[{"publication_status":"published","ec_funded":1,"date_updated":"2025-05-28T11:42:45Z","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"_id":"3375","oa":1,"author":[{"id":"2A181218-F248-11E8-B48F-1D18A9856A87","last_name":"de Vladar","orcid":"0000-0002-5985-7653","full_name":"de Vladar, Harold","first_name":"Harold"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"external_id":{"pmid":["21084341"]},"date_published":"2011-05-01T00:00:00Z","status":"public","year":"2011","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"720 - 739","pmid":1,"publication":"Journal of the Royal Society Interface","month":"05","publisher":"The Royal Society","title":"The statistical mechanics of a polygenic character under stabilizing selection mutation and drift","scopus_import":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:02:58Z","department":[{"_id":"NiBa"}],"intvolume":"         8","issue":"58","article_type":"original","abstract":[{"lang":"eng","text":"By exploiting an analogy between population genetics and statistical mechanics, we study the evolution of a polygenic trait under stabilizing selection, mutation and genetic drift. This requires us to track only four macroscopic variables, instead of the distribution of all the allele frequencies that influence the trait. These macroscopic variables are the expectations of: the trait mean and its square, the genetic variance, and of a measure of heterozygosity, and are derived from a generating function that is in turn derived by maximizing an entropy measure. These four macroscopics are enough to accurately describe the dynamics of the trait mean and of its genetic variance (and in principle of any other quantity). Unlike previous approaches that were based on an infinite series of moments or cumulants, which had to be truncated arbitrarily, our calculations provide a well-defined approximation procedure. We apply the framework to abrupt and gradual changes in the optimum, as well as to changes in the strength of stabilizing selection. Our approximations are surprisingly accurate, even for systems with as few as five loci. We find that when the effects of drift are included, the expected genetic variance is hardly altered by directional selection, even though it fluctuates in any particular instance. We also find hysteresis, showing that even after averaging over the microscopic variables, the macroscopic trajectories retain a memory of the underlying genetic states."}],"volume":8,"quality_controlled":"1","doi":"10.1098/rsif.2010.0438","oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061091/"}],"publist_id":"3232","type":"journal_article","day":"01","citation":{"mla":"de Vladar, Harold, and Nicholas H. Barton. “The Statistical Mechanics of a Polygenic Character under Stabilizing Selection Mutation and Drift.” <i>Journal of the Royal Society Interface</i>, vol. 8, no. 58, The Royal Society, 2011, pp. 720–39, doi:<a href=\"https://doi.org/10.1098/rsif.2010.0438\">10.1098/rsif.2010.0438</a>.","apa":"de Vladar, H., &#38; Barton, N. H. (2011). The statistical mechanics of a polygenic character under stabilizing selection mutation and drift. <i>Journal of the Royal Society Interface</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsif.2010.0438\">https://doi.org/10.1098/rsif.2010.0438</a>","ista":"de Vladar H, Barton NH. 2011. The statistical mechanics of a polygenic character under stabilizing selection mutation and drift. Journal of the Royal Society Interface. 8(58), 720–739.","chicago":"Vladar, Harold de, and Nicholas H Barton. “The Statistical Mechanics of a Polygenic Character under Stabilizing Selection Mutation and Drift.” <i>Journal of the Royal Society Interface</i>. The Royal Society, 2011. <a href=\"https://doi.org/10.1098/rsif.2010.0438\">https://doi.org/10.1098/rsif.2010.0438</a>.","short":"H. de Vladar, N.H. Barton, Journal of the Royal Society Interface 8 (2011) 720–739.","ama":"de Vladar H, Barton NH. The statistical mechanics of a polygenic character under stabilizing selection mutation and drift. <i>Journal of the Royal Society Interface</i>. 2011;8(58):720-739. doi:<a href=\"https://doi.org/10.1098/rsif.2010.0438\">10.1098/rsif.2010.0438</a>","ieee":"H. de Vladar and N. H. Barton, “The statistical mechanics of a polygenic character under stabilizing selection mutation and drift,” <i>Journal of the Royal Society Interface</i>, vol. 8, no. 58. The Royal Society, pp. 720–739, 2011."}},{"publication":"Molecular Cell","month":"05","publisher":"Cell Press","date_updated":"2021-01-12T07:43:03Z","publication_status":"published","_id":"3376","acknowledgement":"This work was supported by a Feodor Lynen Fellowship of the Alexander von Humboldt Foundation (to T.B.).","oa":1,"author":[{"last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias"},{"first_name":"Roy","full_name":"Kishony, Roy","last_name":"Kishony"}],"page":"413 - 425","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2011-05-20T00:00:00Z","year":"2011","doi":"10.1016/j.molcel.2011.04.016","quality_controlled":"1","oa_version":"Submitted Version","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3143497/","open_access":"1"}],"citation":{"chicago":"Bollenbach, Mark Tobias, and Roy Kishony. “Resolution of Gene Regulatory Conflicts Caused by Combinations of Antibiotics.” <i>Molecular Cell</i>. Cell Press, 2011. <a href=\"https://doi.org/10.1016/j.molcel.2011.04.016\">https://doi.org/10.1016/j.molcel.2011.04.016</a>.","ista":"Bollenbach MT, Kishony R. 2011. Resolution of gene regulatory conflicts caused by combinations of antibiotics. Molecular Cell. 42(4), 413–425.","apa":"Bollenbach, M. T., &#38; Kishony, R. (2011). Resolution of gene regulatory conflicts caused by combinations of antibiotics. <i>Molecular Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.molcel.2011.04.016\">https://doi.org/10.1016/j.molcel.2011.04.016</a>","ama":"Bollenbach MT, Kishony R. Resolution of gene regulatory conflicts caused by combinations of antibiotics. <i>Molecular Cell</i>. 2011;42(4):413-425. doi:<a href=\"https://doi.org/10.1016/j.molcel.2011.04.016\">10.1016/j.molcel.2011.04.016</a>","ieee":"M. T. Bollenbach and R. Kishony, “Resolution of gene regulatory conflicts caused by combinations of antibiotics,” <i>Molecular Cell</i>, vol. 42, no. 4. Cell Press, pp. 413–425, 2011.","short":"M.T. Bollenbach, R. Kishony, Molecular Cell 42 (2011) 413–425.","mla":"Bollenbach, Mark Tobias, and Roy Kishony. “Resolution of Gene Regulatory Conflicts Caused by Combinations of Antibiotics.” <i>Molecular Cell</i>, vol. 42, no. 4, Cell Press, 2011, pp. 413–25, doi:<a href=\"https://doi.org/10.1016/j.molcel.2011.04.016\">10.1016/j.molcel.2011.04.016</a>."},"publist_id":"3231","type":"journal_article","day":"20","title":"Resolution of gene regulatory conflicts caused by combinations of antibiotics","scopus_import":1,"department":[{"_id":"ToBo"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T12:02:59Z","intvolume":"        42","issue":"4","volume":42,"abstract":[{"lang":"eng","text":"Regulatory conflicts occur when two signals that individually trigger opposite cellular responses are present simultaneously. Here, we investigate regulatory conflicts in the bacterial response to antibiotic combinations. We use an Escherichia coli promoter-GFP library to study the transcriptional response of many promoters to either additive or antagonistic drug pairs at fine two-dimensional (2D) resolution of drug concentration. Surprisingly, we find that this data set can be characterized as a linear sum of only two principal components. Component one, accounting for over 70% of the response, represents the response to growth inhibition by the drugs. Component two describes how regulatory conflicts are resolved. For the additive drug pair, conflicts are resolved by linearly interpolating the single drug responses, while for the antagonistic drug pair, the growth-limiting drug dominates the response. Importantly, for a given drug pair, the same conflict resolution strategy applies to almost all genes. These results provide a recipe for predicting gene expression responses to antibiotic combinations."}]},{"month":"06","publication":"Foundations of Computational Mathematics","publisher":"Springer","_id":"3377","date_updated":"2021-01-12T07:43:04Z","publication_status":"published","page":"345 - 361","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2011","status":"public","date_published":"2011-06-01T00:00:00Z","acknowledgement":"This research is partially supported by the Defense Advanced Research Projects Agency (DARPA) under grants HR0011-05-1-0007 and HR0011-05-1-0057.","oa":1,"author":[{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"},{"last_name":"Morozov","first_name":"Dmitriy","full_name":"Morozov, Dmitriy"},{"id":"34A254A0-F248-11E8-B48F-1D18A9856A87","last_name":"Patel","first_name":"Amit","full_name":"Patel, Amit"}],"oa_version":"Submitted Version","quality_controlled":"1","doi":"10.1007/s10208-011-9090-8","citation":{"apa":"Edelsbrunner, H., Morozov, D., &#38; Patel, A. (2011). Quantifying transversality by measuring the robustness of intersections. <i>Foundations of Computational Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s10208-011-9090-8\">https://doi.org/10.1007/s10208-011-9090-8</a>","chicago":"Edelsbrunner, Herbert, Dmitriy Morozov, and Amit Patel. “Quantifying Transversality by Measuring the Robustness of Intersections.” <i>Foundations of Computational Mathematics</i>. Springer, 2011. <a href=\"https://doi.org/10.1007/s10208-011-9090-8\">https://doi.org/10.1007/s10208-011-9090-8</a>.","ista":"Edelsbrunner H, Morozov D, Patel A. 2011. Quantifying transversality by measuring the robustness of intersections. Foundations of Computational Mathematics. 