[{"arxiv":1,"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”.","external_id":{"arxiv":["1312.1231"],"isi":["000398030400024"]},"publication":"Transactions of the American Mathematical Society","date_published":"2017-05-01T00:00:00Z","month":"05","author":[{"last_name":"Bauer","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich","orcid":"0000-0002-9683-0724","full_name":"Bauer, Ulrich"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833"}],"intvolume":"       369","quality_controlled":"1","doi":"10.1090/tran/6991","year":"2017","article_processing_charge":"No","publication_status":"published","project":[{"call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems","grant_number":"318493"}],"oa_version":"Preprint","language":[{"iso":"eng"}],"volume":369,"date_created":"2018-12-11T11:49:59Z","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."}],"date_updated":"2023-09-20T12:05:56Z","main_file_link":[{"url":"https://arxiv.org/abs/1312.1231","open_access":"1"}],"article_type":"original","isi":1,"oa":1,"citation":{"ieee":"U. Bauer and H. Edelsbrunner, “The Morse theory of Čech and delaunay complexes,” <i>Transactions of the American Mathematical Society</i>, vol. 369, no. 5. American Mathematical Society, pp. 3741–3762, 2017.","chicago":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Complexes.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2017. <a href=\"https://doi.org/10.1090/tran/6991\">https://doi.org/10.1090/tran/6991</a>.","mla":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Complexes.” <i>Transactions of the American Mathematical Society</i>, vol. 369, no. 5, American Mathematical Society, 2017, pp. 3741–62, doi:<a href=\"https://doi.org/10.1090/tran/6991\">10.1090/tran/6991</a>.","ista":"Bauer U, Edelsbrunner H. 2017. The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. 369(5), 3741–3762.","ama":"Bauer U, Edelsbrunner H. The Morse theory of Čech and delaunay complexes. <i>Transactions of the American Mathematical Society</i>. 2017;369(5):3741-3762. doi:<a href=\"https://doi.org/10.1090/tran/6991\">10.1090/tran/6991</a>","apa":"Bauer, U., &#38; Edelsbrunner, H. (2017). The Morse theory of Čech and delaunay complexes. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/6991\">https://doi.org/10.1090/tran/6991</a>","short":"U. Bauer, H. Edelsbrunner, Transactions of the American Mathematical Society 369 (2017) 3741–3762."},"day":"01","_id":"1072","publisher":"American Mathematical Society","department":[{"_id":"HeEd"}],"publist_id":"6311","type":"journal_article","scopus_import":"1","title":"The Morse theory of Čech and delaunay complexes","status":"public","page":"3741 - 3762","ec_funded":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"5"},{"month":"06","author":[{"full_name":"Čadek, Martin","first_name":"Martin","last_name":"Čadek"},{"last_name":"Krcál","id":"33E21118-F248-11E8-B48F-1D18A9856A87","first_name":"Marek","full_name":"Krcál, Marek"},{"last_name":"Vokřínek","first_name":"Lukáš","full_name":"Vokřínek, Lukáš"}],"intvolume":"        54","quality_controlled":"1","publication":"Discrete & Computational Geometry","external_id":{"isi":["000400072700008"]},"date_published":"2017-06-01T00:00:00Z","article_processing_charge":"No","publication_status":"published","oa_version":"Submitted Version","doi":"10.1007/s00454-016-9855-6","year":"2017","citation":{"short":"M. Čadek, M. Krcál, L. Vokřínek, Discrete &#38; Computational Geometry 54 (2017) 915–965.","apa":"Čadek, M., Krcál, M., &#38; Vokřínek, L. (2017). Algorithmic solvability of the lifting extension problem. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-016-9855-6\">https://doi.org/10.1007/s00454-016-9855-6</a>","ama":"Čadek M, Krcál M, Vokřínek L. Algorithmic solvability of the lifting extension problem. <i>Discrete &#38; Computational Geometry</i>. 2017;54(4):915-965. doi:<a href=\"https://doi.org/10.1007/s00454-016-9855-6\">10.1007/s00454-016-9855-6</a>","ista":"Čadek M, Krcál M, Vokřínek L. 2017. Algorithmic solvability of the lifting extension problem. Discrete &#38; Computational Geometry. 54(4), 915–965.","mla":"Čadek, Martin, et al. “Algorithmic Solvability of the Lifting Extension Problem.” <i>Discrete &#38; Computational Geometry</i>, vol. 54, no. 4, Springer, 2017, pp. 915–65, doi:<a href=\"https://doi.org/10.1007/s00454-016-9855-6\">10.1007/s00454-016-9855-6</a>.","chicago":"Čadek, Martin, Marek Krcál, and Lukáš Vokřínek. “Algorithmic Solvability of the Lifting Extension Problem.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00454-016-9855-6\">https://doi.org/10.1007/s00454-016-9855-6</a>.","ieee":"M. Čadek, M. Krcál, and L. Vokřínek, “Algorithmic solvability of the lifting extension problem,” <i>Discrete &#38; Computational Geometry</i>, vol. 54, no. 4. Springer, pp. 915–965, 2017."},"day":"01","_id":"1073","publisher":"Springer","department":[{"_id":"UlWa"}],"language":[{"iso":"eng"}],"abstract":[{"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.","lang":"eng"}],"volume":54,"date_created":"2018-12-11T11:50:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1307.6444","open_access":"1"}],"date_updated":"2023-09-20T12:01:28Z","isi":1,"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"4","publist_id":"6309","type":"journal_article","title":"Algorithmic solvability of the lifting extension problem","status":"public","scopus_import":"1","publication_identifier":{"issn":["01795376"]},"page":"915 - 965"},{"intvolume":"       205","month":"03","author":[{"last_name":"Ringbauer","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4884-9682","full_name":"Ringbauer, Harald","first_name":"Harald"},{"full_name":"Coop, Graham","first_name":"Graham","last_name":"Coop"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"}],"quality_controlled":"1","external_id":{"isi":["000395807200023"]},"publication":"Genetics","date_published":"2017-03-01T00:00:00Z","article_processing_charge":"No","publication_status":"published","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"oa_version":"Preprint","related_material":{"record":[{"id":"200","relation":"dissertation_contains","status":"public"}]},"doi":"10.1534/genetics.116.196220","year":"2017","citation":{"chicago":"Ringbauer, Harald, Graham Coop, and Nicholas H Barton. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” <i>Genetics</i>. Genetics Society of America, 2017. <a href=\"https://doi.org/10.1534/genetics.116.196220\">https://doi.org/10.1534/genetics.116.196220</a>.","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.","mla":"Ringbauer, Harald, et al. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” <i>Genetics</i>, vol. 205, no. 3, Genetics Society of America, 2017, pp. 1335–51, doi:<a href=\"https://doi.org/10.1534/genetics.116.196220\">10.1534/genetics.116.196220</a>.","ieee":"H. Ringbauer, G. Coop, and N. H. Barton, “Inferring recent demography from isolation by distance of long shared sequence blocks,” <i>Genetics</i>, vol. 205, no. 3. Genetics Society of America, pp. 1335–1351, 2017.","apa":"Ringbauer, H., Coop, G., &#38; Barton, N. H. (2017). Inferring recent demography from isolation by distance of long shared sequence blocks. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.116.196220\">https://doi.org/10.1534/genetics.116.196220</a>","ama":"Ringbauer H, Coop G, Barton NH. Inferring recent demography from isolation by distance of long shared sequence blocks. <i>Genetics</i>. 2017;205(3):1335-1351. doi:<a href=\"https://doi.org/10.1534/genetics.116.196220\">10.1534/genetics.116.196220</a>","short":"H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351."},"publisher":"Genetics Society of America","_id":"1074","day":"01","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"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."}],"volume":205,"date_created":"2018-12-11T11:50:00Z","date_updated":"2025-05-28T11:42:51Z","main_file_link":[{"url":"http://www.biorxiv.org/content/early/2016/09/23/076810","open_access":"1"}],"oa":1,"isi":1,"ec_funded":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"3","type":"journal_article","publist_id":"6307","page":"1335 - 1351","status":"public","title":"Inferring recent demography from isolation by distance of long shared sequence blocks","publication_identifier":{"issn":["00166731"]},"scopus_import":"1"},{"oa_version":"Published Version","article_processing_charge":"No","publication_status":"published","year":"2017","quality_controlled":"1","article_number":"P39.00011","month":"03","intvolume":"        62","author":[{"full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","first_name":"Hryhoriy","last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48"},{"last_name":"Naibert","full_name":"Naibert, Tyler","first_name":"Tyler"},{"first_name":"Raffi","full_name":"Budakian, Raffi","last_name":"Budakian"}],"extern":"1","publication":"APS March Meeting 2017","conference":{"start_date":"2017-03-13","end_date":"2017-03-17","location":"New Orleans, LA, United States","name":"APS: American Physical Society"},"date_published":"2017-03-01T00:00:00Z","issue":"4","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"conference","publication_identifier":{"issn":["0003-0503"]},"title":" Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures","status":"public","alternative_title":["Bulletin of the American Physical Society"],"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.","mla":"Polshyn, Hryhoriy, et al. “ Probing and Controlling Fluxoid States in Multiply-Connected Mesoscopic Superconducting Structures.” <i>APS March Meeting 2017</i>, vol. 62, no. 4, P39.00011, American Physical Society, 2017.","chicago":"Polshyn, Hryhoriy, Tyler Naibert, and Raffi Budakian. “ Probing and Controlling Fluxoid States in Multiply-Connected Mesoscopic Superconducting Structures.” In <i>APS March Meeting 2017</i>, Vol. 62. American Physical Society, 2017.","ieee":"H. Polshyn, T. Naibert, and R. Budakian, “ Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures,” in <i>APS March Meeting 2017</i>, New Orleans, LA, United States, 2017, vol. 62, no. 4.","apa":"Polshyn, H., Naibert, T., &#38; Budakian, R. (2017).  Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures. In <i>APS March Meeting 2017</i> (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: <i>APS March Meeting 2017</i>. Vol 62. American Physical Society; 2017.","short":"H. Polshyn, T. Naibert, R. Budakian, in:, APS March Meeting 2017, American Physical Society, 2017."},"day":"01","_id":"10745","publisher":"American Physical Society","main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR17/Session/P39.11"}],"date_updated":"2022-02-08T10:44:35Z","oa":1,"language":[{"iso":"eng"}],"date_created":"2022-02-08T09:49:17Z","volume":62,"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"}]},{"date_published":"2017-02-01T00:00:00Z","publication":"Austria and America: 20th-Century Cross-Cultural Encounters","extern":"1","author":[{"id":"479E9046-F248-11E8-B48F-1D18A9856A87","last_name":"Wenzl","full_name":"Wenzl, Bernhard","first_name":"Bernhard"}],"intvolume":"        15","month":"02","ddc":["001"],"year":"2017","has_accepted_license":"1","file":[{"file_size":380624,"creator":"system","file_name":"IST-2017-732-v1+1_Austria_and_America_Cross-Cultural_Encounters.pdf","date_created":"2018-12-12T10:08:06Z","access_level":"open_access","relation":"main_file","date_updated":"2018-12-12T10:08:06Z","file_id":"4666","content_type":"application/pdf"}],"editor":[{"last_name":"Parker","full_name":"Parker, Joshua","first_name":"Joshua"},{"last_name":"Poole","full_name":"Poole, Ralph","first_name":"Ralph"}],"publication_status":"published","oa_version":"None","volume":15,"date_created":"2018-12-11T11:50:00Z","language":[{"iso":"eng"}],"oa":1,"date_updated":"2021-01-12T06:48:06Z","_id":"1075","publisher":"LIT Verlag Berlin-Münster-Wien-Zürich-London","day":"01","citation":{"mla":"Wenzl, Bernhard. “An American in Allied-Occupied Austria: John Dos Passos Reports on &#38;quot;The Vienna Frontier&#38;quot;” <i>Austria and America: 20th-Century Cross-Cultural Encounters</i>, edited by Joshua Parker and Ralph Poole, vol. 15, LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.","chicago":"Wenzl, Bernhard. “An American in Allied-Occupied Austria: John Dos Passos Reports on &#38;quot;The Vienna Frontier&#38;quot;” In <i>Austria and America: 20th-Century Cross-Cultural Encounters</i>, edited by Joshua Parker and Ralph Poole, 15:73–80. LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017.","ista":"Wenzl B. 2017.An American in Allied-occupied Austria: John Dos Passos Reports on &#38;quot;The Vienna Frontier&#38;quot; In: Austria and America: 20th-Century Cross-Cultural Encounters. American Studies in Austria, vol. 15, 73–80.","ieee":"B. Wenzl, “An American in Allied-occupied Austria: John Dos Passos Reports on &#38;quot;The Vienna Frontier&#38;quot;,” in <i>Austria and America: 20th-Century Cross-Cultural Encounters</i>, vol. 15, J. Parker and R. Poole, Eds. LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.","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.","apa":"Wenzl, B. (2017). An American in Allied-occupied Austria: John Dos Passos Reports on &#38;quot;The Vienna Frontier&#38;quot; In J. Parker &#38; R. Poole (Eds.), <i>Austria and America: 20th-Century Cross-Cultural Encounters</i> (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 &#38;quot;The Vienna Frontier&#38;quot; In: Parker J, Poole R, eds. <i>Austria and America: 20th-Century Cross-Cultural Encounters</i>. Vol 15. LIT Verlag Berlin-Münster-Wien-Zürich-London; 2017:73-80."},"alternative_title":["American Studies in Austria"],"page":"73 - 80","title":"An American in Allied-occupied Austria: John Dos Passos Reports on &quot;The Vienna Frontier&quot;","status":"public","publication_identifier":{"isbn":["978-3643908124"]},"type":"book_chapter","publist_id":"6306","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2018-12-12T10:08:06Z"},{"publication_status":"published","article_processing_charge":"No","oa_version":"Submitted Version","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"year":"2017","doi":"10.1103/PhysRevA.95.023403","author":[{"full_name":"Klaiber, Michael","first_name":"Michael","last_name":"Klaiber"},{"full_name":"Daněk, Jiří","first_name":"Jiří","last_name":"Daněk"},{"orcid":"0000-0001-5973-0874","first_name":"Enderalp","full_name":"Yakaboylu, Enderalp","last_name":"Yakaboylu","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hatsagortsyan","full_name":"Hatsagortsyan, Karen","first_name":"Karen"},{"last_name":"Keitel","full_name":"Keitel, Christoph","first_name":"Christoph"}],"intvolume":"        95","month":"02","article_number":"023403","quality_controlled":"1","date_published":"2017-02-01T00:00:00Z","publication":" Physical Review A - Atomic, Molecular, and Optical Physics","external_id":{"isi":["000400571700011"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ec_funded":1,"issue":"2","status":"public","publication_identifier":{"issn":["24699926"]},"scopus_import":"1","title":"Strong-field ionization via a high-order Coulomb-corrected strong-field approximation","type":"journal_article","publist_id":"6305","day":"01","publisher":"American Physical Society","_id":"1076","citation":{"ama":"Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. Strong-field ionization via a high-order Coulomb-corrected strong-field approximation. <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2017;95(2). doi:<a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">10.1103/PhysRevA.95.023403</a>","apa":"Klaiber, M., Daněk, J., Yakaboylu, E., Hatsagortsyan, K., &#38; Keitel, C. (2017). Strong-field ionization via a high-order Coulomb-corrected strong-field approximation. <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">https://doi.org/10.1103/PhysRevA.95.023403</a>","short":"M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, C. Keitel,  Physical Review A - Atomic, Molecular, and Optical Physics 95 (2017).","ieee":"M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, and C. Keitel, “Strong-field ionization via a high-order Coulomb-corrected strong-field approximation,” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 95, no. 2. American Physical Society, 2017.","ista":"Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. 2017. Strong-field ionization via a high-order Coulomb-corrected strong-field approximation.  Physical Review A - Atomic, Molecular, and Optical Physics. 95(2), 023403.","mla":"Klaiber, Michael, et al. “Strong-Field Ionization via a High-Order Coulomb-Corrected Strong-Field Approximation.” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 95, no. 2, 023403, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">10.1103/PhysRevA.95.023403</a>.","chicago":"Klaiber, Michael, Jiří Daněk, Enderalp Yakaboylu, Karen Hatsagortsyan, and Christoph Keitel. “Strong-Field Ionization via a High-Order Coulomb-Corrected Strong-Field Approximation.” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">https://doi.org/10.1103/PhysRevA.95.023403</a>."},"department":[{"_id":"MiLe"}],"abstract":[{"lang":"eng","text":"Signatures of the Coulomb corrections in the photoelectron momentum distribution during laser-induced ionization of atoms or ions in tunneling and multiphoton regimes are investigated analytically in the case of a one-dimensional problem. A high-order Coulomb-corrected strong-field approximation is applied, where the exact continuum state in the S matrix is approximated by the eikonal Coulomb-Volkov state including the second-order corrections to the eikonal. Although without high-order corrections our theory coincides with the known analytical R-matrix (ARM) theory, we propose a simplified procedure for the matrix element derivation. Rather than matching the eikonal Coulomb-Volkov wave function with the bound state as in the ARM theory to remove the Coulomb singularity, we calculate the matrix element via the saddle-point integration method by time as well as by coordinate, and in this way avoiding the Coulomb singularity. The momentum shift in the photoelectron momentum distribution with respect to the ARM theory due to high-order corrections is analyzed for tunneling and multiphoton regimes. The relation of the quantum corrections to the tunneling delay time is discussed."