[{"type":"journal_article","month":"06","page":"25 - 29","file":[{"file_id":"4998","content_type":"application/pdf","file_size":247657,"creator":"system","relation":"main_file","access_level":"open_access","date_updated":"2019-10-15T07:44:51Z","date_created":"2018-12-12T10:13:17Z","file_name":"IST-2018-991-v1+2_2018_Chatterjee_Pushdown_PREPRINT.pdf"}],"status":"public","department":[{"_id":"KrCh"},{"_id":"HeEd"}],"external_id":{"isi":["000399506600005"]},"date_created":"2018-12-11T11:49:57Z","publication_status":"published","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Osang, Georg F","last_name":"Osang","orcid":"0000-0002-8882-5116","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","scopus_import":"1","file_date_updated":"2019-10-15T07:44:51Z","_id":"1065","project":[{"grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"citation":{"ista":"Chatterjee K, Osang GF. 2017. Pushdown reachability with constant treewidth. Information Processing Letters. 122, 25–29.","short":"K. Chatterjee, G.F. Osang, Information Processing Letters 122 (2017) 25–29.","mla":"Chatterjee, Krishnendu, and Georg F. Osang. “Pushdown Reachability with Constant Treewidth.” Information Processing Letters, vol. 122, Elsevier, 2017, pp. 25–29, doi:10.1016/j.ipl.2017.02.003.","ieee":"K. Chatterjee and G. F. Osang, “Pushdown reachability with constant treewidth,” Information Processing Letters, vol. 122. Elsevier, pp. 25–29, 2017.","apa":"Chatterjee, K., & Osang, G. F. (2017). Pushdown reachability with constant treewidth. Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2017.02.003","ama":"Chatterjee K, Osang GF. Pushdown reachability with constant treewidth. Information Processing Letters. 2017;122:25-29. doi:10.1016/j.ipl.2017.02.003","chicago":"Chatterjee, Krishnendu, and Georg F Osang. “Pushdown Reachability with Constant Treewidth.” Information Processing Letters. Elsevier, 2017. https://doi.org/10.1016/j.ipl.2017.02.003."},"oa":1,"date_updated":"2025-07-10T11:49:53Z","isi":1,"title":"Pushdown reachability with constant treewidth","publication_identifier":{"issn":["0020-0190"]},"doi":"10.1016/j.ipl.2017.02.003","quality_controlled":"1","has_accepted_license":"1","year":"2017","publist_id":"6323","oa_version":"Submitted Version","ddc":["000"],"volume":122,"ec_funded":1,"date_published":"2017-06-01T00:00:00Z","publication":"Information Processing Letters","intvolume":" 122","pubrep_id":"991","abstract":[{"text":"We consider the problem of reachability in pushdown graphs. We study the problem for pushdown graphs with constant treewidth. Even for pushdown graphs with treewidth 1, for the reachability problem we establish the following: (i) the problem is PTIME-complete, and (ii) any subcubic algorithm for the problem would contradict the k-clique conjecture and imply faster combinatorial algorithms for cliques in graphs.","lang":"eng"}],"publisher":"Elsevier","article_processing_charge":"No","language":[{"iso":"eng"}]},{"article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Elsevier","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.ic.2016.10.006"}],"abstract":[{"lang":"eng","text":"Simulation is an attractive alternative to language inclusion for automata as it is an under-approximation of language inclusion, but usually has much lower complexity. Simulation has also been extended in two orthogonal directions, namely, (1) fair simulation, for simulation over specified set of infinite runs; and (2) quantitative simulation, for simulation between weighted automata. While fair trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial time. For weighted automata, the (quantitative) language inclusion problem is undecidable in general, whereas the (quantitative) simulation reduces to quantitative games, which admit pseudo-polynomial time algorithms.\r\n\r\nIn this work, we study (quantitative) simulation for weighted automata with Büchi acceptance conditions, i.e., we generalize fair simulation from non-weighted automata to weighted automata. We show that imposing Büchi acceptance conditions on weighted automata changes many fundamental properties of the simulation games, yet they still admit pseudo-polynomial time algorithms."}],"intvolume":" 254","OA_type":"free access","volume":254,"ec_funded":1,"date_published":"2017-06-01T00:00:00Z","publication":"Information and Computation","article_type":"original","ddc":["000"],"oa_version":"Published Version","publist_id":"6322","year":"2017","doi":"10.1016/j.ic.2016.10.006","quality_controlled":"1","OA_place":"publisher","title":"Quantitative fair simulation games","isi":1,"corr_author":"1","date_updated":"2026-06-18T08:47:01Z","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"oa":1,"citation":{"ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, “Quantitative fair simulation games,” Information and Computation, vol. 254, no. 2. Elsevier, pp. 143–166, 2017.","mla":"Chatterjee, Krishnendu, et al. “Quantitative Fair Simulation Games.” Information and Computation, vol. 254, no. 2, Elsevier, 2017, pp. 143–66, doi:10.1016/j.ic.2016.10.006.","ista":"Chatterjee K, Henzinger TA, Otop J, Velner Y. 2017. Quantitative fair simulation games. Information and Computation. 254(2), 143–166.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Information and Computation 254 (2017) 143–166.","ama":"Chatterjee K, Henzinger TA, Otop J, Velner Y. Quantitative fair simulation games. Information and Computation. 2017;254(2):143-166. doi:10.1016/j.ic.2016.10.006","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner. “Quantitative Fair Simulation Games.” Information and Computation. Elsevier, 2017. https://doi.org/10.1016/j.ic.2016.10.006.","apa":"Chatterjee, K., Henzinger, T. A., Otop, J., & Velner, Y. (2017). Quantitative fair simulation games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2016.10.006"},"_id":"1066","scopus_import":"1","day":"01","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreements 267989 (QUAREM), 279307 (Graph Games), by the Austrian Science Fund (FWF) projects S11402-N23 (RiSE), S11407-N23 (RiSE), P23499-N23, and Microsoft faculty fellows award.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"2","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Velner, Yaron","first_name":"Yaron","last_name":"Velner"}],"publication_status":"published","related_material":{"record":[{"status":"public","id":"5428","relation":"earlier_version"}]},"external_id":{"isi":["000402025600002"]},"date_created":"2018-12-11T11:49:58Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"status":"public","month":"06","type":"journal_article","page":"143 - 166"},{"status":"public","keyword":["physics","superconductivity","magnetic force microscopy","phase slips"],"degree_awarded":"PhD","page":"103","type":"dissertation","month":"09","alternative_title":["Graduate Dissertations and Theses at Illinois"],"author":[{"id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","first_name":"Hryhoriy","orcid":"0000-0001-8223-8896","last_name":"Polshyn","full_name":"Polshyn, Hryhoriy"}],"oa_version":"Published Version","publication_status":"published","date_created":"2022-01-25T14:54:14Z","extern":"1","year":"2017","_id":"10663","supervisor":[{"last_name":"Budakian","first_name":"Raffi","full_name":"Budakian, Raffi"}],"day":"18","date_published":"2017-09-18T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Magnetic force microscopy studies of mesoscopic superconducting structures","language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"University of Illinois at Urbana-Champaign","date_updated":"2024-10-14T11:13:43Z","main_file_link":[{"url":"http://hdl.handle.net/2142/99178","open_access":"1"}],"abstract":[{"text":"The superconducting state of matter enables one to observe quantum effects on the macroscopic scale and hosts many fascinating phenomena. Topological defects of the superconducting order parameter, such as vortices and fluxoid states in multiply connected structures, are often the key ingredients of these phenomena. This dissertation describes a new mode of magnetic force microscopy (Φ0-MFM) for investigating vortex and fluxoid sates in mesoscopic superconducting (SC) structures. The technique relies on the magneto-mechanical coupling of a MFM cantilever to the motion of fluxons. The novelty of the technique is that a magnetic particle attached to the cantilever is used not only to sense the state of a SC structure, but also as a primary source of the inhomogeneous magnetic field which induces that state. Φ0-MFM enables us to map the transitions between tip-induced states during a scan: at the positions of the tip, where the two lowest energy states become degenerate, small oscillations of the tip drive the transitions between these states, which causes a significant shift in the resonant frequency and dissipation of the cantilever. For narrow-wall aluminum rings, the mapped fluxoid transitions form concentric contours on a scan. We show that the changes in the cantilever resonant frequency and dissipation are well-described by a stochastic resonance (SR) of cantilever-driven thermally activated phase slips (TAPS). The SR model allows us to experimentally determine the rate of TAPS and compare it to the Langer-Ambegaokar-McCumber-Halperin (LAMH) theory for TAPS in 1D superconducting structures. Further, we use the SR model to qualitatively study the effects of a locally applied magnetic field on the phase slip rate in rings containing constrictions. The states with multiple vortices or winding numbers could be useful for the development of novel superconducting devices, or the study of vortex interactions and interference effects. Using Φ0-MFM allows us to induce, probe and control fluxoid states in thin wall structures comprised of multiple loops. We show that Φ0-MFM images of the fluxoid transitions allow us to identify the underlying states and to investigate their energetics and dynamics even in complicated structures.","lang":"eng"}],"citation":{"apa":"Polshyn, H. (2017). Magnetic force microscopy studies of mesoscopic superconducting structures. University of Illinois at Urbana-Champaign.","chicago":"Polshyn, Hryhoriy. “Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures.” University of Illinois at Urbana-Champaign, 2017.","ama":"Polshyn H. Magnetic force microscopy studies of mesoscopic superconducting structures. 