[{"author":[{"full_name":"Gundert, Anna","first_name":"Anna","last_name":"Gundert"},{"first_name":"Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:49:36Z","quality_controlled":"1","department":[{"_id":"UlWa"}],"oa_version":"Preprint","citation":{"short":"A. Gundert, U. Wagner, Israel Journal of Mathematics 216 (2016) 545–582.","mla":"Gundert, Anna, and Uli Wagner. “On Eigenvalues of Random Complexes.” <i>Israel Journal of Mathematics</i>, vol. 216, no. 2, Springer, 2016, pp. 545–82, doi:<a href=\"https://doi.org/10.1007/s11856-016-1419-1\">10.1007/s11856-016-1419-1</a>.","apa":"Gundert, A., &#38; Wagner, U. (2016). On eigenvalues of random complexes. <i>Israel Journal of Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s11856-016-1419-1\">https://doi.org/10.1007/s11856-016-1419-1</a>","ista":"Gundert A, Wagner U. 2016. On eigenvalues of random complexes. Israel Journal of Mathematics. 216(2), 545–582.","chicago":"Gundert, Anna, and Uli Wagner. “On Eigenvalues of Random Complexes.” <i>Israel Journal of Mathematics</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s11856-016-1419-1\">https://doi.org/10.1007/s11856-016-1419-1</a>.","ama":"Gundert A, Wagner U. On eigenvalues of random complexes. <i>Israel Journal of Mathematics</i>. 2016;216(2):545-582. doi:<a href=\"https://doi.org/10.1007/s11856-016-1419-1\">10.1007/s11856-016-1419-1</a>","ieee":"A. Gundert and U. Wagner, “On eigenvalues of random complexes,” <i>Israel Journal of Mathematics</i>, vol. 216, no. 2. Springer, pp. 545–582, 2016."},"date_published":"2016-10-01T00:00:00Z","language":[{"iso":"eng"}],"publisher":"Springer","volume":216,"title":"On eigenvalues of random complexes","abstract":[{"lang":"eng","text":"We consider higher-dimensional generalizations of the normalized Laplacian and the adjacency matrix of graphs and study their eigenvalues for the Linial–Meshulam model Xk(n, p) of random k-dimensional simplicial complexes on n vertices. We show that for p = Ω(logn/n), the eigenvalues of each of the matrices are a.a.s. concentrated around two values. The main tool, which goes back to the work of Garland, are arguments that relate the eigenvalues of these matrices to those of graphs that arise as links of (k - 2)-dimensional faces. Garland’s result concerns the Laplacian; we develop an analogous result for the adjacency matrix. The same arguments apply to other models of random complexes which allow for dependencies between the choices of k-dimensional simplices. In the second part of the paper, we apply this to the question of possible higher-dimensional analogues of the discrete Cheeger inequality, which in the classical case of graphs relates the eigenvalues of a graph and its edge expansion. It is very natural to ask whether this generalizes to higher dimensions and, in particular, whether the eigenvalues of the higher-dimensional Laplacian capture the notion of coboundary expansion—a higher-dimensional generalization of edge expansion that arose in recent work of Linial and Meshulam and of Gromov; this question was raised, for instance, by Dotterrer and Kahle. We show that this most straightforward version of a higher-dimensional discrete Cheeger inequality fails, in quite a strong way: For every k ≥ 2 and n ∈ N, there is a k-dimensional complex Yn k on n vertices that has strong spectral expansion properties (all nontrivial eigenvalues of the normalised k-dimensional Laplacian lie in the interval [1−O(1/√1), 1+0(1/√1]) but whose coboundary expansion is bounded from above by O(log n/n) and so tends to zero as n → ∞; moreover, Yn k can be taken to have vanishing integer homology in dimension less than k."}],"publication_status":"published","month":"10","issue":"2","status":"public","day":"01","page":"545 - 582","year":"2016","doi":"10.1007/s11856-016-1419-1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1411.4906"}],"date_created":"2018-12-11T11:51:07Z","oa":1,"_id":"1282","type":"journal_article","intvolume":"       216","publist_id":"6034","publication":"Israel Journal of Mathematics","scopus_import":1},{"issue":"10","file":[{"creator":"system","checksum":"4d569977fad7a7f22b7e3424003d2ab1","file_id":"4679","file_size":229094,"access_level":"local","relation":"main_file","file_name":"IST-2018-1018-v1+1_Zhu_and_Benkova_TIPS_2016.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:08:19Z"}],"has_accepted_license":"1","month":"10","volume":21,"language":[{"iso":"eng"}],"oa_version":"Submitted Version","quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Hormone cross-talk drives nutrient dependent plant development","grant_number":"I 1774-B16","_id":"2542D156-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Zhu","first_name":"Qiang","id":"40A4B9E6-F248-11E8-B48F-1D18A9856A87","full_name":"Zhu, Qiang"},{"last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"}],"pubrep_id":"1018","_id":"1283","type":"journal_article","article_type":"original","date_created":"2018-12-11T11:51:08Z","status":"public","ddc":["575"],"abstract":[{"lang":"eng","text":"The impact of the plant hormone ethylene on seedling development has long been recognized; however, its ecophysiological relevance is unexplored. Three recent studies demonstrate that ethylene is a critical endogenous integrator of various environmental signals including mechanical stress, light, and oxygen availability during seedling germination and growth through the soil."}],"publication_status":"published","title":"Seedlings’ strategy to overcome a soil barrier","publisher":"Cell Press","date_published":"2016-10-01T00:00:00Z","file_date_updated":"2020-07-14T12:44:42Z","citation":{"ieee":"Q. Zhu and E. Benková, “Seedlings’ strategy to overcome a soil barrier,” <i>Trends in Plant Science</i>, vol. 21, no. 10. Cell Press, pp. 809–811, 2016.","ama":"Zhu Q, Benková E. Seedlings’ strategy to overcome a soil barrier. <i>Trends in Plant Science</i>. 2016;21(10):809-811. doi:<a href=\"https://doi.org/10.1016/j.tplants.2016.08.003\">10.1016/j.tplants.2016.08.003</a>","chicago":"Zhu, Qiang, and Eva Benková. “Seedlings’ Strategy to Overcome a Soil Barrier.” <i>Trends in Plant Science</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.tplants.2016.08.003\">https://doi.org/10.1016/j.tplants.2016.08.003</a>.","ista":"Zhu Q, Benková E. 2016. Seedlings’ strategy to overcome a soil barrier. Trends in Plant Science. 21(10), 809–811.","apa":"Zhu, Q., &#38; Benková, E. (2016). Seedlings’ strategy to overcome a soil barrier. <i>Trends in Plant Science</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tplants.2016.08.003\">https://doi.org/10.1016/j.tplants.2016.08.003</a>","mla":"Zhu, Qiang, and Eva Benková. “Seedlings’ Strategy to Overcome a Soil Barrier.” <i>Trends in Plant Science</i>, vol. 21, no. 10, Cell Press, 2016, pp. 809–11, doi:<a href=\"https://doi.org/10.1016/j.tplants.2016.08.003\">10.1016/j.tplants.2016.08.003</a>.","short":"Q. Zhu, E. Benková, Trends in Plant Science 21 (2016) 809–811."},"date_updated":"2021-01-12T06:49:36Z","department":[{"_id":"EvBe"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"publication":"Trends in Plant Science","intvolume":"        21","publist_id":"6033","day":"01","year":"2016","page":"809 - 811","doi":"10.1016/j.tplants.2016.08.003","acknowledgement":"This work was supported by the Austrian Science Fund (FWF01_I1774S) to E.B., the Natural Science Foundation of Fujian Province (2016J01099), and the Fujian–Taiwan Joint Innovative Center for Germplasm Resources and Cultivation of Crops (FJ 2011 Program, No 2015-75) to Q.Z. The\r\nauthors\r\nthank\r\nIsrael\r\nAusin\r\nand\r\nXu\r\nChen\r\nfor\r\ncritical\r\nreading\r\nof\r\nthe\r\nmanuscript."},{"date_updated":"2021-01-12T06:49:37Z","project":[{"call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"},{"grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF"}],"quality_controlled":"1","department":[{"_id":"MiSi"}],"citation":{"ieee":"E. Paluch, I. Aspalter, and M. K. Sixt, “Focal adhesion-independent cell migration,” <i>Annual Review of Cell and Developmental Biology</i>, vol. 32. Annual Reviews, pp. 469–490, 2016.","ista":"Paluch E, Aspalter I, Sixt MK. 2016. Focal adhesion-independent cell migration. Annual Review of Cell and Developmental Biology. 