"Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang"},{"last_name":"Zhao","first_name":"Q","full_name":"Zhao, Q"},{"first_name":"DL","last_name":"Lin","full_name":"Lin, DL"},{"full_name":"Xu, ZH","first_name":"ZH","last_name":"Xu"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Xue, HW","first_name":"HW","last_name":"Xue"}],"issue":"4","department":[{"_id":"JiFr"}],"acknowledgement":"We gratefully acknowledge the Arabidopsis Biological Resource Centre (ABRC) for providing T-DNA insertional mutants, and Prof. Remko Offringa for sharing published seeds. We thank Yuchuan Liu (Shanghai OE Biotech Co., Ltd) for help with proteomics data analysis, Xixi Zhang (IST Austria) for providing the pDONR-P4P1r-mCherry plasmid, and Yao Xiao (Technical University of Munich), Alexander Johnson (IST Austria) and Hana Semeradova (IST Austria) for helpful discussions. The study was supported by National Natural Science Foundation of China (NSFC, 31721001, 91954206, to H.-W. X.), “Ten-Thousand Talent Program” (to H.-W. X.) and Collaborative Innovation Center of Crop Stress Biology, Henan Province, and Austrian Science Fund (FWF): I 3630-B25 (to J. F.). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015).","quality_controlled":"1","page":"2003-2020","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","_id":"9368","intvolume":"       186","doi":"10.1093/plphys/kiab199","external_id":{"isi":["000703922000025"],"pmid":["33930167"]},"status":"public","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth","isi":1,"article_processing_charge":"No","citation":{"ista":"Kong W, Tan S, Zhao Q, Lin D, Xu Z, Friml J, Xue H. 2021. mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth. Plant Physiology. 186(4), 2003–2020.","ieee":"W. Kong <i>et al.</i>, “mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth,” <i>Plant Physiology</i>, vol. 186, no. 4. American Society of Plant Biologists, pp. 2003–2020, 2021.","chicago":"Kong, W, Shutang Tan, Q Zhao, DL Lin, ZH Xu, Jiří Friml, and HW Xue. “MRNA Surveillance Complex PELOTA-HBS1 Eegulates Phosphoinositide-Sependent Protein Kinase1 and Plant Growth.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2021. <a href=\"https://doi.org/10.1093/plphys/kiab199\">https://doi.org/10.1093/plphys/kiab199</a>.","ama":"Kong W, Tan S, Zhao Q, et al. mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth. <i>Plant Physiology</i>. 2021;186(4):2003-2020. doi:<a href=\"https://doi.org/10.1093/plphys/kiab199\">10.1093/plphys/kiab199</a>","short":"W. Kong, S. Tan, Q. Zhao, D. Lin, Z. Xu, J. Friml, H. Xue, Plant Physiology 186 (2021) 2003–2020.","apa":"Kong, W., Tan, S., Zhao, Q., Lin, D., Xu, Z., Friml, J., &#38; Xue, H. (2021). mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1093/plphys/kiab199\">https://doi.org/10.1093/plphys/kiab199</a>","mla":"Kong, W., et al. “MRNA Surveillance Complex PELOTA-HBS1 Eegulates Phosphoinositide-Sependent Protein Kinase1 and Plant Growth.” <i>Plant Physiology</i>, vol. 186, no. 4, American Society of Plant Biologists, 2021, pp. 2003–20, doi:<a href=\"https://doi.org/10.1093/plphys/kiab199\">10.1093/plphys/kiab199</a>."},"date_updated":"2023-09-05T12:20:27Z","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"publication_status":"published","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","month":"04"},{"keyword":["Genetics","Ecology","Evolution","Behavior and Systematics","General Agricultural and Biological Sciences"],"publication":"Evolution","day":"19","language":[{"iso":"eng"}],"year":"2021","author":[{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."},{"first_name":"Maria R.","last_name":"Servedio","full_name":"Servedio, Maria R."},{"full_name":"Smadja, Carole M.","last_name":"Smadja","first_name":"Carole M."},{"first_name":"Claudia","last_name":"Bank","full_name":"Bank, Claudia"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"first_name":"Samuel M.","last_name":"Flaxman","full_name":"Flaxman, Samuel M."},{"first_name":"Tatiana","last_name":"Giraud","full_name":"Giraud, Tatiana"},{"first_name":"Robin","last_name":"Hopkins","full_name":"Hopkins, Robin"},{"last_name":"Larson","first_name":"Erica L.","full_name":"Larson, Erica L."},{"full_name":"Maan, Martine E.","first_name":"Martine E.","last_name":"Maan"},{"full_name":"Meier, Joana","last_name":"Meier","first_name":"Joana"},{"first_name":"Richard","last_name":"Merrill","full_name":"Merrill, Richard"},{"full_name":"Noor, Mohamed A. F.","last_name":"Noor","first_name":"Mohamed A. F."},{"full_name":"Ortiz‐Barrientos, Daniel","first_name":"Daniel","last_name":"Ortiz‐Barrientos"},{"last_name":"Qvarnström","first_name":"Anna","full_name":"Qvarnström, Anna"}],"abstract":[{"lang":"eng","text":"If there are no constraints on the process of speciation, then the number of species might be expected to match the number of available niches and this number might be indefinitely large. One possible constraint is the opportunity for allopatric divergence. In 1981, Felsenstein used a simple and elegant model to ask if there might also be genetic constraints. He showed that progress towards speciation could be described by the build‐up of linkage disequilibrium among divergently selected loci and between these loci and those contributing to other forms of reproductive isolation. Therefore, speciation is opposed by recombination, because it tends to break down linkage disequilibria. Felsenstein then introduced a crucial distinction between “two‐allele” models, which are subject to this effect, and “one‐allele” models, which are free from the recombination constraint. These fundamentally important insights have been the foundation for both empirical and theoretical studies of speciation ever since."}],"volume":75,"date_published":"2021-04-19T00:00:00Z","issue":"5","date_created":"2021-05-06T04:34:47Z","article_type":"original","publisher":"Wiley","main_file_link":[{"open_access":"1","url":"https://onlinelibrary.wiley.com/doi/10.1111/evo.14235"}],"publication_status":"published","oa":1,"date_updated":"2023-09-05T15:44:33Z","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"oa_version":"Published Version","month":"04","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"RKB was funded by the Natural Environment Research Council (NE/P012272/1 & NE/P001610/1), the European Research Council (693030 BARRIERS), and the Swedish Research Council (VR) (2018‐03695). MRS was funded by the National Science Foundation (Grant No. DEB1939290).","quality_controlled":"1","department":[{"_id":"NiBa"}],"doi":"10.1111/evo.14235","external_id":{"isi":["000647224000001"]},"_id":"9374","page":"978-988","intvolume":"        75","title":"Homage to Felsenstein 1981, or why are there so few/many species?","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)"},"status":"public","type":"journal_article","citation":{"ieee":"R. K. Butlin <i>et al.</i>, “Homage to Felsenstein 1981, or why are there so few/many species?,” <i>Evolution</i>, vol. 75, no. 5. Wiley, pp. 978–988, 2021.","ista":"Butlin RK, Servedio MR, Smadja CM, Bank C, Barton NH, Flaxman SM, Giraud T, Hopkins R, Larson EL, Maan ME, Meier J, Merrill R, Noor MAF, Ortiz‐Barrientos D, Qvarnström A. 2021. Homage to Felsenstein 1981, or why are there so few/many species? Evolution. 75(5), 978–988.","chicago":"Butlin, Roger K., Maria R. Servedio, Carole M. Smadja, Claudia Bank, Nicholas H Barton, Samuel M. Flaxman, Tatiana Giraud, et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many Species?” <i>Evolution</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/evo.14235\">https://doi.org/10.1111/evo.14235</a>.","ama":"Butlin RK, Servedio MR, Smadja CM, et al. Homage to Felsenstein 1981, or why are there so few/many species? <i>Evolution</i>. 2021;75(5):978-988. doi:<a href=\"https://doi.org/10.1111/evo.14235\">10.1111/evo.14235</a>","short":"R.K. Butlin, M.R. Servedio, C.M. Smadja, C. Bank, N.H. Barton, S.M. Flaxman, T. Giraud, R. Hopkins, E.L. Larson, M.E. Maan, J. Meier, R. Merrill, M.A.F. Noor, D. Ortiz‐Barrientos, A. Qvarnström, Evolution 75 (2021) 978–988.","apa":"Butlin, R. K., Servedio, M. R., Smadja, C. M., Bank, C., Barton, N. H., Flaxman, S. M., … Qvarnström, A. (2021). Homage to Felsenstein 1981, or why are there so few/many species? <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.14235\">https://doi.org/10.1111/evo.14235</a>","mla":"Butlin, Roger K., et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many Species?” <i>Evolution</i>, vol. 75, no. 5, Wiley, 2021, pp. 978–88, doi:<a href=\"https://doi.org/10.1111/evo.14235\">10.1111/evo.14235</a>."