[{"author":[{"first_name":"Ulrike","full_name":"Axen, Ulrike","last_name":"Axen"},{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","first_name":"Herbert"}],"_id":"3570","day":"20","date_published":"1998-10-20T00:00:00Z","publication_status":"published","oa_version":"None","page":"223 - 236","abstract":[{"lang":"eng","text":"Visualization of high-dimensional or large geometric data sets is inherently difficult, so we experiment with the use of audio to display the shape and connectivity of these data sets. Sonification is used as both an addition to and a substitution for the visual display. We describe a new algorithm called wave traversal that provides a necessary intermediate step to sonification of the data; it produces an ordered sequence of subsets, called waves, that allows us to map the data to time. In this paper we focus in detail on the mathematics of wave traversal, in particular, how wave traversal can be used as a discrete Morse function."}],"doi":"10.1007/978-3-662-03567-2_17","language":[{"iso":"eng"}],"year":"1998","date_updated":"2022-08-29T12:47:32Z","publisher":"Springer","status":"public","type":"book_chapter","month":"10","publication_identifier":{"isbn":["9783662035672"]},"publist_id":"2815","quality_controlled":"1","publication":"Mathematical Visualization","title":"Auditory Morse analysis of triangulated manifolds","date_created":"2018-12-11T12:04:01Z","citation":{"chicago":"Axen, Ulrike, and Herbert Edelsbrunner. “Auditory Morse Analysis of Triangulated Manifolds.” In <i>Mathematical Visualization</i>, 223–36. Springer, 1998. <a href=\"https://doi.org/10.1007/978-3-662-03567-2_17\">https://doi.org/10.1007/978-3-662-03567-2_17</a>.","ieee":"U. Axen and H. Edelsbrunner, “Auditory Morse analysis of triangulated manifolds,” in <i>Mathematical Visualization</i>, Springer, 1998, pp. 223–236.","ista":"Axen U, Edelsbrunner H. 1998.Auditory Morse analysis of triangulated manifolds. In: Mathematical Visualization. , 223–236.","short":"U. Axen, H. Edelsbrunner, in:, Mathematical Visualization, Springer, 1998, pp. 223–236.","mla":"Axen, Ulrike, and Herbert Edelsbrunner. “Auditory Morse Analysis of Triangulated Manifolds.” <i>Mathematical Visualization</i>, Springer, 1998, pp. 223–36, doi:<a href=\"https://doi.org/10.1007/978-3-662-03567-2_17\">10.1007/978-3-662-03567-2_17</a>.","apa":"Axen, U., &#38; Edelsbrunner, H. (1998). Auditory Morse analysis of triangulated manifolds. In <i>Mathematical Visualization</i> (pp. 223–236). Springer. <a href=\"https://doi.org/10.1007/978-3-662-03567-2_17\">https://doi.org/10.1007/978-3-662-03567-2_17</a>","ama":"Axen U, Edelsbrunner H. Auditory Morse analysis of triangulated manifolds. In: <i>Mathematical Visualization</i>. Springer; 1998:223-236. doi:<a href=\"https://doi.org/10.1007/978-3-662-03567-2_17\">10.1007/978-3-662-03567-2_17</a>"},"extern":"1","article_processing_charge":"No","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17"},{"date_published":"1998-10-01T00:00:00Z","author":[{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"_id":"3627","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1017/S0016672398003462","publisher":"Cambridge University Press","year":"1998","article_type":"original","volume":72,"month":"10","quality_controlled":"1","publication_identifier":{"issn":["0016-6723"]},"publist_id":"2756","extern":"1","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","article_processing_charge":"No","intvolume":"        72","date_created":"2018-12-11T12:04:19Z","acknowledgement":"S. P. Otto kindly supplied the simulation results shown in Fig. 1. I would like to thank B. Charlesworth, A. Etheridge and S. P. Otto for their comments on the manuscript. This work was supported by the Biotechnology and Biological Sciences Research Council, and by the Darwin Trust of Edinburgh.","page":"123 - 133","oa_version":"None","publication_status":"published","day":"01","abstract":[{"lang":"eng","text":"When a favourable mutation sweeps to fixation, those genes initially linked to it increase in frequency; on average, this reduces diversity in the surrounding region of the genome. In the first analysis of this 'hitch-hiking' effect, Maynard-Smith and Haigh followed the increase of the neutral allele that chanced to be associated with the new mutation in the first generation, and assumed that the subsequent increase was deterministic. Later analyses, based on either coalescence arguments, or on diffusion equations for the mean and variance of allele frequency, have also made one or both of these assumptions. In the early generations, stochastic fluctuations in the frequency of the selected allele, and coalescence of neutral lineages, can be accounted for correctly by following relationships between genes conditional on the number of copies of the favourable allele. This analysis shows that the hitch-hiking effect is increased because an allele that is destined to fix tends to increase more rapidly than exponentially. However, the identity generated by the selective sweep has the same form as in previous work, h[r/s] (2 Ns)(-2r/s), where h[r/s] tends to 1 with tight linkage. This analysis is extended to samples of many genes; then, genes may trace back to several families of lineages, each related through a common ancestor early in the selective sweep. Simulations show that the number and sizes of these families can (in principle) be used to make separate estimates of r/s and Ns."