[{"_id":"1104","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"921","status":"public","date_updated":"2023-09-20T11:41:19Z","ddc":["571"],"department":[{"_id":"GaTk"}],"file_date_updated":"2018-12-12T10:16:06Z","abstract":[{"lang":"eng","text":"In the early visual system, cells of the same type perform the same computation in different places of the visual field. How these cells code together a complex visual scene is unclear. A common assumption is that cells of a single-type extract a single-stimulus feature to form a feature map, but this has rarely been observed directly. Using large-scale recordings in the rat retina, we show that a homogeneous population of fast OFF ganglion cells simultaneously encodes two radically different features of a visual scene. Cells close to a moving object code quasilinearly for its position, while distant cells remain largely invariant to the object's position and, instead, respond nonlinearly to changes in the object's speed. We develop a quantitative model that accounts for this effect and identify a disinhibitory circuit that mediates it. Ganglion cells of a single type thus do not code for one, but two features simultaneously. This richer, flexible neural map might also be present in other sensory systems."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 8","month":"12","publication_status":"published","publication_identifier":{"issn":["20411723"]},"language":[{"iso":"eng"}],"file":[{"file_id":"5191","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2018-921-v1+1_s41467-017-02159-y.pdf","date_created":"2018-12-12T10:16:06Z","file_size":2872887,"date_updated":"2018-12-12T10:16:06Z","creator":"system"}],"ec_funded":1,"license":"https://creativecommons.org/licenses/by/4.0/","issue":"1","volume":8,"article_number":"1964","project":[{"grant_number":"604102","name":"Localization of ion channels and receptors by two and three-dimensional immunoelectron microscopic approaches","call_identifier":"FP7","_id":"25CD3DD2-B435-11E9-9278-68D0E5697425"},{"name":"Sensitivity to higher-order statistics in natural scenes","grant_number":"P 25651-N26","_id":"254D1A94-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"ista":"Deny S, Ferrari U, Mace E, Yger P, Caplette R, Picaud S, Tkačik G, Marre O. 2017. Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. 8(1), 1964.","chicago":"Deny, Stephane, Ulisse Ferrari, Emilie Mace, Pierre Yger, Romain Caplette, Serge Picaud, Gašper Tkačik, and Olivier Marre. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-02159-y.","apa":"Deny, S., Ferrari, U., Mace, E., Yger, P., Caplette, R., Picaud, S., … Marre, O. (2017). Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-02159-y","ama":"Deny S, Ferrari U, Mace E, et al. Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-02159-y","short":"S. Deny, U. Ferrari, E. Mace, P. Yger, R. Caplette, S. Picaud, G. Tkačik, O. Marre, Nature Communications 8 (2017).","ieee":"S. Deny et al., “Multiplexed computations in retinal ganglion cells of a single type,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.","mla":"Deny, Stephane, et al. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.” Nature Communications, vol. 8, no. 1, 1964, Nature Publishing Group, 2017, doi:10.1038/s41467-017-02159-y."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000417241200004"]},"article_processing_charge":"No","publist_id":"6266","author":[{"last_name":"Deny","full_name":"Deny, Stephane","first_name":"Stephane"},{"first_name":"Ulisse","last_name":"Ferrari","full_name":"Ferrari, Ulisse"},{"first_name":"Emilie","full_name":"Mace, Emilie","last_name":"Mace"},{"full_name":"Yger, Pierre","last_name":"Yger","first_name":"Pierre"},{"first_name":"Romain","full_name":"Caplette, Romain","last_name":"Caplette"},{"first_name":"Serge","full_name":"Picaud, Serge","last_name":"Picaud"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"}],"title":"Multiplexed computations in retinal ganglion cells of a single type","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","year":"2017","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"06","date_created":"2018-12-11T11:50:10Z","doi":"10.1038/s41467-017-02159-y","date_published":"2017-12-06T00:00:00Z"},{"article_number":"011012","citation":{"ista":"Fink JM, Dombi A, Vukics A, Wallraff A, Domokos P. 2017. Observation of the photon blockade breakdown phase transition. Physical Review X. 7(1), 011012.","chicago":"Fink, Johannes M, András Dombi, András Vukics, Andreas Wallraff, and Peter Domokos. “Observation of the Photon Blockade Breakdown Phase Transition.” Physical Review X. American Physical Society, 2017. https://doi.org/10.1103/PhysRevX.7.011012.","ieee":"J. M. Fink, A. Dombi, A. Vukics, A. Wallraff, and P. Domokos, “Observation of the photon blockade breakdown phase transition,” Physical Review X, vol. 7, no. 1. American Physical Society, 2017.","short":"J.M. Fink, A. Dombi, A. Vukics, A. Wallraff, P. Domokos, Physical Review X 7 (2017).","ama":"Fink JM, Dombi A, Vukics A, Wallraff A, Domokos P. Observation of the photon blockade breakdown phase transition. Physical Review X. 2017;7(1). doi:10.1103/PhysRevX.7.011012","apa":"Fink, J. M., Dombi, A., Vukics, A., Wallraff, A., & Domokos, P. (2017). Observation of the photon blockade breakdown phase transition. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.7.011012","mla":"Fink, Johannes M., et al. “Observation of the Photon Blockade Breakdown Phase Transition.” Physical Review X, vol. 7, no. 1, 011012, American Physical Society, 2017, doi:10.1103/PhysRevX.7.011012."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"Yes","external_id":{"isi":["000397450500001"]},"publist_id":"6252","author":[{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink"},{"full_name":"Dombi, András","last_name":"Dombi","first_name":"András"},{"full_name":"Vukics, András","last_name":"Vukics","first_name":"András"},{"first_name":"Andreas","full_name":"Wallraff, Andreas","last_name":"Wallraff"},{"first_name":"Peter","last_name":"Domokos","full_name":"Domokos, Peter"}],"title":"Observation of the photon blockade breakdown phase transition","oa":1,"publisher":"American Physical Society","quality_controlled":"1","year":"2017","has_accepted_license":"1","isi":1,"publication":"Physical Review X","day":"31","date_created":"2018-12-11T11:50:13Z","date_published":"2017-01-31T00:00:00Z","doi":"10.1103/PhysRevX.7.011012","_id":"1114","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"753","status":"public","date_updated":"2023-09-20T11:33:07Z","ddc":["539"],"department":[{"_id":"JoFi"}],"file_date_updated":"2018-12-12T10:12:52Z","abstract":[{"text":"Nonequilibrium phase transitions exist in damped-driven open quantum systems when the continuous tuning of an external parameter leads to a transition between two robust steady states. In second-order transitions this change is abrupt at a critical point, whereas in first-order transitions the two phases can coexist in a critical hysteresis domain. Here, we report the observation of a first-order dissipative quantum phase transition in a driven circuit quantum electrodynamics system. It takes place when the photon blockade of the driven cavity-atom system is broken by increasing the drive power. The observed experimental signature is a bimodal phase space distribution with varying weights controlled by the drive strength. Our measurements show an improved stabilization of the classical attractors up to the millisecond range when the size of the quantum system is increased from one to three artificial atoms. The formation of such robust pointer states could be used for new quantum measurement schemes or to investigate multiphoton phases of finite-size, nonlinear, open quantum systems.