},"article_processing_charge":"No","isi":1},{"external_id":{"pmid":["34155138"],"isi":["000671755600001"]},"doi":"10.1073/pnas.2015005118","intvolume":"       118","_id":"9375","quality_controlled":"1","acknowledgement":"We thank Felicity Jones for input into experimental design, helpful discussion and improving the manuscript. We thank the Rolian, Jiggins, Chan and Jones Labs members for support, insightful scientific discussion and improving the manuscript. We thank the Rolian lab members, the Animal Resource Centre staff at the University of Calgary, and Caroline Schmid and Ann-Katrin Geysel at the Friedrich Miescher Laboratory for animal husbandry. We thank Christa Lanz, Rebecca Schwab and Ilja Bezrukov for assistance with high-throughput sequencing and associated data processing; Andre Noll and the MPI Tübingen IT team for computational support. We thank Ben Haller and Richard Durbin for helpful discussions. We thank David M. Kingsley for thoughtful input that has greatly improved our manuscript. J.I.M. is supported by a Research Fellowship from St. John’s College, Cambridge. A.D. was supported by a European Research Council Consolidator Grant (No. 617279 “EvolRecombAdapt”, P/I Felicity Jones). C.R. is supported by Discovery Grant #4181932 from the Natural Sciences and Engineering Research Council of Canada and by the Faculty of Veterinary Medicine at the University of Calgary. C.D.J. is supported by a BBSRC grant BB/R007500 and a European Research Council Advanced Grant (No. 339873 “SpeciationGenetics”). M.K. and Y.F.C. are supported by the Max Planck Society and a European Research Council Starting Grant (No. 639096 “HybridMiX”).","department":[{"_id":"NiBa"}],"citation":{"chicago":"Meier, Joana I., Patricio A. Salazar, Marek Kučka, Robert William Davies, Andreea Dréau, Ismael Aldás, Olivia Box Power, et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid Races in Two Butterfly Species.” <i>PNAS</i>. Proceedings of the National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2015005118\">https://doi.org/10.1073/pnas.2015005118</a>.","short":"J.I. Meier, P.A. Salazar, M. Kučka, R.W. Davies, A. Dréau, I. Aldás, O.B. Power, N.J. Nadeau, J.R. Bridle, C. Rolian, N.H. Barton, W.O. McMillan, C.D. Jiggins, Y.F. Chan, PNAS 118 (2021).","ama":"Meier JI, Salazar PA, Kučka M, et al. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. <i>PNAS</i>. 2021;118(25). doi:<a href=\"https://doi.org/10.1073/pnas.2015005118\">10.1073/pnas.2015005118</a>","apa":"Meier, J. I., Salazar, P. A., Kučka, M., Davies, R. W., Dréau, A., Aldás, I., … Chan, Y. F. (2021). Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. <i>PNAS</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2015005118\">https://doi.org/10.1073/pnas.2015005118</a>","mla":"Meier, Joana I., et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid Races in Two Butterfly Species.” <i>PNAS</i>, vol. 118, no. 25, e2015005118, Proceedings of the National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2015005118\">10.1073/pnas.2015005118</a>.","ista":"Meier JI, Salazar PA, Kučka M, Davies RW, Dréau A, Aldás I, Power OB, Nadeau NJ, Bridle JR, Rolian C, Barton NH, McMillan WO, Jiggins CD, Chan YF. 2021. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. 118(25), e2015005118.","ieee":"J. I. Meier <i>et al.</i>, “Haplotype tagging reveals parallel formation of hybrid races in two butterfly species,” <i>PNAS</i>, vol. 118, no. 25. Proceedings of the National Academy of Sciences, 2021."},"article_processing_charge":"No","isi":1,"title":"Haplotype tagging reveals parallel formation of hybrid races in two butterfly species","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"type":"journal_article","status":"public","oa_version":"Published Version","month":"06","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publication_status":"published","publication_identifier":{"eissn":["0027-8424"]},"date_updated":"2023-08-08T13:33:09Z","ddc":["570"],"has_accepted_license":"1","article_number":"e2015005118","article_type":"original","date_created":"2021-05-07T17:10:21Z","pmid":1,"file":[{"success":1,"file_name":"2021_PNAS_Meier.pdf","access_level":"open_access","file_size":20592929,"date_updated":"2022-03-08T08:18:16Z","content_type":"application/pdf","creator":"dernst","date_created":"2022-03-08T08:18:16Z","checksum":"cb30c6166b2132ee60d616b31a1a7c29","relation":"main_file","file_id":"10835"}],"publisher":"Proceedings of the National Academy of Sciences","scopus_import":"1","publication":"PNAS","year":"2021","language":[{"iso":"eng"}],"day":"21","file_date_updated":"2022-03-08T08:18:16Z","issue":"25","author":[{"full_name":"Meier, Joana I.","last_name":"Meier","first_name":"Joana I."},{"full_name":"Salazar, Patricio A.","first_name":"Patricio A.","last_name":"Salazar"},{"full_name":"Kučka, Marek","first_name":"Marek","last_name":"Kučka"},{"last_name":"Davies","first_name":"Robert William","full_name":"Davies, Robert William"},{"full_name":"Dréau, Andreea","first_name":"Andreea","last_name":"Dréau"},{"last_name":"Aldás","first_name":"Ismael","full_name":"Aldás, Ismael"},{"full_name":"Power, Olivia Box","last_name":"Power","first_name":"Olivia Box"},{"last_name":"Nadeau","first_name":"Nicola J.","full_name":"Nadeau, Nicola J."},{"last_name":"Bridle","first_name":"Jon R.","full_name":"Bridle, Jon R."},{"last_name":"Rolian","first_name":"Campbell","full_name":"Rolian, Campbell"},{"first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"last_name":"McMillan","first_name":"W. Owen","full_name":"McMillan, W. Owen"},{"last_name":"Jiggins","first_name":"Chris D.","full_name":"Jiggins, Chris D."},{"last_name":"Chan","first_name":"Yingguang Frank","full_name":"Chan, Yingguang Frank"}],"date_published":"2021-06-21T00:00:00Z","abstract":[{"lang":"eng","text":"Genetic variation segregates as linked sets of variants, or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. And yet, genomic data often lack haplotype information, due to constraints in sequencing technologies. Here we present “haplotagging”, a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species the geographic clines for the major wing pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the centre of the hybrid zone. We propose that shared warning signalling (Müllerian mimicry) may couple the cline shifts seen in both species, and facilitate the parallel co-emergence of a novel hybrid morph in both co-mimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations."}],"volume":118},{"article_number":"186","has_accepted_license":"1","oa":1,"publication_status":"published","date_updated":"2023-08-08T13:31:38Z","ddc":["000"],"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"month":"10","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Computational design of planar multistable compliant structures","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)"},"type":"journal_article","status":"public","citation":{"ieee":"R. Zhang, T. Auzinger, and B. Bickel, “Computational design of planar multistable compliant structures,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 5. Association for Computing Machinery, 2021.","ista":"Zhang R, Auzinger T, Bickel B. 2021. Computational design of planar multistable compliant structures. ACM Transactions on Graphics. 40(5), 186.","mla":"Zhang, Ran, et al. “Computational Design of Planar Multistable Compliant Structures.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 5, 186, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3453477\">10.1145/3453477</a>.","apa":"Zhang, R., Auzinger, T., &#38; Bickel, B. (2021). Computational design of planar multistable compliant structures. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3453477\">https://doi.org/10.1145/3453477</a>","short":"R. Zhang, T. Auzinger, B. Bickel, ACM Transactions on Graphics 40 (2021).","ama":"Zhang R, Auzinger T, Bickel B. Computational design of planar multistable compliant structures. <i>ACM Transactions on Graphics</i>. 2021;40(5). doi:<a href=\"https://doi.org/10.1145/3453477\">10.1145/3453477</a>","chicago":"Zhang, Ran, Thomas Auzinger, and Bernd Bickel. “Computational Design of Planar Multistable Compliant Structures.