}],"status":"public","date_updated":"2022-08-29T12:42:44Z","publication":"Genetical Research","title":"The effect of hitch-hiking on neutral genealogies","issue":"2","scopus_import":"1","citation":{"ista":"Barton NH. 1998. The effect of hitch-hiking on neutral genealogies. Genetical Research. 72(2), 123–133.","short":"N.H. Barton, Genetical Research 72 (1998) 123–133.","mla":"Barton, Nicholas H. “The Effect of Hitch-Hiking on Neutral Genealogies.” <i>Genetical Research</i>, vol. 72, no. 2, Cambridge University Press, 1998, pp. 123–33, doi:<a href=\"https://doi.org/10.1017/S0016672398003462\">10.1017/S0016672398003462</a>.","apa":"Barton, N. H. (1998). The effect of hitch-hiking on neutral genealogies. <i>Genetical Research</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/S0016672398003462\">https://doi.org/10.1017/S0016672398003462</a>","ama":"Barton NH. The effect of hitch-hiking on neutral genealogies. <i>Genetical Research</i>. 1998;72(2):123-133. doi:<a href=\"https://doi.org/10.1017/S0016672398003462\">10.1017/S0016672398003462</a>","chicago":"Barton, Nicholas H. “The Effect of Hitch-Hiking on Neutral Genealogies.” <i>Genetical Research</i>. Cambridge University Press, 1998. <a href=\"https://doi.org/10.1017/S0016672398003462\">https://doi.org/10.1017/S0016672398003462</a>.","ieee":"N. H. Barton, “The effect of hitch-hiking on neutral genealogies,” <i>Genetical Research</i>, vol. 72, no. 2. Cambridge University Press, pp. 123–133, 1998."}},{"abstract":[{"lang":"eng","text":"Determining the way in which deleterious mutations interact in their effects on fitness is crucial to numerous areas in population genetics and evolutionary biology. For example, if each additional mutation leads to a greater decrease in log fitness than the last (synergistic epistasis), then the evolution of sex and recombination may be favored to facilitate the elimination of deleterious mutations. However, there is a severe shortage of relevant data. Three relatively simple experimental methods to test for epistasis between deleterious mutations in haploid species have recently been proposed. These methods involve crossing individuals and examining the mean and/or skew in log fitness of the offspring and parents. The main aim of this paper is to formalize these methods, and determine the most effective way in which tests for epistasis could be carried out. We show that only one of these methods is likely to give useful results: crossing individuals that have very different numbers of deleterious mutations, and comparing the mean log fitness of the parents with that of their offspring. We also reconsider experimental data collected on Chlamydomonas moewussi using two of the three methods. Finally, we suggest how the test could be applied to diploid species."}],"oa_version":"None","publication_status":"published","page":"435 - 444","day":"01","status":"public","date_updated":"2022-08-29T08:53:09Z","external_id":{"pmid":["9584115"]},"title":"Testing for epistasis between deleterious mutations","publication":"Genetics","main_file_link":[{"open_access":"1","url":"https://academic.oup.com/genetics/article/149/1/435/6034229"}],"issue":"1","scopus_import":"1","citation":{"ama":"West S, Peters A, Barton NH. Testing for epistasis between deleterious mutations. <i>Genetics</i>. 1998;149(1):435-444. doi:<a href=\"https://doi.org/10.1093/genetics/149.1.435\">10.1093/genetics/149.1.435</a>","mla":"West, Stuart, et al. “Testing for Epistasis between Deleterious Mutations.” <i>Genetics</i>, vol. 149, no. 1, Genetics Society of America, 1998, pp. 435–44, doi:<a href=\"https://doi.org/10.1093/genetics/149.1.435\">10.1093/genetics/149.1.435</a>.","short":"S. West, A. Peters, N.H. Barton, Genetics 149 (1998) 435–444.","apa":"West, S., Peters, A., &#38; Barton, N. H. (1998). Testing for epistasis between deleterious mutations. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1093/genetics/149.1.435\">https://doi.org/10.1093/genetics/149.1.435</a>","ista":"West S, Peters A, Barton NH. 1998. Testing for epistasis between deleterious mutations. Genetics. 