2017.","short":"H. Polshyn, Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures, University of Illinois at Urbana-Champaign, 2017.","ista":"Polshyn H. 2017. Magnetic force microscopy studies of mesoscopic superconducting structures. University of Illinois at Urbana-Champaign.","ieee":"H. Polshyn, “Magnetic force microscopy studies of mesoscopic superconducting structures,” University of Illinois at Urbana-Champaign, 2017.","mla":"Polshyn, Hryhoriy. Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures. University of Illinois at Urbana-Champaign, 2017."},"oa":1},{"volume":40,"ec_funded":1,"date_published":"2017-02-27T00:00:00Z","publication":"Developmental Cell","intvolume":" 40","pubrep_id":"869","abstract":[{"lang":"eng","text":"Embryo morphogenesis relies on highly coordinated movements of different tissues. However, remarkably little is known about how tissues coordinate their movements to shape the embryo. In zebrafish embryogenesis, coordinated tissue movements first become apparent during “doming,” when the blastoderm begins to spread over the yolk sac, a process involving coordinated epithelial surface cell layer expansion and mesenchymal deep cell intercalations. Here, we find that active surface cell expansion represents the key process coordinating tissue movements during doming. By using a combination of theory and experiments, we show that epithelial surface cells not only trigger blastoderm expansion by reducing tissue surface tension, but also drive blastoderm thinning by inducing tissue contraction through radial deep cell intercalations. Thus, coordinated tissue expansion and thinning during doming relies on surface cells simultaneously controlling tissue surface tension and radial tissue contraction."}],"publisher":"Cell Press","article_processing_charge":"No","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1534-5807"]},"doi":"10.1016/j.devcel.2017.01.010","acknowledged_ssus":[{"_id":"PreCl"}],"quality_controlled":"1","has_accepted_license":"1","year":"2017","publist_id":"6320","ddc":["572","597"],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"4","day":"27","file_date_updated":"2018-12-12T10:10:57Z","scopus_import":"1","_id":"1067","project":[{"name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","call_identifier":"FP7","grant_number":"201439","_id":"2524F500-B435-11E9-9278-68D0E5697425"}],"oa":1,"citation":{"ieee":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, and C.-P. J. Heisenberg, “The physical basis of coordinated tissue spreading in zebrafish gastrulation,” Developmental Cell, vol. 40, no. 4. Cell Press, pp. 354–366, 2017.","mla":"Morita, Hitoshi, et al. “The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation.” Developmental Cell, vol. 40, no. 4, Cell Press, 2017, pp. 354–66, doi:10.1016/j.devcel.2017.01.010.","short":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, C.-P.J. Heisenberg, Developmental Cell 40 (2017) 354–366.","ista":"Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. 2017. The physical basis of coordinated tissue spreading in zebrafish gastrulation. Developmental Cell. 40(4), 354–366.","chicago":"Morita, Hitoshi, Silvia Grigolon, Martin Bock, Gabriel Krens, Guillaume Salbreux, and Carl-Philipp J Heisenberg. “The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation.” Developmental Cell. Cell Press, 2017. https://doi.org/10.1016/j.devcel.2017.01.010.","ama":"Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. The physical basis of coordinated tissue spreading in zebrafish gastrulation. Developmental Cell. 2017;40(4):354-366. doi:10.1016/j.devcel.2017.01.010","apa":"Morita, H., Grigolon, S., Bock, M., Krens, G., Salbreux, G., & Heisenberg, C.-P. J. (2017). The physical basis of coordinated tissue spreading in zebrafish gastrulation. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2017.01.010"},"date_updated":"2025-07-10T11:49:55Z","isi":1,"corr_author":"1","title":"The physical basis of coordinated tissue spreading in zebrafish gastrulation","month":"02","type":"journal_article","page":"354 - 366","file":[{"file_name":"IST-2017-869-v1+1_1-s2.0-S1534580717300370-main.pdf","date_created":"2018-12-12T10:10:57Z","date_updated":"2018-12-12T10:10:57Z","access_level":"open_access","relation":"main_file","creator":"system","file_size":6866187,"content_type":"application/pdf","file_id":"4849"}],"status":"public","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"department":[{"_id":"CaHe"}],"external_id":{"isi":["000395368300007"]},"date_created":"2018-12-11T11:49:58Z","publication_status":"published","author":[{"full_name":"Morita, Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","last_name":"Morita","first_name":"Hitoshi"},{"first_name":"Silvia","last_name":"Grigolon","full_name":"Grigolon, Silvia"},{"first_name":"Martin","last_name":"Bock","full_name":"Bock, Martin"},{"full_name":"Krens, Gabriel","last_name":"Krens","first_name":"Gabriel","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Salbreux","first_name":"Guillaume","full_name":"Salbreux, Guillaume"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}]},{"isi":1,"arxiv":1,"title":"The Morse theory of Čech and delaunay complexes","oa":1,"citation":{"apa":"Bauer, U., & Edelsbrunner, H. (2017). The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/6991","ama":"Bauer U, Edelsbrunner H. The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. 2017;369(5):3741-3762. doi:10.1090/tran/6991","chicago":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Complexes.” Transactions of the American Mathematical Society. American Mathematical Society, 2017. https://doi.org/10.1090/tran/6991.","ista":"Bauer U, Edelsbrunner H. 2017. The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. 369(5), 3741–3762.","short":"U. Bauer, H. Edelsbrunner, Transactions of the American Mathematical Society 369 (2017) 3741–3762.","mla":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Complexes.” Transactions of the American Mathematical Society, vol. 369, no. 5, American Mathematical Society, 2017, pp. 3741–62, doi:10.1090/tran/6991.","ieee":"U. Bauer and H. Edelsbrunner, “The Morse theory of Čech and delaunay complexes,” Transactions of the American Mathematical Society, vol. 369, no. 5. American Mathematical Society, pp. 3741–3762, 2017."},"project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Topological Complex Systems","grant_number":"318493"}],"date_updated":"2025-04-15T08:37:54Z","scopus_import":"1","_id":"1072","issue":"5","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"This research has been supported by the EU project Toposys(FP7-ICT-318493-STREP), by ESF under the ACAT Research Network Programme, by the Russian Government under mega project 11.G34.31.0053, and by the DFG Collaborative Research Center SFB/TRR 109 “Discretization in Geometry and Dynamics”.","day":"01","publication_status":"published","author":[{"full_name":"Bauer, Ulrich","first_name":"Ulrich","orcid":"0000-0002-9683-0724","last_name":"Bauer","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"}],"department":[{"_id":"HeEd"}],"date_created":"2018-12-11T11:49:59Z","external_id":{"arxiv":["1312.1231"],"isi":["000398030400024"]},"status":"public","page":"3741 - 3762","month":"05","type":"journal_article","language":[{"iso":"eng"}],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Given a finite set of points in Rn and a radius parameter, we study the Čech, Delaunay–Čech, Delaunay (or alpha), and Wrap complexes in the light of generalized discrete Morse theory. Establishing the Čech and Delaunay complexes as sublevel sets of generalized discrete Morse functions, we prove that the four complexes are simple-homotopy equivalent by a sequence of simplicial collapses, which are explicitly described by a single discrete gradient field."}],"publisher":"American Mathematical Society","main_file_link":[{"url":"https://arxiv.org/abs/1312.1231","open_access":"1"}],"date_published":"2017-05-01T00:00:00Z","publication":"Transactions of the American Mathematical Society","ec_funded":1,"volume":369,"intvolume":" 369","oa_version":"Preprint","article_type":"original","year":"2017","publist_id":"6311","quality_controlled":"1","doi":"10.1090/tran/6991"},{"article_processing_charge":"No","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Let X and Y be finite simplicial sets (e.g. finite simplicial complexes), both equipped with a free simplicial action of a finite group G. Assuming that Y is d-connected and dimX≤2d, for some d≥1, we provide an algorithm that computes the set of all equivariant homotopy classes of equivariant continuous maps |X|→|Y|; the existence of such a map can be decided even for dimX≤2d+1. This yields the first algorithm for deciding topological embeddability of a k-dimensional finite simplicial complex into Rn under the condition k≤23n−1. More generally, we present an algorithm that, given a lifting-extension problem satisfying an appropriate stability assumption, computes the set of all homotopy classes of solutions. This result is new even in the non-equivariant situation."