32, 469–490.","chicago":"Paluch, Ewa, Irene Aspalter, and Michael K Sixt. “Focal Adhesion-Independent Cell Migration.” <i>Annual Review of Cell and Developmental Biology</i>. Annual Reviews, 2016. <a href=\"https://doi.org/10.1146/annurev-cellbio-111315-125341\">https://doi.org/10.1146/annurev-cellbio-111315-125341</a>.","ama":"Paluch E, Aspalter I, Sixt MK. Focal adhesion-independent cell migration. <i>Annual Review of Cell and Developmental Biology</i>. 2016;32:469-490. doi:<a href=\"https://doi.org/10.1146/annurev-cellbio-111315-125341\">10.1146/annurev-cellbio-111315-125341</a>","apa":"Paluch, E., Aspalter, I., &#38; Sixt, M. K. (2016). Focal adhesion-independent cell migration. <i>Annual Review of Cell and Developmental Biology</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-cellbio-111315-125341\">https://doi.org/10.1146/annurev-cellbio-111315-125341</a>","mla":"Paluch, Ewa, et al. “Focal Adhesion-Independent Cell Migration.” <i>Annual Review of Cell and Developmental Biology</i>, vol. 32, Annual Reviews, 2016, pp. 469–90, doi:<a href=\"https://doi.org/10.1146/annurev-cellbio-111315-125341\">10.1146/annurev-cellbio-111315-125341</a>.","short":"E. Paluch, I. Aspalter, M.K. Sixt, Annual Review of Cell and Developmental Biology 32 (2016) 469–490."},"oa_version":"None","author":[{"last_name":"Paluch","first_name":"Ewa","full_name":"Paluch, Ewa"},{"last_name":"Aspalter","first_name":"Irene","full_name":"Aspalter, Irene"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Cell migration is central to a multitude of physiological processes, including embryonic development, immune surveillance, and wound healing, and deregulated migration is key to cancer dissemination. Decades of investigations have uncovered many of the molecular and physical mechanisms underlying cell migration. Together with protrusion extension and cell body retraction, adhesion to the substrate via specific focal adhesion points has long been considered an essential step in cell migration. Although this is true for cells moving on two-dimensional substrates, recent studies have demonstrated that focal adhesions are not required for cells moving in three dimensions, in which confinement is sufficient to maintain a cell in contact with its substrate. Here, we review the investigations that have led to challenging the requirement of specific adhesions for migration, discuss the physical mechanisms proposed for cell body translocation during focal adhesion-independent migration, and highlight the remaining open questions for the future."}],"month":"10","publication_status":"published","language":[{"iso":"eng"}],"publisher":"Annual Reviews","date_published":"2016-10-06T00:00:00Z","title":"Focal adhesion-independent cell migration","volume":32,"date_created":"2018-12-11T11:51:08Z","_id":"1285","type":"journal_article","acknowledgement":"We would like to thank Dani Bodor for critical comments on the manuscript and Guillaume Salbreux for discussions. The authors are supported by the United Kingdom's Medical Research Council (MRC) (E.K.P. and I.M.A.; core funding to the MRC Laboratory for Molecular Cell Biology), by the European Research Council [ERC GA 311637 (E.K.P.) and ERC GA 281556 (M.S.)], and by a START award from the Austrian Science Foundation (M.S.).","status":"public","page":"469 - 490","year":"2016","day":"06","doi":"10.1146/annurev-cellbio-111315-125341","scopus_import":1,"ec_funded":1,"intvolume":"        32","publist_id":"6031","publication":"Annual Review of Cell and Developmental Biology"},{"author":[{"last_name":"Midya","first_name":"Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87","full_name":"Midya, Bikashkali"},{"full_name":"Tomza, Michał","first_name":"Michał","last_name":"Tomza"},{"full_name":"Schmidt, Richard","first_name":"Richard","last_name":"Schmidt"},{"first_name":"Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"}],"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa_version":"Preprint","language":[{"iso":"eng"}],"volume":94,"month":"10","issue":"4","article_number":"041601","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1607.06092"}],"status":"public","date_created":"2018-12-11T11:51:09Z","_id":"1286","type":"journal_article","ec_funded":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:49:37Z","department":[{"_id":"MiLe"}],"citation":{"mla":"Midya, Bikashkali, et al. “Rotation of Cold Molecular Ions inside a Bose-Einstein Condensate.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 94, no. 4, 041601, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevA.94.041601\">10.1103/PhysRevA.94.041601</a>.","short":"B. Midya, M. Tomza, R. Schmidt, M. Lemeshko, Physical Review A - Atomic, Molecular, and Optical Physics 94 (2016).","ieee":"B. Midya, M. Tomza, R. Schmidt, and M. Lemeshko, “Rotation of cold molecular ions inside a Bose-Einstein condensate,” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 94, no. 4. American Physical Society, 2016.","apa":"Midya, B., Tomza, M., Schmidt, R., &#38; Lemeshko, M. (2016). Rotation of cold molecular ions inside a Bose-Einstein condensate. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.94.041601\">https://doi.org/10.1103/PhysRevA.94.041601</a>","chicago":"Midya, Bikashkali, Michał Tomza, Richard Schmidt, and Mikhail Lemeshko. “Rotation of Cold Molecular Ions inside a Bose-Einstein Condensate.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevA.94.041601\">https://doi.org/10.1103/PhysRevA.94.041601</a>.","ama":"Midya B, Tomza M, Schmidt R, Lemeshko M. Rotation of cold molecular ions inside a Bose-Einstein condensate. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2016;94(4). doi:<a href=\"https://doi.org/10.1103/PhysRevA.94.041601\">10.1103/PhysRevA.94.041601</a>","ista":"Midya B, Tomza M, Schmidt R, Lemeshko M. 2016. Rotation of cold molecular ions inside a Bose-Einstein condensate. Physical Review A - Atomic, Molecular, and Optical Physics. 94(4), 041601."},"date_published":"2016-10-13T00:00:00Z","publisher":"American Physical Society","title":"Rotation of cold molecular ions inside a Bose-Einstein condensate","abstract":[{"lang":"eng","text":"We use recently developed angulon theory [R. Schmidt and M. Lemeshko, Phys. Rev. Lett. 114, 203001 (2015)PRLTAO0031-900710.1103/PhysRevLett.114.203001] to study the rotational spectrum of a cyanide molecular anion immersed into Bose-Einstein condensates of rubidium and strontium. Based on ab initio potential energy surfaces, we provide a detailed study of the rotational Lamb shift and many-body-induced fine structure which arise due to dressing of molecular rotation by a field of phonon excitations. We demonstrate that the magnitude of these effects is large enough in order to be observed in modern experiments on cold molecular ions. Furthermore, we introduce a novel method to construct pseudopotentials starting from the ab initio potential energy surfaces, which provides a means to obtain effective coupling constants for low-energy polaron models."}],"publication_status":"published","acknowledgement":"The work was supported by the NSF through a grant for the Institute for Theoretical Atomic, Molecular, and Optical Physics at Harvard University and the Smithsonian Astrophysical Observatory. B.M. acknowledges financial support received from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. 