149(1), 435–444.","ieee":"S. West, A. Peters, and N. H. Barton, “Testing for epistasis between deleterious mutations,” <i>Genetics</i>, vol. 149, no. 1. Genetics Society of America, pp. 435–444, 1998.","chicago":"West, Stuart, Andrew Peters, and Nicholas H Barton. “Testing for Epistasis between Deleterious Mutations.” <i>Genetics</i>. Genetics Society of America, 1998. <a href=\"https://doi.org/10.1093/genetics/149.1.435\">https://doi.org/10.1093/genetics/149.1.435</a>."},"date_published":"1998-05-01T00:00:00Z","oa":1,"_id":"3628","author":[{"first_name":"Stuart","full_name":"West, Stuart","last_name":"West"},{"last_name":"Peters","first_name":"Andrew","full_name":"Peters, Andrew"},{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","publisher":"Genetics Society of America","year":"1998","language":[{"iso":"eng"}],"doi":"10.1093/genetics/149.1.435","volume":149,"article_type":"original","quality_controlled":"1","publication_identifier":{"issn":["0016-6731"]},"publist_id":"2755","month":"05","intvolume":"       149","article_processing_charge":"No","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","extern":"1","pmid":1,"acknowledgement":"We thank BRIAN  CHARLESWORTH, ANDREW  CLARK, LAURENCE  HURST, PETER  KEIGHTLEY, ALEXEY  KONDRASHOV, CURT  LIVELY, MARGARET  MACKINNON, KATRINA  LYTHGOE, SALLY  OTTO, ANDREW  READ and ARJAN DE  VISSER for useful discussion and comments on the manuscript. This work was supported by the Biotechnology and Biological Sciences Research Council.","date_created":"2018-12-11T12:04:19Z"},{"publication":"Evolution","title":"Habitat preference in the Bombina hybrid zone in Croatia","external_id":{"pmid":["28568140"]},"citation":{"ieee":"C. Maccallum, B. Nürnberger, N. H. Barton, and J. Szymura, “Habitat preference in the Bombina hybrid zone in Croatia,” <i>Evolution</i>, vol. 52, no. 1. Wiley-Blackwell, pp. 227–239, 1998.","chicago":"Maccallum, Catriona, Beate Nürnberger, Nicholas H Barton, and Jacek Szymura. “Habitat Preference in the Bombina Hybrid Zone in Croatia.” <i>Evolution</i>. Wiley-Blackwell, 1998. <a href=\"https://doi.org/10.1111/j.1558-5646.1998.tb05156.x\">https://doi.org/10.1111/j.1558-5646.1998.tb05156.x</a>.","ama":"Maccallum C, Nürnberger B, Barton NH, Szymura J. Habitat preference in the Bombina hybrid zone in Croatia. <i>Evolution</i>. 1998;52(1):227-239. doi:<a href=\"https://doi.org/10.1111/j.1558-5646.1998.tb05156.x\">10.1111/j.1558-5646.1998.tb05156.x</a>","short":"C. Maccallum, B. Nürnberger, N.H. Barton, J. Szymura, Evolution 52 (1998) 227–239.","apa":"Maccallum, C., Nürnberger, B., Barton, N. H., &#38; Szymura, J. (1998). Habitat preference in the Bombina hybrid zone in Croatia. <i>Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1558-5646.1998.tb05156.x\">https://doi.org/10.1111/j.1558-5646.1998.tb05156.x</a>","ista":"Maccallum C, Nürnberger B, Barton NH, Szymura J. 1998. Habitat preference in the Bombina hybrid zone in Croatia. Evolution. 52(1), 227–239.","mla":"Maccallum, Catriona, et al. “Habitat Preference in the Bombina Hybrid Zone in Croatia.” <i>Evolution</i>, vol. 52, no. 1, Wiley-Blackwell, 1998, pp. 227–39, doi:<a href=\"https://doi.org/10.1111/j.1558-5646.1998.tb05156.x\">10.1111/j.1558-5646.1998.tb05156.x</a>."},"scopus_import":"1","issue":"1","day":"01","page":"227 - 239","publication_status":"published","oa_version":"None","abstract":[{"text":"This paper demonstrates the effect of habitat heterogeneity and a habitat preference on the genetic structure of a hybrid zone between the toads Bombina bombina and B. variegata (Anura: Discoglossidae); 1613 toads from 85 sites across a transect near Pešćenica, Croatia, were scored for five unlinked diagnostic allozyme markers. These were found to be largely concordant. Aside from minor systematic deviations, there was little variance in allele frequency among loci within sites. Yet the allele frequencies did not follow a smooth cline, but formed a mosaic in the center, such that neighboring sites could differ markedly in their enzyme score. A detailed ecological survey revealed a correlation between this pattern and habitat. In keeping with the typical breeding sites of the parental taxa, B. bombina-like hybrids were found more often in ponds, whereas B. variegata-like hybrids were more common in puddles. In addition, there was significant heterozygote deficit (FIS) and strong linkage disequilibrium (R), both of which were stronger on the B. bombina side of the transect, and stronger in puddles than ponds. Mark-recapture data showed: (1) that the animals disperse beyond the scale of the habitat pattern; (2) frequent turn-over of individuals within sites; and (3) nonrandom movement between two sites of different habitat type. We conclude that an active habitat preference must contribute to the observed association between marker alleles and habitat. As a consequence, there is incomplete mixing of the two gene