}],"publisher":"Springer","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1307.6444"}],"volume":54,"publication":"Discrete & Computational Geometry","date_published":"2017-06-01T00:00:00Z","intvolume":" 54","oa_version":"Submitted Version","year":"2017","publist_id":"6309","doi":"10.1007/s00454-016-9855-6","quality_controlled":"1","publication_identifier":{"issn":["01795376"]},"arxiv":1,"isi":1,"title":"Algorithmic solvability of the lifting extension problem","citation":{"ista":"Čadek M, Krcál M, Vokřínek L. 2017. Algorithmic solvability of the lifting extension problem. Discrete & Computational Geometry. 54(4), 915–965.","short":"M. Čadek, M. Krcál, L. Vokřínek, Discrete & Computational Geometry 54 (2017) 915–965.","mla":"Čadek, Martin, et al. “Algorithmic Solvability of the Lifting Extension Problem.” Discrete & Computational Geometry, vol. 54, no. 4, Springer, 2017, pp. 915–65, doi:10.1007/s00454-016-9855-6.","ieee":"M. Čadek, M. Krcál, and L. Vokřínek, “Algorithmic solvability of the lifting extension problem,” Discrete & Computational Geometry, vol. 54, no. 4. Springer, pp. 915–965, 2017.","apa":"Čadek, M., Krcál, M., & Vokřínek, L. (2017). Algorithmic solvability of the lifting extension problem. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-016-9855-6","chicago":"Čadek, Martin, Marek Krcál, and Lukáš Vokřínek. “Algorithmic Solvability of the Lifting Extension Problem.” Discrete & Computational Geometry. Springer, 2017. https://doi.org/10.1007/s00454-016-9855-6.","ama":"Čadek M, Krcál M, Vokřínek L. Algorithmic solvability of the lifting extension problem. Discrete & Computational Geometry. 2017;54(4):915-965. doi:10.1007/s00454-016-9855-6"},"oa":1,"date_updated":"2025-06-04T08:11:10Z","scopus_import":"1","_id":"1073","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"4","day":"01","publication_status":"published","author":[{"first_name":"Martin","last_name":"Čadek","full_name":"Čadek, Martin"},{"full_name":"Krcál, Marek","last_name":"Krcál","first_name":"Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vokřínek, Lukáš","last_name":"Vokřínek","first_name":"Lukáš"}],"department":[{"_id":"UlWa"}],"external_id":{"arxiv":["1307.6444"],"isi":["000400072700008"]},"date_created":"2018-12-11T11:50:00Z","status":"public","month":"06","type":"journal_article","page":"915 - 965"},{"type":"journal_article","month":"03","page":"1335 - 1351","status":"public","department":[{"_id":"NiBa"}],"date_created":"2018-12-11T11:50:00Z","external_id":{"isi":["000395807200023"]},"publication_status":"published","related_material":{"record":[{"id":"200","status":"public","relation":"dissertation_contains"}]},"author":[{"id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","first_name":"Harald","orcid":"0000-0002-4884-9682","last_name":"Ringbauer","full_name":"Ringbauer, Harald"},{"first_name":"Graham","last_name":"Coop","full_name":"Coop, Graham"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","day":"01","scopus_import":"1","_id":"1074","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"oa":1,"citation":{"ista":"Ringbauer H, Coop G, Barton NH. 2017. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 205(3), 1335–1351.","short":"H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351.","mla":"Ringbauer, Harald, et al. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics, vol. 205, no. 3, Genetics Society of America, 2017, pp. 1335–51, doi:10.1534/genetics.116.196220.","ieee":"H. Ringbauer, G. Coop, and N. H. Barton, “Inferring recent demography from isolation by distance of long shared sequence blocks,” Genetics, vol. 205, no. 3. Genetics Society of America, pp. 1335–1351, 2017.","apa":"Ringbauer, H., Coop, G., & Barton, N. H. (2017). Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.196220","ama":"Ringbauer H, Coop G, Barton NH. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 2017;205(3):1335-1351. doi:10.1534/genetics.116.196220","chicago":"Ringbauer, Harald, Graham Coop, and Nicholas H Barton. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.196220."},"date_updated":"2026-04-08T14:06:35Z","isi":1,"title":"Inferring recent demography from isolation by distance of long shared sequence blocks","publication_identifier":{"issn":["0016-6731"]},"doi":"10.1534/genetics.116.196220","quality_controlled":"1","year":"2017","publist_id":"6307","oa_version":"Preprint","ec_funded":1,"volume":205,"date_published":"2017-03-01T00:00:00Z","publication":"Genetics","intvolume":" 205","abstract":[{"lang":"eng","text":"Recently it has become feasible to detect long blocks of nearly identical sequence shared between pairs of genomes. These IBD blocks are direct traces of recent coalescence events and, as such, contain ample signal to infer recent demography. Here, we examine sharing of such blocks in two-dimensional populations with local migration. Using a diffusion approximation to trace genetic ancestry, we derive analytical formulae for patterns of isolation by distance of IBD blocks, which can also incorporate recent population density changes. We introduce an inference scheme that uses a composite likelihood approach to fit these formulae. We then extensively evaluate our theory and inference method on a range of scenarios using simulated data. We first validate the diffusion approximation by showing that the theoretical results closely match the simulated block sharing patterns. We then demonstrate that our inference scheme can accurately and robustly infer dispersal rate and effective density, as well as bounds on recent dynamics of population density. To demonstrate an application, we use our estimation scheme to explore the fit of a diffusion model to Eastern European samples in the POPRES data set. We show that ancestry diffusing with a rate of σ ≈ 50–100 km/√gen during the last centuries, combined with accelerating population growth, can explain the observed exponential decay of block sharing with increasing pairwise sample distance."}],"publisher":"Genetics Society of America","main_file_link":[{"open_access":"1","url":"http://www.biorxiv.org/content/early/2016/09/23/076810"}],"article_processing_charge":"No","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"American Physical Society","main_file_link":[{"url":"https://meetings.aps.org/Meeting/MAR17/Session/P39.11","open_access":"1"}],"abstract":[{"text":"New ways to investigate and manipulate fluxoid and vortex states of mesoscopic superconducting structures are of great interest. The states with multiple vortices or winding numbers could be useful for the study of vortex interactions and interference effects, the braiding of Majorana bound states by winding vortices, and the development of novel superconducting devices. We demonstrate a methodology based on magnetic force microscopy that allows us to induce, probe and control fluxoid states in thin wall structures comprised of multiple loops. By using micro-magnet as a source of inhomogeneous magnetic field, we can efficiently explore the configuration space of fluxoid states. Scanning over the structure reveals the energy crossing points of the lowest laying fluxoid states. This is due the strong interaction of cantilever with thermally activated fluxoid transitions at points of degeneracy. We show that measured patterns of fluxoid transitions allow to identify the states, investigate their energetics, and manipulate them. Further, we show that the dynamics of driven fluxoid transitions can be described by stochastic resonance model, which provides a unique way of measuring fluxoid transition rate and related energy barrier for chosen transitions even in complicated structures","lang":"eng"}],"intvolume":" 62","publication":"APS March Meeting 2017","date_published":"2017-03-01T00:00:00Z","volume":62,"oa_version":"Published Version","year":"2017","quality_controlled":"1","conference":{"end_date":"2017-03-17","location":"New Orleans, LA, United States","start_date":"2017-03-13","name":"APS: American Physical Society"},"publication_identifier":{"issn":["0003-0503"]},"title":" Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures","date_updated":"2022-02-08T10:44:35Z","oa":1,"citation":{"ista":"Polshyn H, Naibert T, Budakian R. 2017. Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures. APS March Meeting 2017. APS: American Physical Society, Bulletin of the American Physical Society, vol. 62, P39.00011.","short":"H. Polshyn, T. Naibert, R. Budakian, in:, APS March Meeting 2017, American Physical Society, 2017.","mla":"Polshyn, Hryhoriy, et al. “ Probing and Controlling Fluxoid States in Multiply-Connected Mesoscopic Superconducting Structures.” APS March Meeting 2017, vol. 62, no. 4, P39.00011, American Physical Society, 2017.","ieee":"H. Polshyn, T. Naibert, and R. Budakian, “ Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures,” in APS March Meeting 2017, New Orleans, LA, United States, 2017, vol. 62, no. 4.","apa":"Polshyn, H., Naibert, T., & Budakian, R. (2017). Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures. In APS March Meeting 2017 (Vol. 62). New Orleans, LA, United States: American Physical Society.","ama":"Polshyn H, Naibert T, Budakian R. Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures. In: APS March Meeting 2017. Vol 62. American Physical Society; 2017.","chicago":"Polshyn, Hryhoriy, Tyler Naibert, and Raffi Budakian. “ Probing and Controlling Fluxoid States in Multiply-Connected Mesoscopic Superconducting Structures.” In APS March Meeting 2017, Vol. 62. American Physical Society, 2017."