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3453477\">https://doi.org/10.1145/3453477</a>."},"article_processing_charge":"No","isi":1,"acknowledged_ssus":[{"_id":"M-Shop"}],"acknowledgement":"We would like to thank everyone who contributed to this paper, the authors of artworks for all the examples, including @macrovec-tor_official and Wikimedia for the FLAG semaphore, and @pikisuper-star for the FIGURINE. The photos of iconic poses in the teaser were supplied by (from left to right): Mike Hewitt/Olympics Day 8 - Athletics/Gettty Images, Oneinchpunch/Basketball player training on acourt in New york city/Shutterstock, and Andrew Redington/TigerWoods/Getty Images. We also want to express our gratitude to Christian Hafner for insightful discussions, the IST Austria machine shop SSU, all proof-readers, and anonymous reviewers. This project has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO), and under the European Research Council grant agreement No 715767 (MATERIALIZABLE).","quality_controlled":"1","department":[{"_id":"BeBi"}],"doi":"10.1145/3453477","external_id":{"isi":["000752079300003"]},"_id":"9376","intvolume":"        40","author":[{"id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Ran","orcid":"0000-0002-3808-281X","last_name":"Zhang","first_name":"Ran"},{"id":"4718F954-F248-11E8-B48F-1D18A9856A87","full_name":"Auzinger, Thomas","first_name":"Thomas","last_name":"Auzinger","orcid":"0000-0002-1546-3265"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd"}],"volume":40,"abstract":[{"text":"This paper presents a method for designing planar multistable compliant structures. Given a sequence of desired stable states and the corresponding poses of the structure, we identify the topology and geometric realization of a mechanism—consisting of bars and joints—that is able to physically reproduce the desired multistable behavior. In order to solve this problem efficiently, we build on insights from minimally rigid graph theory to identify simple but effective topologies for the mechanism. We then optimize its geometric parameters, such as joint positions and bar lengths, to obtain correct transitions between the given poses. Simultaneously, we ensure adequate stability of each pose based on an effective approximate error metric related to the elastic energy Hessian of the bars in the mechanism. As demonstrated by our results, we obtain functional multistable mechanisms of manageable complexity that can be fabricated using 3D printing. Further, we evaluated the effectiveness of our method on a large number of examples in the simulation and fabricated several physical prototypes.","lang":"eng"}],"date_published":"2021-10-08T00:00:00Z","file_date_updated":"2021-12-17T08:13:51Z","issue":"5","keyword":["multistability","mechanism","computational design","rigidity"],"ec_funded":1,"publication":"ACM Transactions on Graphics","day":"08","year":"2021","language":[{"iso":"eng"}],"file":[{"date_created":"2021-05-08T17:36:59Z","creator":"bbickel","checksum":"8564b3118457d4c8939a8ef2b1a2f16c","relation":"main_file","file_id":"9377","file_name":"Multistable-authorversion.pdf","file_size":18926557,"access_level":"open_access","date_updated":"2021-05-08T17:36:59Z","content_type":"application/pdf"},{"success":1,"content_type":"video/mp4","date_updated":"2021-05-08T17:38:22Z","file_size":76542901,"access_level":"open_access","file_name":"multistable-video.mp4","file_id":"9378","checksum":"3b6e874e30bfa1bfc3ad3498710145a1","relation":"main_file","date_created":"2021-05-08T17:38:22Z","creator":"bbickel"},{"file_size":3367072,"access_level":"open_access","file_name":"multistable-supplementary material.pdf","content_type":"application/pdf","date_updated":"2021-12-17T08:13:51Z","relation":"supplementary_material","checksum":"20dc3bc42e1a912a5b0247c116772098","description":"This document provides additional results and analyzes the robustness and limitations of our approach.","creator":"bbickel","date_created":"2021-12-17T08:13:51Z","file_id":"10562","title":"Supplementary Material for “Computational Design of Planar Multistable Compliant Structures”"}],"publisher":"Association for Computing Machinery","project":[{"call_identifier":"H2020","grant_number":"642841","_id":"2508E324-B435-11E9-9278-68D0E5697425","name":"Distributed 3D Object Design"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","grant_number":"715767"}],"date_created":"2021-05-08T17:37:08Z","article_type":"original"},{"article_type":"original","date_created":"2021-05-09T22:01:37Z","pmid":1,"publisher":"Frontiers Media","file":[{"success":1,"file_id":"9386","checksum":"8c8a03575d2f7583f88dc3b658b0976b","relation":"main_file","date_created":"2021-05-11T15:09:23Z","creator":"kschuh","content_type":"application/pdf","date_updated":"2021-05-11T15:09:23Z","file_size":4076024,"access_level":"open_access","file_name":"2021_Frontiers_Cell_Bolger-Munro.pdf"}],"scopus_import":"1","publication":"Frontiers in Cell and Developmental Biology","language":[{"iso":"eng"}],"year":"2021","day":"13","keyword":["B cell","actin","immune synapse","cell spreading","cofilin","WDR1 (AIP1)","LIM domain kinase","B cell receptor (BCR)"],"file_date_updated":"2021-05-11T15:09:23Z","author":[{"last_name":"Bolger-Munro","first_name":"Madison","orcid":"0000-0002-8176-4824","full_name":"Bolger-Munro, Madison","id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E"},{"last_name":"Choi","first_name":"Kate","full_name":"Choi, Kate"},{"first_name":"Faith","last_name":"Cheung","full_name":"Cheung, Faith"},{"full_name":"Liu, Yi Tian","last_name":"Liu","first_name":"Yi Tian"},{"last_name":"Dang-Lawson","first_name":"May","full_name":"Dang-Lawson, May"},{"first_name":"Nikola","last_name":"Deretic","full_name":"Deretic, Nikola"},{"last_name":"Keane","first_name":"Connor","full_name":"Keane, Connor"},{"first_name":"Michael R.","last_name":"Gold","full_name":"Gold, Michael R."}],"date_published":"2021-04-13T00:00:00Z","abstract":[{"text":"When B cells encounter membrane-bound antigens, the formation and coalescence of B cell antigen receptor (BCR) microclusters amplifies BCR signaling. The ability of B cells to probe the surface of antigen-presenting cells (APCs) and respond to APC-bound antigens requires remodeling of the actin cytoskeleton. Initial BCR signaling stimulates actin-related protein (Arp) 2/3 complex-dependent actin polymerization, which drives B cell spreading as well as the centripetal movement and coalescence of BCR microclusters at the B cell-APC synapse. Sustained actin polymerization depends on concomitant actin filament depolymerization, which enables the recycling of actin monomers and Arp2/3 complexes. Cofilin-mediated severing of actin filaments is a rate-limiting step in the morphological changes that occur during immune synapse formation. Hence, regulators of cofilin activity such as WD repeat-containing protein 1 (Wdr1), LIM domain kinase (LIMK), and coactosin-like 1 (Cotl1) may also be essential for actin-dependent processes in B cells. Wdr1 enhances cofilin-mediated actin disassembly. Conversely, Cotl1 competes with cofilin for binding to actin and LIMK phosphorylates cofilin and prevents it from binding to actin filaments. We now show that Wdr1 and LIMK have distinct roles in BCR-induced assembly of the peripheral actin structures that drive B cell spreading, and that cofilin, Wdr1, and LIMK all contribute to the actin-dependent amplification of BCR signaling at the immune synapse. Depleting Cotl1 had no effect on these processes. Thus, the Wdr1-LIMK-cofilin axis is critical for BCR-induced actin remodeling and for B cell responses to APC-bound antigens.","lang":"eng"}],"volume":9,"external_id":{"pmid":["33928084"],"isi":["000644419500001"]},"doi":"10.3389/fcell.2021.649433","intvolume":"         9","_id":"9379","quality_controlled":"1","acknowledgement":"We thank the UBC Life Sciences Institute Imaging Facility andthe UBC Flow Cytometry Facility.","department":[{"_id":"CaHe"}],"citation":{"ista":"Bolger-Munro M, Choi K, Cheung F, Liu YT, Dang-Lawson M, Deretic N, Keane C, Gold MR. 2021. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental Biology. 9, 649433.","ieee":"M. Bolger-Munro <i>et al.