pools, which could explain the high level of FIS and R. The asymmetry in these parameters may reflect asymmetry in the preference or in the distribution of habitats across the zone. We discuss the implications of habitat preference for the dynamics of hybrid zones.","lang":"eng"}],"date_updated":"2022-08-26T11:00:17Z","status":"public","month":"02","publication_identifier":{"issn":["0014-3820"]},"publist_id":"2754","quality_controlled":"1","article_type":"original","volume":52,"date_created":"2018-12-11T12:04:20Z","acknowledgement":"This work was supported by a NERC studentshipto CJM, by NERC grants GR3/9353, GR3/8002, andGR9/1909A to NHB,  and by KBN grant 193/P04/95/09to JMS. We are grateful to J. W.Arntzen, L.Kruuk, R. G.Harrison, J. W.Sites, and an anonymous reviewer for their comments on the manuscript.","pmid":1,"user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","article_processing_charge":"No","extern":"1","intvolume":"        52","author":[{"full_name":"Maccallum, Catriona","first_name":"Catriona","last_name":"Maccallum"},{"full_name":"Nürnberger, Beate","first_name":"Beate","last_name":"Nürnberger"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"},{"last_name":"Szymura","first_name":"Jacek","full_name":"Szymura, Jacek"}],"_id":"3629","date_published":"1998-02-01T00:00:00Z","doi":"10.1111/j.1558-5646.1998.tb05156.x","language":[{"iso":"eng"}],"year":"1998","publisher":"Wiley-Blackwell","type":"journal_article"},{"title":"Partitioning the components of sexual selection: attractiveness and agonistic behaviour in male wax moths, Achroia grisella (Lepidoptera, Pyralidae)","publication":"Ethology","scopus_import":"1","issue":"1","citation":{"apa":"Cremer, S., &#38; Greenfield, M. (1998). Partitioning the components of sexual selection: attractiveness and agonistic behaviour in male wax moths, Achroia grisella (Lepidoptera, Pyralidae). <i>Ethology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1439-0310.1998.tb00025.x\">https://doi.org/10.1111/j.1439-0310.1998.tb00025.x</a>","ista":"Cremer S, Greenfield M. 1998. Partitioning the components of sexual selection: attractiveness and agonistic behaviour in male wax moths, Achroia grisella (Lepidoptera, Pyralidae). Ethology. 104(1), 1–9.","mla":"Cremer, Sylvia, and Michael Greenfield. “Partitioning the Components of Sexual Selection: Attractiveness and Agonistic Behaviour in Male Wax Moths, Achroia Grisella (Lepidoptera, Pyralidae).” <i>Ethology</i>, vol. 104, no. 1, Wiley-Blackwell, 1998, pp. 1–9, doi:<a href=\"https://doi.org/10.1111/j.1439-0310.1998.tb00025.x\">10.1111/j.1439-0310.1998.tb00025.x</a>.","short":"S. Cremer, M. Greenfield, Ethology 104 (1998) 1–9.","ama":"Cremer S, Greenfield M. Partitioning the components of sexual selection: attractiveness and agonistic behaviour in male wax moths, Achroia grisella (Lepidoptera, Pyralidae). <i>Ethology</i>. 1998;104(1):1-9. doi:<a href=\"https://doi.org/10.1111/j.1439-0310.1998.tb00025.x\">10.1111/j.1439-0310.1998.tb00025.x</a>","chicago":"Cremer, Sylvia, and Michael Greenfield. “Partitioning the Components of Sexual Selection: Attractiveness and Agonistic Behaviour in Male Wax Moths, Achroia Grisella (Lepidoptera, Pyralidae).” <i>Ethology</i>. Wiley-Blackwell, 1998. <a href=\"https://doi.org/10.1111/j.1439-0310.1998.tb00025.x\">https://doi.org/10.1111/j.1439-0310.1998.tb00025.x</a>.","ieee":"S. Cremer and M. Greenfield, “Partitioning the components of sexual selection: attractiveness and agonistic behaviour in male wax moths, Achroia grisella (Lepidoptera, Pyralidae),” <i>Ethology</i>, vol. 104, no. 1. Wiley-Blackwell, pp. 1–9, 1998."},"abstract":[{"text":"Two components of sexual selection in the lesser wax moth, Achroia grisella, are clearly defined: females choose males based on characters of their ultrasonic advertisement signals, and males display agonistic behaviour patterns in contests over signalling stations. We conducted a series of laboratory trials to determine whether successes in these two sexual selection arenas were related. Our trials showed that winners in contests over signalling stations were characterized by earlier initiation of both signalling and aggression. These characteristics may indicate higher levels of ‘motivation,’ but it is unclear whether this level is a fixed trait. There was no relationship, however, between any measure of a male's attractiveness to females and his success in winning competition trials. Thus, inter- and intra-sexual selection may be acting on different, uncorrelated traits in A. grisella.","lang":"eng"}],"day":"01","page":"1 - 9","publication_status":"published","oa_version":"None","status":"public","date_updated":"2022-08-26T09:11:08Z","volume":104,"article_type":"original","publication_identifier":{"issn":["0044-3573"]},"publist_id":"2227","quality_controlled":"1","month":"01","intvolume":"       