}],"date_created":"2018-12-11T11:50:01Z","volume":95,"language":[{"iso":"eng"}],"isi":1,"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1609.07018","open_access":"1"}],"date_updated":"2023-09-20T11:57:23Z"},{"external_id":{"isi":["000393380400001"]},"publication":"Journal of the Royal Society Interface","date_published":"2017-01-04T00:00:00Z","quality_controlled":"1","article_number":"20160139","author":[{"id":"409D5C96-F248-11E8-B48F-1D18A9856A87","last_name":"Fernandes Redondo","orcid":"0000-0002-5837-2793","full_name":"Fernandes Redondo, Rodrigo A","first_name":"Rodrigo A"},{"last_name":"Vladar","id":"2A181218-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5985-7653","full_name":"Vladar, Harold","first_name":"Harold"},{"first_name":"Tomasz","full_name":"Włodarski, Tomasz","last_name":"Włodarski"},{"orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","first_name":"Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"month":"01","intvolume":"        14","doi":"10.1098/rsif.2016.0139","has_accepted_license":"1","file":[{"file_size":1092015,"relation":"main_file","success":1,"date_updated":"2019-01-18T09:14:02Z","file_id":"5843","content_type":"application/pdf","creator":"dernst","date_created":"2019-01-18T09:14:02Z","file_name":"2017_JRSI_Redondo.pdf","access_level":"open_access"}],"year":"2017","related_material":{"record":[{"id":"9864","relation":"research_data","status":"public"}]},"ddc":["570"],"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"},{"grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer","_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_updated":"2025-05-28T11:42:51Z","oa":1,"isi":1,"language":[{"iso":"eng"}],"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."}],"date_created":"2018-12-11T11:50:01Z","volume":14,"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"citation":{"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.” <i>Journal of the Royal Society Interface</i>. Royal Society of London, 2017. <a href=\"https://doi.org/10.1098/rsif.2016.0139\">https://doi.org/10.1098/rsif.2016.0139</a>.","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.","mla":"Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” <i>Journal of the Royal Society Interface</i>, vol. 14, no. 126, 20160139, Royal Society of London, 2017, doi:<a href=\"https://doi.org/10.1098/rsif.2016.0139\">10.1098/rsif.2016.0139</a>.","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,” <i>Journal of the Royal Society Interface</i>, vol. 14, no. 126. Royal Society of London, 2017.","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017).","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., &#38; Bollback, J. P. (2017). Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. <i>Journal of the Royal Society Interface</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rsif.2016.0139\">https://doi.org/10.1098/rsif.2016.0139</a>","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. <i>Journal of the Royal Society Interface</i>. 2017;14(126). doi:<a href=\"https://doi.org/10.1098/rsif.2016.0139\">10.1098/rsif.2016.0139</a>"},"_id":"1077","publisher":"Royal Society of London","day":"04","type":"journal_article","publist_id":"6303","status":"public","scopus_import":"1","title":"Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","publication_identifier":{"issn":["17425689"]},"issue":"126","file_date_updated":"2019-01-18T09:14:02Z","ec_funded":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"date_published":"2017-01-18T00:00:00Z","external_id":{"isi":["000397847200041"]},"publication":"Journal of visualized experiments JoVE","month":"01","intvolume":"      2017","author":[{"id":"49E91952-F248-11E8-B48F-1D18A9856A87","last_name":"Von Wangenheim","orcid":"0000-0002-6862-1247","full_name":"Von Wangenheim, Daniel","first_name":"Daniel"},{"last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"article_number":"e55044","ddc":["580"],"related_material":{"record":[{"id":"5565","status":"public","relation":"popular_science"}]},"year":"2017","doi":"10.3791/55044","has_accepted_license":"1","file":[{"file_size":57678,"relation":"main_file","file_id":"5219","content_type":"application/pdf","date_updated":"2018-12-12T10:16:31Z","creator":"system","file_name":"IST-2017-808-v1+1_2017_VWangenheim_list.pdf","date_created":"2018-12-12T10:16:31Z","access_level":"open_access"},{"file_size":1317820,"access_level":"open_access","creator":"system","date_created":"2018-12-12T10:16:32Z","file_name":"IST-2017-808-v1+2_2017_VWangenheim_article.pdf","file_id":"5220","content_type":"application/pdf","date_updated":"2018-12-12T10:16:32Z","relation":"main_file"}],"publication_status":"published","article_processing_charge":"No","oa_version":"Published Version","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:50:01Z","volume":2017,"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. "}],"language":[{"iso":"eng"}],"oa":1,"isi":1,"date_updated":"2025-05-07T11:12:33Z","pubrep_id":"808","_id":"1078","publisher":"Journal of Visualized Experiments","day":"18","citation":{"short":"D. von Wangenheim, R. Hauschild, J. Friml, Journal of Visualized Experiments JoVE 2017 (2017).","ama":"von Wangenheim D, Hauschild R, Friml J. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. <i>Journal of visualized experiments JoVE</i>. 2017;2017(119). doi:<a href=\"https://doi.org/10.3791/55044\">10.3791/55044</a>","apa":"von Wangenheim, D., Hauschild, R., &#38; Friml, J. (2017). Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. <i>Journal of Visualized Experiments JoVE</i>. Journal of Visualized Experiments. <a href=\"https://doi.org/10.3791/55044\">https://doi.org/10.3791/55044</a>","ieee":"D. von Wangenheim, R. Hauschild, and J. Friml, “Light sheet fluorescence microscopy of plant roots growing on the surface of a gel,” <i>Journal of visualized experiments JoVE</i>, vol. 2017, no. 119. Journal of Visualized Experiments, 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.","chicago":"Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” <i>Journal of Visualized Experiments JoVE</i>. Journal of Visualized Experiments, 2017. <a href=\"https://doi.org/10.3791/55044\">https://doi.org/10.3791/55044</a>.","mla":"von Wangenheim, Daniel, et al. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” <i>Journal of Visualized Experiments JoVE</i>, vol. 2017, no. 119, e55044, Journal of Visualized Experiments, 2017, doi:<a href=\"https://doi.org/10.3791/55044\">10.3791/55044</a>."},"department":[{"_id":"JiFr"},{"_id":"Bio"}],"scopus_import":"1","status":"public","title":"Light sheet fluorescence microscopy of plant roots growing on the surface of a gel","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"publist_id":"6302","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ec_funded":1,"file_date_updated":"2018-12-12T10:16:32Z","issue":"119"},{"publication":"Mathematical Physics, Analysis and Geometry","external_id":{"isi":["000401270000004"]},"date_published":"2017-06-01T00:00:00Z","quality_controlled":"1","article_number":"6","author":[{"last_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan","full_name":"Nam, Phan"},{"last_name":"Van Den Bosch","full_name":"Van Den Bosch, Hanne","first_name":"Hanne"}],"month":"06","intvolume":"        20","doi":"10.1007/s11040-017-9238-0","year":"2017","oa_version":"Submitted Version","project":[{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"}],"article_processing_charge":"No","publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/1603.07368","open_access":"1"}],"date_updated":"2023-09-20T11:53:35Z","oa":1,"isi":1,"language":[{"iso":"eng"}],"volume":20,"date_created":"2018-12-11T11:50:02Z","abstract":[{"lang":"eng","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."}],"department":[{"_id":"RoSe"}],"citation":{"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.","mla":"Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 20, no. 2, 6, Springer, 2017, doi:<a href=\"https://doi.org/10.1007/s11040-017-9238-0\">10.1007/s11040-017-9238-0</a>.","chicago":"Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” <i>Mathematical Physics, Analysis and Geometry</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s11040-017-9238-0\">https://doi.org/10.1007/s11040-017-9238-0</a>.","ieee":"P. Nam and H. Van Den Bosch, “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges,” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 20, no. 2. Springer, 2017.","apa":"Nam, P., &#38; Van Den Bosch, H. (2017). Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. <i>Mathematical Physics, Analysis and Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s11040-017-9238-0\">https://doi.org/10.1007/s11040-017-9238-0</a>","ama":"Nam P, Van Den Bosch H. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. <i>Mathematical Physics, Analysis and Geometry</i>. 2017;20(2). doi:<a href=\"https://doi.org/10.1007/s11040-017-9238-0\">10.1007/s11040-017-9238-0</a>","short":"P. Nam, H. Van Den Bosch, Mathematical Physics, Analysis and Geometry 20 (2017)."},"_id":"1079","publisher":"Springer","day":"01","publist_id":"6300","type":"journal_article","title":"Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges","status":"public","scopus_import":"1","publication_identifier":{"issn":["13850172"]},"issue":"2","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"department":[{"_id":"KrCh"}],"pubrep_id":"786","_id":"1080","publisher":"Nature Publishing Group","day":"31","citation":{"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. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms14114\">https://doi.org/10.1038/ncomms14114</a>","ama":"Reiter J, Makohon Moore A, Gerold J, et al. Reconstructing metastatic seeding patterns of human cancers. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms14114\">10.1038/ncomms14114</a>","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.","mla":"Reiter, Johannes, et al. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” <i>Nature Communications</i>, vol. 8, 14114, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms14114\">10.1038/ncomms14114</a>.","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.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms14114\">https://doi.org/10.1038/ncomms14114</a>.","ieee":"J. Reiter <i>et al.</i>, “Reconstructing metastatic seeding patterns of human cancers,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017."},"oa":1,"isi":1,"date_updated":"2023-09-20T11:55:31Z","volume":8,"abstract":[{"lang":"eng","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."}],"date_created":"2018-12-11T11:50:02Z","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2018-12-12T10:15:15Z","ec_funded":1,"status":"public","publication_identifier":{"issn":["20411723"]},"title":"Reconstructing metastatic seeding patterns of human cancers","scopus_import":"1","publist_id":"6301","type":"journal_article","article_number":"14114","quality_controlled":"1","intvolume":"         8","author":[{"id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter","full_name":"Reiter, Johannes","first_name":"Johannes","orcid":"0000-0002-0170-7353"},{"first_name":"Alvin","full_name":"Makohon Moore, Alvin","last_name":"Makohon Moore"},{"last_name":"Gerold","first_name":"Jeffrey","full_name":"Gerold, Jeffrey"},{"last_name":"Božić","first_name":"Ivana","full_name":"Božić, Ivana"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Iacobuzio Donahue","full_name":"Iacobuzio Donahue, Christine","first_name":"Christine"},{"last_name":"Vogelstein","full_name":"Vogelstein, Bert","first_name":"Bert"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"month":"01","date_published":"2017-01-31T00:00:00Z","external_id":{"isi":["000393096600001"]},"publication":"Nature Communications","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"article_processing_charge":"No","year":"2017","doi":"10.1038/ncomms14114","has_accepted_license":"1","file":[{"file_size":897050,"file_id":"5133","content_type":"application/pdf","date_updated":"2018-12-12T10:15:15Z","relation":"main_file","access_level":"open_access","creator":"system","date_created":"2018-12-12T10:15:15Z","file_name":"IST-2017-786-v1+1_ncomms14114.pdf"}],"ddc":["004","006"]},{"issue":"6345","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ec_funded":1,"page":"1379 - 1383","status":"public","scopus_import":"1","title":"Decoding of position in the developing neural tube from antiparallel morphogen gradients","publication_identifier":{"issn":["00368075"]},"type":"journal_article","publist_id":"6474","department":[{"_id":"AnKi"},{"_id":"GaTk"}],"publisher":"American Association for the Advancement of Science","_id":"943","day":"30","citation":{"ieee":"M. P. Zagórski <i>et al.</i>, “Decoding of position in the developing neural tube from antiparallel morphogen gradients,” <i>Science</i>, vol. 356, no. 6345. American Association for the Advancement of Science, pp. 1379–1383, 2017.","ista":"Zagórski MP, Tabata Y, Brandenberg N, Lutolf M, Tkačik G, Bollenbach T, Briscoe J, Kicheva A. 2017. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 356(6345), 1379–1383.","mla":"Zagórski, Marcin P., et al. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” <i>Science</i>, vol. 356, no. 6345, American Association for the Advancement of Science, 2017, pp. 1379–83, doi:<a href=\"https://doi.org/10.1126/science.aam5887\">10.1126/science.aam5887</a>.","chicago":"Zagórski, Marcin P, Yoji Tabata, Nathalie Brandenberg, Matthias Lutolf, Gašper Tkačik, Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” <i>Science</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/science.aam5887\">https://doi.org/10.1126/science.aam5887</a>.","ama":"Zagórski MP, Tabata Y, Brandenberg N, et al. Decoding of position in the developing neural tube from antiparallel morphogen gradients. <i>Science</i>. 2017;356(6345):1379-1383. doi:<a href=\"https://doi.org/10.1126/science.aam5887\">10.1126/science.aam5887</a>","apa":"Zagórski, M. P., Tabata, Y., Brandenberg, N., Lutolf, M., Tkačik, G., Bollenbach, T., … Kicheva, A. (2017). Decoding of position in the developing neural tube from antiparallel morphogen gradients. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aam5887\">https://doi.org/10.1126/science.aam5887</a>","short":"M.P. Zagórski, Y. Tabata, N. Brandenberg, M. Lutolf, G. Tkačik, T. Bollenbach, J. Briscoe, A. Kicheva, Science 356 (2017) 1379–1383."},"oa":1,"isi":1,"date_updated":"2023-09-26T15:38:05Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568706/","open_access":"1"}],"volume":356,"abstract":[{"text":"Like many developing tissues, the vertebrate neural tube is patterned by antiparallel morphogen gradients. To understand how these inputs are interpreted, we measured morphogen signaling and target gene expression in mouse embryos and chick ex vivo assays. From these data, we derived and validated a characteristic decoding map that relates morphogen input to the positional identity of neural progenitors. Analysis of the observed responses indicates that the underlying interpretation strategy minimizes patterning errors in response to the joint input of noisy opposing gradients. We reverse-engineered a transcriptional network that provides a mechanistic basis for the observed cell fate decisions and accounts for the precision and dynamics of pattern formation. Together, our data link opposing gradient dynamics in a growing tissue to precise pattern formation.","lang":"eng"}],"date_created":"2018-12-11T11:49:20Z","language":[{"iso":"eng"}],"project":[{"name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"},{"_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020","grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","grant_number":"201439","call_identifier":"FP7","_id":"2524F500-B435-11E9-9278-68D0E5697425"}],"oa_version":"Submitted Version","publication_status":"published","article_processing_charge":"No","year":"2017","doi":"10.1126/science.aam5887","quality_controlled":"1","intvolume":"       356","month":"06","author":[{"last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7896-7762","full_name":"Zagórski, Marcin P","first_name":"Marcin P"},{"full_name":"Tabata, Yoji","first_name":"Yoji","last_name":"Tabata"},{"first_name":"Nathalie","full_name":"Brandenberg, Nathalie","last_name":"Brandenberg"},{"first_name":"Matthias","full_name":"Lutolf, Matthias","last_name":"Lutolf"},{"first_name":"Gasper","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik"},{"first_name":"Tobias","full_name":"Bollenbach, Tobias","last_name":"Bollenbach"},{"first_name":"James","full_name":"Briscoe, James","last_name":"Briscoe"},{"first_name":"Anna","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva"}],"date_published":"2017-06-30T00:00:00Z","external_id":{"isi":["000404351500036"],"pmid":["28663499"]},"publication":"Science","pmid":1},{"date_published":"2017-11-15T00:00:00Z","publication":"eLife","external_id":{"pmid":["29140247"]},"pmid":1,"article_number":"e30674","quality_controlled":"1","extern":"1","month":"11","intvolume":"         6","author":[{"full_name":"Lyons, David B","first_name":"David B","last_name":"Lyons"},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"year":"2017","doi":"10.7554/elife.30674","has_accepted_license":"1","file":[{"relation":"main_file","success":1,"content_type":"application/pdf","file_id":"9446","date_updated":"2021-06-02T14:33:36Z","date_created":"2021-06-02T14:33:36Z","file_name":"2017_eLife_Lyons.pdf","creator":"cziletti","access_level":"open_access","file_size":1603102,"checksum":"4cfcdd67511ae4aed3d993550e46e146"}],"ddc":["570"],"oa_version":"Published Version","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"article_processing_charge":"No","oa":1,"article_type":"original","date_updated":"2021-12-14T07:54:36Z","date_created":"2021-06-02T14:28:58Z","abstract":[{"lang":"eng","text":"Cytosine methylation regulates essential genome functions across eukaryotes, but the fundamental question of whether nucleosomal or naked DNA is the preferred substrate of plant and animal methyltransferases remains unresolved. Here, we show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome, suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases in vivo. Furthermore, we show that simultaneous mutation of DDM1 and linker histone H1 in Arabidopsis reproduces the strong linker-specific methylation patterns of species that diverged from flowering plants and animals over a billion years ago. Our results indicate that in the absence of remodeling, nucleosomes are strong barriers to DNA methyltransferases. Linker-specific methylation can evolve simply by breaking the connection between nucleosome remodeling and DNA methylation."