291734. M.T. acknowledges support from the EU Marie Curie COFUND action (ICFOnest), the EU Grants ERC AdG OSYRIS, FP7 SIQS and EQuaM, FETPROACT QUIC, the Spanish Ministry Grants FOQUS (FIS2013-46768-P) and Severo Ochoa (SEV-2015-0522), Generalitat de Catalunya (SGR 874), Fundacio Cellex, the National Science Centre (2015/19/D/ST4/02173), and the PL-Grid Infrastructure.","year":"2016","day":"13","doi":"10.1103/PhysRevA.94.041601","oa":1,"intvolume":"        94","publist_id":"6030","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","scopus_import":1},{"month":"10","issue":"20","language":[{"iso":"eng"}],"volume":41,"article_processing_charge":"No","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"quality_controlled":"1","oa_version":"Preprint","author":[{"full_name":"Midya, Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87","first_name":"Bikashkali","last_name":"Midya"},{"full_name":"Konotop, Vladimir","last_name":"Konotop","first_name":"Vladimir"}],"ec_funded":1,"date_created":"2018-12-11T11:51:09Z","type":"journal_article","_id":"1287","status":"public","main_file_link":[{"url":"https://arxiv.org/abs/1609.02863","open_access":"1"}],"publication_status":"published","abstract":[{"lang":"eng","text":"A planar waveguide with an impedance boundary, composed of nonperfect metallic plates, and with passive or active dielectric filling, is considered. We show the possibility of selective mode guiding and amplification when a homogeneous pump is added to the dielectric and analyze differences in TE and TM mode propagation. Such a non-conservative system is also shown to feature exceptional points for specific and experimentally tunable parameters, which are described for a particular case of transparent dielectric."}],"publisher":"Optica Publishing Group","date_published":"2016-10-15T00:00:00Z","title":"Modes and exceptional points in waveguides with impedance boundary conditions","department":[{"_id":"MiLe"}],"date_updated":"2023-10-17T12:16:24Z","citation":{"short":"B. Midya, V. Konotop, Optics Letters 41 (2016) 4621–4624.","mla":"Midya, Bikashkali, and Vladimir Konotop. “Modes and Exceptional Points in Waveguides with Impedance Boundary Conditions.” <i>Optics Letters</i>, vol. 41, no. 20, Optica Publishing Group, 2016, pp. 4621–24, doi:<a href=\"https://doi.org/10.1364/OL.41.004621\">10.1364/OL.41.004621</a>.","ieee":"B. Midya and V. Konotop, “Modes and exceptional points in waveguides with impedance boundary conditions,” <i>Optics Letters</i>, vol. 41, no. 20. Optica Publishing Group, pp. 4621–4624, 2016.","apa":"Midya, B., &#38; Konotop, V. (2016). Modes and exceptional points in waveguides with impedance boundary conditions. <i>Optics Letters</i>. Optica Publishing Group. <a href=\"https://doi.org/10.1364/OL.41.004621\">https://doi.org/10.1364/OL.41.004621</a>","ista":"Midya B, Konotop V. 2016. Modes and exceptional points in waveguides with impedance boundary conditions. Optics Letters. 41(20), 4621–4624.","ama":"Midya B, Konotop V. Modes and exceptional points in waveguides with impedance boundary conditions. <i>Optics Letters</i>. 2016;41(20):4621-4624. doi:<a href=\"https://doi.org/10.1364/OL.41.004621\">10.1364/OL.41.004621</a>","chicago":"Midya, Bikashkali, and Vladimir Konotop. “Modes and Exceptional Points in Waveguides with Impedance Boundary Conditions.” <i>Optics Letters</i>. Optica Publishing Group, 2016. <a href=\"https://doi.org/10.1364/OL.41.004621\">https://doi.org/10.1364/OL.41.004621</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","publist_id":"6029","intvolume":"        41","publication":"Optics Letters","oa":1,"acknowledgement":"The research of B.M. is supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant No. [291734].","year":"2016","day":"15","doi":"10.1364/OL.41.004621","page":"4621 - 4624"},{"publication":"Biochimica et Biophysica Acta - Bioenergetics","publist_id":"6028","intvolume":"      1857","scopus_import":1,"status":"public","doi":"10.1016/j.bbabio.2016.08.008","page":"1777 - 1785","year":"2016","day":"01","acknowledgement":"This work was funded by the UK Medical Research Council.","type":"journal_article","_id":"1288","date_created":"2018-12-11T11:51:09Z","volume":1857,"title":"Reversible FMN dissociation from Escherichia coli respiratory complex I","language":[{"iso":"eng"}],"publisher":"Elsevier","date_published":"2016-11-01T00:00:00Z","issue":"11","month":"11","publication_status":"published","abstract":[{"text":"Respiratory complex I transfers electrons from NADH to quinone, utilizing the reaction energy to translocate protons across the membrane. It is a key enzyme of the respiratory chain of many prokaryotic and most eukaryotic organisms. The reversible NADH oxidation reaction is facilitated in complex I by non-covalently bound flavin mononucleotide (FMN). Here we report that the catalytic activity of E. coli complex I with artificial electron acceptors potassium ferricyanide (FeCy) and hexaamineruthenium (HAR) is significantly inhibited in the enzyme pre-reduced by NADH. Further, we demonstrate that the inhibition is caused by reversible dissociation of FMN. The binding constant (Kd) for FMN increases from the femto- or picomolar range in oxidized complex I to the nanomolar range in the NADH reduced enzyme, with an FMN dissociation time constant of ~ 5 s. The oxidation state of complex I, rather than that of FMN, proved critical to the dissociation. Such dissociation is not observed with the T. thermophilus enzyme and our analysis suggests that the difference may be due to the unusually high redox potential of Fe-S cluster N1a in E. coli. It is possible that the enzyme attenuates ROS production in vivo by releasing FMN under highly reducing conditions.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Peter","last_name":"Holt","full_name":"Holt, Peter"},{"full_name":"Efremov, Rouslan","first_name":"Rouslan","last_name":"Efremov"},{"full_name":"Nakamaru Ogiso, Eiko","first_name":"Eiko","last_name":"Nakamaru Ogiso"},{"last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A"}],"citation":{"mla":"Holt, Peter, et al. “Reversible FMN Dissociation from Escherichia Coli Respiratory Complex I.” <i>Biochimica et Biophysica Acta - Bioenergetics</i>, vol. 1857, no. 11, Elsevier, 2016, pp. 1777–85, doi:<a href=\"https://doi.org/10.1016/j.bbabio.2016.08.008\">10.1016/j.bbabio.2016.08.008</a>.","short":"P. Holt, R. Efremov, E. Nakamaru Ogiso, L.A. Sazanov, Biochimica et Biophysica Acta - Bioenergetics 1857 (2016) 1777–1785.","ista":"Holt P, Efremov R, Nakamaru Ogiso E, Sazanov LA. 2016. Reversible FMN dissociation from Escherichia coli respiratory complex I. Biochimica et Biophysica Acta - Bioenergetics. 1857(11), 1777–1785.","ama":"Holt P, Efremov R, Nakamaru Ogiso E, Sazanov LA. Reversible FMN dissociation from Escherichia coli respiratory complex I. <i>Biochimica et Biophysica Acta - Bioenergetics</i>. 2016;1857(11):1777-1785. doi:<a href=\"https://doi.org/10.1016/j.bbabio.2016.08.008\">10.1016/j.bbabio.2016.08.008</a>","chicago":"Holt, Peter, Rouslan Efremov, Eiko Nakamaru Ogiso, and Leonid A Sazanov. “Reversible FMN Dissociation from Escherichia Coli Respiratory Complex I.” <i>Biochimica et Biophysica Acta - Bioenergetics</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.bbabio.2016.08.008\">https://doi.org/10.1016/j.bbabio.2016.08.008</a>.","apa":"Holt, P., Efremov, R., Nakamaru Ogiso, E., &#38; Sazanov, L. A. (2016). Reversible FMN dissociation from Escherichia coli respiratory complex I. <i>Biochimica et Biophysica Acta - Bioenergetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bbabio.2016.08.008\">https://doi.org/10.1016/j.bbabio.2016.08.008</a>","ieee":"P. Holt, R. Efremov, E. Nakamaru Ogiso, and L. A. Sazanov, “Reversible FMN dissociation from Escherichia coli respiratory complex I,” <i>Biochimica et Biophysica Acta - Bioenergetics</i>, vol. 1857, no. 11. Elsevier, pp. 1777–1785, 2016."},"oa_version":"None","quality_controlled":"1","department":[{"_id":"LeSa"}],"date_updated":"2021-01-12T06:49:38Z"},{"oa":1,"doi":"10.1016/j.patrec.2015.12.012","day":"01","year":"2016","page":"13 - 22","scopus_import":1,"related_material":{"record":[{"status":"public","id":"1568","relation":"earlier_version"}]},"publist_id":"6027","intvolume":"        83","publication":"Pattern Recognition Letters","department":[{"_id":"HeEd"}],"date_updated":"2023-02-23T10:04:40Z","citation":{"ama":"Dunaeva O, Edelsbrunner H, Lukyanov A, et al. The classification of endoscopy images with persistent homology. <i>Pattern Recognition Letters</i>. 