},"_id":"10745","article_number":"P39.00011","day":"01","issue":"4","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Polshyn, Hryhoriy","last_name":"Polshyn","first_name":"Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48"},{"first_name":"Tyler","last_name":"Naibert","full_name":"Naibert, Tyler"},{"last_name":"Budakian","first_name":"Raffi","full_name":"Budakian, Raffi"}],"publication_status":"published","date_created":"2022-02-08T09:49:17Z","extern":"1","status":"public","month":"03","type":"conference","alternative_title":["Bulletin of the American Physical Society"]},{"has_accepted_license":"1","publication_identifier":{"isbn":["978-3643908124"]},"oa_version":"None","ddc":["001"],"year":"2017","publist_id":"6306","volume":15,"publication":"Austria and America: 20th-Century Cross-Cultural Encounters","date_published":"2017-02-01T00:00:00Z","intvolume":" 15","editor":[{"last_name":"Parker","first_name":"Joshua","full_name":"Parker, Joshua"},{"full_name":"Poole, Ralph","last_name":"Poole","first_name":"Ralph"}],"language":[{"iso":"eng"}],"publisher":"LIT Verlag Berlin-Münster-Wien-Zürich-London","status":"public","alternative_title":["American Studies in Austria"],"month":"02","type":"book_chapter","page":"73 - 80","file":[{"date_created":"2018-12-12T10:08:06Z","date_updated":"2018-12-12T10:08:06Z","file_name":"IST-2017-732-v1+1_Austria_and_America_Cross-Cultural_Encounters.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":380624,"file_id":"4666","creator":"system"}],"publication_status":"published","author":[{"full_name":"Wenzl, Bernhard","last_name":"Wenzl","first_name":"Bernhard","id":"479E9046-F248-11E8-B48F-1D18A9856A87"}],"extern":"1","date_created":"2018-12-11T11:50:00Z","file_date_updated":"2018-12-12T10:08:06Z","_id":"1075","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","day":"01","title":"An American in Allied-occupied Austria: John Dos Passos Reports on "The Vienna Frontier"","oa":1,"citation":{"short":"B. Wenzl, in:, J. Parker, R. Poole (Eds.), Austria and America: 20th-Century Cross-Cultural Encounters, LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.","ista":"Wenzl B. 2017.An American in Allied-occupied Austria: John Dos Passos Reports on &quot;The Vienna Frontier&quot; In: Austria and America: 20th-Century Cross-Cultural Encounters. American Studies in Austria, vol. 15, 73–80.","mla":"Wenzl, Bernhard. “An American in Allied-Occupied Austria: John Dos Passos Reports on &quot;The Vienna Frontier&quot;” Austria and America: 20th-Century Cross-Cultural Encounters, edited by Joshua Parker and Ralph Poole, vol. 15, LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.","ieee":"B. Wenzl, “An American in Allied-occupied Austria: John Dos Passos Reports on &quot;The Vienna Frontier&quot;,” in Austria and America: 20th-Century Cross-Cultural Encounters, vol. 15, J. Parker and R. Poole, Eds. LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.","apa":"Wenzl, B. (2017). An American in Allied-occupied Austria: John Dos Passos Reports on &quot;The Vienna Frontier&quot; In J. Parker & R. Poole (Eds.), Austria and America: 20th-Century Cross-Cultural Encounters (Vol. 15, pp. 73–80). LIT Verlag Berlin-Münster-Wien-Zürich-London.","ama":"Wenzl B. An American in Allied-occupied Austria: John Dos Passos Reports on &quot;The Vienna Frontier&quot; In: Parker J, Poole R, eds. Austria and America: 20th-Century Cross-Cultural Encounters. Vol 15. LIT Verlag Berlin-Münster-Wien-Zürich-London; 2017:73-80.","chicago":"Wenzl, Bernhard. “An American in Allied-Occupied Austria: John Dos Passos Reports on &quot;The Vienna Frontier&quot;” In Austria and America: 20th-Century Cross-Cultural Encounters, edited by Joshua Parker and Ralph Poole, 15:73–80. LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017."},"date_updated":"2021-01-12T06:48:06Z"},{"file_date_updated":"2019-01-18T09:14:02Z","scopus_import":"1","_id":"1077","issue":"126","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"20160139","day":"04","isi":1,"title":"Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","citation":{"ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family,” Journal of the Royal Society Interface, vol. 14, no. 126. Royal Society of London, 2017.","mla":"Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface, vol. 14, no. 126, 20160139, Royal Society of London, 2017, doi:10.1098/rsif.2016.0139.","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 14(126), 20160139.","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017).","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface. Royal Society of London, 2017. https://doi.org/10.1098/rsif.2016.0139.","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 2017;14(126). doi:10.1098/rsif.2016.0139","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J. P. (2017). Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. Royal Society of London. https://doi.org/10.1098/rsif.2016.0139"},"oa":1,"project":[{"grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer"}],"date_updated":"2025-07-10T11:49:59Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"status":"public","file":[{"relation":"main_file","access_level":"open_access","date_updated":"2019-01-18T09:14:02Z","date_created":"2019-01-18T09:14:02Z","file_name":"2017_JRSI_Redondo.pdf","creator":"dernst","success":1,"file_id":"5843","content_type":"application/pdf","file_size":1092015}],"type":"journal_article","month":"01","related_material":{"record":[{"status":"public","id":"9864","relation":"research_data"}]},"publication_status":"published","author":[{"id":"409D5C96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5837-2793","first_name":"Rodrigo A","last_name":"Fernandes Redondo","full_name":"Fernandes Redondo, Rodrigo A"},{"id":"2A181218-F248-11E8-B48F-1D18A9856A87","first_name":"Harold","orcid":"0000-0002-5985-7653","last_name":"Vladar","full_name":"Vladar, Harold"},{"full_name":"Włodarski, Tomasz","first_name":"Tomasz","last_name":"Włodarski"},{"last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P"}],"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"external_id":{"isi":["000393380400001"]},"date_created":"2018-12-11T11:50:01Z","publication":"Journal of the Royal Society Interface","date_published":"2017-01-04T00:00:00Z","volume":14,"ec_funded":1,"intvolume":" 14","language":[{"iso":"eng"}],"article_processing_charge":"Yes (in subscription journal)","abstract":[{"lang":"eng","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 fX174 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."}],"publisher":"Royal Society of London","quality_controlled":"1","doi":"10.1098/rsif.2016.0139","has_accepted_license":"1","publication_identifier":{"issn":["1742-5689"]},"ddc":["570"],"oa_version":"Published Version","year":"2017","publist_id":"6303"},{"isi":1,"title":"Light sheet fluorescence microscopy of plant roots growing on the surface of a gel","project":[{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"oa":1,"citation":{"chicago":"Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” Journal of Visualized Experiments JoVE. Journal of Visualized Experiments, 2017. https://doi.org/10.3791/55044.","ama":"von Wangenheim D, Hauschild R, Friml J. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of visualized experiments JoVE. 2017;2017(119). doi:10.3791/55044","apa":"von Wangenheim, D., Hauschild, R., & Friml, J. (2017). Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of Visualized Experiments JoVE. Journal of Visualized Experiments. https://doi.org/10.3791/55044","ieee":"D. von Wangenheim, R. Hauschild, and J. Friml, “Light sheet fluorescence microscopy of plant roots growing on the surface of a gel,” Journal of visualized experiments JoVE, vol. 2017, no. 119. Journal of Visualized Experiments, 2017.","mla":"von Wangenheim, Daniel, et al. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” Journal of Visualized Experiments JoVE, vol. 2017, no. 119, e55044, Journal of Visualized Experiments, 2017, doi:10.3791/55044.","short":"D. von Wangenheim, R. Hauschild, J. Friml, Journal of Visualized Experiments JoVE 2017 (2017).","ista":"von Wangenheim D, Hauschild R, Friml J. 2017. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of visualized experiments JoVE. 2017(119), e55044."},"date_updated":"2025-04-15T06:50:23Z","scopus_import":"1","file_date_updated":"2018-12-12T10:16:32Z","_id":"1078","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"119","article_number":"e55044","day":"18","publication_status":"published","related_material":{"record":[{"status":"public","id":"5565","relation":"popular_science"}]},"author":[{"id":"49E91952-F248-11E8-B48F-1D18A9856A87","last_name":"Von Wangenheim","first_name":"Daniel","orcid":"0000-0002-6862-1247","full_name":"Von Wangenheim, Daniel"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","orcid":"0000-0001-9843-3522","first_name":"Robert"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"}],"department":[{"_id":"JiFr"},{"_id":"Bio"}],"external_id":{"isi":["000397847200041"]},"date_created":"2018-12-11T11:50:01Z","status":"public","type":"journal_article","month":"01","file":[{"relation":"main_file","access_level":"open_access","date_updated":"2018-12-12T10:16:31Z","date_created":"2018-12-12T10:16:31Z","file_name":"IST-2017-808-v1+1_2017_VWangenheim_list.pdf","file_id":"5219","content_type":"application/pdf","file_size":57678,"creator":"system"},{"creator":"system","file_id":"5220","file_size":1317820,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_name":"IST-2017-808-v1+2_2017_VWangenheim_article.pdf","date_created":"2018-12-12T10:16:32Z","date_updated":"2018-12-12T10:16:32Z"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. "}],"publisher":"Journal of Visualized Experiments","pubrep_id":"808","volume":2017,"ec_funded":1,"publication":"Journal of visualized experiments JoVE","date_published":"2017-01-18T00:00:00Z","intvolume":" 2017","ddc":["580"],"oa_version":"Published Version","year":"2017","publist_id":"6302","doi":"10.3791/55044","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"has_accepted_license":"1"},{"project":[{"call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"oa":1,"citation":{"mla":"Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” Mathematical Physics, Analysis and Geometry, vol. 20, no. 2, 6, Springer, 2017, doi:10.1007/s11040-017-9238-0.","ieee":"P. Nam and H. Van Den Bosch, “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges,” Mathematical Physics, Analysis and Geometry, vol. 20, no. 2. Springer, 2017.","ista":"Nam P, Van Den Bosch H. 2017. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis and Geometry. 20(2), 6.","short":"P. Nam, H. Van Den Bosch, Mathematical Physics, Analysis and Geometry 20 (2017).","chicago":"Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” Mathematical Physics, Analysis and Geometry. Springer, 2017. https://doi.org/10.1007/s11040-017-9238-0.","ama":"Nam P, Van Den Bosch H. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis and Geometry. 2017;20(2). doi:10.1007/s11040-017-9238-0","apa":"Nam, P., & Van Den Bosch, H. (2017). Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-017-9238-0"},"date_updated":"2025-06-04T08:11:50Z","arxiv":1,"isi":1,"title":"Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"2","article_number":"6","day":"01","scopus_import":"1","_id":"1079","department":[{"_id":"RoSe"}],"external_id":{"isi":["000401270000004"],"arxiv":["1603.07368"]},"date_created":"2018-12-11T11:50:02Z","publication_status":"published","author":[{"full_name":"Nam, Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan","last_name":"Nam"},{"first_name":"Hanne","last_name":"Van Den Bosch","full_name":"Van Den Bosch, Hanne"}],"type":"journal_article","month":"06","status":"public","abstract":[{"text":"We study the ionization problem in the Thomas-Fermi-Dirac-von Weizsäcker theory for atoms and molecules. We prove the nonexistence of minimizers for the energy functional when the number of electrons is large and the total nuclear charge is small. This nonexistence result also applies to external potentials decaying faster than the Coulomb potential. In the case of arbitrary nuclear charges, we obtain the nonexistence of stable minimizers and radial minimizers.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1603.07368"}],"publisher":"Springer","article_processing_charge":"No","language":[{"iso":"eng"}],"volume":20,"publication":"Mathematical Physics, Analysis and Geometry","date_published":"2017-06-01T00:00:00Z","intvolume":" 20","year":"2017","publist_id":"6300","oa_version":"Submitted Version","publication_identifier":{"issn":["1385-0172"]},"doi":"10.1007/s11040-017-9238-0","quality_controlled":"1"},{"ec_funded":1,"volume":8,"date_published":"2017-01-31T00:00:00Z","publication":"Nature Communications","intvolume":" 8","pubrep_id":"786","abstract":[{"text":"Reconstructing the evolutionary history of metastases is critical for understanding their basic biological principles and has profound clinical implications. Genome-wide sequencing data has enabled modern phylogenomic methods to accurately dissect subclones and their phylogenies from noisy and impure bulk tumour samples at unprecedented depth. However, existing methods are not designed to infer metastatic seeding patterns. Here we develop a tool, called Treeomics, to reconstruct the phylogeny of metastases and map subclones to their anatomic locations. Treeomics infers comprehensive seeding patterns for pancreatic, ovarian, and prostate cancers. Moreover, Treeomics correctly disambiguates true seeding patterns from sequencing artifacts; 7% of variants were misclassified by conventional statistical methods. These artifacts can skew phylogenies by creating illusory tumour heterogeneity among distinct samples. In silico benchmarking on simulated tumour phylogenies across a wide range of sample purities (15–95%) and sequencing depths (25-800 × ) demonstrates the accuracy of Treeomics compared with existing methods.","lang":"eng"}],"publisher":"Nature Publishing Group","article_processing_charge":"No","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2041-1723"]},"doi":"10.1038/ncomms14114","quality_controlled":"1","has_accepted_license":"1","year":"2017","publist_id":"6301","oa_version":"Published Version","ddc":["004","006"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"14114","day":"31","scopus_import":"1","file_date_updated":"2018-12-12T10:15:15Z","_id":"1080","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"citation":{"short":"J. Reiter, A. Makohon Moore, J. Gerold, I. Božić, K. Chatterjee, C. Iacobuzio Donahue, B. Vogelstein, M. Nowak, Nature Communications 8 (2017).","ista":"Reiter J, Makohon Moore A, Gerold J, Božić I, Chatterjee K, Iacobuzio Donahue C, Vogelstein B, Nowak M. 2017. Reconstructing metastatic seeding patterns of human cancers. Nature Communications. 8, 14114.","ieee":"J. Reiter et al., “Reconstructing metastatic seeding patterns of human cancers,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","mla":"Reiter, Johannes, et al. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” Nature Communications, vol. 8, 14114, Nature Publishing Group, 2017, doi:10.1038/ncomms14114.","apa":"Reiter, J., Makohon Moore, A., Gerold, J., Božić, I., Chatterjee, K., Iacobuzio Donahue, C., … Nowak, M. (2017). Reconstructing metastatic seeding patterns of human cancers. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14114","chicago":"Reiter, Johannes, Alvin Makohon Moore, Jeffrey Gerold, Ivana Božić, Krishnendu Chatterjee, Christine Iacobuzio Donahue, Bert Vogelstein, and Martin Nowak. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms14114.","ama":"Reiter J, Makohon Moore A, Gerold J, et al. Reconstructing metastatic seeding patterns of human cancers. Nature Communications. 2017;8. doi:10.1038/ncomms14114"},"oa":1,"date_updated":"2025-07-10T11:50:00Z","isi":1,"title":"Reconstructing metastatic seeding patterns of human cancers","type":"journal_article","month":"01","file":[{"relation":"main_file","access_level":"open_access","date_updated":"2018-12-12T10:15:15Z","date_created":"2018-12-12T10:15:15Z","file_name":"IST-2017-786-v1+1_ncomms14114.pdf","file_id":"5133","content_type":"application/pdf","file_size":897050,"creator":"system"}],"status":"public","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"department":[{"_id":"KrCh"}],"external_id":{"isi":["000393096600001"]},"date_created":"2018-12-11T11:50:02Z","publication_status":"published","author":[{"last_name":"Reiter","first_name":"Johannes","orcid":"0000-0002-0170-7353","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","full_name":"Reiter, Johannes"},{"first_name":"Alvin","last_name":"Makohon Moore","full_name":"Makohon Moore, Alvin"},{"last_name":"Gerold","first_name":"Jeffrey","full_name":"Gerold, Jeffrey"},{"full_name":"Božić, Ivana","last_name":"Božić","first_name":"Ivana"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Christine","last_name":"Iacobuzio Donahue","full_name":"Iacobuzio Donahue, Christine"},{"last_name":"Vogelstein","first_name":"Bert","full_name":"Vogelstein, Bert"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}]},{"status":"public","quality_controlled":"1","doi":"10.1038/s41559-017-0373-6","page":"100-107","month":"11","type":"journal_article","publication_identifier":{"issn":["2397-334X"]},"article_type":"original","author":[{"last_name":"Reger","first_name":"Julia","full_name":"Reger, Julia"},{"full_name":"Lind, Martin I.","first_name":"Martin I.","last_name":"Lind"},{"full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","last_name":"Robinson"},{"full_name":"Beckerman, Andrew P.","first_name":"Andrew P.","last_name":"Beckerman"}],"oa_version":"None","publication_status":"published","date_created":"2020-04-30T10:46:02Z","extern":"1","year":"2017","_id":"7725","day":"27","intvolume":" 2","date_published":"2017-11-27T00:00:00Z","publication":"Nature Ecology & Evolution","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":2,"language":[{"iso":"eng"}],"title":"Predation drives local adaptation of phenotypic plasticity","article_processing_charge":"No","publisher":"Springer Nature","date_updated":"2021-01-12T08:15:07Z","abstract":[{"text":"Phenotypic plasticity is the ability of an individual genotype to alter aspects of its phenotype depending on the current environment. It is central to the persistence, resistance and resilience of populations facing variation in physical or biological factors. Genetic variation in plasticity is pervasive, which suggests its local adaptation is plausible. Existing studies on the adaptation of plasticity typically focus on single traits and a few populations, while theory about interactions among genes (for example, pleiotropy) suggests that a multi-trait, landscape scale (for example, multiple populations) perspective is required. We present data from a landscape scale, replicated, multi-trait experiment using a classic predator–prey system centred on the water flea Daphnia pulex. We find predator regime-driven differences in genetic variation of multivariate plasticity. These differences are associated with strong divergent selection linked to a predation regime. Our findings are evidence for local adaptation of plasticity, suggesting that responses of populations to environmental variation depend on the conditions in which they evolved in the past.","lang":"eng"}],"citation":{"ama":"Reger J, Lind MI, Robinson MR, Beckerman AP. Predation drives local adaptation of phenotypic plasticity. Nature Ecology & Evolution. 