11(3), 345–361.","ama":"Edelsbrunner H, Morozov D, Patel A. Quantifying transversality by measuring the robustness of intersections. <i>Foundations of Computational Mathematics</i>. 2011;11(3):345-361. doi:<a href=\"https://doi.org/10.1007/s10208-011-9090-8\">10.1007/s10208-011-9090-8</a>","ieee":"H. Edelsbrunner, D. Morozov, and A. Patel, “Quantifying transversality by measuring the robustness of intersections,” <i>Foundations of Computational Mathematics</i>, vol. 11, no. 3. Springer, pp. 345–361, 2011.","short":"H. Edelsbrunner, D. Morozov, A. Patel, Foundations of Computational Mathematics 11 (2011) 345–361.","mla":"Edelsbrunner, Herbert, et al. “Quantifying Transversality by Measuring the Robustness of Intersections.” <i>Foundations of Computational Mathematics</i>, vol. 11, no. 3, Springer, 2011, pp. 345–61, doi:<a href=\"https://doi.org/10.1007/s10208-011-9090-8\">10.1007/s10208-011-9090-8</a>."},"type":"journal_article","day":"01","publist_id":"3230","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0911.2142"}],"department":[{"_id":"HeEd"}],"date_created":"2018-12-11T12:02:59Z","language":[{"iso":"eng"}],"scopus_import":1,"title":"Quantifying transversality by measuring the robustness of intersections","abstract":[{"lang":"eng","text":"By definition, transverse intersections are stable under in- finitesimal perturbations. Using persistent homology, we ex- tend this notion to sizeable perturbations. Specifically, we assign to each homology class of the intersection its robust- ness, the magnitude of a perturbation necessary to kill it, and prove that robustness is stable. Among the applications of this result is a stable notion of robustness for fixed points of continuous mappings and a statement of stability for con- tours of smooth mappings."}],"volume":11,"issue":"3","intvolume":"        11"},{"date_updated":"2021-01-12T07:43:04Z","title":"Persistent intersection homology","publication_status":"published","scopus_import":1,"department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"_id":"3378","date_created":"2018-12-11T12:02:59Z","acknowledgement":"This research was partially supported by the Defense Advanced Research Projects Agency (DARPA) under grant HR0011-05-1-0007.","author":[{"id":"43F6EC54-F248-11E8-B48F-1D18A9856A87","last_name":"Bendich","first_name":"Paul","full_name":"Bendich, Paul"},{"last_name":"Harer","first_name":"John","full_name":"Harer, John"}],"intvolume":"        11","issue":"3","page":"305 - 336","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2011-06-01T00:00:00Z","volume":11,"year":"2011","abstract":[{"text":"The theory of intersection homology was developed to study the singularities of a topologically stratified space. This paper in- corporates this theory into the already developed framework of persistent homology. We demonstrate that persistent intersec- tion homology gives useful information about the relationship between an embedded stratified space and its singularities. We give, and prove the correctness of, an algorithm for the computa- tion of the persistent intersection homology groups of a filtered simplicial complex equipped with a stratification by subcom- plexes. We also derive, from Poincare ́ Duality, some structural results about persistent intersection homology.","lang":"eng"}],"publication":"Foundations of Computational Mathematics","quality_controlled":"1","doi":"10.1007/s10208-010-9081-1","month":"06","oa_version":"None","publisher":"Springer","citation":{"mla":"Bendich, Paul, and John Harer. “Persistent Intersection Homology.” <i>Foundations of Computational Mathematics</i>, vol. 11, no. 3, Springer, 2011, pp. 305–36, doi:<a href=\"https://doi.org/10.1007/s10208-010-9081-1\">10.1007/s10208-010-9081-1</a>.","ieee":"P. Bendich and J. Harer, “Persistent intersection homology,” <i>Foundations of Computational Mathematics</i>, vol. 11, no. 3. Springer, pp. 305–336, 2011.","short":"P. Bendich, J. Harer, Foundations of Computational Mathematics 11 (2011) 305–336.","ama":"Bendich P, Harer J. Persistent intersection homology. <i>Foundations of Computational Mathematics</i>. 2011;11(3):305-336. doi:<a href=\"https://doi.org/10.1007/s10208-010-9081-1\">10.1007/s10208-010-9081-1</a>","chicago":"Bendich, Paul, and John Harer. “Persistent Intersection Homology.” <i>Foundations of Computational Mathematics</i>. Springer, 2011. <a href=\"https://doi.org/10.1007/s10208-010-9081-1\">https://doi.org/10.1007/s10208-010-9081-1</a>.","ista":"Bendich P, Harer J. 2011. Persistent intersection homology. Foundations of Computational Mathematics. 11(3), 305–336.","apa":"Bendich, P., &#38; Harer, J. (2011). Persistent intersection homology. <i>Foundations of Computational Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s10208-010-9081-1\">https://doi.org/10.1007/s10208-010-9081-1</a>"},"publist_id":"3229","type":"journal_article","day":"01"},{"scopus_import":1,"title":"Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail","department":[{"_id":"CaHe"}],"date_created":"2018-12-11T12:03:00Z","language":[{"iso":"eng"}],"issue":"1","article_type":"original","intvolume":"       354","volume":354,"abstract":[{"lang":"eng","text":"The process of gastrulation is highly conserved across vertebrates on both the genetic and morphological levels, despite great variety in embryonic shape and speed of development. This mechanism spatially separates the germ layers and establishes the organizational foundation for future development. Mesodermal identity is specified in a superficial layer of cells, the epiblast, where cells maintain an epithelioid morphology. These cells involute to join the deeper hypoblast layer where they adopt a migratory, mesenchymal morphology. Expression of a cascade of related transcription factors orchestrates the parallel genetic transition from primitive to mature mesoderm. Although the early and late stages of this process are increasingly well understood, the transition between them has remained largely mysterious. We present here the first high resolution in vivo observations of the blebby transitional morphology of involuting mesodermal cells in a vertebrate embryo. We further demonstrate that the zebrafish spadetail mutation creates a reversible block in the maturation program, stalling cells in the transition state. This mutation creates an ideal system for dissecting the specific properties of cells undergoing the morphological transition of maturing mesoderm, as we demonstrate with a direct measurement of cell–cell adhesion."}],"doi":"10.1016/j.ydbio.2011.03.025","quality_controlled":"1","oa_version":"Submitted Version","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3090540/","open_access":"1"}],"citation":{"mla":"Row, Richard, et al. “Completion of the Epithelial to Mesenchymal Transition in Zebrafish Mesoderm Requires Spadetail.” <i>Developmental Biology</i>, vol. 354, no. 1, Elsevier, 2011, pp. 102–10, doi:<a href=\"https://doi.org/10.1016/j.ydbio.2011.03.025\">10.1016/j.ydbio.2011.03.025</a>.","chicago":"Row, Richard, Jean-Léon Maître, Benjamin Martin, Petra Stockinger, Carl-Philipp J Heisenberg, and David Kimelman. “Completion of the Epithelial to Mesenchymal Transition in Zebrafish Mesoderm Requires Spadetail.” <i>Developmental Biology</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.ydbio.2011.03.025\">https://doi.org/10.1016/j.ydbio.2011.03.025</a>.","ista":"Row R, Maître J-L, Martin B, Stockinger P, Heisenberg C-PJ, Kimelman D. 2011. Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail. Developmental Biology. 354(1), 102–110.","apa":"Row, R., Maître, J.-L., Martin, B., Stockinger, P., Heisenberg, C.-P. J., &#38; Kimelman, D. (2011). Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail. <i>Developmental Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ydbio.2011.03.025\">https://doi.org/10.1016/j.ydbio.2011.03.025</a>","ama":"Row R, Maître J-L, Martin B, Stockinger P, Heisenberg C-PJ, Kimelman D. Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail. <i>Developmental Biology</i>. 2011;354(1):102-110. doi:<a href=\"https://doi.org/10.1016/j.ydbio.2011.03.025\">10.1016/j.ydbio.2011.03.025</a>","ieee":"R. Row, J.-L. Maître, B. Martin, P. Stockinger, C.-P. J. Heisenberg, and D. Kimelman, “Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail,” <i>Developmental Biology</i>, vol. 354, no. 1. Elsevier, pp. 102–110, 2011.","short":"R. Row, J.-L. Maître, B. Martin, P. Stockinger, C.-P.J. Heisenberg, D. Kimelman, Developmental Biology 354 (2011) 102–110."},"day":"01","type":"journal_article","publist_id":"3228","date_updated":"2021-01-12T07:43:04Z","publication_status":"published","_id":"3379","oa":1,"author":[{"last_name":"Row","full_name":"Row, Richard","first_name":"Richard"},{"orcid":"0000-0002-3688-1474","first_name":"Jean-Léon","full_name":"Maître, Jean-Léon","last_name":"Maître","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Benjamin","full_name":"Martin, Benjamin","last_name":"Martin"},{"id":"261CB030-E90D-11E9-B182-F697D44B663C","last_name":"Stockinger","full_name":"Stockinger, Petra","first_name":"Petra"},{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kimelman","full_name":"Kimelman, David","first_name":"David"}],"external_id":{"pmid":["1463614"]},"page":"102 - 110","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2011","date_published":"2011-06-01T00:00:00Z","status":"public","publication":"Developmental Biology","pmid":1,"month":"06","publisher":"Elsevier"},{"doi":"10.1017/S0016672311000115","quality_controlled":"1","oa_version":"Published Version","main_file_link":[{"url":"https://www.pure.ed.ac.uk/ws/files/8144621/GR_2011_Barton.pdf","open_access":"1"}],"citation":{"chicago":"Logeswaran, Sayanthan, and Nicholas H Barton. “Mapping Mendelian Traits in Asexual Progeny Using Changes in Marker Allele Frequency.” <i>Genetical Research</i>. Cambridge University Press, 2011. <a href=\"https://doi.org/10.1017/S0016672311000115\">https://doi.org/10.1017/S0016672311000115</a>.","apa":"Logeswaran, S., &#38; Barton, N. H. (2011). Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. <i>Genetical Research</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/S0016672311000115\">https://doi.org/10.1017/S0016672311000115</a>","ista":"Logeswaran S, Barton NH. 2011. Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. Genetical Research. 93(3), 221–232.","ama":"Logeswaran S, Barton NH. Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. <i>Genetical Research</i>. 2011;93(3):221-232. doi:<a href=\"https://doi.org/10.1017/S0016672311000115\">10.1017/S0016672311000115</a>","short":"S. Logeswaran, N.H. Barton, Genetical Research 93 (2011) 221–232.","ieee":"S. Logeswaran and N. H. Barton, “Mapping Mendelian traits in asexual progeny using changes in marker allele frequency,” <i>Genetical Research</i>, vol. 93, no. 3. Cambridge University Press, pp. 221–232, 2011.","mla":"Logeswaran, Sayanthan, and Nicholas H. Barton. “Mapping Mendelian Traits in Asexual Progeny Using Changes in Marker Allele Frequency.” <i>Genetical Research</i>, vol. 93, no. 3, Cambridge University Press, 2011, pp. 221–32, doi:<a href=\"https://doi.org/10.1017/S0016672311000115\">10.1017/S0016672311000115</a>."},"type":"journal_article","day":"18","publist_id":"3227","scopus_import":1,"title":"Mapping Mendelian traits in asexual progeny using changes in marker allele frequency","department":[{"_id":"NiBa"}],"date_created":"2018-12-11T12:03:00Z","language":[{"iso":"eng"}],"article_type":"original","issue":"3","intvolume":"        93","abstract":[{"lang":"eng","text":"Linkage between markers and genes that affect a phenotype of interest may be determined by examining differences in marker allele frequency in the extreme progeny of a cross between two inbred lines. This strategy is usually employed when pooling is used to reduce genotyping costs. When the cross progeny are asexual, the extreme progeny may be selected by multiple generations of asexual reproduction and selection. We analyse this method of measuring phenotype in asexual progeny and examine the changes in marker allele frequency due to selection over many generations. Stochasticity in marker frequency in the selected population arises due to the finite initial population size. We derive the distribution of marker frequency as a result of selection at a single major locus, and show that in order to avoid spurious changes in marker allele frequency in the selected population, the initial population size should be in the low to mid hundreds."}],"volume":93,"publication":"Genetical Research","month":"05","publisher":"Cambridge University Press","date_updated":"2021-01-12T07:43:05Z","publication_status":"published","_id":"3380","oa":1,"author":[{"last_name":"Logeswaran","full_name":"Logeswaran, Sayanthan","first_name":"Sayanthan"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"page":"221 - 232","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","year":"2011","date_published":"2011-05-18T00:00:00Z","status":"public"},{"quality_controlled":"1","doi":"10.1142/S0129054111008441","oa_version":"Submitted Version","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"3841"}]},"citation":{"mla":"Henzinger, Thomas A., et al. “Formalisms for Specifying Markovian Population Models.” <i>IJFCS: International Journal of Foundations of Computer Science</i>, vol. 22, no. 4, World Scientific Publishing, 2011, pp. 823–41, doi:<a href=\"https://doi.org/10.1142/S0129054111008441\">10.1142/S0129054111008441</a>.","ama":"Henzinger TA, Jobstmann B, Wolf V. Formalisms for specifying Markovian population models. <i>IJFCS: International Journal of Foundations of Computer Science</i>. 2011;22(4):823-841. doi:<a href=\"https://doi.org/10.1142/S0129054111008441\">10.1142/S0129054111008441</a>","short":"T.A. Henzinger, B. Jobstmann, V. Wolf, IJFCS: International Journal of Foundations of Computer Science 22 (2011) 823–841.","ieee":"T. A. Henzinger, B. Jobstmann, and V. Wolf, “Formalisms for specifying Markovian population models,” <i>IJFCS: International Journal of Foundations of Computer Science</i>, vol. 22, no. 4. World Scientific Publishing, pp. 823–841, 2011.","apa":"Henzinger, T. A., Jobstmann, B., &#38; Wolf, V. (2011). Formalisms for specifying Markovian population models. <i>IJFCS: International Journal of Foundations of Computer Science</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0129054111008441\">https://doi.org/10.1142/S0129054111008441</a>","chicago":"Henzinger, Thomas A, Barbara Jobstmann, and Verena Wolf. “Formalisms for Specifying Markovian Population Models.” <i>IJFCS: International Journal of Foundations of Computer Science</i>. World Scientific Publishing, 2011. <a href=\"https://doi.org/10.1142/S0129054111008441\">https://doi.org/10.1142/S0129054111008441</a>.","ista":"Henzinger TA, Jobstmann B, Wolf V. 2011. Formalisms for specifying Markovian population models. IJFCS: International Journal of Foundations of Computer Science. 22(4), 823–841."},"publist_id":"3226","type":"journal_article","day":"01","title":"Formalisms for specifying Markovian population models","scopus_import":1,"department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T12:03:00Z","intvolume":"        22","issue":"4","volume":22,"abstract":[{"text":"In this survey, we compare several languages for specifying Markovian population models such as queuing networks and chemical reaction networks. All these languages — matrix descriptions, stochastic Petri nets, stoichiometric equations, stochastic process algebras, and guarded command models — describe continuous-time Markov chains, but they differ according to important properties, such as compositionality, expressiveness and succinctness, executability, and ease of use. Moreover, they provide different support for checking the well-formedness of a model and for analyzing a model.","lang":"eng"}],"publication":"IJFCS: International Journal of Foundations of Computer Science","month":"06","pubrep_id":"628","file":[{"relation":"main_file","content_type":"application/pdf","checksum":"df88431872586c773fbcfea37d7b36a2","file_size":222840,"date_created":"2018-12-12T10:08:45Z","file_name":"IST-2016-628-v1+1_journals-ijfcs-HenzingerJW11.pdf","creator":"system","date_updated":"2020-07-14T12:46:11Z","access_level":"open_access","file_id":"4707"}],"publisher":"World Scientific Publishing","has_accepted_license":"1","file_date_updated":"2020-07-14T12:46:11Z","date_updated":"2023-02-23T11:45:03Z","publication_status":"published","_id":"3381","oa":1,"author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Jobstmann","full_name":"Jobstmann, Barbara","first_name":"Barbara"},{"first_name":"Verena","full_name":"Wolf, Verena","last_name":"Wolf"}],"page":"823 - 841","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_published":"2011-06-01T00:00:00Z","ddc":["000"],"status":"public","year":"2011"},{"month":"05","oa_version":"None","publication":"IEEE Transactions on Robotics","quality_controlled":"1","doi":"10.1109/TRO.2011.2121130","citation":{"mla":"Kroemer, Oliver, et al. “Learning Dynamic Tactile Sensing with Robust Vision Based Training.” <i>IEEE Transactions on Robotics</i>, vol. 27, no. 3, IEEE, 2011, pp. 545–57, doi:<a href=\"https://doi.org/10.1109/TRO.2011.2121130\">10.1109/TRO.2011.2121130</a>.","ieee":"O. Kroemer, C. Lampert, and J. Peters, “Learning dynamic tactile sensing with robust vision based training,” <i>IEEE Transactions on Robotics</i>, vol. 27, no. 3. IEEE, pp. 545–557, 2011.","ama":"Kroemer O, Lampert C, Peters J. Learning dynamic tactile sensing with robust vision based training. <i>IEEE Transactions on Robotics</i>. 2011;27(3):545-557. doi:<a href=\"https://doi.org/10.1109/TRO.2011.2121130\">10.1109/TRO.2011.2121130</a>","short":"O. Kroemer, C. Lampert, J. Peters, IEEE Transactions on Robotics 27 (2011) 545–557.","apa":"Kroemer, O., Lampert, C., &#38; Peters, J. (2011). Learning dynamic tactile sensing with robust vision based training. <i>IEEE Transactions on Robotics</i>. IEEE. <a href=\"https://doi.org/10.1109/TRO.2011.2121130\">https://doi.org/10.1109/TRO.2011.2121130</a>","chicago":"Kroemer, Oliver, Christoph Lampert, and Jan Peters. “Learning Dynamic Tactile Sensing with Robust Vision Based Training.” <i>IEEE Transactions on Robotics</i>. IEEE, 2011. <a href=\"https://doi.org/10.1109/TRO.2011.2121130\">https://doi.org/10.1109/TRO.2011.2121130</a>.","ista":"Kroemer O, Lampert C, Peters J. 2011. Learning dynamic tactile sensing with robust vision based training. IEEE Transactions on Robotics. 27(3), 545–557."