</i>, “The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse,” <i>Frontiers in Cell and Developmental Biology</i>, vol. 9. Frontiers Media, 2021.","mla":"Bolger-Munro, Madison, et al. “The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse.” <i>Frontiers in Cell and Developmental Biology</i>, vol. 9, 649433, Frontiers Media, 2021, doi:<a href=\"https://doi.org/10.3389/fcell.2021.649433\">10.3389/fcell.2021.649433</a>.","apa":"Bolger-Munro, M., Choi, K., Cheung, F., Liu, Y. T., Dang-Lawson, M., Deretic, N., … Gold, M. R. (2021). The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. <i>Frontiers in Cell and Developmental Biology</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fcell.2021.649433\">https://doi.org/10.3389/fcell.2021.649433</a>","chicago":"Bolger-Munro, Madison, Kate Choi, Faith Cheung, Yi Tian Liu, May Dang-Lawson, Nikola Deretic, Connor Keane, and Michael R. Gold. “The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse.” <i>Frontiers in Cell and Developmental Biology</i>. Frontiers Media, 2021. <a href=\"https://doi.org/10.3389/fcell.2021.649433\">https://doi.org/10.3389/fcell.2021.649433</a>.","short":"M. Bolger-Munro, K. Choi, F. Cheung, Y.T. Liu, M. Dang-Lawson, N. Deretic, C. Keane, M.R. Gold, Frontiers in Cell and Developmental Biology 9 (2021).","ama":"Bolger-Munro M, Choi K, Cheung F, et al. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. <i>Frontiers in Cell and Developmental Biology</i>. 2021;9. doi:<a href=\"https://doi.org/10.3389/fcell.2021.649433\">10.3389/fcell.2021.649433</a>"},"article_processing_charge":"No","isi":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)"},"title":"The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse","type":"journal_article","status":"public","oa_version":"Published Version","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publication_status":"published","publication_identifier":{"eissn":["2296-634X"]},"ddc":["570"],"date_updated":"2023-10-18T08:19:49Z","has_accepted_license":"1","article_number":"649433"},{"type":"journal_article","status":"public","title":"High rates of genome rearrangements and pathogenicity of Shigella spp","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)"},"isi":1,"article_processing_charge":"No","citation":{"ista":"Seferbekova Z, Zabelkin A, Yakovleva Y, Afasizhev R, Dranenko NO, Alexeev N, Gelfand MS, Bochkareva O. 2021. High rates of genome rearrangements and pathogenicity of Shigella spp. Frontiers in Microbiology. 12, 628622.","ieee":"Z. Seferbekova <i>et al.</i>, “High rates of genome rearrangements and pathogenicity of Shigella spp,” <i>Frontiers in Microbiology</i>, vol. 12. Frontiers, 2021.","chicago":"Seferbekova, Zaira, Alexey Zabelkin, Yulia Yakovleva, Robert Afasizhev, Natalia O. Dranenko, Nikita Alexeev, Mikhail S. Gelfand, and Olga Bochkareva. “High Rates of Genome Rearrangements and Pathogenicity of Shigella Spp.” <i>Frontiers in Microbiology</i>. Frontiers, 2021. <a href=\"https://doi.org/10.3389/fmicb.2021.628622\">https://doi.org/10.3389/fmicb.2021.628622</a>.","short":"Z. Seferbekova, A. Zabelkin, Y. Yakovleva, R. Afasizhev, N.O. Dranenko, N. Alexeev, M.S. Gelfand, O. Bochkareva, Frontiers in Microbiology 12 (2021).","ama":"Seferbekova Z, Zabelkin A, Yakovleva Y, et al. High rates of genome rearrangements and pathogenicity of Shigella spp. <i>Frontiers in Microbiology</i>. 2021;12. doi:<a href=\"https://doi.org/10.3389/fmicb.2021.628622\">10.3389/fmicb.2021.628622</a>","apa":"Seferbekova, Z., Zabelkin, A., Yakovleva, Y., Afasizhev, R., Dranenko, N. O., Alexeev, N., … Bochkareva, O. (2021). High rates of genome rearrangements and pathogenicity of Shigella spp. <i>Frontiers in Microbiology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fmicb.2021.628622\">https://doi.org/10.3389/fmicb.2021.628622</a>","mla":"Seferbekova, Zaira, et al. “High Rates of Genome Rearrangements and Pathogenicity of Shigella Spp.” <i>Frontiers in Microbiology</i>, vol. 12, 628622, Frontiers, 2021, doi:<a href=\"https://doi.org/10.3389/fmicb.2021.628622\">10.3389/fmicb.2021.628622</a>."},"department":[{"_id":"FyKo"}],"acknowledgement":"We thank Fyodor Kondrashov for valuable advice and manuscript proofreading. We also thank Alla Mikheenko for assistance with Circos.","quality_controlled":"1","_id":"9380","intvolume":"        12","doi":"10.3389/fmicb.2021.628622","external_id":{"isi":["000643713300001"]},"article_number":"628622","has_accepted_license":"1","ddc":["570"],"date_updated":"2023-08-08T13:30:39Z","publication_identifier":{"eissn":["1664-302X"]},"publication_status":"published","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"04","oa_version":"Published Version","scopus_import":"1","publisher":"Frontiers","file":[{"date_created":"2021-05-11T13:05:52Z","creator":"kschuh","relation":"main_file","checksum":"2f856543add59273a482a7f326fc0400","file_id":"9384","file_name":"2021_Frontiers_Microbiology_Seferbekova.pdf","file_size":14362316,"access_level":"open_access","date_updated":"2021-05-11T13:05:52Z","content_type":"application/pdf","success":1}],"date_created":"2021-05-09T22:01:38Z","article_type":"original","project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"abstract":[{"lang":"eng","text":"Shigella are pathogens originating within the Escherichia lineage but frequently classified as a separate genus. Shigella genomes contain numerous insertion sequences (ISs) that lead to pseudogenisation of affected genes and an increase of non-homologous recombination. Here, we study 414 genomes of E. coli and Shigella strains to assess the contribution of genomic rearrangements to Shigella evolution. We found that Shigella experienced exceptionally high rates of intragenomic rearrangements and had a decreased rate of homologous recombination compared to pathogenic and non-pathogenic E. coli. The high rearrangement rate resulted in independent disruption of syntenic regions and parallel rearrangements in different Shigella lineages. Specifically, we identified two types of chromosomally encoded E3 ubiquitin-protein ligases acquired independently by all Shigella strains that also showed a high level of sequence conservation in the promoter and further in the 5′-intergenic region. In the only available enteroinvasive E. coli (EIEC) strain, which is a pathogenic E. coli with a phenotype intermediate between Shigella and non-pathogenic E. coli, we found a rate of genome rearrangements comparable to those in other E. coli and no functional copies of the two Shigella-specific E3 ubiquitin ligases. These data indicate that the accumulation of ISs influenced many aspects of genome evolution and played an important role in the evolution of intracellular pathogens. Our research demonstrates the power of comparative genomics-based on synteny block composition and an important role of non-coding regions in the evolution of genomic islands."}],"volume":12,"date_published":"2021-04-12T00:00:00Z","author":[{"first_name":"Zaira","last_name":"Seferbekova","full_name":"Seferbekova, Zaira"},{"last_name":"Zabelkin","first_name":"Alexey","full_name":"Zabelkin, Alexey"},{"full_name":"Yakovleva, Yulia","first_name":"Yulia","last_name":"Yakovleva"},{"last_name":"Afasizhev","first_name":"Robert","full_name":"Afasizhev, Robert"},{"first_name":"Natalia O.","last_name":"Dranenko","full_name":"Dranenko, Natalia O."},{"last_name":"Alexeev","first_name":"Nikita","full_name":"Alexeev, Nikita"},{"last_name":"Gelfand","first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S."},{"orcid":"0000-0003-1006-6639","last_name":"Bochkareva","first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","full_name":"Bochkareva, Olga"}],"file_date_updated":"2021-05-11T13:05:52Z","ec_funded":1,"day":"12","year":"2021","language":[{"iso":"eng"}],"publication":"Frontiers in Microbiology"},{"intvolume":"        17","_id":"9381","external_id":{"isi":["000639711200001"]},"doi":"10.1371/journal.pcbi.1008523","department":[{"_id":"KrCh"}],"quality_controlled":"1","acknowledgement":"Authors would like to thank Christian Hilbe and Martin Nowak for their inspiring and very helpful feedback on the manuscript.","isi":1,"article_processing_charge":"No","citation":{"chicago":"Kleshnina, Maria, Sabrina S. Streipert, Jerzy A. Filar, and Krishnendu Chatterjee. “Mistakes Can Stabilise the Dynamics of Rock-Paper-Scissors Games.” <i>PLoS Computational Biology</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pcbi.1008523\">https://doi.org/10.1371/journal.pcbi.1008523</a>.","short":"M. Kleshnina, S.S. Streipert, J.A. Filar, K. Chatterjee, PLoS Computational Biology 17 (2021).","ama":"Kleshnina M, Streipert SS, Filar JA, Chatterjee K. Mistakes can stabilise the dynamics of rock-paper-scissors games. <i>PLoS Computational Biology</i>. 