2017;2:100-107. doi:10.1038/s41559-017-0373-6","chicago":"Reger, Julia, Martin I. Lind, Matthew Richard Robinson, and Andrew P. Beckerman. “Predation Drives Local Adaptation of Phenotypic Plasticity.” Nature Ecology & Evolution. Springer Nature, 2017. https://doi.org/10.1038/s41559-017-0373-6.","apa":"Reger, J., Lind, M. I., Robinson, M. R., & Beckerman, A. P. (2017). Predation drives local adaptation of phenotypic plasticity. Nature Ecology & Evolution. Springer Nature. https://doi.org/10.1038/s41559-017-0373-6","mla":"Reger, Julia, et al. “Predation Drives Local Adaptation of Phenotypic Plasticity.” Nature Ecology & Evolution, vol. 2, Springer Nature, 2017, pp. 100–07, doi:10.1038/s41559-017-0373-6.","ieee":"J. Reger, M. I. Lind, M. R. Robinson, and A. P. Beckerman, “Predation drives local adaptation of phenotypic plasticity,” Nature Ecology & Evolution, vol. 2. Springer Nature, pp. 100–107, 2017.","ista":"Reger J, Lind MI, Robinson MR, Beckerman AP. 2017. Predation drives local adaptation of phenotypic plasticity. Nature Ecology & Evolution. 2, 100–107.","short":"J. Reger, M.I. Lind, M.R. Robinson, A.P. Beckerman, Nature Ecology & Evolution 2 (2017) 100–107."}},{"issue":"1868","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"20171824","day":"06","_id":"7727","citation":{"apa":"Burger, D., Thomas, S., Aepli, H., Dreyer, M., Fabre, G., Marti, E., … Wedekind, C. (2017). Major histocompatibility complex-linked social signalling affects female fertility. Proceedings of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2017.1824","ama":"Burger D, Thomas S, Aepli H, et al. Major histocompatibility complex-linked social signalling affects female fertility. Proceedings of the Royal Society B: Biological Sciences. 2017;284(1868). doi:10.1098/rspb.2017.1824","chicago":"Burger, D., S. Thomas, H. Aepli, M. Dreyer, G. Fabre, E. Marti, H. Sieme, Matthew Richard Robinson, and C. Wedekind. “Major Histocompatibility Complex-Linked Social Signalling Affects Female Fertility.” Proceedings of the Royal Society B: Biological Sciences. The Royal Society, 2017. https://doi.org/10.1098/rspb.2017.1824.","ista":"Burger D, Thomas S, Aepli H, Dreyer M, Fabre G, Marti E, Sieme H, Robinson MR, Wedekind C. 2017. Major histocompatibility complex-linked social signalling affects female fertility. Proceedings of the Royal Society B: Biological Sciences. 284(1868), 20171824.","short":"D. Burger, S. Thomas, H. Aepli, M. Dreyer, G. Fabre, E. Marti, H. Sieme, M.R. Robinson, C. Wedekind, Proceedings of the Royal Society B: Biological Sciences 284 (2017).","mla":"Burger, D., et al. “Major Histocompatibility Complex-Linked Social Signalling Affects Female Fertility.” Proceedings of the Royal Society B: Biological Sciences, vol. 284, no. 1868, 20171824, The Royal Society, 2017, doi:10.1098/rspb.2017.1824.","ieee":"D. Burger et al., “Major histocompatibility complex-linked social signalling affects female fertility,” Proceedings of the Royal Society B: Biological Sciences, vol. 284, no. 1868. The Royal Society, 2017."},"date_updated":"2021-01-12T08:15:08Z","title":"Major histocompatibility complex-linked social signalling affects female fertility","type":"journal_article","month":"12","status":"public","extern":"1","external_id":{"pmid":["29212724"]},"date_created":"2020-04-30T10:46:43Z","publication_status":"published","author":[{"full_name":"Burger, D.","first_name":"D.","last_name":"Burger"},{"full_name":"Thomas, S.","last_name":"Thomas","first_name":"S."},{"full_name":"Aepli, H.","last_name":"Aepli","first_name":"H."},{"last_name":"Dreyer","first_name":"M.","full_name":"Dreyer, M."},{"full_name":"Fabre, G.","first_name":"G.","last_name":"Fabre"},{"full_name":"Marti, E.","first_name":"E.","last_name":"Marti"},{"last_name":"Sieme","first_name":"H.","full_name":"Sieme, H."},{"full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","last_name":"Robinson"},{"full_name":"Wedekind, C.","last_name":"Wedekind","first_name":"C."}],"pmid":1,"publication":"Proceedings of the Royal Society B: Biological Sciences","date_published":"2017-12-06T00:00:00Z","volume":284,"intvolume":" 284","abstract":[{"lang":"eng","text":"Genes of the major histocompatibility complex (MHC) have been shown to influence social signalling and mate preferences in many species, including humans. First observations suggest that MHC signalling may also affect female fertility. To test this hypothesis, we exposed 191 female horses (Equus caballus) to either an MHC-similar or an MHC-dissimilar stimulus male around the time of ovulation and conception. A within-subject experimental design controlled for non-MHC-linked male characteristics, and instrumental insemination with semen of other males (n = 106) controlled for potential confounding effects of semen or embryo characteristics. We found that females were more likely to become pregnant if exposed to an MHC-dissimilar than to an MHC-similar male, while overall genetic distance to the stimulus males (based on microsatellite markers on 20 chromosomes) had no effect. Our results demonstrate that early pregnancy failures can be due to maternal life-history decisions (cryptic female choice) influenced by MHC-linked social signalling."}],"publisher":"The Royal Society","language":[{"iso":"eng"}],"article_processing_charge":"No","publication_identifier":{"issn":["0962-8452","1471-2954"]},"quality_controlled":"1","doi":"10.1098/rspb.2017.1824","year":"2017","oa_version":"None","article_type":"original"},{"publication_identifier":{"issn":["2397-3374"]},"month":"09","type":"journal_article","page":"757-765","doi":"10.1038/s41562-017-0195-1","quality_controlled":"1","status":"public","year":"2017","extern":"1","date_created":"2020-04-30T10:47:02Z","publication_status":"published","oa_version":"None","article_type":"original","author":[{"last_name":"Tropf","first_name":"Felix C.","full_name":"Tropf, Felix C."},{"last_name":"Lee","first_name":"S. Hong","full_name":"Lee, S. Hong"},{"full_name":"Verweij, Renske M.","first_name":"Renske M.","last_name":"Verweij"},{"full_name":"Stulp, Gert","last_name":"Stulp","first_name":"Gert"},{"full_name":"van der Most, Peter J.","last_name":"van der Most","first_name":"Peter J."},{"last_name":"de Vlaming","first_name":"Ronald","full_name":"de Vlaming, Ronald"},{"full_name":"Bakshi, Andrew","last_name":"Bakshi","first_name":"Andrew"},{"full_name":"Briley, Daniel A.","last_name":"Briley","first_name":"Daniel A."},{"first_name":"Charles","last_name":"Rahal","full_name":"Rahal, Charles"},{"full_name":"Hellpap, Robert","last_name":"Hellpap","first_name":"Robert"},{"full_name":"Iliadou, Anastasia N.","first_name":"Anastasia N.","last_name":"Iliadou"},{"full_name":"Esko, Tõnu","first_name":"Tõnu","last_name":"Esko"},{"last_name":"Metspalu","first_name":"Andres","full_name":"Metspalu, Andres"},{"last_name":"Medland","first_name":"Sarah E.","full_name":"Medland, Sarah E."},{"last_name":"Martin","first_name":"Nicholas G.","full_name":"Martin, Nicholas G."},{"first_name":"Nicola","last_name":"Barban","full_name":"Barban, Nicola"},{"first_name":"Harold","last_name":"Snieder","full_name":"Snieder, Harold"},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard"},{"full_name":"Mills, Melinda C.","first_name":"Melinda C.","last_name":"Mills"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":1,"date_published":"2017-09-11T00:00:00Z","publication":"Nature Human Behaviour","issue":"10","day":"11","intvolume":" 1","_id":"7728","citation":{"ista":"Tropf FC, Lee SH, Verweij RM, Stulp G, van der Most PJ, de Vlaming R, Bakshi A, Briley DA, Rahal C, Hellpap R, Iliadou AN, Esko T, Metspalu A, Medland SE, Martin NG, Barban N, Snieder H, Robinson MR, Mills MC. 2017. Hidden heritability due to heterogeneity across seven populations. Nature Human Behaviour. 1(10), 757–765.","short":"F.C. Tropf, S.H. Lee, R.M. Verweij, G. Stulp, P.J. van der Most, R. de Vlaming, A. Bakshi, D.A. Briley, C. Rahal, R. Hellpap, A.N. Iliadou, T. Esko, A. Metspalu, S.E. Medland, N.G. Martin, N. Barban, H. Snieder, M.R. Robinson, M.C. Mills, Nature Human Behaviour 1 (2017) 757–765.","mla":"Tropf, Felix C., et al. “Hidden Heritability Due to Heterogeneity across Seven Populations.” Nature Human Behaviour, vol. 1, no. 10, Springer Nature, 2017, pp. 757–65, doi:10.1038/s41562-017-0195-1.","ieee":"F. C. Tropf et al., “Hidden heritability due to heterogeneity across seven populations,” Nature Human Behaviour, vol. 1, no. 10. Springer Nature, pp. 757–765, 2017.","apa":"Tropf, F. C., Lee, S. H., Verweij, R. M., Stulp, G., van der Most, P. J., de Vlaming, R., … Mills, M. C. (2017). Hidden heritability due to heterogeneity across seven populations. Nature Human Behaviour. Springer Nature. https://doi.org/10.1038/s41562-017-0195-1","ama":"Tropf FC, Lee SH, Verweij RM, et al. Hidden heritability due to heterogeneity across seven populations. Nature Human Behaviour. 2017;1(10):757-765. doi:10.1038/s41562-017-0195-1","chicago":"Tropf, Felix C., S. Hong Lee, Renske M. Verweij, Gert Stulp, Peter J. van der Most, Ronald de Vlaming, Andrew Bakshi, et al. “Hidden Heritability Due to Heterogeneity across Seven Populations.” Nature Human Behaviour. Springer Nature, 2017. https://doi.org/10.1038/s41562-017-0195-1."},"abstract":[{"lang":"eng","text":"Meta-analyses of genome-wide association studies, which dominate genetic discovery, are based on data from diverse historical time periods and populations. Genetic scores derived from genome-wide association studies explain only a fraction of the heritability estimates obtained from whole-genome studies on single populations, known as the ‘hidden heritability’ puzzle. Using seven sampling populations (n = 35,062), we test whether hidden heritability is attributed to heterogeneity across sampling populations and time, showing that estimates are substantially smaller across populations compared with within populations. We show that the hidden heritability varies substantially: from zero for height to 20% for body mass index, 37% for education, 40% for age at first birth and up to 75% for number of children. Simulations demonstrate that our results are more likely to reflect heterogeneity in phenotypic measurement or gene–environment interactions than genetic heterogeneity. These findings have substantial implications for genetic discovery, suggesting that large homogenous datasets are required for behavioural phenotypes and that gene–environment interaction may be a central challenge for genetic discovery."