},"publist_id":"3225","type":"journal_article","day":"21","publisher":"IEEE","department":[{"_id":"ChLa"}],"_id":"3382","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:03:01Z","date_updated":"2021-01-12T07:43:06Z","publication_status":"published","title":"Learning dynamic tactile sensing with robust vision based training","scopus_import":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","page":"545 - 557","date_published":"2011-05-21T00:00:00Z","status":"public","year":"2011","abstract":[{"text":"Dynamic tactile sensing is a fundamental ability to recognize materials and objects. However, while humans are born with partially developed dynamic tactile sensing and quickly master this skill, today's robots remain in their infancy. The development of such a sense requires not only better sensors but the right algorithms to deal with these sensors' data as well. For example, when classifying a material based on touch, the data are noisy, high-dimensional, and contain irrelevant signals as well as essential ones. Few classification methods from machine learning can deal with such problems. In this paper, we propose an efficient approach to infer suitable lower dimensional representations of the tactile data. In order to classify materials based on only the sense of touch, these representations are autonomously discovered using visual information of the surfaces during training. However, accurately pairing vision and tactile samples in real-robot applications is a difficult problem. The proposed approach, therefore, works with weak pairings between the modalities. Experiments show that the resulting approach is very robust and yields significantly higher classification performance based on only dynamic tactile sensing.","lang":"eng"}],"volume":27,"author":[{"last_name":"Kroemer","first_name":"Oliver","full_name":"Kroemer, Oliver"},{"full_name":"Lampert, Christoph","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert"},{"full_name":"Peters, Jan","first_name":"Jan","last_name":"Peters"}],"intvolume":"        27","issue":"3"},{"type":"journal_article","day":"01","publist_id":"3224","citation":{"mla":"Heisenberg, Carl-Philipp J. “Invited Lectures ‐ Symposia Area.” <i>FEBS Journal</i>, vol. 278, no. S1, Wiley-Blackwell, 2011, pp. 24–24, doi:<a href=\"https://doi.org/10.1111/j.1742-4658.2011.08136.x\">10.1111/j.1742-4658.2011.08136.x</a>.","short":"C.-P.J. Heisenberg, FEBS Journal 278 (2011) 24–24.","ama":"Heisenberg C-PJ. Invited Lectures ‐ Symposia Area. <i>FEBS Journal</i>. 2011;278(S1):24-24. doi:<a href=\"https://doi.org/10.1111/j.1742-4658.2011.08136.x\">10.1111/j.1742-4658.2011.08136.x</a>","ieee":"C.-P. J. Heisenberg, “Invited Lectures ‐ Symposia Area,” <i>FEBS Journal</i>, vol. 278, no. S1. Wiley-Blackwell, pp. 24–24, 2011.","ista":"Heisenberg C-PJ. 2011. Invited Lectures ‐ Symposia Area. FEBS Journal. 278(S1), 24–24.","apa":"Heisenberg, C.-P. J. (2011). Invited Lectures ‐ Symposia Area. <i>FEBS Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1742-4658.2011.08136.x\">https://doi.org/10.1111/j.1742-4658.2011.08136.x</a>","chicago":"Heisenberg, Carl-Philipp J. “Invited Lectures ‐ Symposia Area.” <i>FEBS Journal</i>. Wiley-Blackwell, 2011. <a href=\"https://doi.org/10.1111/j.1742-4658.2011.08136.x\">https://doi.org/10.1111/j.1742-4658.2011.08136.x</a>."},"publisher":"Wiley-Blackwell","oa_version":"None","month":"07","doi":"10.1111/j.1742-4658.2011.08136.x","publication":"FEBS Journal","year":"2011","volume":278,"status":"public","date_published":"2011-07-01T00:00:00Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","page":"24 - 24","issue":"S1","author":[{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"       278","date_created":"2018-12-11T12:03:01Z","language":[{"iso":"eng"}],"_id":"3383","department":[{"_id":"CaHe"}],"title":"Invited Lectures ‐ Symposia Area","publication_status":"published","date_updated":"2021-01-12T07:43:06Z"},{"file_date_updated":"2020-07-14T12:46:11Z","has_accepted_license":"1","publisher":"Public Library of Science","file":[{"file_name":"IST-2015-379-v1+1_journal.pone.0020409.pdf","date_created":"2018-12-12T10:09:25Z","file_id":"4749","creator":"system","date_updated":"2020-07-14T12:46:11Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"307d4356916471306e3705ac65b82fa1","file_size":1424768}],"pubrep_id":"379","month":"06","publication":"PLoS One","year":"2011","date_published":"2011-06-16T00:00:00Z","ddc":["570"],"status":"public","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Patrick","full_name":"Garrigan, Patrick","last_name":"Garrigan"},{"last_name":"Ratliff","first_name":"Charles","full_name":"Ratliff, Charles"},{"last_name":"Milcinski","full_name":"Milcinski, Grega","first_name":"Grega"},{"last_name":"Klein","full_name":"Klein, Jennifer","first_name":"Jennifer"},{"last_name":"Seyfarth","first_name":"Lucia","full_name":"Seyfarth, Lucia"},{"full_name":"Sterling, Peter","first_name":"Peter","last_name":"Sterling"},{"first_name":"David","full_name":"Brainard, David","last_name":"Brainard"},{"first_name":"Vijay","full_name":"Balasubramanian, Vijay","last_name":"Balasubramanian"}],"oa":1,"_id":"3384","publication_status":"published","date_updated":"2021-01-12T07:43:07Z","day":"16","type":"journal_article","publist_id":"3223","citation":{"ieee":"G. Tkačik <i>et al.</i>, “Natural images from the birthplace of the human eye,” <i>PLoS One</i>, vol. 6, no. 6. Public Library of Science, 2011.","short":"G. Tkačik, P. Garrigan, C. Ratliff, G. Milcinski, J. Klein, L. Seyfarth, P. Sterling, D. Brainard, V. Balasubramanian, PLoS One 6 (2011).","ama":"Tkačik G, Garrigan P, Ratliff C, et al. Natural images from the birthplace of the human eye. <i>PLoS One</i>. 2011;6(6). doi:<a href=\"https://doi.org/10.1371/journal.pone.0020409\">10.1371/journal.pone.0020409</a>","apa":"Tkačik, G., Garrigan, P., Ratliff, C., Milcinski, G., Klein, J., Seyfarth, L., … Balasubramanian, V. (2011). Natural images from the birthplace of the human eye. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0020409\">https://doi.org/10.1371/journal.pone.0020409</a>","ista":"Tkačik G, Garrigan P, Ratliff C, Milcinski G, Klein J, Seyfarth L, Sterling P, Brainard D, Balasubramanian V. 2011. Natural images from the birthplace of the human eye. PLoS One. 6(6), e20409.","chicago":"Tkačik, Gašper, Patrick Garrigan, Charles Ratliff, Grega Milcinski, Jennifer Klein, Lucia Seyfarth, Peter Sterling, David Brainard, and Vijay Balasubramanian. “Natural Images from the Birthplace of the Human Eye.” <i>PLoS One</i>. Public Library of Science, 2011. <a href=\"https://doi.org/10.1371/journal.pone.0020409\">https://doi.org/10.1371/journal.pone.0020409</a>.","mla":"Tkačik, Gašper, et al. “Natural Images from the Birthplace of the Human Eye.” <i>PLoS One</i>, vol. 6, no. 6, e20409, Public Library of Science, 2011, doi:<a href=\"https://doi.org/10.1371/journal.pone.0020409\">10.1371/journal.pone.0020409</a>."},"oa_version":"Published Version","doi":"10.1371/journal.pone.0020409","quality_controlled":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":6,"abstract":[{"text":"Here we introduce a database of calibrated natural images publicly available through an easy-to-use web interface. Using a Nikon D70 digital SLR camera, we acquired about  six-megapixel images of Okavango Delta of Botswana, a tropical savanna habitat similar to where the human eye is thought to have evolved. Some sequences of images were captured unsystematically while following a baboon troop, while others were designed to vary a single parameter such as aperture, object distance, time of day or position on the horizon. Images are available in the raw RGB format and in grayscale. Images are also available in units relevant to the physiology of human cone photoreceptors, where pixel values represent the expected number of photoisomerizations per second for cones sensitive to long (L), medium (M) and short (S) wavelengths. This database is distributed under a Creative Commons Attribution-Noncommercial Unported license to facilitate research in computer vision, psychophysics of perception, and visual neuroscience.","lang":"eng"}],"issue":"6","article_number":"e20409","intvolume":"         6","date_created":"2018-12-11T12:03:01Z","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"}],"scopus_import":1,"title":"Natural images from the birthplace of the human eye"},{"department":[{"_id":"MiSi"}],"date_created":"2018-12-11T12:03:02Z","_id":"3385","language":[{"iso":"eng"}],"date_updated":"2021-01-12T07:43:07Z","scopus_import":1,"publication_status":"published","title":"Interstitial locomotion of leukocytes","page":"32 - 34","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":138,"year":"2011","date_published":"2011-07-01T00:00:00Z","status":"public","issue":"1","article_type":"review","intvolume":"       138","author":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K"}],"month":"07","oa_version":"None","publication":"Immunology Letters","doi":"10.1016/j.imlet.2011.02.013","quality_controlled":"1","citation":{"chicago":"Sixt, Michael K. “Interstitial Locomotion of Leukocytes.” <i>Immunology Letters</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.imlet.2011.02.013\">https://doi.org/10.1016/j.imlet.2011.02.013</a>.","apa":"Sixt, M. K. (2011). Interstitial locomotion of leukocytes. <i>Immunology Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.imlet.2011.02.013\">https://doi.org/10.1016/j.imlet.2011.02.013</a>","ista":"Sixt MK. 2011. Interstitial locomotion of leukocytes. Immunology Letters. 138(1), 32–34.","short":"M.K. Sixt, Immunology Letters 138 (2011) 32–34.","ama":"Sixt MK. Interstitial locomotion of leukocytes. <i>Immunology Letters</i>. 2011;138(1):32-34. doi:<a href=\"https://doi.org/10.1016/j.imlet.2011.02.013\">10.1016/j.imlet.2011.02.013</a>","ieee":"M. K. Sixt, “Interstitial locomotion of leukocytes,” <i>Immunology Letters</i>, vol. 138, no. 1. Elsevier, pp. 32–34, 2011.","mla":"Sixt, Michael K. “Interstitial Locomotion of Leukocytes.” <i>Immunology Letters</i>, vol. 138, no. 1, Elsevier, 2011, pp. 32–34, doi:<a href=\"https://doi.org/10.1016/j.imlet.2011.02.013\">10.1016/j.imlet.2011.02.013</a>."},"type":"journal_article","day":"01","publist_id":"3222","publisher":"Elsevier"},{"oa_version":"None","month":"04","doi":"10.1111/j.1420-9101.2011.02278.x","quality_controlled":"1","publication":"Journal of Evolutionary Biology","day":"21","type":"journal_article","publist_id":"3221","citation":{"ama":"Schrempf A, Cremer S, Heinze J. Social influence on age and reproduction reduced lifespan and fecundity in multi queen ant colonies. <i>Journal of Evolutionary Biology</i>. 