[{"oa_version":"None","publication_status":"published","doi":"10.1101/gr.6144007","publication":"Genome Research","_id":"4225","date_created":"2018-12-11T12:07:42Z","day":"09","status":"public","citation":{"chicago":"Bollenbach, Mark Tobias, Kalin Vetsigian, and Roy Kishony. “Evolution and Multilevel Optimization of the Genetic Code.” <i>Genome Research</i>. Cold Spring Harbor Laboratory Press, 2007. <a href=\"https://doi.org/10.1101/gr.6144007\">https://doi.org/10.1101/gr.6144007</a>.","ista":"Bollenbach MT, Vetsigian K, Kishony R. 2007. Evolution and multilevel optimization of the genetic code. Genome Research. 17(4), 401–404.","short":"M.T. Bollenbach, K. Vetsigian, R. Kishony, Genome Research 17 (2007) 401–404.","ieee":"M. T. Bollenbach, K. Vetsigian, and R. Kishony, “Evolution and multilevel optimization of the genetic code,” <i>Genome Research</i>, vol. 17, no. 4. Cold Spring Harbor Laboratory Press, pp. 401–404, 2007.","ama":"Bollenbach MT, Vetsigian K, Kishony R. Evolution and multilevel optimization of the genetic code. <i>Genome Research</i>. 2007;17(4):401-404. doi:<a href=\"https://doi.org/10.1101/gr.6144007\">10.1101/gr.6144007</a>","mla":"Bollenbach, Mark Tobias, et al. “Evolution and Multilevel Optimization of the Genetic Code.” <i>Genome Research</i>, vol. 17, no. 4, Cold Spring Harbor Laboratory Press, 2007, pp. 401–04, doi:<a href=\"https://doi.org/10.1101/gr.6144007\">10.1101/gr.6144007</a>.","apa":"Bollenbach, M. T., Vetsigian, K., &#38; Kishony, R. (2007). Evolution and multilevel optimization of the genetic code. <i>Genome Research</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gr.6144007\">https://doi.org/10.1101/gr.6144007</a>"},"extern":"1","volume":17,"type":"journal_article","abstract":[{"lang":"eng","text":"The discovery of the genetic code was one of the most important advances of modern biology. But there is more to a DNA code than protein sequence; DNA carries signals for splicing, localization, folding, and regulation that are often embedded within the protein-coding sequence. In this issue, Itzkovitz and Alon show that the specific 64-to-20 mapping found in the genetic code may have been optimized for permitting protein-coding regions to carry this extra information and suggest that this property may have evolved as a side benefit of selection to minimize the negative effects of frameshift errors."}],"language":[{"iso":"eng"}],"year":"2007","page":"401 - 404","article_processing_charge":"No","publist_id":"1891","date_updated":"2021-01-12T07:55:26Z","issue":"4","author":[{"full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","orcid":"0000-0003-4398-476X"},{"full_name":"Vetsigian, Kalin","last_name":"Vetsigian","first_name":"Kalin"},{"full_name":"Kishony, Roy","last_name":"Kishony","first_name":"Roy"}],"title":"Evolution and multilevel optimization of the genetic code","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","intvolume":"        17","date_published":"2007-03-09T00:00:00Z","publisher":"Cold Spring Harbor Laboratory Press"},{"page":"521 - 525","publist_id":"1892","year":"2007","date_published":"2007-01-26T00:00:00Z","month":"01","intvolume":"       315","publisher":"American Association for the Advancement of Science","date_updated":"2021-01-12T07:55:26Z","author":[{"full_name":"Anna Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva"},{"first_name":"Periklis","last_name":"Pantazis","full_name":"Pantazis, Periklis"},{"last_name":"Bollenbach","first_name":"Tobias","full_name":"Bollenbach, Tobias"},{"first_name":"Yannis","last_name":"Kalaidzidis","full_name":"Kalaidzidis, Yannis"},{"first_name":"Thomas","last_name":"Bittig","full_name":"Bittig, Thomas"},{"first_name":"Frank","last_name":"Julicher","full_name":"Julicher, Frank"},{"full_name":"Gonzalez-Gaitan, Marcos","last_name":"Gonzalez Gaitan","first_name":"Marcos"}],"title":"Kinetics of morphogen gradient formation","issue":"5811","publication":"Science","publication_status":"published","doi":"10.1126/science.1135774","volume":315,"extern":1,"citation":{"mla":"Kicheva, Anna, et al. “Kinetics of Morphogen Gradient Formation.” <i>Science</i>, vol. 315, no. 5811, American Association for the Advancement of Science, 2007, pp. 521–25, doi:<a href=\"https://doi.org/10.1126/science.1135774\">10.1126/science.1135774</a>.","apa":"Kicheva, A., Pantazis, P., Bollenbach, T., Kalaidzidis, Y., Bittig, T., Julicher, F., &#38; Gonzalez Gaitan, M. (2007). Kinetics of morphogen gradient formation. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1135774\">https://doi.org/10.1126/science.1135774</a>","chicago":"Kicheva, Anna, Periklis Pantazis, Tobias Bollenbach, Yannis Kalaidzidis, Thomas Bittig, Frank Julicher, and Marcos Gonzalez Gaitan. “Kinetics of Morphogen Gradient Formation.” <i>Science</i>. American Association for the Advancement of Science, 2007. <a href=\"https://doi.org/10.1126/science.1135774\">https://doi.org/10.1126/science.1135774</a>.","ama":"Kicheva A, Pantazis P, Bollenbach T, et al. Kinetics of morphogen gradient formation. <i>Science</i>. 2007;315(5811):521-525. doi:<a href=\"https://doi.org/10.1126/science.1135774\">10.1126/science.1135774</a>","ieee":"A. Kicheva <i>et al.</i>, “Kinetics of morphogen gradient formation,” <i>Science</i>, vol. 315, no. 5811. American Association for the Advancement of Science, pp. 521–525, 2007.","short":"A. Kicheva, P. Pantazis, T. Bollenbach, Y. Kalaidzidis, T. Bittig, F. Julicher, M. Gonzalez Gaitan, Science 315 (2007) 521–525.","ista":"Kicheva A, Pantazis P, Bollenbach T, Kalaidzidis Y, Bittig T, Julicher F, Gonzalez Gaitan M. 2007. Kinetics of morphogen gradient formation. Science. 315(5811), 521–525."},"abstract":[{"lang":"eng","text":"In the developing fly wing, secreted morphogens such as Decapentaplegic (Dpp) and Wingless (Wg) form gradients of concentration providing positional information. Dpp forms a longer-range gradient than Wg. To understand how the range is controlled, we measured the four key kinetic parameters governing morphogen spreading: the production rate, the effective diffusion coefficient, the degradation rate, and the immobile fraction. The four parameters had different values for Dpp versus Wg. In addition, Dynamin-dependent endocytosis was required for spreading of Dpp, but not Wg. Thus, the cellular mechanisms of Dpp and Wingless spreading are different: Dpp spreading requires endocytic, intracellular trafficking."}],"type":"journal_article","_id":"4226","date_created":"2018-12-11T12:07:42Z","day":"26","status":"public","quality_controlled":0},{"extern":1,"citation":{"ista":"de Vladar H. 2007. Alternativas prebióticas para la síntesis de amino- ácidos y otras moléculas relacionadas. Ab Initio: Orígenes Del Universo, La Vida, Y La Inteligencia, 91–109.","short":"H. de Vladar, in:, N. Falcón, Y. Loyo De Sardi (Eds.), Consejo de Desarrollo Cientifico y Tecnologico, 2007, pp. 91–109.","ieee":"H. de Vladar, “Alternativas prebióticas para la síntesis de amino- ácidos y otras moléculas relacionadas,” presented at the Ab Initio: Orígenes Del Universo, La Vida, Y La Inteligencia, 2007, pp. 91–109.","ama":"de Vladar H. Alternativas prebióticas para la síntesis de amino- ácidos y otras moléculas relacionadas. In: Falcón N, Loyo De Sardi Y, eds. Consejo de Desarrollo Cientifico y Tecnologico; 2007:91-109. doi:<a href=\"https://doi.org/3808\">3808</a>","chicago":"Vladar, Harold de. “Alternativas Prebióticas Para La Síntesis de Amino- Ácidos y Otras Moléculas Relacionadas.” edited by N. Falcón and Y. Loyo De Sardi, 91–109. Consejo de Desarrollo Cientifico y Tecnologico, 2007. <a href=\"https://doi.org/3808\">https://doi.org/3808</a>.","apa":"de Vladar, H. (2007). Alternativas prebióticas para la síntesis de amino- ácidos y otras moléculas relacionadas. In N. Falcón &#38; Y. Loyo De Sardi (Eds.) (pp. 91–109). Presented at the Ab Initio: Orígenes Del Universo, La Vida, Y La Inteligencia, Consejo de Desarrollo Cientifico y Tecnologico. <a href=\"https://doi.org/3808\">https://doi.org/3808</a>","mla":"de Vladar, Harold. <i>Alternativas Prebióticas Para La Síntesis de Amino- Ácidos y Otras Moléculas Relacionadas</i>. Edited by N. Falcón and Y. Loyo De Sardi, Consejo de Desarrollo Cientifico y Tecnologico, 2007, pp. 91–109, doi:<a href=\"https://doi.org/3808\">3808</a>."