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 7","month":"01","publication_status":"published","publication_identifier":{"issn":["21603308"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4972","creator":"system","date_updated":"2018-12-12T10:12:52Z","file_size":1172926,"date_created":"2018-12-12T10:12:52Z","file_name":"IST-2017-753-v1+1_PhysRevX.7.011012.pdf"}],"issue":"1","volume":7},{"oa":1,"publisher":"Genetics Society of America","quality_controlled":"1","date_created":"2018-12-11T11:50:12Z","doi":"10.1534/genetics.116.189340","date_published":"2017-02-01T00:00:00Z","page":"803 - 825","publication":"Genetics","day":"01","year":"2017","isi":1,"project":[{"call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091"}],"title":"Selection limits to adaptive walks on correlated landscapes","article_processing_charge":"No","external_id":{"isi":["000394144900025"],"pmid":["27881471"]},"publist_id":"6256","author":[{"full_name":"Heredia, Jorge","last_name":"Heredia","first_name":"Jorge"},{"last_name":"Trubenova","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora"},{"first_name":"Dirk","last_name":"Sudholt","full_name":"Sudholt, Dirk"},{"first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"J. Heredia, B. Trubenova, D. Sudholt, and T. Paixao, “Selection limits to adaptive walks on correlated landscapes,” Genetics, vol. 205, no. 2. Genetics Society of America, pp. 803–825, 2017.","short":"J. Heredia, B. Trubenova, D. Sudholt, T. Paixao, Genetics 205 (2017) 803–825.","ama":"Heredia J, Trubenova B, Sudholt D, Paixao T. Selection limits to adaptive walks on correlated landscapes. Genetics. 2017;205(2):803-825. doi:10.1534/genetics.116.189340","apa":"Heredia, J., Trubenova, B., Sudholt, D., & Paixao, T. (2017). Selection limits to adaptive walks on correlated landscapes. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.189340","mla":"Heredia, Jorge, et al. “Selection Limits to Adaptive Walks on Correlated Landscapes.” Genetics, vol. 205, no. 2, Genetics Society of America, 2017, pp. 803–25, doi:10.1534/genetics.116.189340.","ista":"Heredia J, Trubenova B, Sudholt D, Paixao T. 2017. Selection limits to adaptive walks on correlated landscapes. Genetics. 205(2), 803–825.","chicago":"Heredia, Jorge, Barbora Trubenova, Dirk Sudholt, and Tiago Paixao. “Selection Limits to Adaptive Walks on Correlated Landscapes.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.189340."},"intvolume":" 205","month":"02","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1534/genetics.116.189340"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Adaptation depends critically on the effects of new mutations and their dependency on the genetic background in which they occur. These two factors can be summarized by the fitness landscape. However, it would require testing all mutations in all backgrounds, making the definition and analysis of fitness landscapes mostly inaccessible. Instead of postulating a particular fitness landscape, we address this problem by considering general classes of landscapes and calculating an upper limit for the time it takes for a population to reach a fitness peak, circumventing the need to have full knowledge about the fitness landscape. We analyze populations in the weak-mutation regime and characterize the conditions that enable them to quickly reach the fitness peak as a function of the number of sites under selection. We show that for additive landscapes there is a critical selection strength enabling populations to reach high-fitness genotypes, regardless of the distribution of effects. This threshold scales with the number of sites under selection, effectively setting a limit to adaptation, and results from the inevitable increase in deleterious mutational pressure as the population adapts in a space of discrete genotypes. Furthermore, we show that for the class of all unimodal landscapes this condition is sufficient but not necessary for rapid adaptation, as in some highly epistatic landscapes the critical strength does not depend on the number of sites under selection; effectively removing this barrier to adaptation."}],"ec_funded":1,"issue":"2","volume":205,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00166731"]},"status":"public","article_type":"original","type":"journal_article","_id":"1111","department":[{"_id":"NiBa"}],"date_updated":"2023-09-20T11:35:03Z"},{"abstract":[{"text":"Rotation of molecules embedded in He nanodroplets is explored by a combination of fs laser-induced alignment experiments and angulon quasiparticle theory. We demonstrate that at low fluence of the fs alignment pulse, the molecule and its solvation shell can be set into coherent collective rotation lasting long enough to form revivals. With increasing fluence, however, the revivals disappear -- instead, rotational dynamics as rapid as for an isolated molecule is observed during the first few picoseconds. Classical calculations trace this phenomenon to transient decoupling of the molecule from its He shell. Our results open novel opportunities for studying non-equilibrium solute-solvent dynamics and quantum thermalization. ","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1702.01977","open_access":"1"}],"scopus_import":"1","intvolume":" 118","month":"05","publication_status":"published","language":[{"iso":"eng"}],"issue":"20","volume":118,"_id":"1109","type":"journal_article","status":"public","date_updated":"2023-09-20T11:36:17Z","department":[{"_id":"MiLe"}],"oa":1,"publisher":"American Physical Society","quality_controlled":"1","year":"2017","isi":1,"publication":"Physical Review Letters","day":"19","date_created":"2018-12-11T11:50:12Z","doi":"10.1103/PhysRevLett.118.203203","date_published":"2017-05-19T00:00:00Z","article_number":"203203","project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment"}],"citation":{"short":"B. Shepperson, A. Søndergaard, L. Christiansen, J. Kaczmarczyk, R. Zillich, M. Lemeshko, H. Stapelfeldt, Physical Review Letters 118 (2017).","ieee":"B. Shepperson et al., “Laser-induced rotation of iodine molecules in helium nanodroplets: Revivals and breaking-free,” Physical Review Letters, vol. 118, no. 20. American Physical Society, 2017.","apa":"Shepperson, B., Søndergaard, A., Christiansen, L., Kaczmarczyk, J., Zillich, R., Lemeshko, M., & Stapelfeldt, H. (2017). Laser-induced rotation of iodine molecules in helium nanodroplets: Revivals and breaking-free. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.118.203203","ama":"Shepperson B, Søndergaard A, Christiansen L, et al. Laser-induced rotation of iodine molecules in helium nanodroplets: Revivals and breaking-free. Physical Review Letters. 2017;118(20). doi:10.1103/PhysRevLett.118.203203","mla":"Shepperson, Benjamin, et al. “Laser-Induced Rotation of Iodine Molecules in Helium Nanodroplets: Revivals and Breaking-Free.” Physical Review Letters, vol. 118, no. 20, 203203, American Physical Society, 2017, doi:10.1103/PhysRevLett.118.203203.","ista":"Shepperson B, Søndergaard A, Christiansen L, Kaczmarczyk J, Zillich R, Lemeshko M, Stapelfeldt H. 2017. Laser-induced rotation of iodine molecules in helium nanodroplets: Revivals and breaking-free. Physical Review Letters. 118(20), 203203.","chicago":"Shepperson, Benjamin, Anders Søndergaard, Lars Christiansen, Jan Kaczmarczyk, Robert Zillich, Mikhail Lemeshko, and Henrik Stapelfeldt. “Laser-Induced Rotation of Iodine Molecules in Helium Nanodroplets: Revivals and Breaking-Free.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.118.203203."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000401664000005"]},"article_processing_charge":"No","author":[{"full_name":"Shepperson, Benjamin","last_name":"Shepperson","first_name":"Benjamin"},{"full_name":"Søndergaard, Anders","last_name":"Søndergaard","first_name":"Anders"},{"full_name":"Christiansen, Lars","last_name":"Christiansen","first_name":"Lars"},{"first_name":"Jan","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","last_name":"Kaczmarczyk","orcid":"0000-0002-1629-3675","full_name":"Kaczmarczyk, Jan"},{"last_name":"Zillich","full_name":"Zillich, Robert","first_name":"Robert"},{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stapelfeldt, Henrik","last_name":"Stapelfeldt","first_name":"Henrik"}],"publist_id":"6260","title":"Laser-induced rotation of iodine molecules in helium nanodroplets: Revivals and breaking-free"},{"date_updated":"2023-09-20T11:47:22Z","department":[{"_id":"BjHo"}],"_id":"1087","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"issn":["00221120"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":813,"acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"Using extensive direct numerical simulations, the dynamics of laminar-turbulent fronts in pipe flow is investigated for Reynolds numbers between and 5500. We here investigate the physical distinction between the fronts of weak and strong slugs both by analysing the turbulent kinetic energy budget and by comparing the downstream front motion to the advection speed of bulk turbulent structures. Our study shows that weak downstream fronts travel slower than turbulent structures in the bulk and correspond to decaying turbulence at the front. At