2011;24(7):1455-1461. doi:<a href=\"https://doi.org/10.1111/j.1420-9101.2011.02278.x\">10.1111/j.1420-9101.2011.02278.x</a>","short":"A. Schrempf, S. Cremer, J. Heinze, Journal of Evolutionary Biology 24 (2011) 1455–1461.","ieee":"A. Schrempf, S. Cremer, and J. Heinze, “Social influence on age and reproduction reduced lifespan and fecundity in multi queen ant colonies,” <i>Journal of Evolutionary Biology</i>, vol. 24, no. 7. Wiley-Blackwell, pp. 1455–1461, 2011.","chicago":"Schrempf, Alexandra, Sylvia Cremer, and Jürgen Heinze. “Social Influence on Age and Reproduction Reduced Lifespan and Fecundity in Multi Queen Ant Colonies.” <i>Journal of Evolutionary Biology</i>. Wiley-Blackwell, 2011. <a href=\"https://doi.org/10.1111/j.1420-9101.2011.02278.x\">https://doi.org/10.1111/j.1420-9101.2011.02278.x</a>.","ista":"Schrempf A, Cremer S, Heinze J. 2011. Social influence on age and reproduction reduced lifespan and fecundity in multi queen ant colonies. Journal of Evolutionary Biology. 24(7), 1455–1461.","apa":"Schrempf, A., Cremer, S., &#38; Heinze, J. (2011). Social influence on age and reproduction reduced lifespan and fecundity in multi queen ant colonies. <i>Journal of Evolutionary Biology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1420-9101.2011.02278.x\">https://doi.org/10.1111/j.1420-9101.2011.02278.x</a>","mla":"Schrempf, Alexandra, et al. “Social Influence on Age and Reproduction Reduced Lifespan and Fecundity in Multi Queen Ant Colonies.” <i>Journal of Evolutionary Biology</i>, vol. 24, no. 7, Wiley-Blackwell, 2011, pp. 1455–61, doi:<a href=\"https://doi.org/10.1111/j.1420-9101.2011.02278.x\">10.1111/j.1420-9101.2011.02278.x</a>."},"publisher":"Wiley-Blackwell","date_created":"2018-12-11T12:03:02Z","language":[{"iso":"eng"}],"_id":"3386","department":[{"_id":"SyCr"}],"scopus_import":1,"title":"Social influence on age and reproduction reduced lifespan and fecundity in multi queen ant colonies","publication_status":"published","date_updated":"2021-01-12T07:43:08Z","year":"2011","volume":24,"abstract":[{"lang":"eng","text":"Evolutionary theories of ageing predict that life span increases with decreasing extrinsic mortality, and life span variation among queens in ant species seems to corroborate this prediction: queens, which are the only reproductive in a colony, live much longer than queens in multi-queen colonies. The latter often inhabit ephemeral nest sites and accordingly are assumed to experience a higher mortality risk. Yet, all prior studies compared queens from different single- and multi-queen species. Here, we demonstrate an effect of queen number on longevity and fecundity within a single, socially plastic species, where queens experience the similar level of extrinsic mortality. Queens from single- and two-queen colonies had significantly longer lifespan and higher fecundity than queens living in associations of eight queens. As queens also differ neither in morphology nor the mode of colony foundation, our study shows that the social environment itself strongly affects ageing rate."}],"status":"public","date_published":"2011-04-21T00:00:00Z","page":"1455 - 1461","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"7","author":[{"last_name":"Schrempf","full_name":"Schrempf, Alexandra","first_name":"Alexandra"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","full_name":"Cremer, Sylvia","first_name":"Sylvia","orcid":"0000-0002-2193-3868"},{"full_name":"Heinze, Jürgen","first_name":"Jürgen","last_name":"Heinze"}],"intvolume":"        24"},{"pubrep_id":"372","file":[{"date_updated":"2020-07-14T12:46:11Z","creator":"system","access_level":"open_access","file_id":"5058","date_created":"2018-12-12T10:14:09Z","file_name":"IST-2015-372-v1+1_1471-2148-11-205.pdf","checksum":"68da8d04af1b97b4cbe8606e2f92ddd8","file_size":465042,"content_type":"application/pdf","relation":"main_file"}],"month":"07","publication":"BMC Evolutionary Biology","file_date_updated":"2020-07-14T12:46:11Z","has_accepted_license":"1","publisher":"BioMed Central","_id":"3387","publication_status":"published","date_updated":"2021-01-12T07:43:08Z","status":"public","date_published":"2011-07-13T00:00:00Z","ddc":["576"],"year":"2011","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Anne","full_name":"Kupczok, Anne","last_name":"Kupczok","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"oa_version":"Published Version","quality_controlled":"1","doi":"10.1186/1471-2148-11-205","publist_id":"3219","type":"journal_article","day":"13","citation":{"ista":"Kupczok A. 2011. Split based computation of majority rule supertrees. BMC Evolutionary Biology. 11(205), 205.","apa":"Kupczok, A. (2011). Split based computation of majority rule supertrees. <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2148-11-205\">https://doi.org/10.1186/1471-2148-11-205</a>","chicago":"Kupczok, Anne. “Split Based Computation of Majority Rule Supertrees.” <i>BMC Evolutionary Biology</i>. BioMed Central, 2011. <a href=\"https://doi.org/10.1186/1471-2148-11-205\">https://doi.org/10.1186/1471-2148-11-205</a>.","ama":"Kupczok A. Split based computation of majority rule supertrees. <i>BMC Evolutionary Biology</i>. 2011;11(205). doi:<a href=\"https://doi.org/10.1186/1471-2148-11-205\">10.1186/1471-2148-11-205</a>","short":"A. Kupczok, BMC Evolutionary Biology 11 (2011).","ieee":"A. Kupczok, “Split based computation of majority rule supertrees,” <i>BMC Evolutionary Biology</i>, vol. 11, no. 205. BioMed Central, 2011.","mla":"Kupczok, Anne. “Split Based Computation of Majority Rule Supertrees.” <i>BMC Evolutionary Biology</i>, vol. 11, no. 205, 205, BioMed Central, 2011, doi:<a href=\"https://doi.org/10.1186/1471-2148-11-205\">10.1186/1471-2148-11-205</a>."},"language":[{"iso":"eng"}],"date_created":"2018-12-11T12:03:03Z","department":[{"_id":"JoBo"}],"title":"Split based computation of majority rule supertrees","scopus_import":1,"abstract":[{"text":"Background: Supertree methods combine overlapping input trees into a larger supertree. Here, I consider split-based supertree methods that first extract the split information of the input trees and subsequently combine this split information into a phylogeny. Well known split-based supertree methods are matrix representation with parsimony and matrix representation with compatibility. Combining input trees on the same taxon set, as in the consensus setting, is a well-studied task and it is thus desirable to generalize consensus methods to supertree methods. Results: Here, three variants of majority-rule (MR) supertrees that generalize majority-rule consensus trees are investigated. I provide simple formulas for computing the respective score for bifurcating input- and supertrees. These score computations, together with a heuristic tree search minmizing the scores, were implemented in the python program PluMiST (Plus- and Minus SuperTrees) available from http://www.cibiv.at/software/ plumist. The different MR methods were tested by simulation and on real data sets. The search heuristic was successful in combining compatible input trees. When combining incompatible input trees, especially one variant, MR(-) supertrees, performed well. Conclusions: The presented framework allows for an efficient score computation of three majority-rule supertree variants and input trees. I combined the score computation with a heuristic search over the supertree space. The implementation was tested by simulation and on real data sets and showed promising results. Especially the MR(-) variant seems to be a reasonable score for supertree reconstruction. Generalizing these computations to multifurcating trees is an open problem, which may be tackled using this framework.","lang":"eng"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":11,"intvolume":"        11","issue":"205","article_number":"205"},{"scopus_import":1,"title":"Reconstructing eight decades of genetic variation in an isolated Danish population of the large blue butterfly Maculinea arion","date_created":"2018-12-11T12:03:03Z","language":[{"iso":"eng"}],"department":[{"_id":"SyCr"}],"issue":"201","article_number":"201","intvolume":"        11","volume":11,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"abstract":[{"text":"Background: Fragmentation of terrestrial ecosystems has had detrimental effects on metapopulations of habitat specialists. Maculinea butterflies have been particularly affected because of their specialized lifecycles, requiring both specific food-plants and host-ants. However, the interaction between dispersal, effective population size, and long-term genetic erosion of these endangered butterflies remains unknown. Using non-destructive sampling, we investigated the genetic diversity of the last extant population of M. arion in Denmark, which experienced critically low numbers in the 1980s. Results: Using nine microsatellite markers, we show that the population is genetically impoverished compared to nearby populations in Sweden, but less so than monitoring programs suggested. Ten additional short repeat microsatellites were used to reconstruct changes in genetic diversity and population structure over the last 77 years from museum specimens. We also tested amplification efficiency in such historical samples as a function of repeat length and sample age. Low population numbers in the 1980s did not affect genetic diversity, but considerable turnover of alleles has characterized this population throughout the time-span of our analysis. Conclusions: Our results suggest that M. arion is less sensitive to genetic erosion via population bottlenecks than previously thought, and that managing clusters of high quality habitat may be key for long-term conservation.","lang":"eng"}],"quality_controlled":"1","doi":"10.1186/1471-2148-11-201","oa_version":"Published Version","type":"journal_article","day":"11","publist_id":"3220","citation":{"ieee":"L. V. Ugelvig, P. Nielsen, J. Boomsma, and D. Nash, “Reconstructing eight decades of genetic variation in an isolated Danish population of the large blue butterfly Maculinea arion,” <i>BMC Evolutionary Biology</i>, vol. 11, no. 201. BioMed Central, 2011.","short":"L.V. Ugelvig, P. Nielsen, J. Boomsma, D. Nash, BMC Evolutionary Biology 11 (2011).","ama":"Ugelvig LV, Nielsen P, Boomsma J, Nash D. Reconstructing eight decades of genetic variation in an isolated Danish population of the large blue butterfly Maculinea arion. <i>BMC Evolutionary Biology</i>. 