}],"volume":6,"language":[{"iso":"eng"}],"department":[{"_id":"DaZi"}],"_id":"9445","publisher":"eLife Sciences Publications","day":"15","citation":{"short":"D.B. Lyons, D. Zilberman, ELife 6 (2017).","apa":"Lyons, D. B., &#38; Zilberman, D. (2017). DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.30674\">https://doi.org/10.7554/elife.30674</a>","ama":"Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/elife.30674\">10.7554/elife.30674</a>","mla":"Lyons, David B., and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” <i>ELife</i>, vol. 6, e30674, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/elife.30674\">10.7554/elife.30674</a>.","chicago":"Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/elife.30674\">https://doi.org/10.7554/elife.30674</a>.","ista":"Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 6, e30674.","ieee":"D. B. Lyons and D. Zilberman, “DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017."},"status":"public","title":"DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes","publication_identifier":{"eissn":["2050-084X"]},"scopus_import":"1","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file_date_updated":"2021-06-02T14:33:36Z"},{"day":"06","_id":"945","publisher":"Oxford University Press","pubrep_id":"848","citation":{"ieee":"A. K. Huylmans, A. Macon, and B. Vicoso, “Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome,” <i>Molecular Biology and Evolution</i>, vol. 34, no. 10. Oxford University Press, pp. 2637–2649, 2017.","mla":"Huylmans, Ann K., et al. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” <i>Molecular Biology and Evolution</i>, vol. 34, no. 10, Oxford University Press, 2017, pp. 2637–49, doi:<a href=\"https://doi.org/10.1093/molbev/msx190\">10.1093/molbev/msx190</a>.","chicago":"Huylmans, Ann K, Ariana Macon, and Beatriz Vicoso. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/molbev/msx190\">https://doi.org/10.1093/molbev/msx190</a>.","ista":"Huylmans AK, Macon A, Vicoso B. 2017. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. 34(10), 2637–2649.","ama":"Huylmans AK, Macon A, Vicoso B. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. <i>Molecular Biology and Evolution</i>. 2017;34(10):2637-2649. doi:<a href=\"https://doi.org/10.1093/molbev/msx190\">10.1093/molbev/msx190</a>","apa":"Huylmans, A. K., Macon, A., &#38; Vicoso, B. (2017). Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msx190\">https://doi.org/10.1093/molbev/msx190</a>","short":"A.K. Huylmans, A. Macon, B. Vicoso, Molecular Biology and Evolution 34 (2017) 2637–2649."},"department":[{"_id":"BeVi"}],"abstract":[{"lang":"eng","text":"While chromosome-wide dosage compensation of the X chromosome has been found in many species, studies in ZW clades have indicated that compensation of the Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show complete compensation of the Z chromosome, while others lack full equalization, but what drives these inconsistencies is unclear. Here, we compare patterns of male and female gene expression on the Z chromosome of two closely related butterfly species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths species, Plodia interpunctella and Bombyx mori, which were previously found to differ in the extent to which they equalize Z-linked gene expression between the sexes. We find that, while some species and tissues seem to have incomplete dosage compensation, this is in fact due to the accumulation of male-biased genes and the depletion of female-biased genes on the Z chromosome. Once this is accounted for, the Z chromosome is fully compensated in all four species, through the up-regulation of Z expression in females and in some cases additional down-regulation in males. We further find that both sex-biased genes and Z-linked genes have increased rates of expression divergence in this clade, and that this can lead to fast shifts in patterns of gene expression even between closely related species. Taken together, these results show that the uneven distribution of sex-biased genes on sex chromosomes can confound conclusions about dosage compensation and that Z chromosome-wide dosage compensation is not only possible but ubiquitous among Lepidoptera."}],"date_created":"2018-12-11T11:49:20Z","volume":34,"language":[{"iso":"eng"}],"isi":1,"oa":1,"date_updated":"2023-09-26T15:36:34Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2020-07-14T12:48:15Z","issue":"10","title":"Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome","publication_identifier":{"issn":["07374038"]},"status":"public","scopus_import":"1","page":"2637 - 2649","publist_id":"6472","type":"journal_article","author":[{"last_name":"Huylmans","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K","orcid":"0000-0001-8871-4961","full_name":"Huylmans, Ann K"},{"last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","full_name":"Macon, Ariana"},{"first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"        34","month":"07","quality_controlled":"1","date_published":"2017-07-06T00:00:00Z","external_id":{"isi":["000411814800016"]},"publication":"Molecular Biology and Evolution","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","article_processing_charge":"Yes (in subscription journal)","project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","ddc":["570","576"],"year":"2017","has_accepted_license":"1","file":[{"file_id":"4810","content_type":"application/pdf","date_updated":"2020-07-14T12:48:15Z","relation":"main_file","access_level":"open_access","creator":"system","date_created":"2018-12-12T10:10:23Z","file_name":"IST-2017-848-v1+1_2017_Vicoso_GlobalDosage.pdf","file_size":462863,"checksum":"009fd68043211d645ceb9d1de28274f2"}],"doi":"10.1093/molbev/msx190"},{"quality_controlled":"1","article_number":"e26792","intvolume":"         6","author":[{"id":"49E91952-F248-11E8-B48F-1D18A9856A87","last_name":"Von Wangenheim","first_name":"Daniel","orcid":"0000-0002-6862-1247","full_name":"Von Wangenheim, Daniel"},{"orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","first_name":"Matyas"},{"last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367","first_name":"Vanessa","full_name":"Barone, Vanessa"},{"full_name":"Benková, Eva","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí"}],"month":"06","publication":"eLife","external_id":{"isi":["000404728300001"]},"date_published":"2017-06-19T00:00:00Z","acknowledgement":"Funding: Marie Curie Actions (FP7/2007-2013 no 291734) to Daniel von Wangenheim; Austrian Science Fund (M 2128-B21) to Matyáš Fendrych; Austrian Science Fund (FWF01_I1774S) to Eva Benková; European Research Council (FP7/2007-2013 no 282300) to Jiří Friml. \r\nThe authors are grateful to the Miba Machine Shop at IST Austria for their contribution to the microscope setup and to Yvonne Kemper for reading, understanding and correcting the manuscript.\r\n#BioimagingFacility","oa_version":"Published Version","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"M02128","name":"Molecular basis of root growth inhibition by auxin","_id":"2572ED28-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"I 1774-B16","name":"Hormone cross-talk drives nutrient dependent plant development","_id":"2542D156-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"Yes","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","has_accepted_license":"1","file":[{"access_level":"open_access","creator":"system","date_created":"2018-12-12T10:17:57Z","file_name":"IST-2017-847-v1+1_elife-26792-v2.pdf","content_type":"application/pdf","file_id":"5315","date_updated":"2020-07-14T12:48:15Z","relation":"main_file","checksum":"9af3398cb0d81f99d79016a616df22e9","file_size":19581847}],"doi":"10.7554/eLife.26792","year":"2017","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5566"}]},"ddc":["570"],"department":[{"_id":"JiFr"},{"_id":"Bio"},{"_id":"CaHe"},{"_id":"EvBe"}],"citation":{"ista":"von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. 2017. Live tracking of moving samples in confocal microscopy for vertically grown roots. eLife. 6, e26792.","mla":"von Wangenheim, Daniel, et al. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” <i>ELife</i>, vol. 6, e26792, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/eLife.26792\">10.7554/eLife.26792</a>.","chicago":"Wangenheim, Daniel von, Robert Hauschild, Matyas Fendrych, Vanessa Barone, Eva Benková, and Jiří Friml. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/eLife.26792\">https://doi.org/10.7554/eLife.26792</a>.","ieee":"D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, and J. Friml, “Live tracking of moving samples in confocal microscopy for vertically grown roots,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017.","short":"D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, J. Friml, ELife 6 (2017).","apa":"von Wangenheim, D., Hauschild, R., Fendrych, M., Barone, V., Benková, E., &#38; Friml, J. (2017). Live tracking of moving samples in confocal microscopy for vertically grown roots. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.26792\">https://doi.org/10.7554/eLife.26792</a>","ama":"von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. Live tracking of moving samples in confocal microscopy for vertically grown roots. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/eLife.26792\">10.7554/eLife.26792</a>"},"day":"19","publisher":"eLife Sciences Publications","_id":"946","pubrep_id":"847","date_updated":"2025-05-07T11:12:33Z","isi":1,"oa":1,"language":[{"iso":"eng"}],"volume":6,"abstract":[{"lang":"eng","text":"Roots navigate through soil integrating environmental signals to orient their growth. The Arabidopsis root is a widely used model for developmental, physiological and cell biological studies. Live imaging greatly aids these efforts, but the horizontal sample position and continuous root tip displacement present significant difficulties. Here, we develop a confocal microscope setup for vertical sample mounting and integrated directional illumination. We present TipTracker – a custom software for automatic tracking of diverse moving objects usable on various microscope setups. Combined, this enables observation of root tips growing along the natural gravity vector over prolonged periods of time, as well as the ability to induce rapid gravity or light stimulation. We also track migrating cells in the developing zebrafish embryo, demonstrating the utility of this system in the acquisition of high-resolution data sets of dynamic samples. We provide detailed descriptions of the tools enabling the easy implementation on other microscopes."}],"date_created":"2018-12-11T11:49:21Z","file_date_updated":"2020-07-14T12:48:15Z","ec_funded":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6471","type":"journal_article","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"status":"public","scopus_import":"1","title":"Live tracking of moving samples in confocal microscopy for vertically grown roots"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.00219"}],"date_updated":"2023-09-22T10:03:50Z","oa":1,"isi":1,"language":[{"iso":"eng"}],"volume":96,"abstract":[{"lang":"eng","text":"Viewing the ways a living cell can organize its metabolism as the phase space of a physical system, regulation can be seen as the ability to reduce the entropy of that space by selecting specific cellular configurations that are, in some sense, optimal. Here we quantify the amount of regulation required to control a cell's growth rate by a maximum-entropy approach to the space of underlying metabolic phenotypes, where a configuration corresponds to a metabolic flux pattern as described by genome-scale models. We link the mean growth rate achieved by a population of cells to the minimal amount of metabolic regulation needed to achieve it through a phase diagram that highlights how growth suppression can be as costly (in regulatory terms) as growth enhancement. Moreover, we provide an interpretation of the inverse temperature β controlling maximum-entropy distributions based on the underlying growth dynamics. Specifically, we show that the asymptotic value of β for a cell population can be expected to depend on (i) the carrying capacity of the environment, (ii) the initial size of the colony, and (iii) the probability distribution from which the inoculum was sampled. Results obtained for E. coli and human cells are found to be remarkably consistent with empirical evidence."}],"date_created":"2018-12-11T11:49:21Z","department":[{"_id":"GaTk"}],"citation":{"apa":"De Martino, D., Capuani, F., &#38; De Martino, A. (2017). Quantifying the entropic cost of cellular growth control. <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.96.010401\">https://doi.org/10.1103/PhysRevE.96.010401</a>","ama":"De Martino D, Capuani F, De Martino A. Quantifying the entropic cost of cellular growth control. <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. 2017;96(1). doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.010401\">10.1103/PhysRevE.96.010401</a>","short":"D. De Martino, F. Capuani, A. De Martino,  Physical Review E Statistical Nonlinear and Soft Matter Physics  96 (2017).","chicago":"De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Quantifying the Entropic Cost of Cellular Growth Control.” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. American Institute of Physics, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.96.010401\">https://doi.org/10.1103/PhysRevE.96.010401</a>.","mla":"De Martino, Daniele, et al. “Quantifying the Entropic Cost of Cellular Growth Control.” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>, vol. 96, no. 1, 010401, American Institute of Physics, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.010401\">10.1103/PhysRevE.96.010401</a>.","ista":"De Martino D, Capuani F, De Martino A. 2017. Quantifying the entropic cost of cellular growth control.  Physical Review E Statistical Nonlinear and Soft Matter Physics . 96(1), 010401.","ieee":"D. De Martino, F. Capuani, and A. De Martino, “Quantifying the entropic cost of cellular growth control,” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>, vol. 96, no. 1. American Institute of Physics, 2017."},"_id":"947","publisher":"American Institute of Physics","day":"10","publist_id":"6470","type":"journal_article","status":"public","scopus_import":"1","title":"Quantifying the entropic cost of cellular growth control","publication_identifier":{"issn":["24700045"]},"issue":"1","ec_funded":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000405194200002"]},"publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","date_published":"2017-07-10T00:00:00Z","quality_controlled":"1","article_number":"010401","author":[{"orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","first_name":"Daniele","last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Fabrizio","full_name":"Capuani, Fabrizio","last_name":"Capuani"},{"first_name":"Andrea","full_name":"De Martino, Andrea","last_name":"De Martino"}],"intvolume":"        96","month":"07","doi":"10.1103/PhysRevE.96.010401","year":"2017","oa_version":"Submitted Version","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"article_processing_charge":"No","publication_status":"published"},{"pubrep_id":"845","_id":"949","publisher":"Springer","day":"01","citation":{"ista":"Chatterjee K, Goharshady AK, Pavlogiannis A. 2017. JTDec: A tool for tree decompositions in soot. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 10482, 59–66.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Andreas Pavlogiannis. “JTDec: A Tool for Tree Decompositions in Soot.” edited by Deepak D’Souza, 10482:59–66. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-68167-2_4\">https://doi.org/10.1007/978-3-319-68167-2_4</a>.","mla":"Chatterjee, Krishnendu, et al. <i>JTDec: A Tool for Tree Decompositions in Soot</i>. Edited by Deepak D’Souza, vol. 10482, Springer, 2017, pp. 59–66, doi:<a href=\"https://doi.org/10.1007/978-3-319-68167-2_4\">10.1007/978-3-319-68167-2_4</a>.","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pavlogiannis, “JTDec: A tool for tree decompositions in soot,” presented at the ATVA: Automated Technology for Verification and Analysis, Pune, India, 2017, vol. 10482, pp. 59–66.","apa":"Chatterjee, K., Goharshady, A. K., &#38; Pavlogiannis, A. (2017). JTDec: A tool for tree decompositions in soot. In D. D’Souza (Ed.) (Vol. 10482, pp. 59–66). Presented at the ATVA: Automated Technology for Verification and Analysis, Pune, India: Springer. <a href=\"https://doi.org/10.1007/978-3-319-68167-2_4\">https://doi.org/10.1007/978-3-319-68167-2_4</a>","ama":"Chatterjee K, Goharshady AK, Pavlogiannis A. JTDec: A tool for tree decompositions in soot. In: D’Souza D, ed. Vol 10482. Springer; 2017:59-66. doi:<a href=\"https://doi.org/10.1007/978-3-319-68167-2_4\">10.1007/978-3-319-68167-2_4</a>","short":"K. Chatterjee, A.K. Goharshady, A. Pavlogiannis, in:, D. D’Souza (Ed.), Springer, 2017, pp. 59–66."},"department":[{"_id":"KrCh"}],"alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"The notion of treewidth of graphs has been exploited for faster algorithms for several problems arising in verification and program analysis. Moreover, various notions of balanced tree decompositions have been used for improved algorithms supporting dynamic updates and analysis of concurrent programs. In this work, we present a tool for constructing tree-decompositions of CFGs obtained from Java methods, which is implemented as an extension to the widely used Soot framework. The experimental results show that our implementation on real-world Java benchmarks is very efficient. Our tool also provides the first implementation for balancing tree-decompositions. In summary, we present the first tool support for exploiting treewidth in the static analysis problems on Java programs."