the downstream front speed becomes faster than the advection speed, marking the onset of strong fronts. In contrast to weak fronts, turbulent eddies are generated at strong fronts by feeding on the downstream laminar flow. Our study also suggests that temporal fluctuations of production and dissipation at the downstream laminar-turbulent front drive the dynamical switches between the two types of front observed up to.","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://arxiv.org/abs/1603.04077","open_access":"1"}],"scopus_import":"1","intvolume":" 813","month":"02","citation":{"mla":"Song, Baofang, et al. “Speed and Structure of Turbulent Fronts in Pipe Flow.” Journal of Fluid Mechanics, vol. 813, Cambridge University Press, 2017, pp. 1045–59, doi:10.1017/jfm.2017.14.","short":"B. Song, D. Barkley, B. Hof, M. Avila, Journal of Fluid Mechanics 813 (2017) 1045–1059.","ieee":"B. Song, D. Barkley, B. Hof, and M. Avila, “Speed and structure of turbulent fronts in pipe flow,” Journal of Fluid Mechanics, vol. 813. Cambridge University Press, pp. 1045–1059, 2017.","apa":"Song, B., Barkley, D., Hof, B., & Avila, M. (2017). Speed and structure of turbulent fronts in pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.14","ama":"Song B, Barkley D, Hof B, Avila M. Speed and structure of turbulent fronts in pipe flow. Journal of Fluid Mechanics. 2017;813:1045-1059. doi:10.1017/jfm.2017.14","chicago":"Song, Baofang, Dwight Barkley, Björn Hof, and Marc Avila. “Speed and Structure of Turbulent Fronts in Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2017. https://doi.org/10.1017/jfm.2017.14.","ista":"Song B, Barkley D, Hof B, Avila M. 2017. Speed and structure of turbulent fronts in pipe flow. Journal of Fluid Mechanics. 813, 1045–1059."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000394376400044"]},"author":[{"first_name":"Baofang","full_name":"Song, Baofang","last_name":"Song"},{"full_name":"Barkley, Dwight","last_name":"Barkley","first_name":"Dwight"},{"last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"},{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"}],"publist_id":"6290","title":"Speed and structure of turbulent fronts in pipe flow","project":[{"call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425","grant_number":"306589","name":"Decoding the complexity of turbulence at its origin"}],"year":"2017","isi":1,"publication":"Journal of Fluid Mechanics","day":"25","page":"1045 - 1059","date_created":"2018-12-11T11:50:04Z","doi":"10.1017/jfm.2017.14","date_published":"2017-02-25T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Cambridge University Press"},{"citation":{"mla":"Fallat, Shaun, et al. “Total Positivity in Markov Structures.” Annals of Statistics, vol. 45, no. 3, Institute of Mathematical Statistics, 2017, pp. 1152–84, doi:10.1214/16-AOS1478.","apa":"Fallat, S., Lauritzen, S., Sadeghi, K., Uhler, C., Wermuth, N., & Zwiernik, P. (2017). Total positivity in Markov structures. Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/16-AOS1478","ama":"Fallat S, Lauritzen S, Sadeghi K, Uhler C, Wermuth N, Zwiernik P. Total positivity in Markov structures. Annals of Statistics. 2017;45(3):1152-1184. doi:10.1214/16-AOS1478","short":"S. Fallat, S. Lauritzen, K. Sadeghi, C. Uhler, N. Wermuth, P. Zwiernik, Annals of Statistics 45 (2017) 1152–1184.","ieee":"S. Fallat, S. Lauritzen, K. Sadeghi, C. Uhler, N. Wermuth, and P. Zwiernik, “Total positivity in Markov structures,” Annals of Statistics, vol. 45, no. 3. Institute of Mathematical Statistics, pp. 1152–1184, 2017.","chicago":"Fallat, Shaun, Steffen Lauritzen, Kayvan Sadeghi, Caroline Uhler, Nanny Wermuth, and Piotr Zwiernik. “Total Positivity in Markov Structures.” Annals of Statistics. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/16-AOS1478.","ista":"Fallat S, Lauritzen S, Sadeghi K, Uhler C, Wermuth N, Zwiernik P. 2017. Total positivity in Markov structures. Annals of Statistics. 45(3), 1152–1184."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Shaun","last_name":"Fallat","full_name":"Fallat, Shaun"},{"first_name":"Steffen","last_name":"Lauritzen","full_name":"Lauritzen, Steffen"},{"full_name":"Sadeghi, Kayvan","last_name":"Sadeghi","first_name":"Kayvan"},{"first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline","last_name":"Uhler"},{"first_name":"Nanny","full_name":"Wermuth, Nanny","last_name":"Wermuth"},{"first_name":"Piotr","last_name":"Zwiernik","full_name":"Zwiernik, Piotr"}],"publist_id":"6288","external_id":{"isi":["000404395900008"]},"article_processing_charge":"No","title":"Total positivity in Markov structures","project":[{"_id":"2530CA10-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Y 903-N35","name":"Gaussian Graphical Models: Theory and Applications"}],"isi":1,"year":"2017","day":"01","publication":"Annals of Statistics","page":"1152 - 1184","date_published":"2017-06-01T00:00:00Z","doi":"10.1214/16-AOS1478","date_created":"2018-12-11T11:50:05Z","quality_controlled":"1","publisher":"Institute of Mathematical Statistics","oa":1,"date_updated":"2023-09-20T11:46:53Z","department":[{"_id":"CaUh"}],"_id":"1089","type":"journal_article","status":"public","publication_identifier":{"issn":["00905364"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"3","volume":45,"abstract":[{"text":"We discuss properties of distributions that are multivariate totally positive of order two (MTP2) related to conditional independence. In particular, we show that any independence model generated by an MTP2 distribution is a compositional semigraphoid which is upward-stable and singleton-transitive. In addition, we prove that any MTP2 distribution satisfying an appropriate support condition is faithful to its concentration graph. Finally, we analyze factorization properties of MTP2 distributions and discuss ways of constructing MTP2 distributions; in particular we give conditions on the log-linear parameters of a discrete distribution which ensure MTP2 and characterize conditional Gaussian distributions which satisfy MTP2.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1510.01290"}],"month":"06","intvolume":" 45"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","chicago":"Reiter, Johannes, Alvin Makohon Moore, Jeffrey Gerold, Ivana Božić, Krishnendu Chatterjee, Christine Iacobuzio Donahue, Bert Vogelstein, and Martin Nowak. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms14114.","apa":"Reiter, J., Makohon Moore, A., Gerold, J., Božić, I., Chatterjee, K., Iacobuzio Donahue, C., … Nowak, M. (2017). Reconstructing metastatic seeding patterns of human cancers. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14114","ama":"Reiter J, Makohon Moore A, Gerold J, et al. Reconstructing metastatic seeding patterns of human cancers. Nature Communications. 2017;8. doi:10.1038/ncomms14114","short":"J. Reiter, A. Makohon Moore, J. Gerold, I. Božić, K. Chatterjee, C. Iacobuzio Donahue, B. Vogelstein, M. Nowak, Nature Communications 8 (2017).","ieee":"J. Reiter et al., “Reconstructing metastatic seeding patterns of human cancers,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","mla":"Reiter, Johannes, et al. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” Nature Communications, vol. 8, 14114, Nature Publishing Group, 2017, doi:10.1038/ncomms14114."},"title":"Reconstructing metastatic seeding patterns of human cancers","publist_id":"6301","author":[{"id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","last_name":"Reiter","orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes"},{"full_name":"Makohon Moore, Alvin","last_name":"Makohon Moore","first_name":"Alvin"},{"first_name":"Jeffrey","last_name":"Gerold","full_name":"Gerold, Jeffrey"},{"last_name":"Božić","full_name":"Božić, Ivana","first_name":"Ivana"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Christine","full_name":"Iacobuzio Donahue, Christine","last_name":"Iacobuzio Donahue"},{"first_name":"Bert","full_name":"Vogelstein, Bert","last_name":"Vogelstein"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"article_processing_charge":"No","external_id":{"isi":["000393096600001"]},"article_number":"14114","project":[{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"}],"day":"31","publication":"Nature Communications","isi":1,"has_accepted_license":"1","year":"2017","date_published":"2017-01-31T00:00:00Z","doi":"10.1038/ncomms14114","date_created":"2018-12-11T11:50:02Z","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"ddc":["004","006"],"date_updated":"2023-09-20T11:55:31Z","department":[{"_id":"KrCh"}],"file_date_updated":"2018-12-12T10:15:15Z","_id":"1080","status":"public","pubrep_id":"786","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_id":"5133","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-786-v1+1_ncomms14114.pdf","date_created":"2018-12-12T10:15:15Z","creator":"system","file_size":897050,"date_updated":"2018-12-12T10:15:15Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["20411723"]},"publication_status":"published","volume":8,"ec_funded":1,"oa_version":"Published Version","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."