2011;11(201). doi:<a href=\"https://doi.org/10.1186/1471-2148-11-201\">10.1186/1471-2148-11-201</a>","apa":"Ugelvig, L. V., Nielsen, P., Boomsma, J., &#38; Nash, D. (2011). Reconstructing eight decades of genetic variation in an isolated Danish population of the large blue butterfly Maculinea arion. <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2148-11-201\">https://doi.org/10.1186/1471-2148-11-201</a>","ista":"Ugelvig LV, Nielsen P, Boomsma J, Nash D. 2011. Reconstructing eight decades of genetic variation in an isolated Danish population of the large blue butterfly Maculinea arion. BMC Evolutionary Biology. 11(201), 201.","chicago":"Ugelvig, Line V, Per Nielsen, Jacobus Boomsma, and David Nash. “Reconstructing Eight Decades of Genetic Variation in an Isolated Danish Population of the Large Blue Butterfly Maculinea Arion.” <i>BMC Evolutionary Biology</i>. BioMed Central, 2011. <a href=\"https://doi.org/10.1186/1471-2148-11-201\">https://doi.org/10.1186/1471-2148-11-201</a>.","mla":"Ugelvig, Line V., et al. “Reconstructing Eight Decades of Genetic Variation in an Isolated Danish Population of the Large Blue Butterfly Maculinea Arion.” <i>BMC Evolutionary Biology</i>, vol. 11, no. 201, 201, BioMed Central, 2011, doi:<a href=\"https://doi.org/10.1186/1471-2148-11-201\">10.1186/1471-2148-11-201</a>."},"publication_status":"published","date_updated":"2021-01-12T07:43:08Z","_id":"3388","author":[{"first_name":"Line V","full_name":"Ugelvig, Line V","orcid":"0000-0003-1832-8883","last_name":"Ugelvig","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Per","full_name":"Nielsen, Per","last_name":"Nielsen"},{"full_name":"Boomsma, Jacobus","first_name":"Jacobus","last_name":"Boomsma"},{"first_name":"David","full_name":"Nash, David","last_name":"Nash"}],"oa":1,"year":"2011","date_published":"2011-07-11T00:00:00Z","ddc":["576"],"status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication":"BMC Evolutionary Biology","file":[{"file_size":2166556,"checksum":"9ebfed0740f1fa071d02ec32c2b8c17f","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"system","date_updated":"2020-07-14T12:46:11Z","file_id":"5069","date_created":"2018-12-12T10:14:18Z","file_name":"IST-2015-371-v1+1_1471-2148-11-201.pdf"}],"pubrep_id":"371","month":"07","publisher":"BioMed Central","has_accepted_license":"1","file_date_updated":"2020-07-14T12:46:11Z"},{"oa_version":"None","month":"08","doi":"10.1016/j.patrec.2011.02.011","quality_controlled":"1","publication":"Pattern Recognition Letters","type":"journal_article","day":"01","publist_id":"3218","citation":{"ista":"Blaschko M, Shelton J, Bartels A, Lampert C, Gretton A. 2011. Semi supervised kernel canonical correlation analysis with application to human fMRI. Pattern Recognition Letters. 32(11), 1572–1583.","chicago":"Blaschko, Matthew, Jacquelyn Shelton, Andreas Bartels, Christoph Lampert, and Arthur Gretton. “Semi Supervised Kernel Canonical Correlation Analysis with Application to Human FMRI.” <i>Pattern Recognition Letters</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.patrec.2011.02.011\">https://doi.org/10.1016/j.patrec.2011.02.011</a>.","apa":"Blaschko, M., Shelton, J., Bartels, A., Lampert, C., &#38; Gretton, A. (2011). Semi supervised kernel canonical correlation analysis with application to human fMRI. <i>Pattern Recognition Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.patrec.2011.02.011\">https://doi.org/10.1016/j.patrec.2011.02.011</a>","ama":"Blaschko M, Shelton J, Bartels A, Lampert C, Gretton A. Semi supervised kernel canonical correlation analysis with application to human fMRI. <i>Pattern Recognition Letters</i>. 2011;32(11):1572-1583. doi:<a href=\"https://doi.org/10.1016/j.patrec.2011.02.011\">10.1016/j.patrec.2011.02.011</a>","short":"M. Blaschko, J. Shelton, A. Bartels, C. Lampert, A. Gretton, Pattern Recognition Letters 32 (2011) 1572–1583.","ieee":"M. Blaschko, J. Shelton, A. Bartels, C. Lampert, and A. Gretton, “Semi supervised kernel canonical correlation analysis with application to human fMRI,” <i>Pattern Recognition Letters</i>, vol. 32, no. 11. Elsevier, pp. 1572–1583, 2011.","mla":"Blaschko, Matthew, et al. “Semi Supervised Kernel Canonical Correlation Analysis with Application to Human FMRI.” <i>Pattern Recognition Letters</i>, vol. 32, no. 11, Elsevier, 2011, pp. 1572–83, doi:<a href=\"https://doi.org/10.1016/j.patrec.2011.02.011\">10.1016/j.patrec.2011.02.011</a>."},"publisher":"Elsevier","date_created":"2018-12-11T12:03:03Z","language":[{"iso":"eng"}],"_id":"3389","department":[{"_id":"ChLa"}],"scopus_import":1,"publication_status":"published","title":"Semi supervised kernel canonical correlation analysis with application to human fMRI","date_updated":"2021-01-12T07:43:09Z","volume":32,"abstract":[{"lang":"eng","text":"Kernel canonical correlation analysis (KCCA) is a general technique for subspace learning that incorporates principal components analysis (PCA) and Fisher linear discriminant analysis (LDA) as special cases. By finding directions that maximize correlation, KCCA learns representations that are more closely tied to the underlying process that generates the data and can ignore high-variance noise directions. However, for data where acquisition in one or more modalities is expensive or otherwise limited, KCCA may suffer from small sample effects. We propose to use semi-supervised Laplacian regularization to utilize data that are present in only one modality. This approach is able to find highly correlated directions that also lie along the data manifold, resulting in a more robust estimate of correlated subspaces. Functional magnetic resonance imaging (fMRI) acquired data are naturally amenable to subspace techniques as data are well aligned. fMRI data of the human brain are a particularly interesting candidate. In this study we implemented various supervised and semi-supervised versions of KCCA on human fMRI data, with regression to single and multi-variate labels (corresponding to video content subjects viewed during the image acquisition). In each variate condition, the semi-supervised variants of KCCA performed better than the supervised variants, including a supervised variant with Laplacian regularization. We additionally analyze the weights learned by the regression in order to infer brain regions that are important to different types of visual processing."}],"year":"2011","date_published":"2011-08-01T00:00:00Z","status":"public","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","page":"1572 - 1583","issue":"11","intvolume":"        32","author":[{"last_name":"Blaschko","first_name":"Matthew","full_name":"Blaschko, Matthew"},{"last_name":"Shelton","first_name":"Jacquelyn","full_name":"Shelton, Jacquelyn"},{"first_name":"Andreas","full_name":"Bartels, Andreas","last_name":"Bartels"},{"full_name":"Lampert, Christoph","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert"},{"last_name":"Gretton","full_name":"Gretton, Arthur","first_name":"Arthur"}],"acknowledgement":"The research leading to these results has received funding from the European Research Council under the European Community’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement No. 228180. This work was funded in part by the EC project CLASS, IST 027978, and the PASCAL2 network of excellence, IST 2002-506778."},{"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176105/","open_access":"1"}],"citation":{"ama":"Barton NH, Etheridge A. The relation between reproductive value and genetic contribution. <i>Genetics</i>. 2011;188(4):953-973. doi:<a href=\"https://doi.org/10.1534/genetics.111.127555\">10.1534/genetics.111.127555</a>","ieee":"N. H. Barton and A. Etheridge, “The relation between reproductive value and genetic contribution,” <i>Genetics</i>, vol. 188, no. 4. Genetics Society of America, pp. 953–973, 2011.","short":"N.H. Barton, A. Etheridge, Genetics 188 (2011) 953–973.","apa":"Barton, N. H., &#38; Etheridge, A. (2011). The relation between reproductive value and genetic contribution. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.111.127555\">https://doi.org/10.1534/genetics.111.127555</a>","chicago":"Barton, Nicholas H, and Alison Etheridge. “The Relation between Reproductive Value and Genetic Contribution.” <i>Genetics</i>. Genetics Society of America, 2011. <a href=\"https://doi.org/10.1534/genetics.111.127555\">https://doi.org/10.1534/genetics.111.127555</a>.","ista":"Barton NH, Etheridge A. 2011. The relation between reproductive value and genetic contribution. Genetics. 188(4), 953–973.","mla":"Barton, Nicholas H., and Alison Etheridge. “The Relation between Reproductive Value and Genetic Contribution.” <i>Genetics</i>, vol. 188, no. 4, Genetics Society of America, 2011, pp. 953–73, doi:<a href=\"https://doi.org/10.1534/genetics.111.127555\">10.1534/genetics.111.127555</a>."