},"type":"conference","date_created":"2018-12-11T12:07:45Z","_id":"4233","editor":[{"full_name":"Falcón,N.","first_name":"N.","last_name":"Falcón"},{"full_name":"Loyo de Sardi,Y.","last_name":"Loyo De Sardi","first_name":"Y."}],"day":"01","status":"public","quality_controlled":0,"doi":"3808","publication_status":"published","date_published":"2007-01-01T00:00:00Z","month":"01","publisher":"Consejo de Desarrollo Cientifico y Tecnologico","date_updated":"2021-01-12T07:55:29Z","author":[{"full_name":"Harold Vladar","orcid":"0000-0002-5985-7653","last_name":"Vladar","id":"2A181218-F248-11E8-B48F-1D18A9856A87","first_name":"Harold"}],"title":"Alternativas prebióticas para la síntesis de amino- ácidos y otras moléculas relacionadas","page":"91 - 109","conference":{"name":"Ab Initio: Orígenes Del Universo, La Vida, Y La Inteligencia"},"publist_id":"1880","year":"2007"},{"publisher":"Elsevier","month":"01","intvolume":"       373","date_published":"2007-01-01T00:00:00Z","author":[{"full_name":"de Vladar, Harold","id":"2A181218-F248-11E8-B48F-1D18A9856A87","first_name":"Harold","last_name":"de Vladar","orcid":"0000-0002-5985-7653"},{"full_name":"Pen, I.","first_name":"I.","last_name":"Pen"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Determinism, noise, and spurious estimations in a generalised model of population growth","date_updated":"2021-01-12T07:55:30Z","publist_id":"1881","external_id":{"arxiv":["abs/q-bio/0602018"]},"page":"477 - 485","article_processing_charge":"No","year":"2007","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"We study a generalised model of population growth in which the state variable is population growth rate instead of population size. Stochastic parametric perturbations, modelling phenotypic variability, lead to a Langevin system with two sources of multiplicative noise. The stationary probability distributions have two characteristic power-law scales. Numerical simulations show that noise suppresses the explosion of the growth rate which occurs in the deterministic counterpart. Instead, in different parameter regimes populations will grow with &quot;anomalous&quot; stochastic rates and (i) stabilise at &quot;random carrying capacities&quot;, or (ii) go extinct in random times. Using logistic fits to reconstruct the simulated data, we find that even highly significant estimations do not recover or reflect information about the deterministic part of the process. Therefore, the logistic interpretation is not biologically meaningful. These results have implications for distinct model-aided calculations in biological situations because these kinds of estimations could lead to spurious conclusions. (c) 2006 Elsevier B.V. All rights reserved.","lang":"eng"}],"arxiv":1,"extern":"1","citation":{"chicago":"Vladar, Harold de, and I. Pen. “Determinism, Noise, and Spurious Estimations in a Generalised Model of Population Growth.” <i>Physica A</i>. Elsevier, 2007. <a href=\"https://doi.org/10.1016/j.physa.2006.06.025\">https://doi.org/10.1016/j.physa.2006.06.025</a>.","ista":"de Vladar H, Pen I. 2007. Determinism, noise, and spurious estimations in a generalised model of population growth. Physica A. 373, 477–485.","ieee":"H. de Vladar and I. Pen, “Determinism, noise, and spurious estimations in a generalised model of population growth,” <i>Physica A</i>, vol. 373. Elsevier, pp. 477–485, 2007.","short":"H. de Vladar, I. Pen, Physica A 373 (2007) 477–485.","ama":"de Vladar H, Pen I. Determinism, noise, and spurious estimations in a generalised model of population growth. <i>Physica A</i>. 2007;373:477-485. doi:<a href=\"https://doi.org/10.1016/j.physa.2006.06.025\">10.1016/j.physa.2006.06.025</a>","mla":"de Vladar, Harold, and I. Pen. “Determinism, Noise, and Spurious Estimations in a Generalised Model of Population Growth.” <i>Physica A</i>, vol. 373, Elsevier, 2007, pp. 477–85, doi:<a href=\"https://doi.org/10.1016/j.physa.2006.06.025\">10.1016/j.physa.2006.06.025</a>.","apa":"de Vladar, H., &#38; Pen, I. (2007). Determinism, noise, and spurious estimations in a generalised model of population growth. <i>Physica A</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.physa.2006.06.025\">https://doi.org/10.1016/j.physa.2006.06.025</a>"},"volume":373,"status":"public","day":"01","_id":"4234","date_created":"2018-12-11T12:07:45Z","doi":"10.1016/j.physa.2006.06.025","publication_status":"published","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/q-bio/0602018"}],"publication":"Physica A","oa_version":"Preprint"},{"year":"2007","publist_id":"1856","page":"611 - 619","author":[{"first_name":"Andrew","last_name":"Free","full_name":"Free, Andrew"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Nicholas Barton"}],"title":"Do evolution and ecology need the Gaia hypothesis?","issue":"11","date_updated":"2021-01-12T07:55:35Z","publisher":"Cell Press","date_published":"2007-11-01T00:00:00Z","month":"11","intvolume":"        22","publication":"Trends in Ecology and Evolution","publication_status":"published","doi":"10.1016/j.tree.2007.07.007","status":"public","quality_controlled":0,"day":"01","_id":"4246","date_created":"2018-12-11T12:07:49Z","abstract":[{"lang":"eng","text":"Gaia theory, which describes the life–environment system of the Earth as stable and self-regulating, has remained at the fringes of mainstream biological science owing to its historically inadequate definition and apparent incompatibility with individual-level natural selection. The key issue is whether and why the biosphere might tend towards stability and self-regulation. We review the various ways in which these issues have been addressed by evolutionary and ecological theory, and relate these to ‘Gaia theory’. We then ask how this theory extends the perspectives offered by these disciplines, and how it might be tested by novel modelling approaches and laboratory experiments using emergent technologies."}],"type":"journal_article","volume":22,"citation":{"mla":"Free, Andrew, and Nicholas H. Barton. “Do Evolution and Ecology Need the Gaia Hypothesis?” <i>Trends in Ecology and Evolution</i>, vol. 22, no. 11, Cell Press, 2007, pp. 611–19, doi:<a href=\"https://doi.org/10.1016/j.tree.2007.07.007\">10.1016/j.tree.2007.07.007</a>.","apa":"Free, A., &#38; Barton, N. H. (2007). Do evolution and ecology need the Gaia hypothesis? <i>Trends in Ecology and Evolution</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tree.2007.07.007\">https://doi.org/10.1016/j.tree.2007.07.007</a>","chicago":"Free, Andrew, and Nicholas H Barton. “Do Evolution and Ecology Need the Gaia Hypothesis?” <i>Trends in Ecology and Evolution</i>. Cell Press, 2007. <a href=\"https://doi.org/10.1016/j.tree.2007.07.007\">https://doi.org/10.1016/j.tree.2007.07.007</a>.","short":"A. Free, N.H. Barton, Trends in Ecology and Evolution 22 (2007) 611–619.","ista":"Free A, Barton NH. 2007. Do evolution and ecology need the Gaia hypothesis? Trends in Ecology and Evolution. 