}],"month":"01","intvolume":" 8","scopus_import":"1"},{"scopus_import":"1","intvolume":" 8","month":"01","abstract":[{"lang":"eng","text":"Sex chromosomes evolve once recombination is halted between a homologous pair of chromosomes. The dominant model of sex chromosome evolution posits that recombination is suppressed between emerging X and Y chromosomes in order to resolve sexual conflict. Here we test this model using whole genome and transcriptome resequencing data in the guppy, a model for sexual selection with many Y-linked colour traits. We show that although the nascent Y chromosome encompasses nearly half of the linkage group, there has been no perceptible degradation of Y chromosome gene content or activity. Using replicate wild populations with differing levels of sexually antagonistic selection for colour, we also show that sexual selection leads to greater expansion of the non-recombining region and increased Y chromosome divergence. These results provide empirical support for longstanding models of sex chromosome catalysis, and suggest an important role for sexual selection and sexual conflict in genome evolution."}],"oa_version":"Published Version","volume":8,"publication_status":"published","publication_identifier":{"issn":["20411723"]},"language":[{"iso":"eng"}],"file":[{"file_id":"5141","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2017-791-v1+1_ncomms14251.pdf","date_created":"2018-12-12T10:15:22Z","file_size":955256,"date_updated":"2018-12-12T10:15:22Z","creator":"system"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"791","status":"public","_id":"1085","department":[{"_id":"BeVi"}],"file_date_updated":"2018-12-12T10:15:22Z","date_updated":"2023-09-20T11:48:16Z","ddc":["570","576"],"oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","date_created":"2018-12-11T11:50:04Z","doi":"10.1038/ncomms14251","date_published":"2017-01-31T00:00:00Z","year":"2017","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"31","article_number":"14251","external_id":{"isi":["000392953700001"]},"article_processing_charge":"No","publist_id":"6292","author":[{"first_name":"Alison","full_name":"Wright, Alison","last_name":"Wright"},{"full_name":"Darolti, Iulia","last_name":"Darolti","first_name":"Iulia"},{"last_name":"Bloch","full_name":"Bloch, Natasha","first_name":"Natasha"},{"last_name":"Oostra","full_name":"Oostra, Vicencio","first_name":"Vicencio"},{"full_name":"Sandkam, Benjamin","last_name":"Sandkam","first_name":"Benjamin"},{"first_name":"Séverine","full_name":"Buechel, Séverine","last_name":"Buechel"},{"last_name":"Kolm","full_name":"Kolm, Niclas","first_name":"Niclas"},{"full_name":"Breden, Felix","last_name":"Breden","first_name":"Felix"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"},{"last_name":"Mank","full_name":"Mank, Judith","first_name":"Judith"}],"title":"Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation","citation":{"chicago":"Wright, Alison, Iulia Darolti, Natasha Bloch, Vicencio Oostra, Benjamin Sandkam, Séverine Buechel, Niclas Kolm, Felix Breden, Beatriz Vicoso, and Judith Mank. “Convergent Recombination Suppression Suggests Role of Sexual Selection in Guppy Sex Chromosome Formation.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms14251.","ista":"Wright A, Darolti I, Bloch N, Oostra V, Sandkam B, Buechel S, Kolm N, Breden F, Vicoso B, Mank J. 2017. Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nature Communications. 8, 14251.","mla":"Wright, Alison, et al. “Convergent Recombination Suppression Suggests Role of Sexual Selection in Guppy Sex Chromosome Formation.” Nature Communications, vol. 8, 14251, Nature Publishing Group, 2017, doi:10.1038/ncomms14251.","apa":"Wright, A., Darolti, I., Bloch, N., Oostra, V., Sandkam, B., Buechel, S., … Mank, J. (2017). Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14251","ama":"Wright A, Darolti I, Bloch N, et al. Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nature Communications. 2017;8. doi:10.1038/ncomms14251","short":"A. Wright, I. Darolti, N. Bloch, V. Oostra, B. Sandkam, S. Buechel, N. Kolm, F. Breden, B. Vicoso, J. Mank, Nature Communications 8 (2017).","ieee":"A. Wright et al., “Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation,” Nature Communications, vol. 8. Nature Publishing Group, 2017."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"day":"01","publication":"Scientific Reports","isi":1,"has_accepted_license":"1","year":"2017","date_published":"2017-02-01T00:00:00Z","doi":"10.1038/srep41002","date_created":"2018-12-11T11:50:04Z","page":"41002","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Di Giglio M, Muttenthaler M, Harpsøe K, Liutkeviciute Z, Keov P, Eder T, Rattei T, Arrowsmith S, Wray S, Marek A, Elbert T, Alewood P, Gloriam D, Gruber C. 2017. Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide. Scientific Reports. 7, 41002.","chicago":"Di Giglio, Maria, Markus Muttenthaler, Kasper Harpsøe, Zita Liutkeviciute, Peter Keov, Thomas Eder, Thomas Rattei, et al. “Development of a Human Vasopressin V1a-Receptor Antagonist from an Evolutionary-Related Insect Neuropeptide.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/srep41002.","ieee":"M. Di Giglio et al., “Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide,” Scientific Reports, vol. 7. Nature Publishing Group, p. 41002, 2017.","short":"M. Di Giglio, M. Muttenthaler, K. Harpsøe, Z. Liutkeviciute, P. Keov, T. Eder, T. Rattei, S. Arrowsmith, S. Wray, A. Marek, T. Elbert, P. Alewood, D. Gloriam, C. Gruber, Scientific Reports 7 (2017) 41002.","apa":"Di Giglio, M., Muttenthaler, M., Harpsøe, K., Liutkeviciute, Z., Keov, P., Eder, T., … Gruber, C. (2017). Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep41002","ama":"Di Giglio M, Muttenthaler M, Harpsøe K, et al. Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide. Scientific Reports. 2017;7:41002. doi:10.1038/srep41002","mla":"Di Giglio, Maria, et al. “Development of a Human Vasopressin V1a-Receptor Antagonist from an Evolutionary-Related Insect Neuropeptide.” Scientific Reports, vol. 7, Nature Publishing Group, 2017, p. 41002, doi:10.1038/srep41002."},"title":"Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide","author":[{"first_name":"Maria","last_name":"Di Giglio","full_name":"Di Giglio, Maria"},{"last_name":"Muttenthaler","full_name":"Muttenthaler, Markus","first_name":"Markus"},{"last_name":"Harpsøe","full_name":"Harpsøe, Kasper","first_name":"Kasper"},{"full_name":"Liutkeviciute, Zita","last_name":"Liutkeviciute","first_name":"Zita"},{"first_name":"Peter","last_name":"Keov","full_name":"Keov, Peter"},{"full_name":"Eder, Thomas","last_name":"Eder","first_name":"Thomas"},{"first_name":"Thomas","full_name":"Rattei, Thomas","last_name":"Rattei"},{"first_name":"Sarah","last_name":"Arrowsmith","full_name":"Arrowsmith, Sarah"},{"last_name":"Wray","full_name":"Wray, Susan","first_name":"Susan"},{"full_name":"Marek, Ales","last_name":"Marek","first_name":"Ales"},{"first_name":"Tomas","last_name":"Elbert","full_name":"Elbert, Tomas"},{"full_name":"Alewood, Paul","last_name":"Alewood","first_name":"Paul"},{"first_name":"David","full_name":"Gloriam, David","last_name":"Gloriam"},{"last_name":"Gruber","full_name":"Gruber, Christian","first_name":"Christian"}],"publist_id":"6291","external_id":{"isi":["000393163800001"]},"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"text":"Characterisation of G protein-coupled receptors (GPCR) relies on the availability of a toolbox of ligands that selectively modulate different functional states of the receptors. To uncover such molecules, we explored a unique strategy for ligand discovery that takes advantage of the evolutionary conservation of the 600-million-year-old oxytocin/vasopressin signalling system. We isolated the insect oxytocin/vasopressin orthologue inotocin from the black garden ant (Lasius