},"publist_id":"3217","day":"01","type":"journal_article","quality_controlled":"1","doi":"10.1534/genetics.111.127555","oa_version":"Submitted Version","intvolume":"       188","issue":"4","volume":188,"abstract":[{"lang":"eng","text":"What determines the genetic contribution that an individual makes to future generations? With biparental reproduction, each individual leaves a 'pedigree' of descendants, determined by the biparental relationships in the population. The pedigree of an individual constrains the lines of descent of each of its genes. An individual's reproductive value is the expected number of copies of each of its genes that is passed on to distant generations conditional on its pedigree. For the simplest model of biparental reproduction analogous to the Wright-Fisher model, an individual's reproductive value is determined within ~10 generations, independent of population size. Partial selfing and subdivision do not greatly slow this convergence. Our central result is that the probability that a gene will survive is proportional to the reproductive value of the individual that carries it, and that conditional on survival, after a few tens of generations, the distribution of the number of surviving copies is the same for all individuals, whatever their reproductive value. These results can be generalized to the joint distribution of surviving blocks of ancestral genome. Selection on unlinked loci in the genetic background may greatly increase the variance in reproductive value, but the above results nevertheless still hold. The almost linear relationship between survival probability and reproductive value also holds for weakly favored alleles. Thus, the influence of the complex pedigree of descendants on an individual's genetic contribution to the population can be summarized through a single number: its reproductive value."}],"title":"The relation between reproductive value and genetic contribution","scopus_import":1,"department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T12:03:04Z","publisher":"Genetics Society of America","publication":"Genetics","month":"08","oa":1,"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H"},{"last_name":"Etheridge","full_name":"Etheridge, Alison","first_name":"Alison"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","page":"953 - 973","date_published":"2011-08-01T00:00:00Z","status":"public","year":"2011","date_updated":"2021-01-12T07:43:09Z","project":[{"call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation"}],"ec_funded":1,"publication_status":"published","_id":"3390"},{"publisher":"Cell Press","publication":"Trends in Ecology and Evolution","month":"08","oa":1,"author":[{"orcid":"0000-0002-5985-7653","first_name":"Harold","full_name":"de Vladar, Harold","id":"2A181218-F248-11E8-B48F-1D18A9856A87","last_name":"de Vladar"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"year":"2011","status":"public","date_published":"2011-08-01T00:00:00Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","page":"424 - 432","publication_status":"published","ec_funded":1,"project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"date_updated":"2021-01-12T07:43:10Z","_id":"3391","main_file_link":[{"url":"http://arxiv.org/abs/1104.2854","open_access":"1"}],"day":"01","type":"journal_article","publist_id":"3216","citation":{"short":"H. de Vladar, N.H. Barton, Trends in Ecology and Evolution 26 (2011) 424–432.","ama":"de Vladar H, Barton NH. The contribution of statistical physics to evolutionary biology. <i>Trends in Ecology and Evolution</i>. 2011;26(8):424-432. doi:<a href=\"https://doi.org/10.1016/j.tree.2011.04.002\">10.1016/j.tree.2011.04.002</a>","ieee":"H. de Vladar and N. H. Barton, “The contribution of statistical physics to evolutionary biology,” <i>Trends in Ecology and Evolution</i>, vol. 26, no. 8. Cell Press, pp. 424–432, 2011.","chicago":"Vladar, Harold de, and Nicholas H Barton. “The Contribution of Statistical Physics to Evolutionary Biology.” <i>Trends in Ecology and Evolution</i>. Cell Press, 2011. <a href=\"https://doi.org/10.1016/j.tree.2011.04.002\">https://doi.org/10.1016/j.tree.2011.04.002</a>.","apa":"de Vladar, H., &#38; Barton, N. H. (2011). The contribution of statistical physics to evolutionary biology. <i>Trends in Ecology and Evolution</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tree.2011.04.002\">https://doi.org/10.1016/j.tree.2011.04.002</a>","ista":"de Vladar H, Barton NH. 2011. The contribution of statistical physics to evolutionary biology. Trends in Ecology and Evolution. 26(8), 424–432.","mla":"de Vladar, Harold, and Nicholas H. Barton. “The Contribution of Statistical Physics to Evolutionary Biology.” <i>Trends in Ecology and Evolution</i>, vol. 26, no. 8, Cell Press, 2011, pp. 424–32, doi:<a href=\"https://doi.org/10.1016/j.tree.2011.04.002\">10.1016/j.tree.2011.04.002</a>."},"quality_controlled":"1","doi":"10.1016/j.tree.2011.04.002","oa_version":"Submitted Version","issue":"8","intvolume":"        26","volume":26,"abstract":[{"text":"Evolutionary biology shares many concepts with statistical physics: both deal with populations, whether of molecules or organisms, and both seek to simplify evolution in very many dimensions. Often, methodologies have undergone parallel and independent development, as with stochastic methods in population genetics. Here, we discuss aspects of population genetics that have embraced methods from physics: non-equilibrium statistical mechanics, travelling waves and Monte-Carlo methods, among others, have been used to study polygenic evolution, rates of adaptation and range expansions. These applications indicate that evolutionary biology can further benefit from interactions with other areas of statistical physics; for example, by following the distribution of paths taken by a population through time","lang":"eng"}],"scopus_import":1,"title":"The contribution of statistical physics to evolutionary biology","date_created":"2018-12-11T12:03:04Z","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}]},{"oa_version":"None","quality_controlled":"1","doi":"10.4049/jimmunol.1100935","day":"01","type":"journal_article","publist_id":"3215","citation":{"apa":"Soriano, S., Hons, M., Schumann, K., Kumar, V., Dennier, T., Lyck, R., … Stein, J. (2011). In vivo analysis of uropod function during physiological T cell trafficking. <i>Journal of Immunology</i>. American Association of Immunologists. <a href=\"https://doi.org/10.4049/jimmunol.1100935\">https://doi.org/10.4049/jimmunol.1100935</a>","chicago":"Soriano, Silvia, Miroslav Hons, Kathrin Schumann, Varsha Kumar, Timo Dennier, Ruth Lyck, Michael K Sixt, and Jens Stein. “In Vivo Analysis of Uropod Function during Physiological T Cell Trafficking.” <i>Journal of Immunology</i>. American Association of Immunologists, 2011. <a href=\"https://doi.org/10.4049/jimmunol.1100935\">https://doi.org/10.4049/jimmunol.1100935</a>.","ista":"Soriano S, Hons M, Schumann K, Kumar V, Dennier T, Lyck R, Sixt MK, Stein J. 2011. In vivo analysis of uropod function during physiological T cell trafficking. Journal of Immunology. 187(5), 2356–2364.","ama":"Soriano S, Hons M, Schumann K, et al. In vivo analysis of uropod function during physiological T cell trafficking. <i>Journal of Immunology</i>. 2011;187(5):2356-2364. doi:<a href=\"https://doi.org/10.4049/jimmunol.1100935\">10.4049/jimmunol.1100935</a>","ieee":"S. Soriano <i>et al.</i>, “In vivo analysis of uropod function during physiological T cell trafficking,” <i>Journal of Immunology</i>, vol. 187, no. 5. American Association of Immunologists, pp. 2356–2364, 2011.","short":"S. Soriano, M. Hons, K. Schumann, V. Kumar, T. Dennier, R. Lyck, M.K. Sixt, J. Stein, Journal of Immunology 187 (2011) 2356–2364.","mla":"Soriano, Silvia, et al. “In Vivo Analysis of Uropod Function during Physiological T Cell Trafficking.” <i>Journal of Immunology</i>, vol. 187, no. 5, American Association of Immunologists, 2011, pp. 2356–64, doi:<a href=\"https://doi.org/10.4049/jimmunol.1100935\">10.4049/jimmunol.1100935</a>."},"date_created":"2018-12-11T12:03:04Z","language":[{"iso":"eng"}],"department":[{"_id":"MiSi"}],"scopus_import":"1","title":"In vivo analysis of uropod function during physiological T cell trafficking","abstract":[{"lang":"eng","text":"Migrating lymphocytes acquire a polarized phenotype with a leading and a trailing edge, or uropod. Although in vitro experiments in cell lines or activated primary cell cultures have established that Rho-p160 coiled-coil kinase (ROCK)-myosin II-mediated uropod contractility is required for integrin de-adhesion on two-dimensional surfaces and nuclear propulsion through narrow pores in three-dimensional matrices, less is known about the role of these two events during the recirculation of primary, nonactivated lymphocytes. Using pharmacological antagonists of ROCK and myosin II, we report that inhibition of uropod contractility blocked integrin-independent mouse T cell migration through narrow, but not large, pores in vitro. T cell crawling on chemokine-coated endothelial cells under shear was severely impaired by ROCK inhibition, whereas transendothelial migration was only reduced through endothelial cells with high, but not low, barrier properties. Using three-dimensional thick-tissue imaging and dynamic two-photon microscopy of T cell motility in lymphoid tissue, we demonstrated a significant role for uropod contractility in intraluminal crawling and transendothelial migration through lymph node, but not bone marrow, endothelial cells. Finally, we demonstrated that ICAM-1, but not anatomical constraints or integrin-independent interactions, reduced parenchymal motility of inhibitor-treated T cells within the dense lymphoid microenvironment, thus assigning context-dependent roles for uropod contraction during lymphocyte recirculation."