2016;83(1):13-22. doi:<a href=\"https://doi.org/10.1016/j.patrec.2015.12.012\">10.1016/j.patrec.2015.12.012</a>","chicago":"Dunaeva, Olga, Herbert Edelsbrunner, Anton Lukyanov, Michael Machin, Daria Malkova, Roman Kuvaev, and Sergey Kashin. “The Classification of Endoscopy Images with Persistent Homology.” <i>Pattern Recognition Letters</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.patrec.2015.12.012\">https://doi.org/10.1016/j.patrec.2015.12.012</a>.","ista":"Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D, Kuvaev R, Kashin S. 2016. The classification of endoscopy images with persistent homology. Pattern Recognition Letters. 83(1), 13–22.","apa":"Dunaeva, O., Edelsbrunner, H., Lukyanov, A., Machin, M., Malkova, D., Kuvaev, R., &#38; Kashin, S. (2016). The classification of endoscopy images with persistent homology. <i>Pattern Recognition Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.patrec.2015.12.012\">https://doi.org/10.1016/j.patrec.2015.12.012</a>","ieee":"O. Dunaeva <i>et al.</i>, “The classification of endoscopy images with persistent homology,” <i>Pattern Recognition Letters</i>, vol. 83, no. 1. Elsevier, pp. 13–22, 2016.","short":"O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, D. Malkova, R. Kuvaev, S. Kashin, Pattern Recognition Letters 83 (2016) 13–22.","mla":"Dunaeva, Olga, et al. “The Classification of Endoscopy Images with Persistent Homology.” <i>Pattern Recognition Letters</i>, vol. 83, no. 1, Elsevier, 2016, pp. 13–22, doi:<a href=\"https://doi.org/10.1016/j.patrec.2015.12.012\">10.1016/j.patrec.2015.12.012</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"text":"Aiming at the automatic diagnosis of tumors using narrow band imaging (NBI) magnifying endoscopic (ME) images of the stomach, we combine methods from image processing, topology, geometry, and machine learning to classify patterns into three classes: oval, tubular and irregular. Training the algorithm on a small number of images of each type, we achieve a high rate of correct classifications. The analysis of the learning algorithm reveals that a handful of geometric and topological features are responsible for the overwhelming majority of decisions.","lang":"eng"}],"ddc":["004","514"],"file_date_updated":"2020-07-14T12:44:42Z","date_published":"2016-11-01T00:00:00Z","publisher":"Elsevier","title":"The classification of endoscopy images with persistent homology","date_created":"2018-12-11T11:51:10Z","type":"journal_article","_id":"1289","status":"public","pubrep_id":"975","quality_controlled":"1","oa_version":"Submitted Version","author":[{"first_name":"Olga","last_name":"Dunaeva","full_name":"Dunaeva, Olga"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert"},{"last_name":"Lukyanov","first_name":"Anton","full_name":"Lukyanov, Anton"},{"full_name":"Machin, Michael","last_name":"Machin","first_name":"Michael"},{"last_name":"Malkova","first_name":"Daria","full_name":"Malkova, Daria"},{"first_name":"Roman","last_name":"Kuvaev","full_name":"Kuvaev, Roman"},{"first_name":"Sergey","last_name":"Kashin","full_name":"Kashin, Sergey"}],"has_accepted_license":"1","month":"11","file":[{"content_type":"application/pdf","date_created":"2019-04-17T07:55:51Z","date_updated":"2020-07-14T12:44:42Z","file_name":"2016-Edelsbrunner_The_classification.pdf","relation":"main_file","checksum":"33458bbb8c32a339e1adeca6d5a1112d","file_id":"6334","creator":"dernst","access_level":"open_access","file_size":1921113}],"issue":"1","language":[{"iso":"eng"}],"volume":83,"article_processing_charge":"No"},{"status":"public","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069154/"}],"_id":"1290","type":"journal_article","date_created":"2018-12-11T11:51:10Z","author":[{"full_name":"Stone, Laura","first_name":"Laura","last_name":"Stone"},{"last_name":"Baym","first_name":"Michael","full_name":"Baym, Michael"},{"first_name":"Tami","last_name":"Lieberman","full_name":"Lieberman, Tami"},{"id":"3464AE84-F248-11E8-B48F-1D18A9856A87","full_name":"Chait, Remy P","last_name":"Chait","first_name":"Remy P","orcid":"0000-0003-0876-3187"},{"full_name":"Clardy, Jon","last_name":"Clardy","first_name":"Jon"},{"last_name":"Kishony","first_name":"Roy","full_name":"Kishony, Roy"}],"oa_version":"Preprint","quality_controlled":"1","volume":12,"language":[{"iso":"eng"}],"issue":"11","month":"11","day":"01","year":"2016","doi":"10.1038/nchembio.2176","page":"902 - 904","acknowledgement":"This work was supported in part by National Institute of Allergy and Infectious Diseases grant U54 AI057159, US National Institutes of Health grants R01 GM081617 (to R.K.) and GM086258 (to J.C.), European Research Council FP7 ERC grant 281891 (to R.K.) and a National Science Foundation Graduate Fellowship (to L.K.S.).\r\n","oa":1,"publication":"Nature Chemical Biology","publist_id":"6026","intvolume":"        12","scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Stone, Laura, et al. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” <i>Nature Chemical Biology</i>, vol. 12, no. 11, Nature Publishing Group, 2016, pp. 902–04, doi:<a href=\"https://doi.org/10.1038/nchembio.2176\">10.1038/nchembio.2176</a>.","short":"L. Stone, M. Baym, T. Lieberman, R.P. Chait, J. Clardy, R. Kishony, Nature Chemical Biology 12 (2016) 902–904.","ieee":"L. Stone, M. Baym, T. Lieberman, R. P. Chait, J. Clardy, and R. Kishony, “Compounds that select against the tetracycline-resistance efflux pump,” <i>Nature Chemical Biology</i>, vol. 12, no. 11. Nature Publishing Group, pp. 902–904, 2016.","ama":"Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. Compounds that select against the tetracycline-resistance efflux pump. <i>Nature Chemical Biology</i>. 2016;12(11):902-904. doi:<a href=\"https://doi.org/10.1038/nchembio.2176\">10.1038/nchembio.2176</a>","ista":"Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. 2016. Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. 12(11), 902–904.","chicago":"Stone, Laura, Michael Baym, Tami Lieberman, Remy P Chait, Jon Clardy, and Roy Kishony. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” <i>Nature Chemical Biology</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/nchembio.2176\">https://doi.org/10.1038/nchembio.2176</a>.","apa":"Stone, L., Baym, M., Lieberman, T., Chait, R. P., Clardy, J., &#38; Kishony, R. (2016). Compounds that select against the tetracycline-resistance efflux pump. <i>Nature Chemical Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nchembio.2176\">https://doi.org/10.1038/nchembio.2176</a>"},"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"date_updated":"2021-01-12T06:49:39Z","title":"Compounds that select against the tetracycline-resistance efflux pump","date_published":"2016-11-01T00:00:00Z","publisher":"Nature Publishing Group","publication_status":"published","abstract":[{"lang":"eng","text":"We developed a competition-based screening strategy to identify compounds that invert the selective advantage of antibiotic resistance. Using our assay, we screened over 19,000 compounds for the ability to select against the TetA tetracycline-resistance efflux pump in Escherichia coli and identified two hits, β-thujaplicin and disulfiram. Treating a tetracycline-resistant population with β-thujaplicin selects for loss of the resistance gene, enabling an effective second-phase treatment with doxycycline."