}],"date_updated":"2021-01-12T08:15:08Z","publisher":"Springer Nature","article_processing_charge":"No","title":"Hidden heritability due to heterogeneity across seven populations","language":[{"iso":"eng"}]},{"type":"journal_article","month":"08","page":"8602-8607","publication_identifier":{"issn":["0027-8424","1091-6490"]},"status":"public","doi":"10.1073/pnas.1621096114","quality_controlled":"1","date_created":"2020-04-30T10:47:19Z","year":"2017","extern":"1","article_type":"original","author":[{"first_name":"Loic","last_name":"Yengo","full_name":"Yengo, Loic"},{"full_name":"Zhu, Zhihong","first_name":"Zhihong","last_name":"Zhu"},{"first_name":"Naomi R.","last_name":"Wray","full_name":"Wray, Naomi R."},{"full_name":"Weir, Bruce S.","last_name":"Weir","first_name":"Bruce S."},{"full_name":"Yang, Jian","last_name":"Yang","first_name":"Jian"},{"first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard"},{"first_name":"Peter M.","last_name":"Visscher","full_name":"Visscher, Peter M."}],"publication_status":"published","oa_version":"None","related_material":{"link":[{"url":"https://doi.org/10.1073/pnas.1718598115","relation":"other"}]},"day":"08","intvolume":" 114","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":114,"publication":"Proceedings of the National Academy of Sciences","issue":"32","date_published":"2017-08-08T00:00:00Z","_id":"7729","date_updated":"2021-01-12T08:15:09Z","publisher":"Proceedings of the National Academy of Sciences","abstract":[{"text":"Quantifying the effects of inbreeding is critical to characterizing the genetic architecture of complex traits. This study highlights through theory and simulations the strengths and shortcomings of three SNP-based inbreeding measures commonly used to estimate inbreeding depression (ID). We demonstrate that heterogeneity in linkage disequilibrium (LD) between causal variants and SNPs biases ID estimates, and we develop an approach to correct this bias using LD and minor allele frequency stratified inference (LDMS). We quantified ID in 25 traits measured in ∼140,000 participants of the UK Biobank, using LDMS, and confirmed previously published ID for 4 traits. We find unique evidence of ID for handgrip strength, waist/hip ratio, and visual and auditory acuity (ID between −2.3 and −5.2 phenotypic SDs for complete inbreeding; P<0.001). Our results illustrate that a careful choice of the measure of inbreeding combined with LDMS stratification improves both detection and quantification of ID using SNP data.","lang":"eng"}],"citation":{"ama":"Yengo L, Zhu Z, Wray NR, et al. Detection and quantification of inbreeding depression for complex traits from SNP data. Proceedings of the National Academy of Sciences. 2017;114(32):8602-8607. doi:10.1073/pnas.1621096114","chicago":"Yengo, Loic, Zhihong Zhu, Naomi R. Wray, Bruce S. Weir, Jian Yang, Matthew Richard Robinson, and Peter M. Visscher. “Detection and Quantification of Inbreeding Depression for Complex Traits from SNP Data.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1621096114.","apa":"Yengo, L., Zhu, Z., Wray, N. R., Weir, B. S., Yang, J., Robinson, M. R., & Visscher, P. M. (2017). Detection and quantification of inbreeding depression for complex traits from SNP data. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1621096114","mla":"Yengo, Loic, et al. “Detection and Quantification of Inbreeding Depression for Complex Traits from SNP Data.” Proceedings of the National Academy of Sciences, vol. 114, no. 32, Proceedings of the National Academy of Sciences, 2017, pp. 8602–07, doi:10.1073/pnas.1621096114.","ieee":"L. Yengo et al., “Detection and quantification of inbreeding depression for complex traits from SNP data,” Proceedings of the National Academy of Sciences, vol. 114, no. 32. Proceedings of the National Academy of Sciences, pp. 8602–8607, 2017.","short":"L. Yengo, Z. Zhu, N.R. Wray, B.S. Weir, J. Yang, M.R. Robinson, P.M. Visscher, Proceedings of the National Academy of Sciences 114 (2017) 8602–8607.","ista":"Yengo L, Zhu Z, Wray NR, Weir BS, Yang J, Robinson MR, Visscher PM. 2017. Detection and quantification of inbreeding depression for complex traits from SNP data. Proceedings of the National Academy of Sciences. 114(32), 8602–8607."},"article_processing_charge":"No","language":[{"iso":"eng"}],"title":"Detection and quantification of inbreeding depression for complex traits from SNP data"},{"status":"public","doi":"10.1534/genetics.116.193383","quality_controlled":"1","type":"journal_article","month":"06","page":"1113-1126","publication_identifier":{"issn":["0016-6731","1943-2631"]},"article_type":"original","author":[{"last_name":"Lloyd-Jones","first_name":"Luke R.","full_name":"Lloyd-Jones, Luke R."},{"full_name":"Robinson, Matthew Richard","last_name":"Robinson","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"full_name":"Moser, Gerhard","last_name":"Moser","first_name":"Gerhard"},{"full_name":"Zeng, Jian","first_name":"Jian","last_name":"Zeng"},{"full_name":"Beleza, Sandra","last_name":"Beleza","first_name":"Sandra"},{"first_name":"Gregory S.","last_name":"Barsh","full_name":"Barsh, Gregory S."},{"full_name":"Tang, Hua","first_name":"Hua","last_name":"Tang"},{"full_name":"Visscher, Peter M.","first_name":"Peter M.","last_name":"Visscher"}],"publication_status":"published","oa_version":"None","date_created":"2020-04-30T10:47:50Z","year":"2017","extern":"1","_id":"7731","day":"01","intvolume":" 206","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":206,"publication":"Genetics","issue":"2","date_published":"2017-06-01T00:00:00Z","article_processing_charge":"No","language":[{"iso":"eng"}],"title":"Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models","date_updated":"2021-01-12T08:15:10Z","publisher":"Genetics Society of America","citation":{"apa":"Lloyd-Jones, L. R., Robinson, M. R., Moser, G., Zeng, J., Beleza, S., Barsh, G. S., … Visscher, P. M. (2017). Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.193383","chicago":"Lloyd-Jones, Luke R., Matthew Richard Robinson, Gerhard Moser, Jian Zeng, Sandra Beleza, Gregory S. Barsh, Hua Tang, and Peter M. Visscher. “Inference on the Genetic Basis of Eye and Skin Color in an Admixed Population via Bayesian Linear Mixed Models.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.193383.","ama":"Lloyd-Jones LR, Robinson MR, Moser G, et al. Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models. Genetics. 2017;206(2):1113-1126. doi:10.1534/genetics.116.193383","ista":"Lloyd-Jones LR, Robinson MR, Moser G, Zeng J, Beleza S, Barsh GS, Tang H, Visscher PM. 2017. Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models. Genetics. 206(2), 1113–1126.","short":"L.R. Lloyd-Jones, M.R. Robinson, G. Moser, J. Zeng, S. Beleza, G.S. Barsh, H. Tang, P.M. Visscher, Genetics 206 (2017) 1113–1126.","ieee":"L. R. Lloyd-Jones et al., “Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models,” Genetics, vol. 206, no. 2. Genetics Society of America, pp. 1113–1126, 2017.","mla":"Lloyd-Jones, Luke R., et al. “Inference on the Genetic Basis of Eye and Skin Color in an Admixed Population via Bayesian Linear Mixed Models.” Genetics, vol. 206, no. 2, Genetics Society of America, 2017, pp. 1113–26, doi:10.1534/genetics.116.193383."},"abstract":[{"text":"Genetic association studies in admixed populations are underrepresented in the genomics literature, with a key concern for researchers being the adequate control of spurious associations due to population structure. Linear mixed models (LMMs) are well suited for genome-wide association studies (GWAS) because they account for both population stratification and cryptic relatedness and achieve increased statistical power by jointly modeling all genotyped markers. Additionally, Bayesian LMMs allow for more flexible assumptions about the underlying distribution of genetic effects, and can concurrently estimate the proportion of phenotypic variance explained by genetic markers. Using three recently published Bayesian LMMs, Bayes R, BSLMM, and BOLT-LMM, we investigate an existing data set on eye (n = 625) and skin (n = 684) color from Cape Verde, an island nation off West Africa that is home to individuals with a broad range of phenotypic values for eye and skin color due to the mix of West African and European ancestry. We use simulations to demonstrate the utility of Bayesian LMMs for mapping loci and studying the genetic architecture of quantitative traits in admixed populations. The Bayesian LMMs provide evidence for two new pigmentation loci: one for eye color (AHRR) and one for skin color (DDB1).","lang":"eng"}]},{"status":"public","page":"418-428","month":"07","type":"journal_article","publication_status":"published","author":[{"full_name":"Garton, Fleur C.","last_name":"Garton","first_name":"Fleur C."},{"full_name":"Benyamin, Beben","first_name":"Beben","last_name":"Benyamin"},{"full_name":"Zhao, Qiongyi","last_name":"Zhao","first_name":"Qiongyi"},{"full_name":"Liu, Zhijun","last_name":"Liu","first_name":"Zhijun"},{"last_name":"Gratten","first_name":"Jacob","full_name":"Gratten, Jacob"},{"first_name":"Anjali K.","last_name":"Henders","full_name":"Henders, Anjali K."},{"first_name":"Zong-Hong","last_name":"Zhang","full_name":"Zhang, Zong-Hong"},{"full_name":"Edson, Janette","first_name":"Janette","last_name":"Edson"},{"first_name":"Sarah","last_name":"Furlong","full_name":"Furlong, Sarah"},{"full_name":"Morgan, Sarah","last_name":"Morgan","first_name":"Sarah"},{"first_name":"Susan","last_name":"Heggie","full_name":"Heggie, Susan"},{"full_name":"Thorpe, Kathryn","first_name":"Kathryn","last_name":"Thorpe"},{"full_name":"Pfluger, Casey","first_name":"Casey","last_name":"Pfluger"},{"first_name":"Karen A.","last_name":"Mather","full_name":"Mather, Karen A."