}],"volume":187,"issue":"5","article_type":"original","intvolume":"       187","month":"09","publication":"Journal of Immunology","publisher":"American Association of Immunologists","_id":"3392","publication_status":"published","date_updated":"2023-10-10T13:14:59Z","year":"2011","publication_identifier":{"issn":["0022-1767"],"eissn":["1550-6606"]},"date_published":"2011-09-01T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"2356 - 2364","article_processing_charge":"No","author":[{"last_name":"Soriano","full_name":"Soriano, Silvia","first_name":"Silvia"},{"first_name":"Miroslav","full_name":"Hons, Miroslav","orcid":"0000-0002-6625-3348","last_name":"Hons"},{"last_name":"Schumann","first_name":"Kathrin","full_name":"Schumann, Kathrin"},{"first_name":"Varsha","full_name":"Kumar, Varsha","last_name":"Kumar"},{"first_name":"Timo","full_name":"Dennier, Timo","last_name":"Dennier"},{"last_name":"Lyck","full_name":"Lyck, Ruth","first_name":"Ruth"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K","orcid":"0000-0002-6620-9179"},{"first_name":"Jens","full_name":"Stein, Jens","last_name":"Stein"}]},{"abstract":[{"text":"Unlike unconditionally advantageous “Fisherian” variants that tend to spread throughout a species range once introduced anywhere, “bistable” variants, such as chromosome translocations, have two alternative stable frequencies, absence and (near) fixation. Analogous to populations with Allee effects, bistable variants tend to increase locally only once they become sufficiently common, and their spread depends on their rate of increase averaged over all frequencies. Several proposed manipulations of insect populations, such as using Wolbachia or “engineered underdominance” to suppress vector-borne diseases, produce bistable rather than Fisherian dynamics. We synthesize and extend theoretical analyses concerning three features of their spatial behavior: rate of spread, conditions to initiate spread from a localized introduction, and wave stopping caused by variation in population densities or dispersal rates. Unlike Fisherian variants, bistable variants tend to spread spatially only for particular parameter combinations and initial conditions. Wave initiation requires introduction over an extended region, while subsequent spatial spread is slower than for Fisherian waves and can easily be halted by local spatial inhomogeneities. We present several new results, including robust sufficient conditions to initiate (and stop) spread, using a one-parameter cubic approximation applicable to several models. The results have both basic and applied implications.","lang":"eng"}],"volume":178,"issue":"3","article_type":"original","intvolume":"       178","department":[{"_id":"NiBa"}],"date_created":"2018-12-11T12:03:05Z","language":[{"iso":"eng"}],"scopus_import":"1","title":"Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects","citation":{"chicago":"Barton, Nicholas H, and Michael Turelli. “Spatial Waves of Advance with Bistable Dynamics: Cytoplasmic and Genetic Analogues of Allee Effects.” <i>American Naturalist</i>. The University of Chicago Press, 2011. <a href=\"https://doi.org/10.1086/661246\">https://doi.org/10.1086/661246</a>.","ista":"Barton NH, Turelli M. 2011. Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects. American Naturalist. 178(3), E48–E75.","apa":"Barton, N. H., &#38; Turelli, M. (2011). Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects. <i>American Naturalist</i>. The University of Chicago Press. <a href=\"https://doi.org/10.1086/661246\">https://doi.org/10.1086/661246</a>","ieee":"N. H. Barton and M. Turelli, “Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects,” <i>American Naturalist</i>, vol. 178, no. 3. The University of Chicago Press, pp. E48–E75, 2011.","ama":"Barton NH, Turelli M. Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects. <i>American Naturalist</i>. 2011;178(3):E48-E75. doi:<a href=\"https://doi.org/10.1086/661246\">10.1086/661246</a>","short":"N.H. Barton, M. Turelli, American Naturalist 178 (2011) E48–E75.","mla":"Barton, Nicholas H., and Michael Turelli. “Spatial Waves of Advance with Bistable Dynamics: Cytoplasmic and Genetic Analogues of Allee Effects.” <i>American Naturalist</i>, vol. 178, no. 3, The University of Chicago Press, 2011, pp. E48–75, doi:<a href=\"https://doi.org/10.1086/661246\">10.1086/661246</a>."},"type":"journal_article","day":"01","publist_id":"3214","oa_version":"Submitted Version","quality_controlled":"1","doi":"10.1086/661246","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"E48 - E75","article_processing_charge":"No","publication_identifier":{"eissn":["1537-5323"],"issn":["0003-0147"]},"year":"2011","date_published":"2011-09-01T00:00:00Z","ddc":["570"],"status":"public","oa":1,"author":[{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Turelli, Michael","first_name":"Michael","last_name":"Turelli"}],"_id":"3393","date_updated":"2023-10-18T08:01:43Z","publication_status":"published","file_date_updated":"2020-07-14T12:46:11Z","has_accepted_license":"1","publisher":"The University of Chicago Press","month":"09","file":[{"access_level":"open_access","creator":"system","date_updated":"2020-07-14T12:46:11Z","file_id":"4692","date_created":"2018-12-12T10:08:31Z","file_name":"IST-2016-554-v1+1_BartonTurelli2011_copy.pdf","file_size":629130,"checksum":"7fd22a2ef3321a6fca6a439b3be5d8f4","content_type":"application/pdf","relation":"main_file"}],"pubrep_id":"554","publication":"American Naturalist"},{"publication":"Genetics","month":"09","publisher":"Genetics Society of America","ec_funded":1,"publication_status":"published","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"date_updated":"2021-01-12T07:43:11Z","_id":"3394","oa":1,"author":[{"first_name":"Jitka","full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}],"year":"2011","status":"public","date_published":"2011-09-01T00:00:00Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","page":"227 - 235","doi":"10.1534/genetics.111.129817","quality_controlled":"1","oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176109/"}],"type":"journal_article","day":"01","publist_id":"3213","citation":{"mla":"Polechova, Jitka, and Nicholas H. Barton. “Genetic Drift Widens the Expected Cline but Narrows the Expected Cline Width.” <i>Genetics</i>, vol. 189, no. 1, Genetics Society of America, 2011, pp. 227–35, doi:<a href=\"https://doi.org/10.1534/genetics.111.129817\">10.1534/genetics.111.129817</a>.","ieee":"J. Polechova and N. H. Barton, “Genetic drift widens the expected cline but narrows the expected cline width,” <i>Genetics</i>, vol. 189, no. 1. Genetics Society of America, pp. 227–235, 2011.","ama":"Polechova J, Barton NH. Genetic drift widens the expected cline but narrows the expected cline width. <i>Genetics</i>. 2011;189(1):227-235. doi:<a href=\"https://doi.org/10.1534/genetics.111.129817\">10.1534/genetics.111.129817</a>","short":"J. Polechova, N.H. Barton, Genetics 189 (2011) 227–235.","apa":"Polechova, J., &#38; Barton, N. H. (2011). Genetic drift widens the expected cline but narrows the expected cline width. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.111.129817\">https://doi.org/10.1534/genetics.111.129817</a>","chicago":"Polechova, Jitka, and Nicholas H Barton. “Genetic Drift Widens the Expected Cline but Narrows the Expected Cline Width.” <i>Genetics</i>. Genetics Society of America, 2011. <a href=\"https://doi.org/10.1534/genetics.111.129817\">https://doi.org/10.1534/genetics.111.129817</a>.","ista":"Polechova J, Barton NH. 2011. Genetic drift widens the expected cline but narrows the expected cline width. Genetics. 189(1), 227–235."},"scopus_import":1,"title":"Genetic drift widens the expected cline but narrows the expected cline width","date_created":"2018-12-11T12:03:05Z","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"issue":"1","intvolume":"       189","volume":189,"abstract":[{"text":"Random genetic drift shifts clines in space, alters their width, and distorts their shape. Such random fluctuations complicate inferences from cline width and position. Notably, the effect of genetic drift on the expected shape of the cline is opposite to the naive (but quite common) misinterpretation of classic results on the expected cline. While random drift on average broadens the overall cline in expected allele frequency, it narrows the width of any particular cline. The opposing effects arise because locally, drift drives alleles to fixation—but fluctuations in position widen the expected cline. The effect of genetic drift can be predicted from standardized variance in allele frequencies, averaged across the habitat: 〈F〉. A cline maintained by spatially varying selection (step change) is expected to be narrower by a factor of  relative to the cline in the absence of drift. The expected cline is broader by the inverse of this factor. In a tension zone maintained by underdominance, the expected cline width is narrower by about 1 – 〈F〉relative to the width in the absence of drift. Individual clines can differ substantially from the expectation, and we give quantitative predictions for the variance in cline position and width. The predictions apply to clines in almost one-dimensional circumstances such as hybrid zones in rivers, deep valleys, or along a coast line and give a guide to what patterns to expect in two dimensions.","lang":"eng"}]}]