}]},{"type":"conference_abstract","_id":"12903","date_created":"2023-05-05T12:54:47Z","oa":1,"year":"2016","page":"37","main_file_link":[{"open_access":"1","url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc16/BOOKLET_AHPC16.pdf"}],"status":"public","day":"24","publication":"AHPC16 - Austrian HPC Meeting 2016","conference":{"name":"AHPC: Austrian HPC Meeting","location":"Grundlsee, Austria","start_date":"2016-02-22","end_date":"2016-02-24"},"citation":{"ieee":"A. Schlögl and S. Stadlbauer, “High performance computing at IST Austria: Modelling the human hippocampus,” in <i>AHPC16 - Austrian HPC Meeting 2016</i>, Grundlsee, Austria, 2016, p. 37.","apa":"Schlögl, A., &#38; Stadlbauer, S. (2016). High performance computing at IST Austria: Modelling the human hippocampus. In <i>AHPC16 - Austrian HPC Meeting 2016</i> (p. 37). Grundlsee, Austria: VSC - Vienna Scientific Cluster.","ama":"Schlögl A, Stadlbauer S. High performance computing at IST Austria: Modelling the human hippocampus. In: <i>AHPC16 - Austrian HPC Meeting 2016</i>. VSC - Vienna Scientific Cluster; 2016:37.","chicago":"Schlögl, Alois, and Stephan Stadlbauer. “High Performance Computing at IST Austria: Modelling the Human Hippocampus.” In <i>AHPC16 - Austrian HPC Meeting 2016</i>, 37. VSC - Vienna Scientific Cluster, 2016.","ista":"Schlögl A, Stadlbauer S. 2016. High performance computing at IST Austria: Modelling the human hippocampus. AHPC16 - Austrian HPC Meeting 2016. AHPC: Austrian HPC Meeting, 37.","short":"A. Schlögl, S. Stadlbauer, in:, AHPC16 - Austrian HPC Meeting 2016, VSC - Vienna Scientific Cluster, 2016, p. 37.","mla":"Schlögl, Alois, and Stephan Stadlbauer. “High Performance Computing at IST Austria: Modelling the Human Hippocampus.” <i>AHPC16 - Austrian HPC Meeting 2016</i>, VSC - Vienna Scientific Cluster, 2016, p. 37."},"oa_version":"Published Version","quality_controlled":"1","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"date_updated":"2023-05-16T07:15:14Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","last_name":"Schlögl","first_name":"Alois"},{"first_name":"Stephan","last_name":"Stadlbauer","id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","full_name":"Stadlbauer, Stephan"}],"file":[{"relation":"main_file","success":1,"file_size":1073523,"access_level":"open_access","creator":"dernst","file_id":"12968","checksum":"4a7b00362e81358d568f5e216fa03c3e","date_updated":"2023-05-16T07:03:56Z","date_created":"2023-05-16T07:03:56Z","content_type":"application/pdf","file_name":"2016_AHPC_Schloegl.pdf"}],"ddc":["000"],"publication_status":"published","month":"02","has_accepted_license":"1","title":"High performance computing at IST Austria: Modelling the human hippocampus","article_processing_charge":"No","language":[{"iso":"eng"}],"file_date_updated":"2023-05-16T07:03:56Z","publisher":"VSC - Vienna Scientific Cluster","date_published":"2016-02-24T00:00:00Z"},{"volume":347,"language":[{"iso":"eng"}],"issue":"3","file":[{"relation":"main_file","access_level":"open_access","file_size":794983,"file_id":"4725","checksum":"3c6e08c048fc462e312788be72874bb1","creator":"system","date_created":"2018-12-12T10:09:02Z","date_updated":"2020-07-14T12:44:42Z","content_type":"application/pdf","file_name":"IST-2016-688-v1+1_s00220-016-2665-0.pdf"}],"month":"11","has_accepted_license":"1","author":[{"last_name":"Giuliani","first_name":"Alessandro","full_name":"Giuliani, Alessandro"},{"first_name":"Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"}],"oa_version":"Published Version","quality_controlled":"1","project":[{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27","call_identifier":"FWF"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"pubrep_id":"688","status":"public","_id":"1291","type":"journal_article","date_created":"2018-12-11T11:51:11Z","title":"Periodic striped ground states in Ising models with competing interactions","file_date_updated":"2020-07-14T12:44:42Z","publisher":"Springer","date_published":"2016-11-01T00:00:00Z","ddc":["510","530"],"abstract":[{"lang":"eng","text":"We consider Ising models in two and three dimensions, with short range ferromagnetic and long range, power-law decaying, antiferromagnetic interactions. We let J be the ratio between the strength of the ferromagnetic to antiferromagnetic interactions. The competition between these two kinds of interactions induces the system to form domains of minus spins in a background of plus spins, or vice versa. If the decay exponent p of the long range interaction is larger than d + 1, with d the space dimension, this happens for all values of J smaller than a critical value Jc(p), beyond which the ground state is homogeneous. In this paper, we give a characterization of the infinite volume ground states of the system, for p &gt; 2d and J in a left neighborhood of Jc(p). In particular, we prove that the quasi-one-dimensional states consisting of infinite stripes (d = 2) or slabs (d = 3), all of the same optimal width and orientation, and alternating magnetization, are infinite volume ground states. Our proof is based on localization bounds combined with reflection positivity."}],"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Giuliani, Alessandro, and Robert Seiringer. “Periodic Striped Ground States in Ising Models with Competing Interactions.” <i>Communications in Mathematical Physics</i>, vol. 347, no. 3, Springer, 2016, pp. 983–1007, doi:<a href=\"https://doi.org/10.1007/s00220-016-2665-0\">10.1007/s00220-016-2665-0</a>.","short":"A. Giuliani, R. Seiringer, Communications in Mathematical Physics 347 (2016) 983–1007.","ieee":"A. Giuliani and R. Seiringer, “Periodic striped ground states in Ising models with competing interactions,” <i>Communications in Mathematical Physics</i>, vol. 347, no. 3. Springer, pp. 983–1007, 2016.","ista":"Giuliani A, Seiringer R. 2016. Periodic striped ground states in Ising models with competing interactions. Communications in Mathematical Physics. 347(3), 983–1007.","chicago":"Giuliani, Alessandro, and Robert Seiringer. “Periodic Striped Ground States in Ising Models with Competing Interactions.” <i>Communications in Mathematical Physics</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00220-016-2665-0\">https://doi.org/10.1007/s00220-016-2665-0</a>.","ama":"Giuliani A, Seiringer R. Periodic striped ground states in Ising models with competing interactions. <i>Communications in Mathematical Physics</i>. 2016;347(3):983-1007. doi:<a href=\"https://doi.org/10.1007/s00220-016-2665-0\">10.1007/s00220-016-2665-0</a>","apa":"Giuliani, A., &#38; Seiringer, R. (2016). Periodic striped ground states in Ising models with competing interactions. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-016-2665-0\">https://doi.org/10.1007/s00220-016-2665-0</a>"},"date_updated":"2021-01-12T06:49:40Z","department":[{"_id":"RoSe"}],"publication":"Communications in Mathematical Physics","intvolume":"       347","publist_id":"6025","scopus_import":1,"year":"2016","day":"01","page":"983 - 1007","doi":"10.1007/s00220-016-2665-0","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The\r\nresearch leading to these results has received funding from the European Research Council under the European\r\nUnion’s Seventh Framework Programme ERC Starting Grant CoMBoS (Grant Agreement No. 239694), from\r\nthe Italian PRIN National Grant Geometric and analytic theory of Hamiltonian systems in finite and infinite\r\ndimensions, and the Austrian Science Fund (FWF), project Nr. P 27533-N27. Part of this work was completed\r\nduring a stay at the Erwin Schrödinger Institute for Mathematical Physics in Vienna (ESI program 2015\r\n“Quantum many-body systems, random matrices, and disorder”), whose hospitality and financial support is\r\ngratefully acknowledged.","oa":1},{"author":[{"last_name":"Durst","first_name":"Sebastian","full_name":"Durst, Sebastian"},{"last_name":"Kegel","first_name":"Marc","full_name":"Kegel, Marc"},{"full_name":"Klukas, Mirko D","id":"34927512-F248-11E8-B48F-1D18A9856A87","first_name":"Mirko D","last_name":"Klukas"}],"oa_version":"Preprint","quality_controlled":"1","volume":150,"language":[{"iso":"eng"}],"issue":"2","month":"12","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1605.00794"}],"status":"public","type":"journal_article","_id":"1292","date_created":"2018-12-11T11:51:11Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Durst, Sebastian, Marc Kegel, and Mirko D Klukas. “Computing the Thurston–Bennequin Invariant in Open Books.” <i>Acta Mathematica Hungarica</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s10474-016-0648-4\">https://doi.org/10.1007/s10474-016-0648-4</a>.","ista":"Durst S, Kegel M, Klukas MD. 2016. Computing the Thurston–Bennequin invariant in open books. Acta Mathematica Hungarica. 150(2), 441–455.","ama":"Durst S, Kegel M, Klukas MD. Computing the Thurston–Bennequin invariant in open books. <i>Acta Mathematica Hungarica</i>. 