104","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","extern":"1","article_processing_charge":"No","acknowledgement":"We thank Robert MINCKI-EY for collecting A. griseh from infested honeybee colonies and Yikweon J,4M;. Feng-You JIA, James MCLLOUGH and Kelly WILLAMS for indispensable laboratory assistaiice. Analyses of the ultrasonic advertisement signals was made possible by digital signal-processing programs written by Tom PETERS and Ric ROGERO (both of the University of Kansas Instrumentation Development Laboratory) and Martin CREMER. Marc BRANHAM and Klaus-Gerhardt HELLER offered valuable discussion during the project and Yikweon JAG, Klaus REINHOLD and several anonymous referees provided critical  reviews of the manuscript. Financial support was provided by US National Science Foundation grant IBN-9407162.","date_created":"2018-12-11T12:05:56Z","date_published":"1998-01-01T00:00:00Z","_id":"3926","author":[{"orcid":"0000-0002-2193-3868","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","first_name":"Sylvia"},{"last_name":"Greenfield","first_name":"Michael","full_name":"Greenfield, Michael"}],"type":"journal_article","year":"1998","publisher":"Wiley-Blackwell","doi":"10.1111/j.1439-0310.1998.tb00025.x","language":[{"iso":"eng"}]},{"abstract":[{"text":"The size and shape of macromolecules such as proteins and nucleic acids play an important role in their functions. Prior efforts to quantify these properties have been based on various discretization or tessellation procedures involving analytical or numerical computations. In this article, we present an analytically exact method for computing the metric properties of macromolecules based on the alpha shape theory. This method uses the duality between alpha complex and the weighted Voronoi decomposition of a molecule. We describe the intuitive ideas and concepts behind the alpha shape theory and the algorithm for computing areas and volumes of macromolecules. We apply our method to compute areas and volumes of a number of protein systems. We also discuss several difficulties commonly encountered in molecular shape computations and outline methods to overcome these problems. (C) 1998 Wiley-Liss, Inc.","lang":"eng"}],"publication_status":"published","page":"1 - 17","oa_version":"None","day":"01","date_updated":"2022-08-25T13:32:59Z","status":"public","title":"Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape","publication":"Proteins: Structure, Function and Bioinformatics","citation":{"ama":"Liang J, Edelsbrunner H, Fu P, Sudhakar P, Subramaniam S. Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape. <i>Proteins: Structure, Function and Bioinformatics</i>. 1998;33(1):1-17. doi:<a href=\"https://doi.org/10.1002/(SICI)1097-0134(19981001)33:1&#38;lt;1::AID-PROT1&#38;gt;3.0.CO;2-O\">10.1002/(SICI)1097-0134(19981001)33:1&#38;lt;1::AID-PROT1&#38;gt;3.0.CO;2-O</a>","short":"J. Liang, H. Edelsbrunner, P. Fu, P. Sudhakar, S. Subramaniam, Proteins: Structure, Function and Bioinformatics 33 (1998) 1–17.","apa":"Liang, J., Edelsbrunner, H., Fu, P., Sudhakar, P., &#38; Subramaniam, S. (1998). Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape. <i>Proteins: Structure, Function and Bioinformatics</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/(SICI)1097-0134(19981001)33:1&#38;lt;1::AID-PROT1&#38;gt;3.0.CO;2-O\">https://doi.org/10.1002/(SICI)1097-0134(19981001)33:1&#38;lt;1::AID-PROT1&#38;gt;3.0.CO;2-O</a>","mla":"Liang, Jie, et al. “Analytical Shape Computation of Macromolecules: I. Molecular Area and Volume through Alpha Shape.” <i>Proteins: Structure, Function and Bioinformatics</i>, vol. 33, no. 1, Wiley-Blackwell, 1998, pp. 1–17, doi:<a href=\"https://doi.org/10.1002/(SICI)1097-0134(19981001)33:1&#38;lt;1::AID-PROT1&#38;gt;3.0.CO;2-O\">10.1002/(SICI)1097-0134(19981001)33:1&#38;lt;1::AID-PROT1&#38;gt;3.0.CO;2-O</a>.","ista":"Liang J, Edelsbrunner H, Fu P, Sudhakar P, Subramaniam S. 1998. Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape. Proteins: Structure, Function and Bioinformatics. 33(1), 1–17.","ieee":"J. Liang, H. Edelsbrunner, P. Fu, P. Sudhakar, and S. Subramaniam, “Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape,” <i>Proteins: Structure, Function and Bioinformatics</i>, vol. 33, no. 1. Wiley-Blackwell, pp. 1–17, 1998.","chicago":"Liang, Jie, Herbert Edelsbrunner, Ping Fu, Pamidighantam Sudhakar, and Shankar Subramaniam. “Analytical Shape Computation of Macromolecules: I. Molecular Area and Volume through Alpha Shape.” <i>Proteins: Structure, Function and Bioinformatics</i>. Wiley-Blackwell, 1998. <a href=\"https://doi.org/10.1002/(SICI)1097-0134(19981001)33:1&#38;lt;1::AID-PROT1&#38;gt;3.0.CO;2-O\">https://doi.org/10.1002/(SICI)1097-0134(19981001)33:1&#38;lt;1::AID-PROT1&#38;gt;3.0.CO;2-O</a>."