22(11), 611–619.","ieee":"A. Free and N. H. Barton, “Do evolution and ecology need the Gaia hypothesis?,” <i>Trends in Ecology and Evolution</i>, vol. 22, no. 11. Cell Press, pp. 611–619, 2007.","ama":"Free A, Barton NH. Do evolution and ecology need the Gaia hypothesis? <i>Trends in Ecology and Evolution</i>. 2007;22(11):611-619. doi:<a href=\"https://doi.org/10.1016/j.tree.2007.07.007\">10.1016/j.tree.2007.07.007</a>"},"extern":1},{"year":"2007","page":"207 - 226","publist_id":"1857","date_updated":"2021-01-12T07:55:35Z","issue":"2","author":[{"last_name":"Gardner","first_name":"Andy","full_name":"Gardner, Andy"},{"first_name":"Stuart","last_name":"West","full_name":"West, Stuart A"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Nicholas Barton"}],"title":"The relation between multilocus population genetics and social evolution theory","intvolume":"       169","month":"02","date_published":"2007-02-01T00:00:00Z","publisher":"University of Chicago Press","doi":"10.1086/510602","publication_status":"published","publication":"American Naturalist","_id":"4247","date_created":"2018-12-11T12:07:50Z","day":"01","status":"public","quality_controlled":0,"citation":{"apa":"Gardner, A., West, S., &#38; Barton, N. H. (2007). The relation between multilocus population genetics and social evolution theory. <i>American Naturalist</i>. University of Chicago Press. <a href=\"https://doi.org/10.1086/510602\">https://doi.org/10.1086/510602</a>","mla":"Gardner, Andy, et al. “The Relation between Multilocus Population Genetics and Social Evolution Theory.” <i>American Naturalist</i>, vol. 169, no. 2, University of Chicago Press, 2007, pp. 207–26, doi:<a href=\"https://doi.org/10.1086/510602\">10.1086/510602</a>.","ieee":"A. Gardner, S. West, and N. H. Barton, “The relation between multilocus population genetics and social evolution theory,” <i>American Naturalist</i>, vol. 169, no. 2. University of Chicago Press, pp. 207–226, 2007.","ista":"Gardner A, West S, Barton NH. 2007. The relation between multilocus population genetics and social evolution theory. American Naturalist. 169(2), 207–226.","short":"A. Gardner, S. West, N.H. Barton, American Naturalist 169 (2007) 207–226.","ama":"Gardner A, West S, Barton NH. The relation between multilocus population genetics and social evolution theory. <i>American Naturalist</i>. 2007;169(2):207-226. doi:<a href=\"https://doi.org/10.1086/510602\">10.1086/510602</a>","chicago":"Gardner, Andy, Stuart West, and Nicholas H Barton. “The Relation between Multilocus Population Genetics and Social Evolution Theory.” <i>American Naturalist</i>. University of Chicago Press, 2007. <a href=\"https://doi.org/10.1086/510602\">https://doi.org/10.1086/510602</a>."},"extern":1,"volume":169,"type":"journal_article","abstract":[{"lang":"eng","text":"Evolution at multiple gene positions is complicated. Direct selection on one gene disturbs the evolutionary dynamics of associated genes. Recent years have seen the development of a multilocus methodology for modeling evolution at arbitrary numbers of gene positions with arbitrary dominance and epistatic relations, mode of inheritance, genetic linkage, and recombination. We show that the approach is conceptually analogous to social evolutionary methodology, which focuses on selection acting on associated individuals. In doing so, we (1) make explicit the links between the multilocus methodology and the foundations of social evolution theory, namely, Price’s theorem and Hamilton’s rule; (2) relate the multilocus approach to levels‐of‐selection and neighbor‐modulated‐fitness approaches in social evolution; (3) highlight the equivalence between genetical hitchhiking and kin selection; (4) demonstrate that the multilocus methodology allows for social evolutionary analyses involving coevolution of multiple traits and genetical associations between nonrelatives, including individuals of different species; (5) show that this methodology helps solve problems of dynamic sufficiency in social evolution theory; (6) form links between invasion criteria in multilocus systems and Hamilton’s rule of kin selection; (7) illustrate the generality and exactness of Hamilton’s rule, which has previously been described as an approximate, heuristic result."}]},{"date_updated":"2021-01-12T07:56:16Z","title":"Library 2.0 and User-Generated Content - What can the users do for us?","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Danowski, Patrick","orcid":"0000-0002-6026-4409","last_name":"Danowski","first_name":"Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2007-05-25T00:00:00Z","month":"05","publisher":"IFLA","language":[{"iso":"eng"}],"year":"2007","conference":{"end_date":"2007-08-23","start_date":"2007-08-19","name":"WLIC: World Library and Information Congress","location":"Durban, South Africa"},"publist_id":"1232","_id":"4342","date_created":"2018-12-11T12:08:22Z","day":"25","status":"public","citation":{"ama":"Danowski P. Library 2.0 and User-Generated Content - What can the users do for us? In: IFLA; 2007. doi:<a href=\"https://doi.org/601\">601</a>","ieee":"P. Danowski, “Library 2.0 and User-Generated Content - What can the users do for us?,” presented at the WLIC: World Library and Information Congress, Durban, South Africa, 2007.","short":"P. Danowski, in:, IFLA, 2007.","ista":"Danowski P. 2007. Library 2.0 and User-Generated Content - What can the users do for us? WLIC: World Library and Information Congress.","chicago":"Danowski, Patrick. “Library 2.0 and User-Generated Content - What Can the Users Do for Us?” IFLA, 2007. <a href=\"https://doi.org/601\">https://doi.org/601</a>.","apa":"Danowski, P. (2007). Library 2.0 and User-Generated Content - What can the users do for us? Presented at the WLIC: World Library and Information Congress, Durban, South Africa: IFLA. <a href=\"https://doi.org/601\">https://doi.org/601</a>","mla":"Danowski, Patrick. <i>Library 2.0 and User-Generated Content - What Can the Users Do for Us?</i> IFLA, 2007, doi:<a href=\"https://doi.org/601\">601</a>."},"extern":"1","abstract":[{"text":"Library 2.0 and user-generated content are two terms, which are closely connected. In the\r\n\r\npresentation, I will briefly define both terms. Two example projects where user- generated content and libraries interact will be presented. The cooperation of Wikipedia and the Personennamendatei, the German cooperative name authority files is the first. The second will be Wikisource where users provide transcribed source material. Another important area of user-generated content is social tagging where users index different resources. And if the users will do so much in the future, is there still a place for librarians? But in the future user\r\n\r\nand librarians become partners and the library will provide the platform: the library 2.0.","lang":"eng"}],"type":"conference","oa_version":"None","doi":"601","publication_status":"published","main_file_link":[{"url":"http://www.ifla.org/IV/ifla73/papers/113-Danowski-en.pdf"}]},{"publication":"Bibliothek - Forschung Und Praxis","doi":"485","publication_status":"published","type":"journal_article","volume":31,"extern":1,"citation":{"chicago":"Danowski, Patrick, and Barbara Pfeifer. “Wikipedia Und Normdateien: Wege Der Vernetzung Am Beispiel Der Kooperation Mit Der Personennamendatei.” <i>Bibliothek - Forschung Und Praxis</i>. De Gruyter, 2007. <a href=\"https://doi.org/485\">https://doi.org/485</a>.","ama":"Danowski P, Pfeifer B. Wikipedia und Normdateien: Wege der Vernetzung am Beispiel der Kooperation mit der Personennamendatei. <i>Bibliothek - Forschung Und Praxis</i>. 