2016;150(2):441-455. doi:<a href=\"https://doi.org/10.1007/s10474-016-0648-4\">10.1007/s10474-016-0648-4</a>","apa":"Durst, S., Kegel, M., &#38; Klukas, M. D. (2016). Computing the Thurston–Bennequin invariant in open books. <i>Acta Mathematica Hungarica</i>. Springer. <a href=\"https://doi.org/10.1007/s10474-016-0648-4\">https://doi.org/10.1007/s10474-016-0648-4</a>","ieee":"S. Durst, M. Kegel, and M. D. Klukas, “Computing the Thurston–Bennequin invariant in open books,” <i>Acta Mathematica Hungarica</i>, vol. 150, no. 2. Springer, pp. 441–455, 2016.","mla":"Durst, Sebastian, et al. “Computing the Thurston–Bennequin Invariant in Open Books.” <i>Acta Mathematica Hungarica</i>, vol. 150, no. 2, Springer, 2016, pp. 441–55, doi:<a href=\"https://doi.org/10.1007/s10474-016-0648-4\">10.1007/s10474-016-0648-4</a>.","short":"S. Durst, M. Kegel, M.D. Klukas, Acta Mathematica Hungarica 150 (2016) 441–455."},"date_updated":"2021-01-12T06:49:40Z","department":[{"_id":"HeEd"}],"title":"Computing the Thurston–Bennequin invariant in open books","publisher":"Springer","date_published":"2016-12-01T00:00:00Z","abstract":[{"text":"We give explicit formulas and algorithms for the computation of the Thurston–Bennequin invariant of a nullhomologous Legendrian knot on a page of a contact open book and on Heegaard surfaces in convex position. Furthermore, we extend the results to rationally nullhomologous knots in arbitrary 3-manifolds.","lang":"eng"}],"publication_status":"published","page":"441 - 455","doi":"10.1007/s10474-016-0648-4","year":"2016","day":"01","acknowledgement":"The authors are veryg rateful to Hansj ̈org Geiges \r\nfor fruitful discussions and advice and Christian Evers for helpful remarks on a draft version.","oa":1,"publication":"Acta Mathematica Hungarica","intvolume":"       150","publist_id":"6023","scopus_import":1},{"publication":"Linear Algebra and Its Applications","intvolume":"       509","publist_id":"6024","scopus_import":1,"year":"2016","day":"15","doi":"10.1016/j.laa.2016.07.026","page":"247 - 275","acknowledgement":"We wish to thank Alexander Engström and Bernd Sturmfels for various valuable discussions and insights. We also thank the two anonymous referees for their thoughtful feedback on the paper. CU was partially supported by the Austrian Science Fund (FWF) Y 903-N35.","oa":1,"title":"Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors","date_published":"2016-11-15T00:00:00Z","publisher":"Elsevier","abstract":[{"text":"For a graph G with p vertices the closed convex cone S⪰0(G) consists of all real positive semidefinite p×p matrices whose sparsity pattern is given by G, that is, those matrices with zeros in the off-diagonal entries corresponding to nonedges of G. The extremal rays of this cone and their associated ranks have applications to matrix completion problems, maximum likelihood estimation in Gaussian graphical models in statistics, and Gauss elimination for sparse matrices. While the maximum rank of an extremal ray in S⪰0(G), known as the sparsity order of G, has been characterized for different classes of graphs, we here study all possible extremal ranks of S⪰0(G). We investigate when the geometry of the (±1)-cut polytope of G yields a polyhedral characterization of the set of extremal ranks of S⪰0(G). For a graph G without K5 minors, we show that appropriately chosen normal vectors to the facets of the (±1)-cut polytope of G specify the off-diagonal entries of extremal matrices in S⪰0(G). We also prove that for appropriately chosen scalars the constant term of the linear equation of each facet-supporting hyperplane is the rank of its corresponding extremal matrix in S⪰0(G). Furthermore, we show that if G is series-parallel then this gives a complete characterization of all possible extremal ranks of S⪰0(G). Consequently, the sparsity order problem for series-parallel graphs can be solved in terms of polyhedral geometry.","lang":"eng"}],"publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Solus LT, Uhler C, Yoshida R. Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors. <i>Linear Algebra and Its Applications</i>. 2016;509:247-275. doi:<a href=\"https://doi.org/10.1016/j.laa.2016.07.026\">10.1016/j.laa.2016.07.026</a>","chicago":"Solus, Liam T, Caroline Uhler, and Ruriko Yoshida. “Extremal Positive Semidefinite Matrices Whose Sparsity Pattern Is given by Graphs without K5 Minors.” <i>Linear Algebra and Its Applications</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.laa.2016.07.026\">https://doi.org/10.1016/j.laa.2016.07.026</a>.","ista":"Solus LT, Uhler C, Yoshida R. 2016. Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors. Linear Algebra and Its Applications. 509, 247–275.","apa":"Solus, L. T., Uhler, C., &#38; Yoshida, R. (2016). Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors. <i>Linear Algebra and Its Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.laa.2016.07.026\">https://doi.org/10.1016/j.laa.2016.07.026</a>","ieee":"L. T. Solus, C. Uhler, and R. Yoshida, “Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors,” <i>Linear Algebra and Its Applications</i>, vol. 509. Elsevier, pp. 247–275, 2016.","short":"L.T. Solus, C. Uhler, R. Yoshida, Linear Algebra and Its Applications 509 (2016) 247–275.","mla":"Solus, Liam T., et al. “Extremal Positive Semidefinite Matrices Whose Sparsity Pattern Is given by Graphs without K5 Minors.” <i>Linear Algebra and Its Applications</i>, vol. 509, Elsevier, 2016, pp. 247–75, doi:<a href=\"https://doi.org/10.1016/j.laa.2016.07.026\">10.1016/j.laa.2016.07.026</a>."},"date_updated":"2021-01-12T06:49:40Z","department":[{"_id":"CaUh"}],"status":"public","main_file_link":[{"url":"https://arxiv.org/pdf/1506.06702.pdf","open_access":"1"}],"_id":"1293","type":"journal_article","date_created":"2018-12-11T11:51:11Z","volume":509,"language":[{"iso":"eng"}],"month":"11","author":[{"first_name":"Liam T","last_name":"Solus","full_name":"Solus, Liam T","id":"2AADA620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Caroline","last_name":"Uhler","orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Uhler, Caroline"},{"last_name":"Yoshida","first_name":"Ruriko","full_name":"Yoshida, Ruriko"}],"oa_version":"Preprint","quality_controlled":"1","project":[{"name":"Gaussian Graphical Models: Theory and Applications","grant_number":"Y 903-N35","_id":"2530CA10-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}]},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Iglesias Ham, Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","first_name":"Mabel","last_name":"Iglesias Ham"}],"citation":{"mla":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls II: Weighted Averages.” <i>Electronic Notes in Discrete Mathematics</i>, vol. 54, Elsevier, 2016, pp. 169–74, doi:<a href=\"https://doi.org/10.1016/j.endm.2016.09.030\">10.1016/j.endm.2016.09.030</a>.","short":"H. Edelsbrunner, M. Iglesias Ham, Electronic Notes in Discrete Mathematics 54 (2016) 169–174.","ieee":"H. Edelsbrunner and M. Iglesias Ham, “Multiple covers with balls II: Weighted averages,” <i>Electronic Notes in Discrete Mathematics</i>, vol. 54. Elsevier, pp. 169–174, 2016.","apa":"Edelsbrunner, H., &#38; Iglesias Ham, M. (2016). Multiple covers with balls II: Weighted averages. <i>Electronic Notes in Discrete Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.endm.2016.09.030\">https://doi.org/10.1016/j.endm.2016.09.030</a>","chicago":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls II: Weighted Averages.” <i>Electronic Notes in Discrete Mathematics</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.endm.2016.09.030\">https://doi.org/10.1016/j.endm.2016.09.030</a>.","ista":"Edelsbrunner H, Iglesias Ham M. 2016. Multiple covers with balls II: Weighted averages. Electronic Notes in Discrete Mathematics. 54, 169–174.","ama":"Edelsbrunner H, Iglesias Ham M. Multiple covers with balls II: Weighted averages. <i>Electronic Notes in Discrete Mathematics</i>. 