niger), identified and cloned its cognate receptor and determined its pharmacological properties on the insect and human oxytocin/vasopressin receptors. Subsequently, we identified a functional dichotomy: inotocin activated the insect inotocin and the human vasopressin V1b receptors, but inhibited the human V1aR. Replacement of Arg8 of inotocin by D-Arg8 led to a potent, stable and competitive V1aR-antagonist ([D-Arg8]-inotocin) with a 3,000-fold binding selectivity for the human V1aR over the other three subtypes, OTR, V1bR and V2R. The Arg8/D-Arg8 ligand-pair was further investigated to gain novel insights into the oxytocin/vasopressin peptide-receptor interaction, which led to the identification of key residues of the receptors that are important for ligand functionality and selectivity. These observations could play an important role for development of oxytocin/vasopressin receptor modulators that would enable clear distinction of the physiological and pathological responses of the individual receptor subtypes.","lang":"eng"}],"month":"02","intvolume":" 7","scopus_import":"1","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5115","creator":"system","file_size":1994139,"date_updated":"2018-12-12T10:14:59Z","file_name":"IST-2017-790-v1+1_srep41002_1_.pdf","date_created":"2018-12-12T10:14:59Z"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":7,"_id":"1086","status":"public","pubrep_id":"790","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570","590"],"date_updated":"2023-09-20T11:47:47Z","file_date_updated":"2018-12-12T10:14:59Z"},{"department":[{"_id":"CaGu"}],"date_updated":"2023-09-20T11:48:43Z","status":"public","type":"journal_article","_id":"1084","volume":104,"issue":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":[" 0950382X"]},"intvolume":" 104","month":"04","scopus_import":"1","oa_version":"None","abstract":[{"text":"BceRS and PsdRS are paralogous two-component systems in Bacillus subtilis controlling the response to antimicrobial peptides. In the presence of extracellular bacitracin and nisin, respectively, the two response regulators (RRs) bind their target promoters, PbceA or PpsdA, resulting in a strong up-regulation of target gene expression and ultimately antibiotic resistance. Despite high sequence similarity between the RRs BceR and PsdR and their known binding sites, no cross-regulation has been observed between them. We therefore investigated the specificity determinants of PbceA and PpsdA that ensure the insulation of these two paralogous pathways at the RR–promoter interface. In vivo and in vitro analyses demonstrate that the regulatory regions within these two promoters contain three important elements: in addition to the known (main) binding site, we identified a linker region and a secondary binding site that are crucial for functionality. Initial binding to the high-affinity, low-specificity main binding site is a prerequisite for the subsequent highly specific binding of a second RR dimer to the low-affinity secondary binding site. In addition to this hierarchical cooperative binding, discrimination requires a competition of the two RRs for their respective binding site mediated by only slight differences in binding affinities.","lang":"eng"}],"title":"Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis","article_processing_charge":"No","external_id":{"isi":["000398059200002"]},"author":[{"last_name":"Fang","full_name":"Fang, Chong","first_name":"Chong"},{"id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","first_name":"Anna A","orcid":"0000-0002-1391-8377","full_name":"Nagy-Staron, Anna A","last_name":"Nagy-Staron"},{"first_name":"Martin","full_name":"Grafe, Martin","last_name":"Grafe"},{"full_name":"Heermann, Ralf","last_name":"Heermann","first_name":"Ralf"},{"first_name":"Kirsten","full_name":"Jung, Kirsten","last_name":"Jung"},{"last_name":"Gebhard","full_name":"Gebhard, Susanne","first_name":"Susanne"},{"last_name":"Mascher","full_name":"Mascher, Thorsten","first_name":"Thorsten"}],"publist_id":"6294","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Fang, Chong, et al. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” Molecular Microbiology, vol. 104, no. 1, Wiley-Blackwell, 2017, pp. 16–31, doi:10.1111/mmi.13597.","short":"C. Fang, A.A. Nagy-Staron, M. Grafe, R. Heermann, K. Jung, S. Gebhard, T. Mascher, Molecular Microbiology 104 (2017) 16–31.","ieee":"C. Fang et al., “Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis,” Molecular Microbiology, vol. 104, no. 1. Wiley-Blackwell, pp. 16–31, 2017.","ama":"Fang C, Nagy-Staron AA, Grafe M, et al. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. 2017;104(1):16-31. doi:10.1111/mmi.13597","apa":"Fang, C., Nagy-Staron, A. A., Grafe, M., Heermann, R., Jung, K., Gebhard, S., & Mascher, T. (2017). Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. Wiley-Blackwell. https://doi.org/10.1111/mmi.13597","chicago":"Fang, Chong, Anna A Nagy-Staron, Martin Grafe, Ralf Heermann, Kirsten Jung, Susanne Gebhard, and Thorsten Mascher. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” Molecular Microbiology. Wiley-Blackwell, 2017. https://doi.org/10.1111/mmi.13597.","ista":"Fang C, Nagy-Staron AA, Grafe M, Heermann R, Jung K, Gebhard S, Mascher T. 2017. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. 104(1), 16–31."},"date_created":"2018-12-11T11:50:03Z","date_published":"2017-04-01T00:00:00Z","doi":"10.1111/mmi.13597","page":"16 - 31","publication":"Molecular Microbiology","day":"01","year":"2017","isi":1,"publisher":"Wiley-Blackwell","quality_controlled":"1"},{"date_updated":"2023-09-20T11:53:35Z","department":[{"_id":"RoSe"}],"_id":"1079","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["13850172"]},"volume":20,"issue":"2","oa_version":"Submitted Version","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."}],"intvolume":" 20","month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1603.07368"}],"scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” Mathematical Physics, Analysis and Geometry. Springer, 2017. https://doi.org/10.1007/s11040-017-9238-0.","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.” Mathematical Physics, Analysis and Geometry, vol. 20, no. 2, 6, Springer, 2017, doi:10.1007/s11040-017-9238-0.","ieee":"P. Nam and H. Van Den Bosch, “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges,” Mathematical Physics, Analysis and Geometry, vol. 20, no. 2. Springer, 2017.","short":"P. Nam, H. Van Den Bosch, Mathematical Physics, Analysis and Geometry 20 (2017).","apa":"Nam, P., & Van Den Bosch, H. (2017). Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-017-9238-0","ama":"Nam P, Van Den Bosch H. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis and Geometry. 2017;20(2). doi:10.1007/s11040-017-9238-0"},"title":"Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges","article_processing_charge":"No","external_id":{"isi":["000401270000004"]},"author":[{"last_name":"Nam","full_name":"Nam, Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan"},{"first_name":"Hanne","full_name":"Van Den Bosch, Hanne","last_name":"Van Den Bosch"}],"publist_id":"6300","article_number":"6","project":[{"call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27"}],"publication":"Mathematical Physics, Analysis and Geometry","day":"01","year":"2017","isi":1,"date_created":"2018-12-11T11:50:02Z","date_published":"2017-06-01T00:00:00Z","doi":"10.1007/s11040-017-9238-0","oa":1,"publisher":"Springer","quality_controlled":"1"},{"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"},{"name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"article_number":"20160139","title":"Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000393380400001"]},"author":[{"id":"409D5C96-F248-11E8-B48F-1D18A9856A87","first_name":"Rodrigo A","full_name":"Fernandes Redondo, Rodrigo A","orcid":"0000-0002-5837-2793","last_name":"Fernandes Redondo"},{"first_name":"Harold","id":"2A181218-F248-11E8-B48F-1D18A9856A87","full_name":"Vladar, Harold","orcid":"0000-0002-5985-7653","last_name":"Vladar"},{"first_name":"Tomasz","full_name":"Włodarski, Tomasz","last_name":"Włodarski"},{"full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","last_name":"Bollback","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6303","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017).","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family,” Journal of the Royal Society Interface, vol. 14, no. 126. Royal Society of London, 2017.","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J. P. (2017). Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. Royal Society of London. https://doi.org/10.1098/rsif.2016.0139","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 2017;14(126). doi:10.1098/rsif.2016.0139","mla":"Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface, vol. 14, no. 126, 20160139, Royal Society of London, 2017, doi:10.1098/rsif.2016.0139.","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 14(126), 20160139.","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface. Royal Society of London, 2017. https://doi.org/10.1098/rsif.2016.0139."},"oa":1,"publisher":"Royal Society of London","quality_controlled":"1","date_created":"2018-12-11T11:50:01Z","doi":"10.1098/rsif.2016.0139","date_published":"2017-01-04T00:00:00Z","publication":"Journal of the Royal Society Interface","day":"04","year":"2017","isi":1,"has_accepted_license":"1","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"1077","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"file_date_updated":"2019-01-18T09:14:02Z","ddc":["570"],"date_updated":"2023-09-20T11:56:34Z","intvolume":" 14","month":"01","scopus_import":"1","oa_version":"Published Version","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."}],"ec_funded":1,"volume":14,"issue":"126","related_material":{"record":[{"id":"9864","status":"public","relation":"research_data"}]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"5843","creator":"dernst","file_size":1092015,"date_updated":"2019-01-18T09:14:02Z","file_name":"2017_JRSI_Redondo.pdf","date_created":"2019-01-18T09:14:02Z"}],"publication_status":"published","publication_identifier":{"issn":["17425689"]}},{"department":[{"_id":"CaHe"}],"file_date_updated":"2018-12-12T10:10:57Z","ddc":["572","597"],"date_updated":"2023-09-20T12:06:27Z","pubrep_id":"869","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"1067","ec_funded":1,"volume":40,"issue":"4","language":[{"iso":"eng"}],"file":[{"date_updated":"2018-12-12T10:10:57Z","file_size":6866187,"creator":"system","date_created":"2018-12-12T10:10:57Z","file_name":"IST-2017-869-v1+1_1-s2.0-S1534580717300370-main.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"4849"}],"publication_status":"published","publication_identifier":{"issn":["15345807"]},"intvolume":" 40","month":"02","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Embryo morphogenesis relies on highly coordinated movements of different tissues. However, remarkably little is known about how tissues coordinate their movements to shape the embryo. In zebrafish embryogenesis, coordinated tissue movements first become apparent during “doming,” when the blastoderm begins to spread over the yolk sac, a process involving coordinated epithelial surface cell layer expansion and mesenchymal deep cell intercalations. Here, we find that active surface cell expansion represents the key process coordinating tissue movements during doming. By using a combination of theory and experiments, we show that epithelial surface cells not only trigger blastoderm expansion by reducing tissue surface tension, but also drive blastoderm thinning by inducing tissue contraction through radial deep cell intercalations. Thus, coordinated tissue expansion and thinning during doming relies on surface cells simultaneously controlling tissue surface tension and radial tissue contraction.","lang":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"}],"title":"The physical basis of coordinated tissue spreading in zebrafish gastrulation","external_id":{"isi":["000395368300007"]},"article_processing_charge":"No","author":[{"first_name":"Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","full_name":"Morita, Hitoshi","last_name":"Morita"},{"full_name":"Grigolon, Silvia","last_name":"Grigolon","first_name":"Silvia"},{"first_name":"Martin","full_name":"Bock, Martin","last_name":"Bock"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","last_name":"Krens","orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel"},{"first_name":"Guillaume","last_name":"Salbreux","full_name":"Salbreux, Guillaume"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"publist_id":"6320","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. 2017. The physical basis of coordinated tissue spreading in zebrafish gastrulation. Developmental Cell. 40(4), 354–366.","chicago":"Morita, Hitoshi, Silvia Grigolon, Martin Bock, Gabriel Krens, Guillaume Salbreux, and Carl-Philipp J Heisenberg. “The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation.” Developmental Cell. Cell Press, 2017. https://doi.org/10.1016/j.devcel.2017.01.010.","apa":"Morita, H., Grigolon, S., Bock, M., Krens, G., Salbreux, G., & Heisenberg, C.-P. J. (2017). The physical basis of coordinated tissue spreading in zebrafish gastrulation. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2017.01.010","ama":"Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. The physical basis of coordinated tissue spreading in zebrafish gastrulation. Developmental Cell. 2017;40(4):354-366. doi:10.1016/j.devcel.2017.01.010","ieee":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, and C.-P. J. Heisenberg, “The physical basis of coordinated tissue spreading in zebrafish gastrulation,” Developmental Cell, vol. 40, no. 4. Cell Press, pp. 354–366, 2017.","short":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, C.-P.J. Heisenberg, Developmental Cell 40 (2017) 354–366.","mla":"Morita, Hitoshi, et al. “The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation.” Developmental Cell, vol. 40, no. 4, Cell Press, 2017, pp. 354–66, doi:10.1016/j.devcel.2017.01.010."},"project":[{"name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","grant_number":"201439","_id":"2524F500-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_created":"2018-12-11T11:49:58Z","doi":"10.1016/j.devcel.2017.01.010","date_published":"2017-02-27T00:00:00Z","page":"354 - 366","publication":"Developmental Cell","day":"27","year":"2017","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"Cell Press"},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00166731"]},"ec_funded":1,"issue":"3","volume":205,"related_material":{"record":[{"id":"200","status":"public","relation":"dissertation_contains"}]},"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"intvolume":" 205","month":"03","main_file_link":[{"open_access":"1","url":"http://www.biorxiv.org/content/early/2016/09/23/076810"}],"scopus_import":"1","date_updated":"2023-09-20T12:00:56Z","department":[{"_id":"NiBa"}],"_id":"1074","status":"public","type":"journal_article","publication":"Genetics","day":"01","year":"2017","isi":1,"date_created":"2018-12-11T11:50:00Z","doi":"10.1534/genetics.116.196220","date_published":"2017-03-01T00:00:00Z","page":"1335 - 1351","oa":1,"publisher":"Genetics Society of America","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Ringbauer, Harald, et al. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics, vol. 205, no. 3, Genetics Society of America, 2017, pp. 1335–51, doi:10.1534/genetics.116.196220.","apa":"Ringbauer, H., Coop, G., & Barton, N. H. (2017). Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.196220","ama":"Ringbauer H, Coop G, Barton NH. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 2017;205(3):1335-1351. doi:10.1534/genetics.116.196220","short":"H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351.","ieee":"H. Ringbauer, G. Coop, and N. H. Barton, “Inferring recent demography from isolation by distance of long shared sequence blocks,” Genetics, vol. 205, no. 3. Genetics Society of America, pp. 1335–1351, 2017.","chicago":"Ringbauer, Harald, Graham Coop, and Nicholas H Barton. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.196220.","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."},"title":"Inferring recent demography from isolation by distance of long shared sequence blocks","article_processing_charge":"No","external_id":{"isi":["000395807200023"]},"publist_id":"6307","author":[{"first_name":"Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","full_name":"Ringbauer, Harald","orcid":"0000-0002-4884-9682","last_name":"Ringbauer"},{"first_name":"Graham","last_name":"Coop","full_name":"Coop, Graham"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}]},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["24699926"]},"ec_funded":1,"issue":"2","volume":95,"oa_version":"Submitted Version","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."