},"issue":"1","scopus_import":"1","_id":"4011","author":[{"last_name":"Liang","full_name":"Liang, Jie","first_name":"Jie"},{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ping","full_name":"Fu, Ping","last_name":"Fu"},{"last_name":"Sudhakar","full_name":"Sudhakar, Pamidighantam","first_name":"Pamidighantam"},{"full_name":"Subramaniam, Shankar","first_name":"Shankar","last_name":"Subramaniam"}],"date_published":"1998-10-01T00:00:00Z","publisher":"Wiley-Blackwell","year":"1998","language":[{"iso":"eng"}],"doi":"10.1002/(SICI)1097-0134(19981001)33:1&lt;1::AID-PROT1&gt;3.0.CO;2-O","type":"journal_article","quality_controlled":"1","publist_id":"2112","publication_identifier":{"issn":["0887-3585"]},"month":"10","volume":33,"article_type":"original","acknowledgement":"We thank Michael Facello for the torus area formula and suggestion regarding computation of MS model from  SA model. We thank Nataraj Akkiraju, Patrick Moran, and Marcus Wagner for interesting discussionson the topic of this article and for help in the generationof two- and three-dimensional illustrations. We thank NSF Meta Center Allocation  for providing computational resources. The software VOLBL is available at:http://alpha.ncsa.uiuc.edu/alpha.","date_created":"2018-12-11T12:06:25Z","intvolume":"        33","article_processing_charge":"No","extern":"1","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17"},{"page":"18 - 29","oa_version":"None","publication_status":"published","day":"01","abstract":[{"text":"The structures of proteins are well-packed, yet they contain numerous cavities which play key roles in accommodating small molecules, or enabling conformational changes. From high-resolution structures it is possible to identify these cavities. We have developed a precise algorithm based on alpha shapes for measuring space-filling-based molecular models (such as van der Waals, solvent accessible, and molecular surface descriptions). We applied this method for accurate computation of the surface area and volume of cavities in several proteins. In addition, all of the atoms/residues Lining the cavities are identified, We use this method to study the structure and the stability of proteins, as well as to locate cavities that could contain structural water molecules in the proton transport pathway in the membrane protein bacteriorhodopsin.","lang":"eng"}],"date_updated":"2022-08-25T13:35:41Z","status":"public","publication":"Proteins: Structure, Function and Bioinformatics","title":"Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins","citation":{"chicago":"Liang, Jie, Herbert Edelsbrunner, Ping Fu, Pamidighantam Sudhakar, and Shankar Subramaniam. “Analytical Shape Computation of Macromolecules: II. Inaccessible Cavities in Proteins.” <i>Proteins: Structure, Function and Bioinformatics</i>. Wiley-Blackwell, 1998. <a href=\"https://doi.org/10.1002/(SICI)1097-0134(19981001)33:1&#38;lt;18::AID-PROT2&#38;gt;3.0.CO;2-H\">https://doi.org/10.1002/(SICI)1097-0134(19981001)33:1&#38;lt;18::AID-PROT2&#38;gt;3.0.CO;2-H</a>.","ieee":"J. Liang, H. Edelsbrunner, P. Fu, P. Sudhakar, and S. Subramaniam, “Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins,” <i>Proteins: Structure, Function and Bioinformatics</i>, vol. 33, no. 1. Wiley-Blackwell, pp. 18–29, 1998.","mla":"Liang, Jie, et al. “Analytical Shape Computation of Macromolecules: II. Inaccessible Cavities in Proteins.” <i>Proteins: Structure, Function and Bioinformatics</i>, vol. 33, no. 1, Wiley-Blackwell, 1998, pp. 18–29, doi:<a href=\"https://doi.org/10.1002/(SICI)1097-0134(19981001)33:1&#38;lt;18::AID-PROT2&#38;gt;3.0.CO;2-H\">10.1002/(SICI)1097-0134(19981001)33:1&#38;lt;18::AID-PROT2&#38;gt;3.0.CO;2-H</a>.","short":"J. Liang, H. Edelsbrunner, P. Fu, P. Sudhakar, S. Subramaniam, Proteins: Structure, Function and Bioinformatics 33 (1998) 18–29.","ista":"Liang J, Edelsbrunner H, Fu P, Sudhakar P, Subramaniam S. 1998. Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins. Proteins: Structure, Function and Bioinformatics. 33(1), 18–29.","apa":"Liang, J., Edelsbrunner, H., Fu, P., Sudhakar, P., &#38; Subramaniam, S. (1998). Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins. <i>Proteins: Structure, Function and Bioinformatics</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/(SICI)1097-0134(19981001)33:1&#38;lt;18::AID-PROT2&#38;gt;3.0.CO;2-H\">https://doi.org/10.1002/(SICI)1097-0134(19981001)33:1&#38;lt;18::AID-PROT2&#38;gt;3.0.CO;2-H</a>","ama":"Liang J, Edelsbrunner H, Fu P, Sudhakar P, Subramaniam S. Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins. <i>Proteins: Structure, Function and Bioinformatics</i>. 