2021;17(4). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008523\">10.1371/journal.pcbi.1008523</a>","mla":"Kleshnina, Maria, et al. “Mistakes Can Stabilise the Dynamics of Rock-Paper-Scissors Games.” <i>PLoS Computational Biology</i>, vol. 17, no. 4, e1008523, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008523\">10.1371/journal.pcbi.1008523</a>.","apa":"Kleshnina, M., Streipert, S. S., Filar, J. A., &#38; Chatterjee, K. (2021). Mistakes can stabilise the dynamics of rock-paper-scissors games. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1008523\">https://doi.org/10.1371/journal.pcbi.1008523</a>","ieee":"M. Kleshnina, S. S. Streipert, J. A. Filar, and K. Chatterjee, “Mistakes can stabilise the dynamics of rock-paper-scissors games,” <i>PLoS Computational Biology</i>, vol. 17, no. 4. Public Library of Science, 2021.","ista":"Kleshnina M, Streipert SS, Filar JA, Chatterjee K. 2021. Mistakes can stabilise the dynamics of rock-paper-scissors games. PLoS Computational Biology. 17(4), e1008523."},"status":"public","type":"journal_article","title":"Mistakes can stabilise the dynamics of rock-paper-scissors games","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)"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","month":"04","publication_identifier":{"issn":["1553734X"],"eissn":["15537358"]},"ddc":["000"],"date_updated":"2025-07-14T09:10:04Z","publication_status":"published","oa":1,"has_accepted_license":"1","article_number":"e1008523","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818"}],"article_type":"original","date_created":"2021-05-09T22:01:38Z","publisher":"Public Library of Science","file":[{"success":1,"file_name":"2021_pcbi_Kleshnina.pdf","file_size":1323820,"access_level":"open_access","date_updated":"2021-05-11T13:50:06Z","content_type":"application/pdf","date_created":"2021-05-11T13:50:06Z","creator":"kschuh","relation":"main_file","checksum":"a94ebe0c4116f5047eaa6029e54d2dac","file_id":"9385"}],"scopus_import":"1","language":[{"iso":"eng"}],"year":"2021","day":"01","publication":"PLoS Computational Biology","ec_funded":1,"issue":"4","file_date_updated":"2021-05-11T13:50:06Z","date_published":"2021-04-01T00:00:00Z","volume":17,"abstract":[{"text":"A game of rock-paper-scissors is an interesting example of an interaction where none of the pure strategies strictly dominates all others, leading to a cyclic pattern. In this work, we consider an unstable version of rock-paper-scissors dynamics and allow individuals to make behavioural mistakes during the strategy execution. We show that such an assumption can break a cyclic relationship leading to a stable equilibrium emerging with only one strategy surviving. We consider two cases: completely random mistakes when individuals have no bias towards any strategy and a general form of mistakes. Then, we determine conditions for a strategy to dominate all other strategies. However, given that individuals who adopt a dominating strategy are still prone to behavioural mistakes in the observed behaviour, we may still observe extinct strategies. That is, behavioural mistakes in strategy execution stabilise evolutionary dynamics leading to an evolutionary stable and, potentially, mixed co-existence equilibrium.","lang":"eng"}],"author":[{"id":"4E21749C-F248-11E8-B48F-1D18A9856A87","full_name":"Kleshnina, Maria","last_name":"Kleshnina","first_name":"Maria"},{"full_name":"Streipert, Sabrina S.","first_name":"Sabrina S.","last_name":"Streipert"},{"full_name":"Filar, Jerzy A.","last_name":"Filar","first_name":"Jerzy A."},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"}]},{"file":[{"success":1,"content_type":"application/pdf","date_updated":"2022-03-25T12:02:04Z","file_size":719991,"access_level":"open_access","file_name":"2021_Evolution_Stankowski.pdf","file_id":"10921","checksum":"96f6ccf15d95a4e9f7c0b27eee570fa6","relation":"main_file","creator":"kschuh","date_created":"2022-03-25T12:02:04Z"}],"publisher":"Oxford University Press","scopus_import":"1","date_created":"2021-05-09T22:01:39Z","article_type":"original","issue":"6","file_date_updated":"2022-03-25T12:02:04Z","date_published":"2021-03-22T00:00:00Z","volume":75,"abstract":[{"lang":"eng","text":"A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that surround us. But what do we really mean when we talk about the speciation continuum, and can it really help us understand speciation? We explored these questions using a literature review and online survey of speciation researchers. Although most researchers were familiar with the concept and thought it was useful, our survey revealed extensive disagreement about what the speciation continuum actually tells us. This is due partly to the lack of a clear definition. Here, we provide an explicit definition that is compatible with the Biological Species Concept. That is, the speciation continuum is a continuum of reproductive isolation. After outlining the logic of the definition in light of alternatives, we explain why attempts to reconstruct the speciation process from present‐day populations will ultimately fail. We then outline how we think the speciation continuum concept can continue to act as a foundation for understanding the continuum of reproductive isolation that surrounds us."}],"author":[{"first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"}],"year":"2021","language":[{"iso":"eng"}],"day":"22","publication":"Evolution","isi":1,"article_processing_charge":"No","citation":{"ista":"Stankowski S, Ravinet M. 2021. Defining the speciation continuum. Evolution. 75(6), 1256–1273.","ieee":"S. Stankowski and M. Ravinet, “Defining the speciation continuum,” <i>Evolution</i>, vol. 75, no. 6. Oxford University Press, pp. 1256–1273, 2021.","mla":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” <i>Evolution</i>, vol. 75, no. 6, Oxford University Press, 2021, pp. 1256–73, doi:<a href=\"https://doi.org/10.1111/evo.14215\">10.1111/evo.14215</a>.","apa":"Stankowski, S., &#38; Ravinet, M. (2021). Defining the speciation continuum. <i>Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1111/evo.14215\">https://doi.org/10.1111/evo.14215</a>","short":"S. Stankowski, M. Ravinet, Evolution 75 (2021) 1256–1273.","chicago":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” <i>Evolution</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1111/evo.14215\">https://doi.org/10.1111/evo.14215</a>.","ama":"Stankowski S, Ravinet M. Defining the speciation continuum. <i>Evolution</i>. 2021;75(6):1256-1273. doi:<a href=\"https://doi.org/10.1111/evo.14215\">10.1111/evo.14215</a>"},"type":"journal_article","status":"public","title":"Defining the speciation continuum","tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"intvolume":"        75","page":"1256-1273","_id":"9383","external_id":{"isi":["000647226400001"]},"doi":"10.1111/evo.14215","department":[{"_id":"NiBa"}],"quality_controlled":"1","acknowledgement":"We thank M. Garlovsky, S. Martin, C. Cooney, C. Roux, J. Larson, and J. Mallet for critical feedback and for discussion. K. Lohse, M. de la Cámara, J. Cerca, M. A. Chase, C. Baskett, A. M. Westram, and N. H. Barton gave feedback on a draft of the manuscript. O. Seehausen, two anonymous reviewers, and the AE (Michael Kopp) provided comments that greatly improved the manuscript. V. Holzmann made many corrections to the proofs. G. Bisschop and K. Lohse kindly contributed the simulations and analyses presented in Box 3. We would also like to extend our thanks to everyone who took part in the speciation survey, which received ethical approval through the University of Sheffield Ethics Review Procedure (Application 029768). We are especially grateful to R. K. Butlin for stimulating discussion throughout the writing of the manuscript and for feedback on an earlier draft.","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","month":"03","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"ddc":["570"],"date_updated":"2023-10-18T08:16:01Z","publication_status":"published","oa":1},{"month":"04","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","oa":1,"date_updated":"2023-08-08T13:32:40Z","publication_identifier":{"issn":["0022-5193"]},"article_number":"110729","doi":"10.1016/j.jtbi.2021.110729","external_id":{"isi":["000659161500002"]},"_id":"9387","intvolume":"       524","acknowledgement":"This work was supported by the Russian Science Foundation grant N 16-14-10173.","quality_controlled":"1","department":[{"_id":"GradSch"}],"citation":{"chicago":"Khudiakova, Kseniia, Tatiana Yu. Neretina, and Alexey S. Kondrashov. “Two Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” <i>Journal of Theoretical Biology</i>. Elsevier , 2021. <a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">https://doi.org/10.1016/j.jtbi.2021.110729</a>.","ama":"Khudiakova K, Neretina TY, Kondrashov AS. Two linked loci under mutation-selection balance and Muller’s ratchet. <i>Journal of Theoretical Biology</i>. 