2007;31(2):149-155. doi:<a href=\"https://doi.org/485\">485</a>","short":"P. Danowski, B. Pfeifer, Bibliothek - Forschung Und Praxis 31 (2007) 149–155.","ista":"Danowski P, Pfeifer B. 2007. Wikipedia und Normdateien: Wege der Vernetzung am Beispiel der Kooperation mit der Personennamendatei. Bibliothek - Forschung Und Praxis. 31(2), 149–155.","ieee":"P. Danowski and B. Pfeifer, “Wikipedia und Normdateien: Wege der Vernetzung am Beispiel der Kooperation mit der Personennamendatei,” <i>Bibliothek - Forschung Und Praxis</i>, vol. 31, no. 2. De Gruyter, pp. 149–155, 2007.","mla":"Danowski, Patrick, and Barbara Pfeifer. “Wikipedia Und Normdateien: Wege Der Vernetzung Am Beispiel Der Kooperation Mit Der Personennamendatei.” <i>Bibliothek - Forschung Und Praxis</i>, vol. 31, no. 2, De Gruyter, 2007, pp. 149–55, doi:<a href=\"https://doi.org/485\">485</a>.","apa":"Danowski, P., &#38; Pfeifer, B. (2007). Wikipedia und Normdateien: Wege der Vernetzung am Beispiel der Kooperation mit der Personennamendatei. <i>Bibliothek - Forschung Und Praxis</i>. De Gruyter. <a href=\"https://doi.org/485\">https://doi.org/485</a>"},"quality_controlled":0,"day":"01","status":"public","date_created":"2018-12-11T12:08:22Z","_id":"4343","publist_id":"1231","page":"149 - 155","year":"2007","publisher":"De Gruyter","date_published":"2007-01-01T00:00:00Z","month":"01","intvolume":"        31","title":"Wikipedia und Normdateien: Wege der Vernetzung am Beispiel der Kooperation mit der Personennamendatei","author":[{"first_name":"Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","last_name":"Danowski","orcid":"0000-0002-6026-4409","full_name":"Patrick Danowski"},{"full_name":"Pfeifer,Barbara","last_name":"Pfeifer","first_name":"Barbara"}],"issue":"2","date_updated":"2021-01-12T07:56:17Z"},{"citation":{"mla":"Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 ? Wird Alles Anders?” <i>Bibliothek - Forschung Und Praxis</i>, vol. 31, no. 2007, De Gruyter, 2007, pp. 130–36, doi:<a href=\"https://doi.org/45\">45</a>.","apa":"Danowski, P., &#38; Heller, L. (2007). Bibliothek 2.0 ? Wird alles anders? <i>Bibliothek - Forschung Und Praxis</i>. De Gruyter. <a href=\"https://doi.org/45\">https://doi.org/45</a>","chicago":"Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 ? Wird Alles Anders?” <i>Bibliothek - Forschung Und Praxis</i>. De Gruyter, 2007. <a href=\"https://doi.org/45\">https://doi.org/45</a>.","short":"P. Danowski, L. Heller, Bibliothek - Forschung Und Praxis 31 (2007) 130–136.","ieee":"P. Danowski and L. Heller, “Bibliothek 2.0 ? Wird alles anders?,” <i>Bibliothek - Forschung Und Praxis</i>, vol. 31, no. 2007. De Gruyter, pp. 130–136, 2007.","ista":"Danowski P, Heller L. 2007. Bibliothek 2.0 ? Wird alles anders? Bibliothek - Forschung Und Praxis. 31(2007), 130–136.","ama":"Danowski P, Heller L. Bibliothek 2.0 ? Wird alles anders? <i>Bibliothek - Forschung Und Praxis</i>. 2007;31(2007):130-136. doi:<a href=\"https://doi.org/45\">45</a>"},"extern":1,"volume":31,"type":"journal_article","_id":"4344","date_created":"2018-12-11T12:08:22Z","day":"01","status":"public","quality_controlled":0,"publication_status":"published","main_file_link":[{"url":"http://www.bibliothek-saur.de/2007_2/130-136.pdf","open_access":"0"}],"doi":"45","publication":"Bibliothek - Forschung Und Praxis","intvolume":"        31","month":"01","date_published":"2007-01-01T00:00:00Z","publisher":"De Gruyter","date_updated":"2021-01-12T07:56:17Z","issue":"2007","title":"Bibliothek 2.0 ? Wird alles anders?","author":[{"first_name":"Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","last_name":"Danowski","orcid":"0000-0002-6026-4409","full_name":"Patrick Danowski"},{"last_name":"Heller","first_name":"Lambert","full_name":"Heller,Lambert"}],"page":"130 - 136","publist_id":"1230","year":"2007"},{"date_created":"2018-12-11T12:08:25Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"4353","quality_controlled":0,"status":"public","day":"14","citation":{"chicago":"Binladen, Jonas, M Thomas Gilbert, Jonathan P Bollback, Frank Panitz, Christian Bendixen, Rasmus Nielsen, and Eske Willerslev. “The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple Homolog Amplification Products by 454 Parallel Sequencing.” <i>PLoS One</i>. Public Library of Science, 2007. <a href=\"https://doi.org/10.1371/journal.pone.0000197\">https://doi.org/10.1371/journal.pone.0000197</a>.","short":"J. Binladen, M.T. Gilbert, J.P. Bollback, F. Panitz, C. Bendixen, R. Nielsen, E. Willerslev, PLoS One 2 (2007).","ieee":"J. Binladen <i>et al.</i>, “The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing,” <i>PLoS One</i>, vol. 2, no. 2. Public Library of Science, 2007.","ista":"Binladen J, Gilbert MT, Bollback JP, Panitz F, Bendixen C, Nielsen R, Willerslev E. 2007. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One. 2(2).","ama":"Binladen J, Gilbert MT, Bollback JP, et al. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. <i>PLoS One</i>. 2007;2(2). doi:<a href=\"https://doi.org/10.1371/journal.pone.0000197\">10.1371/journal.pone.0000197</a>","mla":"Binladen, Jonas, et al. “The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple Homolog Amplification Products by 454 Parallel Sequencing.” <i>PLoS One</i>, vol. 2, no. 2, Public Library of Science, 2007, doi:<a href=\"https://doi.org/10.1371/journal.pone.0000197\">10.1371/journal.pone.0000197</a>.","apa":"Binladen, J., Gilbert, M. T., Bollback, J. P., Panitz, F., Bendixen, C., Nielsen, R., &#38; Willerslev, E. (2007). The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0000197\">https://doi.org/10.1371/journal.pone.0000197</a>"},"extern":1,"volume":2,"type":"journal_article","abstract":[{"text":"BACKGROUND: The invention of the Genome Sequence 20 DNA Sequencing System (454 parallel sequencing platform) has enabled the rapid and high-volume production of sequence data. Until now, however, individual emulsion PCR (emPCR) reactions and subsequent sequencing runs have been unable to combine template DNA from multiple individuals, as homologous sequences cannot be subsequently assigned to their original sources. METHODOLOGY: We use conventional PCR with 5'-nucleotide tagged primers to generate homologous DNA amplification products from multiple specimens, followed by sequencing through the high-throughput Genome Sequence 20 DNA Sequencing System (GS20, Roche/454 Life Sciences). Each DNA sequence is subsequently traced back to its individual source through 5'tag-analysis. CONCLUSIONS: We demonstrate that this new approach enables the assignment of virtually all the generated DNA sequences to the correct source once sequencing anomalies are accounted for (miss-assignment rate&amp;lt;0.4%). Therefore, the method enables accurate sequencing and assignment of homologous DNA sequences from multiple sources in single high-throughput GS20 run. We observe a bias in the distribution of the differently tagged primers that is dependent on the 5' nucleotide of the tag. In particular, primers 5' labelled with a cytosine are heavily overrepresented among the final sequences, while those 5' labelled with a thymine are strongly underrepresented. A weaker bias also exists with regards to the distribution of the sequences as sorted by the second nucleotide of the dinucleotide tags. As the results are based on a single GS20 run, the general applicability of the approach requires confirmation. However, our experiments demonstrate that 5'primer tagging is a useful method in which the sequencing