}],"date_created":"2018-12-11T11:49:22Z","volume":10482,"language":[{"iso":"eng"}],"oa":1,"isi":1,"date_updated":"2024-03-25T23:30:19Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2020-07-14T12:48:16Z","ec_funded":1,"page":"59 - 66","status":"public","scopus_import":"1","title":"JTDec: A tool for tree decompositions in soot","publication_identifier":{"issn":["03029743"]},"publist_id":"6468","type":"conference","intvolume":"     10482","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Amir","full_name":"Goharshady, Amir","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"}],"month":"01","quality_controlled":"1","date_published":"2017-01-01T00:00:00Z","conference":{"end_date":"2017-10-06","start_date":"2017-10-03","location":"Pune, India","name":"ATVA: Automated Technology for Verification and Analysis"},"external_id":{"isi":["000723567800004"]},"editor":[{"last_name":"D'Souza","first_name":"Deepak","full_name":"D'Souza, Deepak"}],"publication_status":"published","article_processing_charge":"No","project":[{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"oa_version":"Submitted Version","ddc":["005"],"related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"year":"2017","doi":"10.1007/978-3-319-68167-2_4","has_accepted_license":"1","file":[{"checksum":"a0d9f5f94dc594c4e71e78525c9942f1","file_size":948514,"file_id":"4835","date_updated":"2020-07-14T12:48:16Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2017-845-v1+1_2017_Chatterjee_JTDec.pdf","date_created":"2018-12-12T10:10:45Z","creator":"system"}]},{"arxiv":1,"external_id":{"arxiv":["1705.01433"]},"conference":{"location":"Berlin, Germany","name":"CONCUR: Concurrency Theory","end_date":"2017-09-07","start_date":"2017-09-05"},"date_published":"2017-09-01T00:00:00Z","month":"09","author":[{"last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","first_name":"Guy","full_name":"Avni, Guy"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"first_name":"Ventsislav K","full_name":"Chonev, Ventsislav K","last_name":"Chonev","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"        85","quality_controlled":"1","article_number":"17","related_material":{"record":[{"status":"public","relation":"later_version","id":"6752"}]},"ddc":["000"],"has_accepted_license":"1","file":[{"creator":"system","file_name":"IST-2017-844-v1+1_concur-cr.pdf","date_created":"2018-12-12T10:18:00Z","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:48:16Z","content_type":"application/pdf","file_id":"5318","file_size":335170,"checksum":"6d5cccf755207b91ccbef95d8275b013"}],"doi":"10.4230/LIPIcs.CONCUR.2017.21","year":"2017","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:49:22Z","abstract":[{"lang":"eng","text":"Two-player games on graphs are widely studied in formal methods as they model the interaction between a system and its environment. The game is played by moving a token throughout a graph to produce an infinite path. There are several common modes to determine how the players move the token through the graph; e.g., in turn-based games the players alternate turns in moving the token. We study the bidding mode of moving the token, which, to the best of our knowledge, has never been studied in infinite-duration games. Both players have separate budgets, which sum up to $1$. In each turn, a bidding takes place. Both players submit bids simultaneously, and a bid is legal if it does not exceed the available budget. The winner of the bidding pays his bid to the other player and moves the token. For reachability objectives, repeated bidding games have been studied and are called Richman games. There, a central question is the existence and computation of threshold budgets; namely, a value t\\in [0,1] such that if\\PO's budget exceeds $t$, he can win the game, and if\\PT's budget exceeds 1-t, he can win the game. We focus on parity games and mean-payoff games. We show the existence of threshold budgets in these games, and reduce the problem of finding them to Richman games. We also determine the strategy-complexity of an optimal strategy. Our most interesting result shows that memoryless strategies suffice for mean-payoff bidding games. \r\n"}],"volume":85,"date_updated":"2023-08-29T07:02:13Z","oa":1,"citation":{"ista":"Avni G, Henzinger TA, Chonev VK. 2017. Infinite-duration bidding games. CONCUR: Concurrency Theory, LIPIcs, vol. 85, 17.","mla":"Avni, Guy, et al. <i>Infinite-Duration Bidding Games</i>. Vol. 85, 17, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2017.21\">10.4230/LIPIcs.CONCUR.2017.21</a>.","chicago":"Avni, Guy, Thomas A Henzinger, and Ventsislav K Chonev. “Infinite-Duration Bidding Games,” Vol. 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2017.21\">https://doi.org/10.4230/LIPIcs.CONCUR.2017.21</a>.","ieee":"G. Avni, T. A. Henzinger, and V. K. Chonev, “Infinite-duration bidding games,” presented at the CONCUR: Concurrency Theory, Berlin, Germany, 2017, vol. 85.","apa":"Avni, G., Henzinger, T. A., &#38; Chonev, V. K. (2017). Infinite-duration bidding games (Vol. 85). Presented at the CONCUR: Concurrency Theory, Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2017.21\">https://doi.org/10.4230/LIPIcs.CONCUR.2017.21</a>","ama":"Avni G, Henzinger TA, Chonev VK. Infinite-duration bidding games. In: Vol 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2017.21\">10.4230/LIPIcs.CONCUR.2017.21</a>","short":"G. Avni, T.A. Henzinger, V.K. Chonev, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017."},"day":"01","_id":"950","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","pubrep_id":"844","alternative_title":["LIPIcs"],"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publist_id":"6466","type":"conference","publication_identifier":{"issn":["1868-8969"]},"title":"Infinite-duration bidding games","status":"public","scopus_import":1,"file_date_updated":"2020-07-14T12:48:16Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"title":"An evolutionary case for functional gene body methylation in plants and animals","publication_identifier":{"eissn":["1465-6906"],"issn":["1474-760X"]},"scopus_import":"1","status":"public","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file_date_updated":"2021-06-07T12:31:36Z","issue":"1","volume":18,"abstract":[{"text":"Methylation in the bodies of active genes is common in animals and vascular plants. Evolutionary patterns indicate homeostatic functions for this type of methylation.","lang":"eng"}],"date_created":"2021-06-07T12:27:39Z","language":[{"iso":"eng"}],"oa":1,"date_updated":"2021-12-14T07:55:02Z","_id":"9506","publisher":"Springer Nature","day":"09","citation":{"ieee":"D. Zilberman, “An evolutionary case for functional gene body methylation in plants and animals,” <i>Genome Biology</i>, vol. 18, no. 1. Springer Nature, 2017.","ista":"Zilberman D. 2017. An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. 18(1), 87.","chicago":"Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation in Plants and Animals.” <i>Genome Biology</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1186/s13059-017-1230-2\">https://doi.org/10.1186/s13059-017-1230-2</a>.","mla":"Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation in Plants and Animals.” <i>Genome Biology</i>, vol. 18, no. 1, 87, Springer Nature, 2017, doi:<a href=\"https://doi.org/10.1186/s13059-017-1230-2\">10.1186/s13059-017-1230-2</a>.","short":"D. Zilberman, Genome Biology 18 (2017).","ama":"Zilberman D. An evolutionary case for functional gene body methylation in plants and animals. <i>Genome Biology</i>. 2017;18(1). doi:<a href=\"https://doi.org/10.1186/s13059-017-1230-2\">10.1186/s13059-017-1230-2</a>","apa":"Zilberman, D. (2017). An evolutionary case for functional gene body methylation in plants and animals. <i>Genome Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13059-017-1230-2\">https://doi.org/10.1186/s13059-017-1230-2</a>"},"department":[{"_id":"DaZi"}],"ddc":["570"],"year":"2017","doi":"10.1186/s13059-017-1230-2","has_accepted_license":"1","file":[{"checksum":"5a455ad914e7d225b1baa4ab07fd925e","file_size":278183,"file_id":"9507","date_updated":"2021-06-07T12:31:36Z","content_type":"application/pdf","relation":"main_file","success":1,"access_level":"open_access","creator":"asandaue","date_created":"2021-06-07T12:31:36Z","file_name":"2017_GenomeBiology_Zilberman.pdf"}],"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"article_processing_charge":"No","oa_version":"Published Version","pmid":1,"date_published":"2017-05-09T00:00:00Z","external_id":{"pmid":["28486944"]},"publication":"Genome Biology","extern":"1","month":"05","intvolume":"        18","author":[{"orcid":"0000-0002-0123-8649","first_name":"Daniel","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman"}],"article_number":"87","quality_controlled":"1"},{"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"article_processing_charge":"No","oa_version":"Published Version","ddc":["576"],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9856"},{"id":"9857","status":"public","relation":"research_data"},{"relation":"research_data","status":"public","id":"9858"}]},"year":"2017","doi":"10.1371/journal.pbio.2001894","file":[{"date_created":"2018-12-12T10:08:30Z","file_name":"IST-2017-843-v1+1_journal.pbio.2001894.pdf","creator":"system","access_level":"open_access","relation":"main_file","file_id":"4691","content_type":"application/pdf","date_updated":"2020-07-14T12:48:16Z","checksum":"107d290bd1159ec77b734eb2824b01c8","file_size":5541206}],"has_accepted_license":"1","month":"05","intvolume":"        15","author":[{"first_name":"Tom","full_name":"Schmidt, Tom","last_name":"Schmidt"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"},{"last_name":"Rasic","first_name":"Gordana","full_name":"Rasic, Gordana"},{"last_name":"Turley","full_name":"Turley, Andrew","first_name":"Andrew"},{"first_name":"Brian","full_name":"Montgomery, Brian","last_name":"Montgomery"},{"first_name":"Inaki","full_name":"Iturbe Ormaetxe, Inaki","last_name":"Iturbe Ormaetxe"},{"last_name":"Cook","first_name":"Peter","full_name":"Cook, Peter"},{"full_name":"Ryan, Peter","first_name":"Peter","last_name":"Ryan"},{"full_name":"Ritchie, Scott","first_name":"Scott","last_name":"Ritchie"},{"first_name":"Ary","full_name":"Hoffmann, Ary","last_name":"Hoffmann"},{"last_name":"O’Neill","full_name":"O’Neill, Scott","first_name":"Scott"},{"first_name":"Michael","full_name":"Turelli, Michael","last_name":"Turelli"}],"article_number":"e2001894","quality_controlled":"1","date_published":"2017-05-30T00:00:00Z","publication":"PLoS Biology","external_id":{"isi":["000402520000012"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2020-07-14T12:48:16Z","issue":"5","publication_identifier":{"issn":["15449173"]},"title":"Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti","status":"public","scopus_import":"1","type":"journal_article","publist_id":"6464","_id":"951","publisher":"Public Library of Science","pubrep_id":"843","day":"30","citation":{"short":"T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, PLoS Biology 15 (2017).","ama":"Schmidt T, Barton NH, Rasic G, et al. Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. <i>PLoS Biology</i>. 2017;15(5). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2001894\">10.1371/journal.pbio.2001894</a>","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2001894\">https://doi.org/10.1371/journal.pbio.2001894</a>","ieee":"T. Schmidt <i>et al.</i>, “Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti,” <i>PLoS Biology</i>, vol. 15, no. 5. Public Library of Science, 2017.","mla":"Schmidt, Tom, et al. “Local Introduction and Heterogeneous Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” <i>PLoS Biology</i>, vol. 15, no. 5, e2001894, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2001894\">10.1371/journal.pbio.2001894</a>.","chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Local Introduction and Heterogeneous Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” <i>PLoS Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pbio.2001894\">https://doi.org/10.1371/journal.pbio.2001894</a>.","ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. 15(5), e2001894."},"department":[{"_id":"NiBa"}],"date_created":"2018-12-11T11:49:22Z","volume":15,"abstract":[{"text":"Dengue-suppressing Wolbachia strains are promising tools for arbovirus control, particularly as they have the potential to self-spread following local introductions. To test this, we followed the frequency of the transinfected Wolbachia strain wMel through Ae. aegypti in Cairns, Australia, following releases at 3 nonisolated locations within the city in early 2013. Spatial spread was analysed graphically using interpolation and by fitting a statistical model describing the position and width of the wave. For the larger 2 of the 3 releases (covering 0.97 km2 and 0.52 km2), we observed slow but steady spatial spread, at about 100–200 m per year, roughly consistent with theoretical predictions. In contrast, the smallest release (0.11 km2) produced erratic temporal and spatial dynamics, with little evidence of spread after 2 years. This is consistent with the prediction concerning fitness-decreasing Wolbachia transinfections that a minimum release area is needed to achieve stable local establishment and spread in continuous habitats. Our graphical and likelihood analyses produced broadly consistent estimates of wave speed and wave width. Spread at all sites was spatially heterogeneous, suggesting that environmental heterogeneity will affect large-scale Wolbachia transformations of urban mosquito populations. The persistence and spread of Wolbachia in release areas meeting minimum area requirements indicates the promise of successful large-scale population transfo","lang":"eng"}],"language":[{"iso":"eng"}],"oa":1,"isi":1,"date_updated":"2023-09-22T10:02:52Z"},{"day":"01","_id":"952","pubrep_id":"972","publisher":"Elsevier","citation":{"apa":"Turelli, M., &#38; Barton, N. H. (2017). Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. <i>Theoretical Population Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tpb.2017.03.003\">https://doi.org/10.1016/j.tpb.2017.03.003</a>","ama":"Turelli M, Barton NH. Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. <i>Theoretical Population Biology</i>. 2017;115:45-60. doi:<a href=\"https://doi.org/10.1016/j.tpb.2017.03.003\">10.1016/j.tpb.2017.03.003</a>","short":"M. Turelli, N.H. Barton, Theoretical Population Biology 115 (2017) 45–60.","mla":"Turelli, Michael, and Nicholas H. Barton. “Deploying Dengue-Suppressing Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” <i>Theoretical Population Biology</i>, vol. 115, Elsevier, 2017, pp. 45–60, doi:<a href=\"https://doi.org/10.1016/j.tpb.2017.03.003\">10.1016/j.tpb.2017.03.003</a>.","ista":"Turelli M, Barton NH. 2017. Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. 115, 45–60.","chicago":"Turelli, Michael, and Nicholas H Barton. “Deploying Dengue-Suppressing Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” <i>Theoretical Population Biology</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.tpb.2017.03.003\">https://doi.org/10.1016/j.tpb.2017.03.003</a>.","ieee":"M. Turelli and N. H. Barton, “Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti,” <i>Theoretical Population Biology</i>, vol. 115. Elsevier, pp. 45–60, 2017."},"department":[{"_id":"NiBa"}],"date_created":"2018-12-11T11:49:22Z","abstract":[{"lang":"eng","text":"A novel strategy for controlling the spread of arboviral diseases such as dengue, Zika and chikungunya is to transform mosquito populations with virus-suppressing Wolbachia. In general, Wolbachia transinfected into mosquitoes induce fitness costs through lower viability or fecundity. These maternally inherited bacteria also produce a frequency-dependent advantage for infected females by inducing cytoplasmic incompatibility (CI), which kills the embryos produced by uninfected females mated to infected males. These competing effects, a frequency-dependent advantage and frequency-independent costs, produce bistable Wolbachia frequency dynamics. Above a threshold frequency, denoted pˆ, CI drives fitness-decreasing Wolbachia transinfections through local populations; but below pˆ, infection frequencies tend to decline to zero. If pˆ is not too high, CI also drives spatial spread once infections become established over sufficiently large areas. We illustrate how simple models provide testable predictions concerning the spatial and temporal dynamics of Wolbachia introductions, focusing on rate of spatial spread, the shape of spreading waves, and the conditions for initiating spread from local introductions. First, we consider the robustness of diffusion-based predictions to incorporating two important features of wMel-Aedes aegypti biology that may be inconsistent with the diffusion approximations, namely fast local dynamics induced by complete CI (i.e., all embryos produced from incompatible crosses die) and long-tailed, non-Gaussian dispersal. With complete CI, our numerical analyses show that long-tailed dispersal changes wave-width predictions only slightly; but it can significantly reduce wave speed relative to the diffusion prediction; it also allows smaller local introductions to initiate spatial spread. Second, we use approximations for pˆ and dispersal distances to predict the outcome of 2013 releases of wMel-infected Aedes aegypti in Cairns, Australia, Third, we describe new data from Ae. aegypti populations near Cairns, Australia that demonstrate long-distance dispersal and provide an approximate lower bound on pˆ for wMel in northeastern Australia. Finally, we apply our analyses to produce operational guidelines for efficient transformation of vector populations over large areas. We demonstrate that even very slow spatial spread, on the order of 10-20 m/month (as predicted), can produce area-wide population transformation within a few years following initial releases covering about 20-30% of the target area."}],"volume":115,"language":[{"iso":"eng"}],"oa":1,"date_updated":"2023-09-22T10:02:21Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2020-07-14T12:48:16Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","title":"Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti","scopus_import":"1","publication_identifier":{"issn":["00405809"]},"status":"public","page":"45 - 60","type":"journal_article","publist_id":"6463","author":[{"last_name":"Turelli","first_name":"Michael","full_name":"Turelli, Michael"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}],"intvolume":"       115","month":"06","quality_controlled":"1","pmid":1,"date_published":"2017-06-01T00:00:00Z","publication":"Theoretical Population Biology","external_id":{"pmid":["28411063"]},"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"publication_status":"published","article_processing_charge":"No","oa_version":"Submitted Version","ddc":["576"],"year":"2017","has_accepted_license":"1","file":[{"access_level":"open_access","creator":"dernst","date_created":"2019-04-17T06:39:45Z","file_name":"2017_TheoreticalPopulationBio_Turelli.pdf","date_updated":"2020-07-14T12:48:16Z","content_type":"application/pdf","file_id":"6327","relation":"main_file","checksum":"9aeff86fa7de69f7a15cf4fc60d57d01","file_size":2073856}],"doi":"10.1016/j.tpb.2017.03.003"}]