2021;524. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">10.1016/j.jtbi.2021.110729</a>","short":"K. Khudiakova, T.Y. Neretina, A.S. Kondrashov, Journal of Theoretical Biology 524 (2021).","apa":"Khudiakova, K., Neretina, T. Y., &#38; Kondrashov, A. S. (2021). Two linked loci under mutation-selection balance and Muller’s ratchet. <i>Journal of Theoretical Biology</i>. Elsevier . <a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">https://doi.org/10.1016/j.jtbi.2021.110729</a>","mla":"Khudiakova, Kseniia, et al. “Two Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” <i>Journal of Theoretical Biology</i>, vol. 524, 110729, Elsevier , 2021, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">10.1016/j.jtbi.2021.110729</a>.","ista":"Khudiakova K, Neretina TY, Kondrashov AS. 2021. Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. 524, 110729.","ieee":"K. Khudiakova, T. Y. Neretina, and A. S. Kondrashov, “Two linked loci under mutation-selection balance and Muller’s ratchet,” <i>Journal of Theoretical Biology</i>, vol. 524. Elsevier , 2021."},"article_processing_charge":"No","isi":1,"title":"Two linked loci under mutation-selection balance and Muller’s ratchet","type":"journal_article","status":"public","publication":"Journal of Theoretical Biology","day":"24","language":[{"iso":"eng"}],"year":"2021","keyword":["General Biochemistry","Genetics and Molecular Biology","Modelling and Simulation","Statistics and Probability","General Immunology and Microbiology","Applied Mathematics","General Agricultural and Biological Sciences","General Medicine"],"author":[{"orcid":"0000-0002-6246-1465","last_name":"Khudiakova","first_name":"Kseniia","full_name":"Khudiakova, Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425"},{"first_name":"Tatiana Yu.","last_name":"Neretina","full_name":"Neretina, Tatiana Yu."},{"last_name":"Kondrashov","first_name":"Alexey S.","full_name":"Kondrashov, Alexey S."}],"abstract":[{"text":"We report the complete analysis of a deterministic model of deleterious mutations and negative selection against them at two haploid loci without recombination. As long as mutation is a weaker force than selection, mutant alleles remain rare at the only stable equilibrium, and otherwise, a variety of dynamics are possible. If the mutation-free genotype is absent, generally the only stable equilibrium is the one that corresponds to fixation of the mutant allele at the locus where it is less deleterious. This result suggests that fixation of a deleterious allele that follows a click of the Muller’s ratchet is governed by natural selection, instead of random drift.","lang":"eng"}],"volume":524,"date_published":"2021-04-24T00:00:00Z","article_type":"original","date_created":"2021-05-12T05:58:42Z","publisher":"Elsevier ","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/477489v1"}]},{"acknowledged_ssus":[{"_id":"NanoFab"}],"publisher":"Institute of Science and Technology Austria","file":[{"relation":"main_file","checksum":"80a905c4eef24dab6fb247e81a3d67f5","creator":"mvalenti","date_created":"2021-05-14T11:42:23Z","file_id":"9390","access_level":"open_access","file_size":10572981,"file_name":"Notebook_Valentini.pdf","content_type":"application/pdf","date_updated":"2021-05-14T11:42:23Z"},{"file_name":"Experimental_data.zip","file_size":99076111,"access_level":"open_access","date_updated":"2021-05-14T11:56:48Z","content_type":"application/x-zip-compressed","date_created":"2021-05-14T11:56:48Z","creator":"mvalenti","relation":"main_file","checksum":"1e61a7e63949448a8db0091cdac23570","file_id":"9391"}],"article_processing_charge":"No","citation":{"ista":"Valentini M. 2021. Research data for ‘Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:9389\">10.15479/AT:ISTA:9389</a>.","ieee":"M. Valentini, “Research data for ‘Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.’” Institute of Science and Technology Austria, 2021.","apa":"Valentini, M. (2021). Research data for “Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9389\">https://doi.org/10.15479/AT:ISTA:9389</a>","mla":"Valentini, Marco. <i>Research Data for “Non-Topological Zero Bias Peaks in Full-Shell Nanowires Induced by Flux Tunable Andreev States.”</i> Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9389\">10.15479/AT:ISTA:9389</a>.","short":"M. Valentini, (2021).","ama":"Valentini M. Research data for “Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.” 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9389\">10.15479/AT:ISTA:9389</a>","chicago":"Valentini, Marco. “Research Data for ‘Non-Topological Zero Bias Peaks in Full-Shell Nanowires Induced by Flux Tunable Andreev States.’” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9389\">https://doi.org/10.15479/AT:ISTA:9389</a>."},"status":"public","type":"research_data","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png"},"title":"Research data for \"Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states\"","_id":"9389","date_created":"2021-05-14T12:07:53Z","doi":"10.15479/AT:ISTA:9389","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"contributor":[{"last_name":"Valentini","first_name":"Marco","contributor_type":"contact_person","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425"}],"file_date_updated":"2021-05-14T11:56:48Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"This .zip File contains the transport data for  \"Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states\" by M. Valentini, et. al.  \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format.\r\nInstructions of how to read the data are in \"Notebook_Valentini.pdf\"."}],"date_published":"2021-01-01T00:00:00Z","author":[{"last_name":"Valentini","first_name":"Marco","full_name":"Valentini, Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"used_in_publication","id":"8910","status":"public"}]},"year":"2021","oa_version":"Published Version","date_updated":"2024-02-21T12:40:09Z","ddc":["530"],"oa":1},{"external_id":{"isi":["000654741200004"],"pmid":["33974865"]},"doi":"10.1016/j.cub.2021.03.060","intvolume":"        31","_id":"9392","page":"R428-R429","quality_controlled":"1","acknowledgement":"We thank Christopher Cooney, Martin Garlovsky, Anja M. Westram, Carina Baskett, Stefanie Belohlavy, Michal Hledik, Arka Pal, Nicholas H. Barton, Roger K. Butlin and members of the University of Sheffield Speciation Journal Club for feedback on draft survey questions and/or comments on a draft manuscript. Three anonymous reviewers gave thoughtful feedback that improved the manuscript. We thank Ahmad Nadeem, who was paid to build the Shiny app. We are especially grateful to everyone who took part in the survey. Ethical approval for the survey was obtained through the University of Sheffield Ethics Review Procedure (Application 029768). S.S. was supported by a NERC grant awarded to Roger K. Butlin.","department":[{"_id":"NiBa"}],"citation":{"ieee":"S. Stankowski and M. Ravinet, “Quantifying the use of species concepts,” <i>Current Biology</i>, vol. 31, no. 9. Cell Press, pp. R428–R429, 2021.","ista":"Stankowski S, Ravinet M. 2021. Quantifying the use of species concepts. Current Biology. 31(9), R428–R429.","mla":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” <i>Current Biology</i>, vol. 31, no. 9, Cell Press, 2021, pp. R428–29, doi:<a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">10.1016/j.cub.2021.03.060</a>.","apa":"Stankowski, S., &#38; Ravinet, M. (2021). Quantifying the use of species concepts. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">https://doi.org/10.1016/j.cub.2021.03.060</a>","chicago":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” <i>Current Biology</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">https://doi.org/10.1016/j.cub.2021.03.060</a>.","ama":"Stankowski S, Ravinet M. Quantifying the use of species concepts. <i>Current Biology</i>. 2021;31(9):R428-R429. doi:<a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">10.1016/j.cub.2021.03.060</a>","short":"S. Stankowski, M. Ravinet, Current Biology 31 (2021) R428–R429."},"article_processing_charge":"No","isi":1,"title":"Quantifying the use of species concepts","type":"journal_article","status":"public","oa_version":"Published Version","month":"05","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publication_status":"published","publication_identifier":{"eissn":["18790445"],"issn":["09609822"]},"date_updated":"2023-08-08T13:34:38Z","article_type":"original","date_created":"2021-05-16T22:01:46Z","main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2021.03.060","open_access":"1"}],"pmid":1,"publisher":"Cell Press","scopus_import":"1","publication":"Current Biology","language":[{"iso":"eng"}],"year":"2021","day":"10","issue":"9","author":[{"id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean"},{"full_name":"Ravinet, Mark","first_name":"Mark","last_name":"Ravinet"}],"date_published":"2021-05-10T00:00:00Z","abstract":[{"text":"Humans conceptualize the diversity of life by classifying individuals into types we call ‘species’1. The species we recognize influence political and financial decisions and guide our understanding of how units of diversity evolve and interact. Although the idea of species may seem intuitive, a debate about the best way to define them has raged even before Darwin2. So much energy has been devoted to the so-called ‘species problem’ that no amount of discourse will ever likely solve it2,3. Dozens of species concepts are currently recognized3, but we lack a concrete understanding of how much researchers actually disagree and the factors that cause them to think differently1,2. To address this, we used a survey to quantify the species problem for the first time. The results indicate that the disagreement is extensive: two randomly chosen respondents will most likely disagree on the nature of species. The probability of disagreement is not predicted by researcher experience or broad study system, but tended to be lower among researchers with similar focus, training and who study the same organism. Should we see this diversity of perspectives as a problem? We argue that we should not.","lang":"eng"}],"volume":31},{"arxiv":1,"publication_identifier":{"issn":["0925-9856"],"eissn":["1572-8102"]},"date_updated":"2023-10-10T11:13:20Z","publication_status":"published","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","oa_version":"Preprint","status":"public","type":"journal_article","title":"Faster algorithms for quantitative verification in bounded treewidth graphs","isi":1,"article_processing_charge":"No","citation":{"ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2021. Faster algorithms for quantitative verification in bounded treewidth graphs. Formal Methods in System Design. 57, 401–428.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for quantitative verification in bounded treewidth graphs,” <i>Formal Methods in System Design</i>, vol. 57. Springer, pp. 401–428, 2021.","apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2021). Faster algorithms for quantitative verification in bounded treewidth graphs. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-021-00373-5\">https://doi.org/10.1007/s10703-021-00373-5</a>","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Quantitative Verification in Bounded Treewidth Graphs.” <i>Formal Methods in System Design</i>, vol. 57, Springer, 2021, pp. 401–28, doi:<a href=\"https://doi.org/10.1007/s10703-021-00373-5\">10.1007/s10703-021-00373-5</a>.","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for quantitative verification in bounded treewidth graphs. <i>Formal Methods in System Design</i>. 2021;57:401-428. doi:<a href=\"https://doi.org/10.1007/s10703-021-00373-5\">10.1007/s10703-021-00373-5</a>","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Formal Methods in System Design 57 (2021) 401–428.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Faster Algorithms for Quantitative Verification in Bounded Treewidth Graphs.” <i>Formal Methods in System Design</i>. Springer, 2021. <a href=\"https://doi.org/10.1007/s10703-021-00373-5\">https://doi.org/10.1007/s10703-021-00373-5</a>."},"department":[{"_id":"KrCh"}],"quality_controlled":"1","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start Grant (279307: Graph Games), and Microsoft faculty fellows award.","intvolume":"        57","_id":"9393","page":"401-428","external_id":{"isi":["000645490300001"],"arxiv":["1504.07384"]},"doi":"10.1007/s10703-021-00373-5","date_published":"2021-09-01T00:00:00Z","abstract":[{"lang":"eng","text":"We consider the core algorithmic problems related to verification of systems with respect to three classical quantitative properties, namely, the mean-payoff, the ratio, and the minimum initial credit for energy property. The algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with bounded treewidth—a class that contains the control flow graphs of most programs. Let n denote the number of nodes of a graph, m the number of edges (for bounded treewidth 𝑚=𝑂(𝑛)) and W the largest absolute value of the weights. Our main theoretical results are as follows. First, for the minimum initial credit problem we show that (1) for general graphs the problem can be solved in 𝑂(𝑛2⋅𝑚) time and the associated decision problem in 𝑂(𝑛⋅𝑚) time, improving the previous known 𝑂(𝑛3⋅𝑚⋅log(𝑛⋅𝑊)) and 𝑂(𝑛2⋅𝑚) bounds, respectively; and (2) for bounded treewidth graphs we present an algorithm that requires 𝑂(𝑛⋅log𝑛) time. Second, for bounded treewidth graphs we present an algorithm that approximates the mean-payoff value within a factor of 1+𝜖 in time 𝑂(𝑛⋅log(𝑛/𝜖)) as compared to the classical exact algorithms on general graphs that require quadratic time. Third, for the ratio property we present an algorithm that for bounded treewidth graphs works in time 𝑂(𝑛⋅log(|𝑎⋅𝑏|))=𝑂(𝑛⋅log(𝑛⋅𝑊)), when the output is 𝑎𝑏, as compared to the previously best known algorithm on general graphs with running time 𝑂(𝑛2⋅log(𝑛⋅𝑊)). We have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks."}],"volume":57,"author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis"}],"ec_funded":1,"language":[{"iso":"eng"}],"year":"2021","day":"01","publication":"Formal Methods in System Design","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1504.07384","open_access":"1"}],"publisher":"Springer","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"},{"grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"article_type":"original","date_created":"2021-05-16T22:01:47Z"},{"file_date_updated":"2021-10-15T08:26:02Z","issue":"3","author":[{"full_name":"Koch, Eva L.","last_name":"Koch","first_name":"Eva L."},{"first_name":"Hernán E.","last_name":"Morales","full_name":"Morales, Hernán E."},{"full_name":"Larsson, Jenny","first_name":"Jenny","last_name":"Larsson"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","first_name":"Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"full_name":"Lemmon, Alan R.","last_name":"Lemmon","first_name":"Alan R."