},{"first_name":"Perminder S.","last_name":"Sachdev","full_name":"Sachdev, Perminder S."},{"last_name":"McRae","first_name":"Allan F.","full_name":"McRae, Allan F."},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard"},{"first_name":"Sonia","last_name":"Shah","full_name":"Shah, Sonia"},{"last_name":"Visscher","first_name":"Peter M.","full_name":"Visscher, Peter M."},{"full_name":"Mangelsdorf, Marie","first_name":"Marie","last_name":"Mangelsdorf"},{"last_name":"Henderson","first_name":"Robert D.","full_name":"Henderson, Robert D."},{"first_name":"Naomi R.","last_name":"Wray","full_name":"Wray, Naomi R."},{"full_name":"McCombe, Pamela A.","first_name":"Pamela A.","last_name":"McCombe"}],"extern":"1","date_created":"2020-04-30T10:48:25Z","_id":"7733","issue":"4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","title":"Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort","citation":{"apa":"Garton, F. C., Benyamin, B., Zhao, Q., Liu, Z., Gratten, J., Henders, A. K., … McCombe, P. A. (2017). Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort. Molecular Genetics & Genomic Medicine. Wiley. https://doi.org/10.1002/mgg3.302","ama":"Garton FC, Benyamin B, Zhao Q, et al. Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort. Molecular Genetics & Genomic Medicine. 2017;5(4):418-428. doi:10.1002/mgg3.302","chicago":"Garton, Fleur C., Beben Benyamin, Qiongyi Zhao, Zhijun Liu, Jacob Gratten, Anjali K. Henders, Zong-Hong Zhang, et al. “Whole Exome Sequencing and DNA Methylation Analysis in a Clinical Amyotrophic Lateral Sclerosis Cohort.” Molecular Genetics & Genomic Medicine. Wiley, 2017. https://doi.org/10.1002/mgg3.302.","short":"F.C. Garton, B. Benyamin, Q. Zhao, Z. Liu, J. Gratten, A.K. Henders, Z.-H. Zhang, J. Edson, S. Furlong, S. Morgan, S. Heggie, K. Thorpe, C. Pfluger, K.A. Mather, P.S. Sachdev, A.F. McRae, M.R. Robinson, S. Shah, P.M. Visscher, M. Mangelsdorf, R.D. Henderson, N.R. Wray, P.A. McCombe, Molecular Genetics & Genomic Medicine 5 (2017) 418–428.","ista":"Garton FC, Benyamin B, Zhao Q, Liu Z, Gratten J, Henders AK, Zhang Z-H, Edson J, Furlong S, Morgan S, Heggie S, Thorpe K, Pfluger C, Mather KA, Sachdev PS, McRae AF, Robinson MR, Shah S, Visscher PM, Mangelsdorf M, Henderson RD, Wray NR, McCombe PA. 2017. Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort. Molecular Genetics & Genomic Medicine. 5(4), 418–428.","mla":"Garton, Fleur C., et al. “Whole Exome Sequencing and DNA Methylation Analysis in a Clinical Amyotrophic Lateral Sclerosis Cohort.” Molecular Genetics & Genomic Medicine, vol. 5, no. 4, Wiley, 2017, pp. 418–28, doi:10.1002/mgg3.302.","ieee":"F. C. Garton et al., “Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort,” Molecular Genetics & Genomic Medicine, vol. 5, no. 4. Wiley, pp. 418–428, 2017."},"oa":1,"date_updated":"2021-01-12T08:15:10Z","quality_controlled":"1","doi":"10.1002/mgg3.302","publication_identifier":{"issn":["2324-9269"]},"oa_version":"Published Version","article_type":"original","year":"2017","publication":"Molecular Genetics & Genomic Medicine","date_published":"2017-07-01T00:00:00Z","volume":5,"intvolume":" 5","language":[{"iso":"eng"}],"article_processing_charge":"No","abstract":[{"text":"Sections\r\nPDFPDF\r\nTools\r\nShare\r\nAbstract\r\nBackground: Gene discovery has provided remarkable biological insights into amyotrophic lateral sclerosis (ALS). One challenge for clinical application of genetic testing is critical evaluation of the significance of reported variants.\r\nMethods: We use whole exome sequencing (WES) to develop a clinically relevant approach to identify a subset of ALS patients harboring likely pathogenic mutations. In parallel, we assess if DNA methylation can be used to screen for pathogenicity of novel variants since a methylation signature has been shown to associate with the pathogenic C9orf72 expansion, but has not been explored for other ALS mutations. Australian patients identified with ALS‐relevant variants were cross‐checked with population databases and case reports to critically assess whether they were “likely causal,” “uncertain significance,” or “unlikely causal.”\r\nResults: Published ALS variants were identified in >10% of patients; however, in only 3% of patients (4/120) could these be confidently considered pathogenic (in SOD1 and TARDBP). We found no evidence for a differential DNA methylation signature in these mutation carriers.\r\nConclusions: The use of WES in a typical ALS clinic demonstrates a critical approach to variant assessment with the capability to combine cohorts to enhance the largely unknown genetic basis of ALS.","lang":"eng"}],"publisher":"Wiley","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/mgg3.302"}]},{"date_created":"2020-04-30T11:38:24Z","year":"2017","extern":"1","author":[{"first_name":"James P.","last_name":"Sethna","full_name":"Sethna, James P."},{"last_name":"Bierbaum","first_name":"Matthew K.","full_name":"Bierbaum, Matthew K."},{"first_name":"Karin A.","last_name":"Dahmen","full_name":"Dahmen, Karin A."},{"first_name":"Carl Peter","orcid":"0000-0002-1307-5074","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","full_name":"Goodrich, Carl Peter"},{"full_name":"Greer, Julia R.","last_name":"Greer","first_name":"Julia R."},{"last_name":"Hayden","first_name":"Lorien X.","full_name":"Hayden, Lorien X."},{"full_name":"Kent-Dobias, Jaron P.","last_name":"Kent-Dobias","first_name":"Jaron P."},{"full_name":"Lee, Edward D.","last_name":"Lee","first_name":"Edward D."},{"first_name":"Danilo B.","last_name":"Liarte","full_name":"Liarte, Danilo B."},{"first_name":"Xiaoyue","last_name":"Ni","full_name":"Ni, Xiaoyue"},{"first_name":"Katherine N.","last_name":"Quinn","full_name":"Quinn, Katherine N."},{"last_name":"Raju","first_name":"Archishman","full_name":"Raju, Archishman"},{"last_name":"Rocklin","first_name":"D. Zeb","full_name":"Rocklin, D. Zeb"},{"first_name":"Ashivni","last_name":"Shekhawat","full_name":"Shekhawat, Ashivni"},{"first_name":"Stefano","last_name":"Zapperi","full_name":"Zapperi, Stefano"}],"article_type":"original","publication_status":"published","oa_version":"Published Version","type":"journal_article","month":"07","page":"217-246","publication_identifier":{"issn":["1531-7331","1545-4118"]},"status":"public","doi":"10.1146/annurev-matsci-070115-032036","quality_controlled":"1","publisher":"Annual Reviews","main_file_link":[{"url":"https://doi.org/10.1146/annurev-matsci-070115-032036","open_access":"1"}],"date_updated":"2021-01-12T08:15:18Z","abstract":[{"lang":"eng","text":"We give a bird's-eye view of the plastic deformation of crystals aimed at the statistical physics community, as well as a broad introduction to the statistical theories of forced rigid systems aimed at the plasticity community. Memory effects in magnets, spin glasses, charge density waves, and dilute colloidal suspensions are discussed in relation to the onset of plastic yielding in crystals. Dislocation avalanches and complex dislocation tangles are discussed via a brief introduction to the renormalization group and scaling. Analogies to emergent scale invariance in fracture, jamming, coarsening, and a variety of depinning transitions are explored. Dislocation dynamics in crystals challenge nonequilibrium statistical physics. Statistical physics provides both cautionary tales of subtle memory effects in nonequilibrium systems and systematic tools designed to address complex scale-invariant behavior on multiple length scales and timescales."}],"citation":{"apa":"Sethna, J. P., Bierbaum, M. K., Dahmen, K. A., Goodrich, C. P., Greer, J. R., Hayden, L. X., … Zapperi, S. (2017). Deformation of crystals: Connections with statistical physics. Annual Review of Materials Research. Annual Reviews. https://doi.org/10.1146/annurev-matsci-070115-032036","ama":"Sethna JP, Bierbaum MK, Dahmen KA, et al. Deformation of crystals: Connections with statistical physics. Annual Review of Materials Research. 2017;47:217-246. doi:10.1146/annurev-matsci-070115-032036","chicago":"Sethna, James P., Matthew K. Bierbaum, Karin A. Dahmen, Carl Peter Goodrich, Julia R. Greer, Lorien X. Hayden, Jaron P. Kent-Dobias, et al. “Deformation of Crystals: Connections with Statistical Physics.” Annual Review of Materials Research. Annual Reviews, 2017. https://doi.org/10.1146/annurev-matsci-070115-032036.","short":"J.P. Sethna, M.K. Bierbaum, K.A. Dahmen, C.P. Goodrich, J.R. Greer, L.X. Hayden, J.P. Kent-Dobias, E.D. Lee, D.B. Liarte, X. Ni, K.N. Quinn, A. Raju, D.Z. Rocklin, A. Shekhawat, S. Zapperi, Annual Review of Materials Research 47 (2017) 217–246.","ista":"Sethna JP, Bierbaum MK, Dahmen KA, Goodrich CP, Greer JR, Hayden LX, Kent-Dobias JP, Lee ED, Liarte DB, Ni X, Quinn KN, Raju A, Rocklin DZ, Shekhawat A, Zapperi S. 2017. Deformation of crystals: Connections with statistical physics. Annual Review of Materials Research. 47, 217–246.","mla":"Sethna, James P., et al. “Deformation of Crystals: Connections with Statistical Physics.” Annual Review of Materials Research, vol. 47, Annual Reviews, 2017, pp. 217–46, doi:10.1146/annurev-matsci-070115-032036.","ieee":"J. P. Sethna et al., “Deformation of crystals: Connections with statistical physics,” Annual Review of Materials Research, vol. 47. Annual Reviews, pp. 217–246, 2017."},"oa":1,"article_processing_charge":"No","language":[{"iso":"eng"}],"title":"Deformation of crystals: Connections with statistical physics","day":"01","intvolume":" 47","volume":47,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Annual Review of Materials Research","date_published":"2017-07-01T00:00:00Z","_id":"7755"}]