2016;54:169-174. doi:<a href=\"https://doi.org/10.1016/j.endm.2016.09.030\">10.1016/j.endm.2016.09.030</a>"},"oa_version":"None","date_updated":"2021-01-12T06:49:41Z","project":[{"call_identifier":"FP7","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems"}],"department":[{"_id":"HeEd"}],"quality_controlled":"1","title":"Multiple covers with balls II: Weighted averages","volume":54,"publisher":"Elsevier","language":[{"iso":"eng"}],"date_published":"2016-10-01T00:00:00Z","abstract":[{"text":"Voronoi diagrams and Delaunay triangulations have been extensively used to represent and compute geometric features of point configurations. We introduce a generalization to poset diagrams and poset complexes, which contain order-k and degree-k Voronoi diagrams and their duals as special cases. Extending a result of Aurenhammer from 1990, we show how to construct poset diagrams as weighted Voronoi diagrams of average balls.","lang":"eng"}],"publication_status":"published","month":"10","page":"169 - 174","status":"public","doi":"10.1016/j.endm.2016.09.030","year":"2016","day":"01","acknowledgement":"This work is partially supported by the Toposys project FP7-ICT-318493-STREP, and by ESF under the ACAT Research Network Programme.","type":"journal_article","_id":"1295","date_created":"2018-12-11T11:51:12Z","publication":"Electronic Notes in Discrete Mathematics","intvolume":"        54","ec_funded":1,"publist_id":"5976","scopus_import":1},{"month":"05","abstract":[{"text":"Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo. The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline.","lang":"eng"}],"title":"Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss","article_processing_charge":"No","publisher":"Dryad","date_published":"2016-05-06T00:00:00Z","citation":{"ieee":"D. Mcmahon <i>et al.</i>, “Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss.” Dryad, 2016.","apa":"Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M., … Paxton, R. (2016). Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Dryad. <a href=\"https://doi.org/10.5061/dryad.cq7t1\">https://doi.org/10.5061/dryad.cq7t1</a>","ista":"Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring A, Paxton R. 2016. Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss, Dryad, <a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>.","ama":"Mcmahon D, Natsopoulou M, Doublet V, et al. Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss. 2016. doi:<a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>","chicago":"Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Data from: Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.cq7t1\">https://doi.org/10.5061/dryad.cq7t1</a>.","mla":"Mcmahon, Dino, et al. <i>Data from: Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss</i>. Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>.","short":"D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A. Gogol Döring, R. Paxton, (2016)."},"oa_version":"Published Version","department":[{"_id":"SyCr"}],"date_updated":"2023-02-21T16:54:31Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Dino","last_name":"Mcmahon","full_name":"Mcmahon, Dino"},{"first_name":"Myrsini","last_name":"Natsopoulou","full_name":"Natsopoulou, Myrsini"},{"full_name":"Doublet, Vincent","last_name":"Doublet","first_name":"Vincent"},{"full_name":"Fürst, Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3712-925X","first_name":"Matthias","last_name":"Fürst"},{"last_name":"Weging","first_name":"Silvio","full_name":"Weging, Silvio"},{"last_name":"Brown","first_name":"Mark","full_name":"Brown, Mark"},{"full_name":"Gogol Döring, Andreas","first_name":"Andreas","last_name":"Gogol Döring"},{"last_name":"Paxton","first_name":"Robert","full_name":"Paxton, Robert"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1262"}]},"_id":"9704","type":"research_data_reference","oa":1,"date_created":"2021-07-23T08:30:38Z","day":"06","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.cq7t1"}],"year":"2016","doi":"10.5061/dryad.cq7t1"},{"month":"09","abstract":[{"text":"Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects.","lang":"eng"}],"publisher":"Dryad","date_published":"2016-09-23T00:00:00Z","title":"Data from: How does epistasis influence the response to selection?","article_processing_charge":"No","department":[{"_id":"NiBa"}],"date_updated":"2025-05-28T11:57:03Z","oa_version":"Published Version","citation":{"mla":"Barton, Nicholas H. <i>Data from: How Does Epistasis Influence the Response to Selection?</i> Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>.","short":"N.H. Barton, (2016).","ieee":"N. H. Barton, “Data from: How does epistasis influence the response to selection?” Dryad, 2016.","apa":"Barton, N. H. (2016). Data from: How does epistasis influence the response to selection? Dryad. <a href=\"https://doi.org/10.5061/dryad.s5s7r\">https://doi.org/10.5061/dryad.s5s7r</a>","ista":"Barton NH. 2016. Data from: How does epistasis influence the response to selection?, Dryad, <a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>.","chicago":"Barton, Nicholas H. “Data from: How Does Epistasis Influence the Response to Selection?” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.s5s7r\">https://doi.org/10.5061/dryad.s5s7r</a>.","ama":"Barton NH. Data from: How does epistasis influence the response to selection? 2016. doi:<a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>"},"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","related_material":{"record":[{"status":"public","id":"1199","relation":"used_in_publication"}]},"oa":1,"date_created":"2021-07-23T11:45:47Z","_id":"9710","type":"research_data_reference","year":"2016","doi":"10.5061/dryad.s5s7r","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.s5s7r"}],"day":"23","status":"public"},{"day":"22","doi":"10.5061/dryad.4b565","year":"2016","status":"public","main_file_link":[{"url":"https://doi.org/10.5061/dryad.4b565","open_access":"1"}],"oa":1,"date_created":"2021-07-26T09:14:19Z","_id":"9720","type":"research_data_reference","related_material":{"record":[{"id":"1855","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Mcmahon, Dino","last_name":"Mcmahon","first_name":"Dino"},{"orcid":"0000-0002-3712-925X","first_name":"Matthias","last_name":"Fürst","full_name":"Fürst, Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Caspar","first_name":"Jesicca","full_name":"Caspar, Jesicca"},{"full_name":"Theodorou, Panagiotis","first_name":"Panagiotis","last_name":"Theodorou"},{"first_name":"Mark","last_name":"Brown","full_name":"Brown, Mark"},{"last_name":"Paxton","first_name":"Robert","full_name":"Paxton, Robert"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"SyCr"}],"date_updated":"2023-02-23T10:17:25Z","citation":{"ieee":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees.” Dryad, 2016.","ama":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees. 2016. doi:<a href=\"https://doi.org/10.5061/dryad.4b565\">10.5061/dryad.4b565</a>","ista":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2016. Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees, Dryad, <a href=\"https://doi.org/10.5061/dryad.4b565\">10.5061/dryad.4b565</a>.","chicago":"Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark Brown, and Robert Paxton. “Data from: A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.4b565\">https://doi.org/10.5061/dryad.4b565</a>.","apa":"Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., &#38; Paxton, R. (2016). Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees. Dryad. <a href=\"https://doi.org/10.5061/dryad.4b565\">https://doi.org/10.5061/dryad.4b565</a>","mla":"Mcmahon, Dino, et al. <i>Data from: A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees</i>. Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.4b565\">10.5061/dryad.4b565</a>.","short":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, (2016)."},"oa_version":"Published Version","date_published":"2016-01-22T00:00:00Z","publisher":"Dryad","title":"Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees","article_processing_charge":"No","month":"01","abstract":[{"lang":"eng","text":"Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline."}]},{"date_updated":"2023-02-21T16:21:20Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"citation":{"apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Simulation study to test the robustness of ABC in face of recent times of divergence. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">https://doi.org/10.1371/journal.pbio.2000234.s016</a>","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">https://doi.org/10.1371/journal.pbio.2000234.s016</a>.","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Simulation study to test the robustness of ABC in face of recent times of divergence. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Simulation study to test the robustness of ABC in face of recent times of divergence, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>.","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Simulation study to test the robustness of ABC in face of recent times of divergence.” Public Library of Science, 2016.","mla":"Roux, Camille, et al. <i>Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016)."},"oa_version":"Published Version","author":[{"first_name":"Camille","last_name":"Roux","full_name":"Roux, Camille"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075"},{"last_name":"Romiguier","first_name":"Jonathan","full_name":"Romiguier, Jonathan"},{"first_name":"Youann","last_name":"Anciaux","full_name":"Anciaux, Youann"},{"last_name":"Galtier","first_name":"Nicolas","full_name":"Galtier, Nicolas"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"12","publisher":"Public Library of Science","article_processing_charge":"No","title":"Simulation study to test the robustness of ABC in face of recent times of divergence","date_created":"2021-08-10T08:20:17Z","_id":"9862","type":"research_data_reference","doi":"10.1371/journal.pbio.2000234.s016","status":"public","year":"2016","day":"27","related_material":{"record":[{"status":"public","id":"1158","relation":"used_in_publication"}]}},{"month":"12","title":"Accessions of surveyed individuals, geographic locations and summary statistics","article_processing_charge":"No","publisher":"Public Library of Science","citation":{"ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Accessions of surveyed individuals, geographic locations and summary statistics.” Public Library of Science, 2016.","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Accessions of surveyed individuals, geographic locations and summary statistics, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>.","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">https://doi.org/10.1371/journal.pbio.2000234.s017</a>.","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Accessions of surveyed individuals, geographic locations and summary statistics. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Accessions of surveyed individuals, geographic locations and summary statistics. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">https://doi.org/10.1371/journal.pbio.2000234.s017</a>","mla":"Roux, Camille, et al. <i>Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016)."},"oa_version":"Published Version","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"date_updated":"2023-02-21T16:21:20Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Roux","first_name":"Camille","full_name":"Roux, Camille"},{"first_name":"Christelle","last_name":"Fraisse","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"},{"first_name":"Jonathan","last_name":"Romiguier","full_name":"Romiguier, Jonathan"},{"last_name":"Anciaux","first_name":"Youann","full_name":"Anciaux, Youann"},{"first_name":"Nicolas","last_name":"Galtier","full_name":"Galtier, Nicolas"},{"last_name":"Bierne","first_name":"Nicolas","full_name":"Bierne, Nicolas"}],"related_material":{"record":[{"status":"public","id":"1158","relation":"used_in_publication"}]},"type":"research_data_reference","_id":"9863","date_created":"2021-08-10T08:22:52Z","year":"2016","doi":"10.1371/journal.pbio.2000234.s017","status":"public","day":"27"},{"related_material":{"record":[{"relation":"used_in_publication","id":"1077","status":"public"}]},"year":"2016","day":"14","status":"public","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.4315652.v1","open_access":"1"}],"doi":"10.6084/m9.figshare.4315652.v1","oa":1,"date_created":"2021-08-10T08:29:47Z","_id":"9864","type":"research_data_reference","date_published":"2016-12-14T00:00:00Z","publisher":"The Royal Society","title":"Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","article_processing_charge":"No","month":"12","abstract":[{"text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.","lang":"eng"}],"author":[{"full_name":"Fernandes Redondo, Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5837-2793","last_name":"Fernandes Redondo","first_name":"Rodrigo A"},{"id":"2A181218-F248-11E8-B48F-1D18A9856A87","full_name":"de Vladar, Harold","first_name":"Harold","last_name":"de Vladar","orcid":"0000-0002-5985-7653"},{"full_name":"Włodarski, Tomasz","last_name":"Włodarski","first_name":"Tomasz"},{"full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"date_updated":"2025-05-28T11:57:06Z","oa_version":"Published Version","citation":{"apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., &#38; Bollback, J. P. (2016). Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. The Royal Society. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family, The Royal Society, <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>.","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>.","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. 2016. doi:<a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family.” The Royal Society, 2016.","mla":"Fernandes Redondo, Rodrigo A., et al. <i>Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family</i>. The Royal Society, 2016, doi:<a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>.","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016)."}},{"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1167"}]},"year":"2016","day":"09","doi":"10.1371/journal.pcbi.1005218.s009","status":"public","date_created":"2021-08-10T08:37:20Z","type":"research_data_reference","_id":"9866","date_published":"2016-12-09T00:00:00Z","publisher":"Public Library of Science","article_processing_charge":"No","title":"ZIP-archived directory containing all data and computer programs","month":"12","author":[{"last_name":"Zagórski","first_name":"Marcin P","orcid":"0000-0001-7896-7762","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","full_name":"Zagórski, Marcin P"},{"full_name":"Burda, Zdzisław","last_name":"Burda","first_name":"Zdzisław"},{"full_name":"Wacław, Bartłomiej","first_name":"Bartłomiej","last_name":"Wacław"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-21T16:24:29Z","department":[{"_id":"AnKi"}],"citation":{"chicago":"Zagórski, Marcin P, Zdzisław Burda, and Bartłomiej Wacław. “ZIP-Archived Directory Containing All Data and Computer Programs.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">https://doi.org/10.1371/journal.pcbi.1005218.s009</a>.","ama":"Zagórski MP, Burda Z, Wacław B. ZIP-archived directory containing all data and computer programs. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">10.1371/journal.pcbi.1005218.s009</a>","ista":"Zagórski MP, Burda Z, Wacław B. 2016. ZIP-archived directory containing all data and computer programs, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">10.1371/journal.pcbi.1005218.s009</a>.","apa":"Zagórski, M. P., Burda, Z., &#38; Wacław, B. (2016). ZIP-archived directory containing all data and computer programs. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">https://doi.org/10.1371/journal.pcbi.1005218.s009</a>","ieee":"M. P. Zagórski, Z. Burda, and B. Wacław, “ZIP-archived directory containing all data and computer programs.” Public Library of Science, 2016.","short":"M.P. Zagórski, Z. Burda, B. Wacław, (2016).","mla":"Zagórski, Marcin P., et al. <i>ZIP-Archived Directory Containing All Data and Computer Programs</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">10.1371/journal.pcbi.1005218.s009</a>."},"oa_version":"Published Version"}]