power of the GS20 can be applied to PCR-based assays of multiple homologous PCR products. The new approach will be of value to a broad range of research areas, such as those of comparative genomics, complete mitochondrial analyses, population genetics, and phylogenetics.","lang":"eng"}],"publication_status":"published","doi":"10.1371/journal.pone.0000197","publication":"PLoS One","date_updated":"2021-01-12T07:56:21Z","issue":"2","title":"The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing","author":[{"full_name":"Binladen, Jonas","last_name":"Binladen","first_name":"Jonas"},{"full_name":"Gilbert, M Thomas","last_name":"Gilbert","first_name":"M Thomas"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","last_name":"Bollback","orcid":"0000-0002-4624-4612","full_name":"Jonathan Bollback"},{"first_name":"Frank","last_name":"Panitz","full_name":"Panitz, Frank"},{"full_name":"Bendixen, Christian","last_name":"Bendixen","first_name":"Christian"},{"full_name":"Nielsen, Rasmus","first_name":"Rasmus","last_name":"Nielsen"},{"first_name":"Eske","last_name":"Willerslev","full_name":"Willerslev, Eske"}],"intvolume":"         2","month":"02","date_published":"2007-02-14T00:00:00Z","publisher":"Public Library of Science","acknowledgement":"JB and EW were supported by the Wellcome Trust, UK, the Carlsberg Foundation, DK, and the National Science Foundation, DK. MTPG acknowledges the Marie Curie Actions FP6-MEIF-CT-2005-025002 ‘FORMAPLEX’ grant for funding his research. JPB and RN were funded by the Danish FSS and the National Science Foundation, DK. None of the sponsors or funders have had any influence on the data or manuscript presented here.","year":"2007","publist_id":"1105"},{"day":"01","quality_controlled":0,"status":"public","date_created":"2018-12-11T12:08:25Z","_id":"4354","type":"journal_article","abstract":[{"lang":"eng","text":"Homology search is one of the most ubiquitous bioinformatic tasks, yet it is unknown how effective the currently available tools are for identifying noncoding RNAs (ncRNAs). In this work, we use reliable ncRNA data sets to assess the effectiveness of methods such as BLAST, FASTA, HMMer, and Infernal. Surprisingly, the most popular homology search methods are often the least accurate. As a result, many studies have used inappropriate tools for their analyses. On the basis of our results, we suggest homology search strategies using the currently available tools and some directions for future development."}],"extern":1,"citation":{"ista":"Freyhult E, Bollback JP, Gardner P. 2007. Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Research. 17(1), 117–25.","short":"E. Freyhult, J.P. Bollback, P. Gardner, Genome Research 17 (2007) 117–25.","ieee":"E. Freyhult, J. P. Bollback, and P. Gardner, “Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA,” <i>Genome Research</i>, vol. 17, no. 1. Cold Spring Harbor Laboratory Press, pp. 117–25, 2007.","ama":"Freyhult E, Bollback JP, Gardner P. Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. <i>Genome Research</i>. 2007;17(1):117-125. doi:<a href=\"https://doi.org/10.1101/gr.5890907\">10.1101/gr.5890907</a>","chicago":"Freyhult, Eva, Jonathan P Bollback, and Paul Gardner. “Exploring Genomic Dark Matter: A Critical Assessment of the Performance of Homology Search Methods on Noncoding RNA.” <i>Genome Research</i>. Cold Spring Harbor Laboratory Press, 2007. <a href=\"https://doi.org/10.1101/gr.5890907\">https://doi.org/10.1101/gr.5890907</a>.","apa":"Freyhult, E., Bollback, J. P., &#38; Gardner, P. (2007). Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. <i>Genome Research</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gr.5890907\">https://doi.org/10.1101/gr.5890907</a>","mla":"Freyhult, Eva, et al. “Exploring Genomic Dark Matter: A Critical Assessment of the Performance of Homology Search Methods on Noncoding RNA.” <i>Genome Research</i>, vol. 17, no. 1, Cold Spring Harbor Laboratory Press, 2007, pp. 117–25, doi:<a href=\"https://doi.org/10.1101/gr.5890907\">10.1101/gr.5890907</a>."},"volume":17,"publication_status":"published","main_file_link":[{"open_access":"0","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716261"}],"doi":"10.1101/gr.5890907","publication":"Genome Research","issue":"1","author":[{"last_name":"Freyhult","first_name":"Eva","full_name":"Freyhult, Eva K"},{"full_name":"Jonathan Bollback","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","orcid":"0000-0002-4624-4612"},{"full_name":"Gardner, Paul P","last_name":"Gardner","first_name":"Paul"}],"title":"Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA","date_updated":"2021-01-12T07:56:21Z","publisher":"Cold Spring Harbor Laboratory Press","month":"01","intvolume":"        17","date_published":"2007-01-01T00:00:00Z","year":"2007","publist_id":"1106","page":"117 - 25"},{"year":"2007","page":"1397 - 1406","publist_id":"1104","date_updated":"2021-01-12T07:56:22Z","title":"Clonal interference is alleviated by high mutation rates in large populations","author":[{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","last_name":"Bollback","full_name":"Jonathan Bollback"},{"full_name":"Huelsenbeck, John P","last_name":"Huelsenbeck","first_name":"John"}],"issue":"6","date_published":"2007-03-22T00:00:00Z","month":"03","intvolume":"        24","publisher":"Oxford University Press","acknowledgement":"R01 GM069801-08/GM/NIGMS NIH HHS/United States","publication":"Molecular Biology and Evolution","doi":"10.1093/molbev/msm056","publication_status":"published","_id":"4355","date_created":"2018-12-11T12:08:26Z","quality_controlled":0,"status":"public","day":"22","volume":24,"extern":1,"citation":{"mla":"Bollback, Jonathan P., and John Huelsenbeck. “Clonal Interference Is Alleviated by High Mutation Rates in Large Populations.” <i>Molecular Biology and Evolution</i>, vol. 24, no. 6, Oxford University Press, 2007, pp. 1397–406, doi:<a href=\"https://doi.org/10.1093/molbev/msm056\">10.1093/molbev/msm056</a>.","apa":"Bollback, J. P., &#38; Huelsenbeck, J. (2007). Clonal interference is alleviated by high mutation rates in large populations. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msm056\">https://doi.org/10.1093/molbev/msm056</a>","chicago":"Bollback, Jonathan P, and John Huelsenbeck. “Clonal Interference Is Alleviated by High Mutation Rates in Large Populations.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2007. <a href=\"https://doi.org/10.1093/molbev/msm056\">https://doi.org/10.1093/molbev/msm056</a>.","ama":"Bollback JP, Huelsenbeck J. Clonal interference is alleviated by high mutation rates in large populations. <i>Molecular Biology and Evolution</i>. 2007;24(6):1397-1406. doi:<a href=\"https://doi.org/10.1093/molbev/msm056\">10.1093/molbev/msm056</a>","short":"J.P. Bollback, J. Huelsenbeck, Molecular Biology and Evolution 24 (2007) 1397–1406.","ieee":"J. P. Bollback and J. Huelsenbeck, “Clonal interference is alleviated by high mutation rates in large populations,” <i>Molecular Biology and Evolution</i>, vol. 24, no. 6. Oxford University Press, pp. 1397–1406, 2007.","ista":"Bollback JP, Huelsenbeck J. 2007. Clonal interference is alleviated by high mutation rates in large populations. Molecular Biology and Evolution. 24(6), 1397–1406."