}],"intvolume":" 95","month":"02","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1609.07018"}],"scopus_import":"1","date_updated":"2023-09-20T11:57:23Z","department":[{"_id":"MiLe"}],"_id":"1076","status":"public","type":"journal_article","publication":" Physical Review A - Atomic, Molecular, and Optical Physics","day":"01","year":"2017","isi":1,"date_created":"2018-12-11T11:50:01Z","doi":"10.1103/PhysRevA.95.023403","date_published":"2017-02-01T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"American Physical Society","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","chicago":"Klaiber, Michael, Jiří Daněk, Enderalp Yakaboylu, Karen Hatsagortsyan, and Christoph Keitel. “Strong-Field Ionization via a High-Order Coulomb-Corrected Strong-Field Approximation.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevA.95.023403.","ama":"Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. Strong-field ionization via a high-order Coulomb-corrected strong-field approximation. Physical Review A - Atomic, Molecular, and Optical Physics. 2017;95(2). doi:10.1103/PhysRevA.95.023403","apa":"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. American Physical Society. https://doi.org/10.1103/PhysRevA.95.023403","ieee":"M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, and C. Keitel, “Strong-field ionization via a high-order Coulomb-corrected strong-field approximation,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 95, no. 2. American Physical Society, 2017.","short":"M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, C. Keitel, Physical Review A - Atomic, Molecular, and Optical Physics 95 (2017).","mla":"Klaiber, Michael, et al. “Strong-Field Ionization via a High-Order Coulomb-Corrected Strong-Field Approximation.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 95, no. 2, 023403, American Physical Society, 2017, doi:10.1103/PhysRevA.95.023403."},"title":"Strong-field ionization via a high-order Coulomb-corrected strong-field approximation","external_id":{"isi":["000400571700011"]},"article_processing_charge":"No","publist_id":"6305","author":[{"first_name":"Michael","full_name":"Klaiber, Michael","last_name":"Klaiber"},{"last_name":"Daněk","full_name":"Daněk, Jiří","first_name":"Jiří"},{"first_name":"Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu","orcid":"0000-0001-5973-0874","full_name":"Yakaboylu, Enderalp"},{"full_name":"Hatsagortsyan, Karen","last_name":"Hatsagortsyan","first_name":"Karen"},{"first_name":"Christoph","last_name":"Keitel","full_name":"Keitel, Christoph"}],"article_number":"023403","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}]},{"status":"public","article_type":"original","type":"journal_article","_id":"1072","department":[{"_id":"HeEd"}],"date_updated":"2023-09-20T12:05:56Z","month":"05","intvolume":" 369","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1312.1231"}],"oa_version":"Preprint","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."}],"volume":369,"issue":"5","ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Topological Complex Systems","grant_number":"318493"}],"title":"The Morse theory of Čech and delaunay complexes","author":[{"last_name":"Bauer","full_name":"Bauer, Ulrich","orcid":"0000-0002-9683-0724","first_name":"Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"}],"publist_id":"6311","article_processing_charge":"No","external_id":{"isi":["000398030400024"],"arxiv":["1312.1231"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Bauer, U., & Edelsbrunner, H. (2017). The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/6991","ama":"Bauer U, Edelsbrunner H. The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. 2017;369(5):3741-3762. doi:10.1090/tran/6991","short":"U. Bauer, H. Edelsbrunner, Transactions of the American Mathematical Society 369 (2017) 3741–3762.","ieee":"U. Bauer and H. Edelsbrunner, “The Morse theory of Čech and delaunay complexes,” Transactions of the American Mathematical Society, vol. 369, no. 5. American Mathematical Society, pp. 3741–3762, 2017.","mla":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Complexes.” Transactions of the American Mathematical Society, vol. 369, no. 5, American Mathematical Society, 2017, pp. 3741–62, doi:10.1090/tran/6991.","ista":"Bauer U, Edelsbrunner H. 2017. The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. 369(5), 3741–3762.","chicago":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Complexes.” Transactions of the American Mathematical Society. American Mathematical Society, 2017. https://doi.org/10.1090/tran/6991."},"publisher":"American Mathematical Society","quality_controlled":"1","oa":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”.","date_published":"2017-05-01T00:00:00Z","doi":"10.1090/tran/6991","date_created":"2018-12-11T11:49:59Z","page":"3741 - 3762","day":"01","publication":"Transactions of the American Mathematical Society","isi":1,"year":"2017"},{"_id":"1073","type":"journal_article","status":"public","date_updated":"2023-09-20T12:01:28Z","department":[{"_id":"UlWa"}],"abstract":[{"lang":"eng","text":"Let X and Y be finite simplicial sets (e.g. finite simplicial complexes), both equipped with a free simplicial action of a finite group G. Assuming that Y is d-connected and dimX≤2d, for some d≥1, we provide an algorithm that computes the set of all equivariant homotopy classes of equivariant continuous maps |X|→|Y|; the existence of such a map can be decided even for dimX≤2d+1. This yields the first algorithm for deciding topological embeddability of a k-dimensional finite simplicial complex into Rn under the condition k≤23n−1. More generally, we present an algorithm that, given a lifting-extension problem satisfying an appropriate stability assumption, computes the set of all homotopy classes of solutions. This result is new even in the non-equivariant situation."}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1307.6444"}],"month":"06","intvolume":" 54","publication_identifier":{"issn":["01795376"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"4","volume":54,"citation":{"ista":"Čadek M, Krcál M, Vokřínek L. 2017. Algorithmic solvability of the lifting extension problem. Discrete & Computational Geometry. 54(4), 915–965.","chicago":"Čadek, Martin, Marek Krcál, and Lukáš Vokřínek. “Algorithmic Solvability of the Lifting Extension Problem.” Discrete & Computational Geometry. Springer, 2017. https://doi.org/10.1007/s00454-016-9855-6.","ieee":"M. Čadek, M. Krcál, and L. Vokřínek, “Algorithmic solvability of the lifting extension problem,” Discrete & Computational Geometry, vol. 54, no. 4. Springer, pp. 915–965, 2017.","short":"M. Čadek, M. Krcál, L. Vokřínek, Discrete & Computational Geometry 54 (2017) 915–965.","apa":"Čadek, M., Krcál, M., & Vokřínek, L. (2017). Algorithmic solvability of the lifting extension problem. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-016-9855-6","ama":"Čadek M, Krcál M, Vokřínek L. Algorithmic solvability of the lifting extension problem. Discrete & Computational Geometry. 2017;54(4):915-965. doi:10.1007/s00454-016-9855-6","mla":"Čadek, Martin, et al. “Algorithmic Solvability of the Lifting Extension Problem.” Discrete & Computational Geometry, vol. 54, no. 4, Springer, 2017, pp. 915–65, doi:10.1007/s00454-016-9855-6."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6309","author":[{"last_name":"Čadek","full_name":"Čadek, Martin","first_name":"Martin"},{"full_name":"Krcál, Marek","last_name":"Krcál","id":"33E21118-F248-11E8-B48F-1D18A9856A87","first_name":"Marek"},{"full_name":"Vokřínek, Lukáš","last_name":"Vokřínek","first_name":"Lukáš"}],"external_id":{"isi":["000400072700008"]},"article_processing_charge":"No","title":"Algorithmic solvability of the lifting extension problem","quality_controlled":"1","publisher":"Springer","oa":1,"isi":1,"year":"2017","day":"01","publication":"Discrete & Computational Geometry","page":"915 - 965","date_published":"2017-06-01T00:00:00Z","doi":"10.1007/s00454-016-9855-6","date_created":"2018-12-11T11:50:00Z"},{"page":"25 - 29","date_published":"2017-06-01T00:00:00Z","doi":"10.1016/j.ipl.2017.02.003","date_created":"2018-12-11T11:49:57Z","has_accepted_license":"1","isi":1,"year":"2017","day":"01","publication":"Information Processing Letters","quality_controlled":"1","publisher":"Elsevier","oa":1,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Osang","full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F"}],"publist_id":"6323","external_id":{"isi":["000399506600005"]},"article_processing_charge":"No","title":"Pushdown reachability with constant treewidth","citation":{"ieee":"K. Chatterjee and G. F. Osang, “Pushdown reachability with constant treewidth,” Information Processing Letters, vol. 122. Elsevier, pp. 25–29, 2017.","short":"K. Chatterjee, G.F. Osang, Information Processing Letters 122 (2017) 25–29.","ama":"Chatterjee K, Osang GF. Pushdown reachability with constant treewidth. Information Processing Letters. 