},{"first_name":"E. Moriarty","last_name":"Lemmon","full_name":"Lemmon, E. Moriarty"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"date_published":"2021-05-07T00:00:00Z","abstract":[{"text":"Chromosomal inversions have long been recognized for their role in local adaptation. By suppressing recombination in heterozygous individuals, they can maintain coadapted gene complexes and protect them from homogenizing effects of gene flow. However, to fully understand their importance for local adaptation we need to know their influence on phenotypes under divergent selection. For this, the marine snail Littorina saxatilis provides an ideal study system. Divergent ecotypes adapted to wave action and crab predation occur in close proximity on intertidal shores with gene flow between them. Here, we used F2 individuals obtained from crosses between the ecotypes to test for associations between genomic regions and traits distinguishing the Crab‐/Wave‐adapted ecotypes including size, shape, shell thickness, and behavior. We show that most of these traits are influenced by two previously detected inversion regions that are divergent between ecotypes. We thus gain a better understanding of one important underlying mechanism responsible for the rapid and repeated formation of ecotypes: divergent selection acting on inversions. We also found that some inversions contributed to more than one trait suggesting that they may contain several loci involved in adaptation, consistent with the hypothesis that suppression of recombination within inversions facilitates differentiation in the presence of gene flow.","lang":"eng"}],"volume":5,"publication":"Evolution Letters","language":[{"iso":"eng"}],"year":"2021","day":"07","ec_funded":1,"publisher":"Wiley","file":[{"success":1,"file_id":"10142","relation":"main_file","checksum":"023b1608e311f0fda30593ba3d0a4e0b","creator":"cchlebak","date_created":"2021-10-15T08:26:02Z","content_type":"application/pdf","date_updated":"2021-10-15T08:26:02Z","access_level":"open_access","file_size":3021108,"file_name":"2021_EvolutionLetters_Koch.pdf"}],"scopus_import":"1","article_type":"original","date_created":"2021-05-16T22:01:47Z","project":[{"name":"Theoretical and empirical approaches to understanding Parallel Adaptation","_id":"265B41B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"797747"}],"has_accepted_license":"1","oa_version":"Published Version","month":"05","related_material":{"record":[{"status":"public","relation":"research_data","id":"12987"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publication_status":"published","publication_identifier":{"eissn":["2056-3744"]},"ddc":["570"],"date_updated":"2023-08-08T13:34:08Z","article_processing_charge":"No","citation":{"ista":"Koch EL, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. 5(3), 196–213.","ieee":"E. L. Koch <i>et al.</i>, “Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis,” <i>Evolution Letters</i>, vol. 5, no. 3. Wiley, pp. 196–213, 2021.","apa":"Koch, E. L., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. <i>Evolution Letters</i>. Wiley. <a href=\"https://doi.org/10.1002/evl3.227\">https://doi.org/10.1002/evl3.227</a>","mla":"Koch, Eva L., et al. “Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” <i>Evolution Letters</i>, vol. 5, no. 3, Wiley, 2021, pp. 196–213, doi:<a href=\"https://doi.org/10.1002/evl3.227\">10.1002/evl3.227</a>.","chicago":"Koch, Eva L., Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” <i>Evolution Letters</i>. Wiley, 2021. <a href=\"https://doi.org/10.1002/evl3.227\">https://doi.org/10.1002/evl3.227</a>.","ama":"Koch EL, Morales HE, Larsson J, et al. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. <i>Evolution Letters</i>. 2021;5(3):196-213. doi:<a href=\"https://doi.org/10.1002/evl3.227\">10.1002/evl3.227</a>","short":"E.L. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, Evolution Letters 5 (2021) 196–213."},"isi":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)"},"title":"Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","status":"public","type":"journal_article","external_id":{"isi":["000647846200001"]},"doi":"10.1002/evl3.227","intvolume":"         5","page":"196-213","_id":"9394","quality_controlled":"1","acknowledgement":"We are very grateful to Irena Senčić for technical assistance and to Michelle Kortyna and Sean Holland at the Center for Anchored Phylogenomics for assistance with data collection. RKB was funded by the Natural Environment Research Council and by the European Research Council. KJ was funded by the Swedish Research Councils VR and Formas (Linnaeus Grant: 217‐2008‐1719). JL was funded by a studentship from the Leverhulme Centre for Advanced Biological Modelling. AMW was funded by the European Union's Horizon 2020 research and innovation program under Marie Skłodowska‐Curie Grant agreement no. 797747. RF was funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska‐Curie Grant agreement No. 706376 and by FEDER Funds through the Operational Competitiveness Factors Program—COMPETE and by National Funds through FCT—Foundation for Science and Technology within the scope of the project “Hybrabbid” (PTDC/BIA‐EVL/30628/2017‐ POCI‐01‐0145‐FEDER‐030628). We are grateful to other members of the Littorina research group for helpful discussions. We thank Claire Mérot and an anonymous referee for insightful comments on an earlier version. ","department":[{"_id":"NiBa"}]},{"date_published":"2021-05-18T00:00:00Z","abstract":[{"lang":"eng","text":"Accumulation of interstitial fluid (IF) between embryonic cells is a common phenomenon in vertebrate embryogenesis. Unlike other model systems, where these accumulations coalesce into a large central cavity – the blastocoel, in zebrafish, IF is more uniformly distributed between the deep cells (DC) before the onset of gastrulation. This is likely due to the presence of a large extraembryonic structure – the yolk cell (YC) at the position where the blastocoel typically forms in other model organisms. IF has long been speculated to play a role in tissue morphogenesis during embryogenesis, but direct evidence supporting such function is still sparse. Here we show that the relocalization of IF to the interface between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion formation and migration along this interface, a key process in embryonic axis formation. We further demonstrate that axial ME cell migration and IF relocalization engage in a positive feedback loop, where axial ME migration triggers IF accumulation ahead of the advancing axial ME tissue by mechanically compressing the overlying epiblast cell layer. Upon compression, locally induced flow relocalizes the IF through the porous epiblast tissue resulting in an IF accumulation ahead of the leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation and migration of the leading axial ME cells, thereby facilitating axial ME extension. Our findings reveal a central role of dynamic IF relocalization in orchestrating germ layer morphogenesis during gastrulation."}],"author":[{"last_name":"Huljev","first_name":"Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","full_name":"Huljev, Karla"}],"file_date_updated":"2022-05-21T22:30:04Z","language":[{"iso":"eng"}],"year":"2021","day":"18","supervisor":[{"first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"file":[{"checksum":"7f98532f5324a0b2f3fa8de2967baa19","relation":"source_file","date_created":"2021-05-17T12:29:12Z","creator":"khuljev","file_id":"9398","file_size":47799741,"access_level":"closed","file_name":"KHuljev_Thesis_corrections.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_updated":"2022-05-21T22:30:04Z"},{"file_id":"9401","creator":"khuljev","date_created":"2021-05-18T14:50:28Z","checksum":"bf512f8a1e572a543778fc4b227c01ba","relation":"main_file","date_updated":"2022-05-21T22:30:04Z","content_type":"application/pdf","file_name":"new_KHuljev_Thesis_corrections.pdf","file_size":16542131,"access_level":"open_access","embargo":"2022-05-20"}],"publisher":"Institute of Science and Technology Austria","date_created":"2021-05-17T12:31:30Z","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"ddc":["571"],"date_updated":"2023-09-07T13:32:32Z","oa":1,"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"05","oa_version":"Published Version","type":"dissertation","status":"public","title":"Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation","article_processing_charge":"No","citation":{"short":"K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute of Science and Technology Austria, 2021.","ama":"Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9397\">10.15479/at:ista:9397</a>","chicago":"Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9397\">https://doi.org/10.15479/at:ista:9397</a>.","apa":"Huljev, K. (2021). <i>Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9397\">https://doi.org/10.15479/at:ista:9397</a>","mla":"Huljev, Karla. <i>Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9397\">10.15479/at:ista:9397</a>.","ista":"Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria.","ieee":"K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation,” Institute of Science and Technology Austria, 2021."},"department":[{"_id":"CaHe"},{"_id":"GradSch"}],"degree_awarded":"PhD","_id":"9397","page":"101","doi":"10.15479/at:ista:9397"}]