},"abstract":[{"text":"When a beneficial mutation is fixed in a population that lacks recombination, the genetic background linked to that mutation is fixed. As a result, beneficial mutations on different backgrounds experience competition, or &quot;clonal interference,&quot; that can cause asexual populations to evolve more slowly than their sexual counterparts. Factors such as a large population size (N) and high mutation rates (mu) increase the number of competing beneficial mutations, and hence are expected to increase the intensity of clonal interference. However, recent theory suggests that, with very large values of Nmu, the severity of clonal interference may instead decline. The reason is that, with large Nmu, genomes including both beneficial mutations are rapidly created by recurrent mutation, obviating the need for recombination. Here, we analyze data from experimentally evolved asexual populations of a bacteriophage and find that, in these nonrecombining populations with very large Nmu, recurrent mutation does appear to ameliorate this cost of asexuality.","lang":"eng"}],"type":"journal_article"},{"issue":"9","title":"Genes under positive selection in Escherichia coli","author":[{"full_name":"Petersen, Lise","last_name":"Petersen","first_name":"Lise"},{"orcid":"0000-0002-4624-4612","last_name":"Bollback","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Jonathan Bollback"},{"full_name":"Dimmic, Matt","first_name":"Matt","last_name":"Dimmic"},{"first_name":"Melissa","last_name":"Hubisz","full_name":"Hubisz, Melissa"},{"full_name":"Nielsen, Rasmus","last_name":"Nielsen","first_name":"Rasmus"}],"date_updated":"2021-01-12T07:56:22Z","publisher":"Cold Spring Harbor Laboratory Press","month":"08","intvolume":"        17","date_published":"2007-08-03T00:00:00Z","year":"2007","publist_id":"1103","page":"1336 - 1343","day":"03","quality_controlled":0,"status":"public","_id":"4356","date_created":"2018-12-11T12:08:26Z","type":"journal_article","abstract":[{"lang":"eng","text":"We used a comparative genomics approach to identify genes that are under positive selection in six strains of Escherichia coli and Shigella flexneri, including five strains that are human pathogens. We find that positive selection targets a wide range of different functions in the E. coli genome, including cell surface proteins such as beta barrel porins, presumably because of the involvement of these genes in evolutionary arms races with other bacteria, phages, and/or the host immune system. Structural mapping of positively selected sites on trans-membrane beta barrel porins reveals that the residues under positive selection occur almost exclusively in the extracellular region of the proteins that are enriched with sites known to be targets of phages, colicins, or the host immune system. More surprisingly, we also find a number of other categories of genes that show very strong evidence for positive selection, such as the enigmatic rhs elements and transposases. Based on structural evidence, we hypothesize that the selection acting on transposases is related to the genomic conflict between transposable elements and the host genome."}],"extern":1,"citation":{"mla":"Petersen, Lise, et al. “Genes under Positive Selection in Escherichia Coli.” <i>Genome Research</i>, vol. 17, no. 9, Cold Spring Harbor Laboratory Press, 2007, pp. 1336–43, doi:<a href=\"https://doi.org/10.1101/gr.6254707\">10.1101/gr.6254707</a>.","apa":"Petersen, L., Bollback, J. P., Dimmic, M., Hubisz, M., &#38; Nielsen, R. (2007). Genes under positive selection in Escherichia coli. <i>Genome Research</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gr.6254707\">https://doi.org/10.1101/gr.6254707</a>","chicago":"Petersen, Lise, Jonathan P Bollback, Matt Dimmic, Melissa Hubisz, and Rasmus Nielsen. “Genes under Positive Selection in Escherichia Coli.” <i>Genome Research</i>. Cold Spring Harbor Laboratory Press, 2007. <a href=\"https://doi.org/10.1101/gr.6254707\">https://doi.org/10.1101/gr.6254707</a>.","ista":"Petersen L, Bollback JP, Dimmic M, Hubisz M, Nielsen R. 2007. Genes under positive selection in Escherichia coli. Genome Research. 17(9), 1336–1343.","short":"L. Petersen, J.P. Bollback, M. Dimmic, M. Hubisz, R. Nielsen, Genome Research 17 (2007) 1336–1343.","ieee":"L. Petersen, J. P. Bollback, M. Dimmic, M. Hubisz, and R. Nielsen, “Genes under positive selection in Escherichia coli,” <i>Genome Research</i>, vol. 17, no. 9. Cold Spring Harbor Laboratory Press, pp. 1336–1343, 2007.","ama":"Petersen L, Bollback JP, Dimmic M, Hubisz M, Nielsen R. Genes under positive selection in Escherichia coli. <i>Genome Research</i>. 2007;17(9):1336-1343. doi:<a href=\"https://doi.org/10.1101/gr.6254707\">10.1101/gr.6254707</a>"},"volume":17,"doi":"10.1101/gr.6254707","publication_status":"published","publication":"Genome Research"},{"publist_id":"1089","conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"page":"304 - 319","year":"2007","publisher":"Springer","alternative_title":["LNCS"],"date_published":"2007-09-20T00:00:00Z","month":"09","title":"AMT: a property-based monitoring tool for analog systems","author":[{"full_name":"Dejan Nickovic","last_name":"Nickovic","first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Maler, Oded","first_name":"Oded","last_name":"Maler"}],"date_updated":"2021-01-12T07:56:27Z","publication_status":"published","doi":"1567","type":"conference","citation":{"apa":"Nickovic, D., &#38; Maler, O. (2007). AMT: a property-based monitoring tool for analog systems (pp. 304–319). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Springer. <a href=\"https://doi.org/1567\">https://doi.org/1567</a>","mla":"Nickovic, Dejan, and Oded Maler. <i>AMT: A Property-Based Monitoring Tool for Analog Systems</i>. Springer, 2007, pp. 304–19, doi:<a href=\"https://doi.org/1567\">1567</a>.","ama":"Nickovic D, Maler O. AMT: a property-based monitoring tool for analog systems. In: Springer; 2007:304-319. doi:<a href=\"https://doi.org/1567\">1567</a>","ista":"Nickovic D, Maler O. 2007. AMT: a property-based monitoring tool for analog systems. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, , 304–319.","short":"D. Nickovic, O. Maler, in:, Springer, 2007, pp. 304–319.","ieee":"D. Nickovic and O. Maler, “AMT: a property-based monitoring tool for analog systems,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2007, pp. 304–319.","chicago":"Nickovic, Dejan, and Oded Maler. “AMT: A Property-Based Monitoring Tool for Analog Systems,” 304–19. Springer, 2007. <a href=\"https://doi.org/1567\">https://doi.org/1567</a>."},"extern":1,"quality_controlled":0,"status":"public","day":"20","_id":"4368","date_created":"2018-12-11T12:08:30Z"},{"publication_status":"published","doi":"1568","day":"01","status":"public","quality_controlled":0,"_id":"4370","date_created":"2018-12-11T12:08:30Z","type":"conference","citation":{"ama":"Maler O, Nickovic D, Pnueli A. On synthesizing controllers from bounded-response properties. In: Springer; 2007:95-107. doi:<a href=\"https://doi.org/1568\">1568</a>","ista":"Maler O, Nickovic D, Pnueli A. 2007. On synthesizing controllers from bounded-response properties. CAV: Computer Aided Verification, Lecture Notes in Computer Science, , 95–107.","short":"O. Maler, D. Nickovic, A. Pnueli, in:, Springer, 2007, pp. 95–107.","ieee":"O. Maler, D. Nickovic, and A. Pnueli, “On synthesizing controllers from bounded-response properties,” presented at the CAV: Computer Aided Verification, 2007, pp. 95–107.","chicago":"Maler, Oded, Dejan Nickovic, and Amir Pnueli. “On Synthesizing Controllers from Bounded-Response Properties,” 95–107. Springer, 2007. <a href=\"https://doi.org/1568\">https://doi.org/1568</a>.","apa":"Maler, O., Nickovic, D., &#38; Pnueli, A. (2007). On synthesizing controllers from bounded-response properties (pp. 95–107). Presented at the CAV: Computer Aided Verification, Springer. <a href=\"https://doi.org/1568\">https://doi.org/1568</a>","mla":"Maler, Oded, et al. <i>On Synthesizing Controllers from Bounded-Response Properties</i>. Springer, 2007, pp. 95–107, doi:<a href=\"https://doi.org/1568\">1568</a>."