2017;122:25-29. doi:10.1016/j.ipl.2017.02.003","apa":"Chatterjee, K., & Osang, G. F. (2017). Pushdown reachability with constant treewidth. Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2017.02.003","mla":"Chatterjee, Krishnendu, and Georg F. Osang. “Pushdown Reachability with Constant Treewidth.” Information Processing Letters, vol. 122, Elsevier, 2017, pp. 25–29, doi:10.1016/j.ipl.2017.02.003.","ista":"Chatterjee K, Osang GF. 2017. Pushdown reachability with constant treewidth. Information Processing Letters. 122, 25–29.","chicago":"Chatterjee, Krishnendu, and Georg F Osang. “Pushdown Reachability with Constant Treewidth.” Information Processing Letters. Elsevier, 2017. https://doi.org/10.1016/j.ipl.2017.02.003."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"volume":122,"ec_funded":1,"publication_identifier":{"issn":["00200190"]},"publication_status":"published","file":[{"file_id":"4998","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:13:17Z","file_name":"IST-2018-991-v1+2_2018_Chatterjee_Pushdown_PREPRINT.pdf","date_updated":"2019-10-15T07:44:51Z","file_size":247657,"creator":"system"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"06","intvolume":" 122","abstract":[{"text":"We consider the problem of reachability in pushdown graphs. We study the problem for pushdown graphs with constant treewidth. Even for pushdown graphs with treewidth 1, for the reachability problem we establish the following: (i) the problem is PTIME-complete, and (ii) any subcubic algorithm for the problem would contradict the k-clique conjecture and imply faster combinatorial algorithms for cliques in graphs.","lang":"eng"}],"oa_version":"Submitted Version","department":[{"_id":"KrCh"},{"_id":"HeEd"}],"file_date_updated":"2019-10-15T07:44:51Z","date_updated":"2023-09-20T12:08:18Z","ddc":["000"],"type":"journal_article","status":"public","pubrep_id":"991","_id":"1065"},{"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Severe environmental change can drive a population extinct unless the population adapts in time to the new conditions (“evolutionary rescue”). How does biparental sexual reproduction influence the chances of population persistence compared to clonal reproduction or selfing? In this article, we set up a one‐locus two‐allele model for adaptation in diploid species, where rescue is contingent on the establishment of the mutant homozygote. Reproduction can occur by random mating, selfing, or clonally. Random mating generates and destroys the rescue mutant; selfing is efficient at generating it but at the same time depletes the heterozygote, which can lead to a low mutant frequency in the standing genetic variation. Due to these (and other) antagonistic effects, we find a nontrivial dependence of population survival on the rate of sex/selfing, which is strongly influenced by the dominance coefficient of the mutation before and after the environmental change. Importantly, since mating with the wild‐type breaks the mutant homozygote up, a slow decay of the wild‐type population size can impede rescue in randomly mating populations."}],"intvolume":" 71","month":"04","main_file_link":[{"open_access":"1","url":"http://biorxiv.org/content/early/2016/10/14/081042"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00143820"]},"ec_funded":1,"volume":71,"issue":"4","_id":"1063","status":"public","type":"journal_article","date_updated":"2023-09-20T12:10:32Z","department":[{"_id":"NiBa"}],"oa":1,"publisher":"Wiley-Blackwell","quality_controlled":"1","publication":"Evolution","day":"01","year":"2017","isi":1,"date_created":"2018-12-11T11:49:57Z","doi":"10.1111/evo.13191","date_published":"2017-04-01T00:00:00Z","page":"845 - 858","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13191.","ista":"Uecker H. 2017. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 71(4), 845–858.","mla":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” Evolution, vol. 71, no. 4, Wiley-Blackwell, 2017, pp. 845–58, doi:10.1111/evo.13191.","short":"H. Uecker, Evolution 71 (2017) 845–858.","ieee":"H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,” Evolution, vol. 71, no. 4. Wiley-Blackwell, pp. 845–858, 2017.","ama":"Uecker H. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 2017;71(4):845-858. doi:10.1111/evo.13191","apa":"Uecker, H. (2017). Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13191"},"title":"Evolutionary rescue in randomly mating, selfing, and clonal populations","article_processing_charge":"No","external_id":{"isi":["000398545200003"]},"publist_id":"6327","author":[{"orcid":"0000-0001-9435-2813","full_name":"Uecker, Hildegard","last_name":"Uecker","first_name":"Hildegard","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87"}]},{"quality_controlled":"1","publisher":"Elsevier","year":"2017","isi":1,"publication":"Information and Computation","day":"01","page":"143 - 166","date_created":"2018-12-11T11:49:58Z","date_published":"2017-06-01T00:00:00Z","doi":"10.1016/j.ic.2016.10.006","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner. “Quantitative Fair Simulation Games.” Information and Computation. Elsevier, 2017. https://doi.org/10.1016/j.ic.2016.10.006.","ista":"Chatterjee K, Henzinger TA, Otop J, Velner Y. 2017. Quantitative fair simulation games. Information and Computation. 254(2), 143–166.","mla":"Chatterjee, Krishnendu, et al. “Quantitative Fair Simulation Games.” Information and Computation, vol. 254, no. 2, Elsevier, 2017, pp. 143–66, doi:10.1016/j.ic.2016.10.006.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Information and Computation 254 (2017) 143–166.","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, “Quantitative fair simulation games,” Information and Computation, vol. 254, no. 2. Elsevier, pp. 143–166, 2017.","ama":"Chatterjee K, Henzinger TA, Otop J, Velner Y. Quantitative fair simulation games. Information and Computation. 2017;254(2):143-166. doi:10.1016/j.ic.2016.10.006","apa":"Chatterjee, K., Henzinger, T. A., Otop, J., & Velner, Y. (2017). Quantitative fair simulation games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2016.10.006"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000402025600002"]},"publist_id":"6322","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"last_name":"Otop","full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"last_name":"Velner","full_name":"Velner, Yaron","first_name":"Yaron"}],"title":"Quantitative fair simulation games","abstract":[{"text":"Simulation is an attractive alternative to language inclusion for automata as it is an under-approximation of language inclusion, but usually has much lower complexity. Simulation has also been extended in two orthogonal directions, namely, (1) fair simulation, for simulation over specified set of infinite runs; and (2) quantitative simulation, for simulation between weighted automata. While fair trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial time. For weighted automata, the (quantitative) language inclusion problem is undecidable in general, whereas the (quantitative) simulation reduces to quantitative games, which admit pseudo-polynomial time algorithms.\r\n\r\nIn this work, we study (quantitative) simulation for weighted automata with Büchi acceptance conditions, i.e., we generalize fair simulation from non-weighted automata to weighted automata. We show that imposing Büchi acceptance conditions on weighted automata changes many fundamental properties of the simulation games, yet they still admit pseudo-polynomial time algorithms.","lang":"eng"}],"oa_version":"None","scopus_import":"1","intvolume":" 254","month":"06","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"issue":"2","related_material":{"record":[{"status":"public","id":"5428","relation":"earlier_version"}]},"volume":254,"_id":"1066","type":"journal_article","status":"public","date_updated":"2023-09-20T12:07:48Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}]}]