},"extern":1,"year":"2007","conference":{"name":"CAV: Computer Aided Verification"},"publist_id":"1086","page":"95 - 107","author":[{"full_name":"Maler, Oded","first_name":"Oded","last_name":"Maler"},{"last_name":"Nickovic","first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","full_name":"Dejan Nickovic"},{"full_name":"Pnueli,Amir","last_name":"Pnueli","first_name":"Amir"}],"title":"On synthesizing controllers from bounded-response properties","date_updated":"2021-01-12T07:56:28Z","publisher":"Springer","date_published":"2007-01-01T00:00:00Z","alternative_title":["Lecture Notes in Computer Science"],"month":"01"},{"date_updated":"2021-01-12T07:56:39Z","title":"Using First-Order Theorem Provers in the Jahob Data Structure Verification System","author":[{"first_name":"Charles","last_name":"Bouillaguet","full_name":"Bouillaguet,Charles"},{"full_name":"Kuncak, Viktor","last_name":"Kuncak","first_name":"Viktor"},{"full_name":"Thomas Wies","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Wies"},{"full_name":"Zee,Karen","last_name":"Zee","first_name":"Karen"},{"full_name":"Rinard,Martin C.","last_name":"Rinard","first_name":"Martin"}],"date_published":"2007-01-01T00:00:00Z","alternative_title":["LNCS 4349"],"month":"01","publisher":"Springer","year":"2007","page":"74 - 88","conference":{"name":"VMCAI: Verification, Model Checking and Abstract Interpretation"},"publist_id":"1062","_id":"4394","date_created":"2018-12-11T12:08:37Z","status":"public","day":"01","quality_controlled":0,"citation":{"ama":"Bouillaguet C, Kuncak V, Wies T, Zee K, Rinard M. Using First-Order Theorem Provers in the Jahob Data Structure Verification System. In: Springer; 2007:74-88. doi:<a href=\"https://doi.org/1552\">1552</a>","ieee":"C. Bouillaguet, V. Kuncak, T. Wies, K. Zee, and M. Rinard, “Using First-Order Theorem Provers in the Jahob Data Structure Verification System,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, 2007, pp. 74–88.","ista":"Bouillaguet C, Kuncak V, Wies T, Zee K, Rinard M. 2007. Using First-Order Theorem Provers in the Jahob Data Structure Verification System. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS 4349, , 74–88.","short":"C. Bouillaguet, V. Kuncak, T. Wies, K. Zee, M. Rinard, in:, Springer, 2007, pp. 74–88.","chicago":"Bouillaguet, Charles, Viktor Kuncak, Thomas Wies, Karen Zee, and Martin Rinard. “Using First-Order Theorem Provers in the Jahob Data Structure Verification System,” 74–88. Springer, 2007. <a href=\"https://doi.org/1552\">https://doi.org/1552</a>.","apa":"Bouillaguet, C., Kuncak, V., Wies, T., Zee, K., &#38; Rinard, M. (2007). Using First-Order Theorem Provers in the Jahob Data Structure Verification System (pp. 74–88). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Springer. <a href=\"https://doi.org/1552\">https://doi.org/1552</a>","mla":"Bouillaguet, Charles, et al. <i>Using First-Order Theorem Provers in the Jahob Data Structure Verification System</i>. Springer, 2007, pp. 74–88, doi:<a href=\"https://doi.org/1552\">1552</a>."},"extern":1,"type":"conference","doi":"1552","publication_status":"published"},{"year":"2007","page":"178 - 192","conference":{"name":"CAV: Computer Aided Verification"},"publist_id":"1058","date_updated":"2021-01-12T07:56:40Z","author":[{"last_name":"Berdine","first_name":"Josh","full_name":"Berdine,Josh"},{"full_name":"Calcagno,Cristiano","last_name":"Calcagno","first_name":"Cristiano"},{"last_name":"Cook","first_name":"Byron","full_name":"Cook,Byron"},{"full_name":"Distefano,Dino","first_name":"Dino","last_name":"Distefano"},{"first_name":"Peter","last_name":"O'Hearn","full_name":"O'Hearn,Peter W."},{"full_name":"Thomas Wies","first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","last_name":"Wies"},{"full_name":"Yang,Hongseok","last_name":"Yang","first_name":"Hongseok"}],"title":"Shape Analysis for Composite Data Structures","month":"01","date_published":"2007-01-01T00:00:00Z","alternative_title":["LNCS 4590"],"publisher":"Springer","publication_status":"published","doi":"1553","date_created":"2018-12-11T12:08:39Z","_id":"4398","day":"01","status":"public","quality_controlled":0,"citation":{"short":"J. Berdine, C. Calcagno, B. Cook, D. Distefano, P. O’Hearn, T. Wies, H. Yang, in:, Springer, 2007, pp. 178–192.","ista":"Berdine J, Calcagno C, Cook B, Distefano D, O’Hearn P, Wies T, Yang H. 2007. Shape Analysis for Composite Data Structures. CAV: Computer Aided Verification, LNCS 4590, , 178–192.","ieee":"J. Berdine <i>et al.</i>, “Shape Analysis for Composite Data Structures,” presented at the CAV: Computer Aided Verification, 2007, pp. 178–192.","ama":"Berdine J, Calcagno C, Cook B, et al. Shape Analysis for Composite Data Structures. In: Springer; 2007:178-192. doi:<a href=\"https://doi.org/1553\">1553</a>","chicago":"Berdine, Josh, Cristiano Calcagno, Byron Cook, Dino Distefano, Peter O’Hearn, Thomas Wies, and Hongseok Yang. “Shape Analysis for Composite Data Structures,” 178–92. Springer, 2007. <a href=\"https://doi.org/1553\">https://doi.org/1553</a>.","apa":"Berdine, J., Calcagno, C., Cook, B., Distefano, D., O’Hearn, P., Wies, T., &#38; Yang, H. (2007). Shape Analysis for Composite Data Structures (pp. 178–192). Presented at the CAV: Computer Aided Verification, Springer. <a href=\"https://doi.org/1553\">https://doi.org/1553</a>","mla":"Berdine, Josh, et al. <i>Shape Analysis for Composite Data Structures</i>. Springer, 2007, pp. 178–92, doi:<a href=\"https://doi.org/1553\">1553</a>."},"extern":1,"type":"conference"},{"status":"public","day":"02","quality_controlled":0,"date_created":"2018-12-11T12:08:39Z","_id":"4399","type":"conference","abstract":[{"text":"A temporal interface for a software component is a finite automaton that specifies the legal sequences of calls to functions that are provided by the component. We compare and evaluate three different algorithms for automatically extracting temporal interfaces from program code: (1) a game algorithm that computes the interface as a representation of the most general environment strategy to avoid a safety violation; (2) a learning algorithm that repeatedly queries the program to construct the minimal interface automaton; and (3) a CEGAR algorithm that iteratively refines an abstract interface hypothesis by adding relevant program variables. For comparison purposes, we present and implement the three algorithms in a unifying formal setting. While the three algorithms compute the same output and have similar worst-case complexities, their actual running times may differ considerably for a given input program. On the theoretical side, we provide for each of the three algorithms a family of input programs on which that algorithm outperforms the two alternatives. On the practical side, we evaluate the three algorithms experimentally on a variety of Java libraries. ","lang":"eng"}],"extern":1,"citation":{"mla":"Beyer, Dirk, et al. <i>Algorithms for Interface Synthesis</i>. Vol. 4590, Springer, 2007, pp. 4–19, doi:<a href=\"https://doi.org/10.1007/978-3-540-73368-3_4\">10.1007/978-3-540-73368-3_4</a>.","apa":"Beyer, D., Henzinger, T. A., &#38; Singh, V. (2007). Algorithms for interface synthesis (Vol. 4590, pp. 4–19). Presented at the CAV: Computer Aided Verification, Springer. <a href=\"https://doi.org/10.1007/978-3-540-73368-3_4\">https://doi.org/10.1007/978-3-540-73368-3_4</a>","chicago":"Beyer, Dirk, Thomas A Henzinger, and Vasu Singh. “Algorithms for Interface Synthesis,” 4590:4–19. Springer, 2007. <a href=\"https://doi.org/10.1007/978-3-540-73368-3_4\">https://doi.org/10.1007/978-3-540-73368-3_4</a>.","short":"D. Beyer, T.A. Henzinger, V. Singh, in:, Springer, 2007, pp. 4–19.","ieee":"D. Beyer, T. A. Henzinger, and V. Singh, “Algorithms for interface synthesis,” presented at the CAV: Computer Aided Verification, 2007, vol. 4590, pp. 4–19.","ista":"Beyer D, Henzinger TA, Singh V. 2007. Algorithms for interface synthesis. CAV: Computer Aided Verification, LNCS, vol. 4590, 4–19.","ama":"Beyer D, Henzinger TA, Singh V. Algorithms for interface synthesis. In: Vol 4590. Springer; 2007:4-19. doi:<a href=\"https://doi.org/10.1007/978-3-540-73368-3_4\">10.1007/978-3-540-73368-3_4</a>"},"volume":4590,"publication_status":"published","doi":"10.1007/978-3-540-73368-3_4","author":[{"full_name":"Beyer, Dirk","last_name":"Beyer","first_name":"Dirk"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Thomas Henzinger"},{"full_name":"Vasu Singh","first_name":"Vasu","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","last_name":"Singh"}],"title":"Algorithms for interface synthesis","date_updated":"2021-01-12T07:56:41Z","acknowledgement":"This research was supported in part by the grant SFU/PRG 06-3, and by the Swiss National Science Foundation.","publisher":"Springer","month":"07","intvolume":"      4590","alternative_title":["LNCS"],"date_published":"2007-07-02T00:00:00Z","year":"2007","conference":{"name":"CAV: Computer Aided Verification"},"publist_id":"1059","page":"4 - 19"},{"type":"conference","extern":1,"citation":{"mla":"Alur, Rajeev, et al. <i>Model Checking on Trees with Path Equivalences</i>. Springer, 2007, pp. 664–78, doi:<a href=\"https://doi.org/1544\">1544</a>.","apa":"Alur, R., Cerny, P., &#38; Chaudhuri, S. (2007). Model Checking on Trees with Path Equivalences (pp. 664–678). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Springer. <a href=\"https://doi.org/1544\">https://doi.org/1544</a>","chicago":"Alur, Rajeev, Pavol Cerny, and Swarat Chaudhuri. “Model Checking on Trees with Path Equivalences,” 664–78. Springer, 2007. <a href=\"https://doi.org/1544\">https://doi.org/1544</a>.","ama":"Alur R, Cerny P, Chaudhuri S. Model Checking on Trees with Path Equivalences. In: Springer; 2007:664-678. doi:<a href=\"https://doi.org/1544\">1544</a>","short":"R. Alur, P. Cerny, S. Chaudhuri, in:, Springer, 2007, pp. 664–678.","ista":"Alur R, Cerny P, Chaudhuri S. 2007. Model Checking on Trees with Path Equivalences. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, , 664–678.","ieee":"R. Alur, P. Cerny, and S. Chaudhuri, “Model Checking on Trees with Path Equivalences,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, 2007, pp. 664–678."},"quality_controlled":0,"day":"01","status":"public","date_created":"2018-12-11T12:08:40Z","_id":"4402","doi":"1544","publication_status":"published","publisher":"Springer","date_published":"2007-01-01T00:00:00Z","alternative_title":["LNCS"],"month":"01","author":[{"full_name":"Alur, Rajeev","last_name":"Alur","first_name":"Rajeev"},{"full_name":"Pavol Cerny","first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny"},{"last_name":"Chaudhuri","first_name":"Swarat","full_name":"Chaudhuri,Swarat"}],"title":"Model Checking on Trees with Path Equivalences","date_updated":"2021-01-12T07:56:43Z","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"publist_id":"1055","page":"664 - 678","year":"2007"},{"publisher":"BioMed Central","date_published":"2007-01-08T00:00:00Z","month":"01","intvolume":"         1","title":"Qualitative networks: A symbolic approach to analyze biological signaling networks","author":[{"full_name":"Schaub, Marc A","first_name":"Marc","last_name":"Schaub"},{"full_name":"Thomas Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"},{"first_name":"Jasmin","last_name":"Fisher","full_name":"Fisher, Jasmin"}],"issue":"4","date_updated":"2021-01-12T07:56:44Z","publist_id":"325","year":"2007","abstract":[{"lang":"eng","text":"Background\nA central goal of Systems Biology is to model and analyze biological signaling pathways that interact with one another to form complex networks. Here we introduce Qualitative networks, an extension of Boolean networks. With this framework, we use formal verification methods to check whether a model is consistent with the laboratory experimental observations on which it is based. If the model does not conform to the data, we suggest a revised model and the new hypotheses are tested in-silico.\n\nResults\nWe consider networks in which elements range over a small finite domain allowing more flexibility than Boolean values, and add target functions that allow to model a rich set of behaviors. We propose a symbolic algorithm for analyzing the steady state of these networks, allowing us to scale up to a system consisting of 144 elements and state spaces of approximately 1086 states. We illustrate the usefulness of this approach through a model of the interaction between the Notch and the Wnt signaling pathways in mammalian skin, and its extensive analysis.\n\nConclusion\nWe introduce an approach for constructing computational models of biological systems that extends the framework of Boolean networks and uses formal verification methods for the analysis of the model. This approach can scale to multicellular models of complex pathways, and is therefore a useful tool for the analysis of complex biological systems. The hypotheses formulated during in-silico testing suggest new avenues to explore experimentally. Hence, this approach has the potential to efficiently complement experimental studies in biology."}],"type":"journal_article","volume":1,"citation":{"apa":"Schaub, M., Henzinger, T. A., &#38; Fisher, J. (2007). Qualitative networks: A symbolic approach to analyze biological signaling networks. <i>BMC Systems Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1752-0509-1-4\">https://doi.org/10.1186/1752-0509-1-4</a>","mla":"Schaub, Marc, et al. “Qualitative Networks: A Symbolic Approach to Analyze Biological Signaling Networks.” <i>BMC Systems Biology</i>, vol. 1, no. 4, BioMed Central, 2007, doi:<a href=\"https://doi.org/10.1186/1752-0509-1-4\">10.1186/1752-0509-1-4</a>.","short":"M. Schaub, T.A. Henzinger, J. Fisher, BMC Systems Biology 1 (2007).","ieee":"M. Schaub, T. A. Henzinger, and J. Fisher, “Qualitative networks: A symbolic approach to analyze biological signaling networks,” <i>BMC Systems Biology</i>, vol. 1, no. 4. BioMed Central, 2007.","ista":"Schaub M, Henzinger TA, Fisher J. 2007. Qualitative networks: A symbolic approach to analyze biological signaling networks. BMC Systems Biology. 1(4).","ama":"Schaub M, Henzinger TA, Fisher J. Qualitative networks: A symbolic approach to analyze biological signaling networks. <i>BMC Systems Biology</i>. 2007;1(4). doi:<a href=\"https://doi.org/10.1186/1752-0509-1-4\">10.1186/1752-0509-1-4</a>","chicago":"Schaub, Marc, Thomas A Henzinger, and Jasmin Fisher. “Qualitative Networks: A Symbolic Approach to Analyze Biological Signaling Networks.” <i>BMC Systems Biology</i>. BioMed Central, 2007. <a href=\"https://doi.org/10.1186/1752-0509-1-4\">https://doi.org/10.1186/1752-0509-1-4</a>."},"extern":1,"day":"08","status":"public","quality_controlled":0,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T12:08:41Z","_id":"4405","publication":"BMC Systems Biology","doi":"10.1186/1752-0509-1-4","publication_status":"published","main_file_link":[{"open_access":"0","url":"http://www.biomedcentral.com/1752-0509/1/4"}]}]