1998;33(1):18-29. doi:<a href=\"https://doi.org/10.1002/(SICI)1097-0134(19981001)33:1&#38;lt;18::AID-PROT2&#38;gt;3.0.CO;2-H\">10.1002/(SICI)1097-0134(19981001)33:1&#38;lt;18::AID-PROT2&#38;gt;3.0.CO;2-H</a>"},"issue":"1","scopus_import":"1","author":[{"last_name":"Liang","full_name":"Liang, Jie","first_name":"Jie"},{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"},{"first_name":"Ping","full_name":"Fu, Ping","last_name":"Fu"},{"last_name":"Sudhakar","first_name":"Pamidighantam","full_name":"Sudhakar, Pamidighantam"},{"full_name":"Subramaniam, Shankar","first_name":"Shankar","last_name":"Subramaniam"}],"_id":"4012","date_published":"1998-10-01T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1002/(SICI)1097-0134(19981001)33:1&lt;18::AID-PROT2&gt;3.0.CO;2-H","publisher":"Wiley-Blackwell","year":"1998","type":"journal_article","month":"10","quality_controlled":"1","publication_identifier":{"issn":["0887-3585"]},"publist_id":"2113","volume":33,"article_type":"original","date_created":"2018-12-11T12:06:26Z","acknowledgement":"The software for constructing weighted Delaunay complexes and the alpha shape filters was written by Ernst Mücke and Michael Facello. We thank them forcreating reliable and robust software so that wecan build on their results. The authors thank NSF Meta Center Allocation for providing computational resources. The software VOLBL is part of the standard distribution of the alpha shapes software, andis available at http://alpha.ncsa.uiuc.edu/alpha.","article_processing_charge":"No","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","extern":"1","intvolume":"        33"},{"citation":{"mla":"Edelsbrunner, Herbert, et al. “On the Definition and the Construction of Pockets in Macromolecules.” <i>Discrete Applied Mathematics</i>, vol. 88, no. 1–3, Elsevier, 1998, pp. 83–102, doi:<a href=\"https://doi.org/10.1016/S0166-218X(98)00067-5\">10.1016/S0166-218X(98)00067-5</a>.","ista":"Edelsbrunner H, Facello M, Liang J. 1998. On the definition and the construction of pockets in macromolecules. Discrete Applied Mathematics. 88(1–3), 83–102.","short":"H. Edelsbrunner, M. Facello, J. Liang, Discrete Applied Mathematics 88 (1998) 83–102.","apa":"Edelsbrunner, H., Facello, M., &#38; Liang, J. (1998). On the definition and the construction of pockets in macromolecules. <i>Discrete Applied Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/S0166-218X(98)00067-5\">https://doi.org/10.1016/S0166-218X(98)00067-5</a>","ama":"Edelsbrunner H, Facello M, Liang J. On the definition and the construction of pockets in macromolecules. <i>Discrete Applied Mathematics</i>. 1998;88(1-3):83-102. doi:<a href=\"https://doi.org/10.1016/S0166-218X(98)00067-5\">10.1016/S0166-218X(98)00067-5</a>","chicago":"Edelsbrunner, Herbert, Michael Facello, and Jie Liang. “On the Definition and the Construction of Pockets in Macromolecules.” <i>Discrete Applied Mathematics</i>. Elsevier, 1998. <a href=\"https://doi.org/10.1016/S0166-218X(98)00067-5\">https://doi.org/10.1016/S0166-218X(98)00067-5</a>.","ieee":"H. Edelsbrunner, M. Facello, and J. Liang, “On the definition and the construction of pockets in macromolecules,” <i>Discrete Applied Mathematics</i>, vol. 88, no. 1–3. Elsevier, pp. 83–102, 1998."},"scopus_import":"1","issue":"1-3","main_file_link":[{"open_access":"1","url":"https://www.sciencedirect.com/science/article/pii/S0166218X98000675?via%3Dihub"}],"publication":"Discrete Applied Mathematics","title":"On the definition and the construction of pockets in macromolecules","external_id":{"pmid":["9390238"]},"date_updated":"2022-08-25T15:06:30Z","status":"public","day":"09","publication_status":"published","page":"83 - 102","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The shape of a protein is important for its functions, This includes the location and size of identifiable regions in its complement space. We formally define pockets as regions in the complement with limited accessibility from the outside. Pockets can be efficiently constructed by an algorithm based on alpha complexes. The algorithm is implemented and applied to proteins with known three-dimensional conformations. 1998 Published by Elsevier Science B.V. All rights reserved."}],"date_created":"2018-12-11T12:06:26Z","acknowledgement":"The authors thank Ping Fu and Ernst Miicke for their contributions to the alpha shapes software in which the pockets software is embedded. ","pmid":1,"user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","article_processing_charge":"No","extern":"1","intvolume":"        88","month":"11","publist_id":"2114","publication_identifier":{"issn":["0166-218X"]},"quality_controlled":"1","article_type":"original","volume":88,"doi":"10.1016/S0166-218X(98)00067-5","language":[{"iso":"eng"}],"year":"1998","publisher":"Elsevier","type":"journal_article","author":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"},{"last_name":"Facello","first_name":"Michael","full_name":"Facello, Michael"},{"last_name":"Liang","first_name":"Jie","full_name":"Liang, Jie"}],"_id":"4013","oa":1,"date_published":"1998-11-09T00:00:00Z"},{"article_processing_charge":"No","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","extern":"1","conference":{"end_date":"1998-04-24","start_date":"1998-04-20","name":"LATIN: Latin American Symposium on Theoretical Informatics ","location":"Campinas, Brazil"},"alternative_title":["LNCS"],"intvolume":"      1380","date_created":"2018-12-11T12:06:27Z","citation":{"ieee":"H. Edelsbrunner, “Shape reconstruction with Delaunay complex,” in <i>Proceedingsof the 3rd Latin American Symposium on Theoretical Informatics</i>, Campinas, Brazil, 1998, vol. 1380, pp. 119–132.","chicago":"Edelsbrunner, Herbert. “Shape Reconstruction with Delaunay Complex.” In <i>Proceedingsof the 3rd Latin American Symposium on Theoretical Informatics</i>, 1380:119–32. Springer, 1998. <a href=\"https://doi.org/10.1007/BFb0054315\">https://doi.org/10.1007/BFb0054315</a>.","ama":"Edelsbrunner H. Shape reconstruction with Delaunay complex. In: <i>Proceedingsof the 3rd Latin American Symposium on Theoretical Informatics</i>. Vol 1380. Springer; 1998:119-132. doi:<a href=\"https://doi.org/10.1007/BFb0054315\">10.1007/BFb0054315</a>","short":"H. Edelsbrunner, in:, Proceedingsof the 3rd Latin American Symposium on Theoretical Informatics, Springer, 1998, pp. 119–132.","apa":"Edelsbrunner, H. (1998). Shape reconstruction with Delaunay complex. In <i>Proceedingsof the 3rd Latin American Symposium on Theoretical Informatics</i> (Vol. 1380, pp. 119–132). Campinas, Brazil: Springer. <a href=\"https://doi.org/10.1007/BFb0054315\">https://doi.org/10.1007/BFb0054315</a>","mla":"Edelsbrunner, Herbert. “Shape Reconstruction with Delaunay Complex.” <i>Proceedingsof the 3rd Latin American Symposium on Theoretical Informatics</i>, vol. 1380, Springer, 1998, pp. 119–32, doi:<a href=\"https://doi.org/10.1007/BFb0054315\">10.1007/BFb0054315</a>.","ista":"Edelsbrunner H. 1998. Shape reconstruction with Delaunay complex. Proceedingsof the 3rd Latin American Symposium on Theoretical Informatics. LATIN: Latin American Symposium on Theoretical Informatics , LNCS, vol. 1380, 119–132."},"publication":"Proceedingsof the 3rd Latin American Symposium on Theoretical Informatics","volume":1380,"title":"Shape reconstruction with Delaunay complex","month":"03","quality_controlled":"1","publication_identifier":{"isbn":["9783540642756"]},"publist_id":"2109","status":"public","type":"conference","language":[{"iso":"eng"}],"doi":"10.1007/BFb0054315","date_updated":"2022-08-25T12:22:10Z","publisher":"Springer","year":"1998","date_published":"1998-03-25T00:00:00Z","page":"119 - 132","publication_status":"published","oa_version":"None","day":"25","abstract":[{"lang":"eng","text":"The reconstruction of a shape or surface from a finite set of points is a practically significant and theoretically challenging problem. This paper presents a unified view of algorithmic solutions proposed in the computer science literature that are based on the Delaunay complex of the points."}],"author":[{"first_name":"Herbert","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"}],"_id":"4015"},{"publist_id":"2110","quality_controlled":"1","month":"01","title":"Wrapping 3D scanning data","volume":3313,"citation":{"ama":"Edelsbrunner H, Facello M, Fu P, Qian J, Nekhayev D. Wrapping 3D scanning data. In: Vol 3313. SPIE; 1998:148-158. doi:<a href=\"https://doi.org/10.1117/12.302448\">10.1117/12.302448</a>","ista":"Edelsbrunner H, Facello M, Fu P, Qian J, Nekhayev D. 1998. Wrapping 3D scanning data. Three-Dimensional Image Capture and Applications, SPIE, vol. 3313, 148–158.","apa":"Edelsbrunner, H., Facello, M., Fu, P., Qian, J., &#38; Nekhayev, D. (1998). Wrapping 3D scanning data (Vol. 3313, pp. 148–158). Presented at the Three-Dimensional Image Capture and Applications, SPIE. <a href=\"https://doi.org/10.1117/12.302448\">https://doi.org/10.1117/12.302448</a>","short":"H. Edelsbrunner, M. Facello, P. Fu, J. Qian, D. Nekhayev, in:, SPIE, 1998, pp. 148–158.","mla":"Edelsbrunner, Herbert, et al. <i>Wrapping 3D Scanning Data</i>. Vol. 3313, SPIE, 1998, pp. 148–58, doi:<a href=\"https://doi.org/10.1117/12.302448\">10.1117/12.302448</a>.","ieee":"H. Edelsbrunner, M. Facello, P. Fu, J. Qian, and D. Nekhayev, “Wrapping 3D scanning data,” presented at the Three-Dimensional Image Capture and Applications, 1998, vol. 3313, pp. 148–158.","chicago":"Edelsbrunner, Herbert, Michael Facello, Ping Fu, Jiang Qian, and Dmitry Nekhayev. “Wrapping 3D Scanning Data,” 3313:148–58. SPIE, 1998. <a href=\"https://doi.org/10.1117/12.302448\">https://doi.org/10.1117/12.302448</a>."},"date_created":"2018-12-11T12:06:27Z","intvolume":"      3313","alternative_title":["SPIE"],"scopus_import":"1","conference":{"name":"Three-Dimensional Image Capture and Applications"},"extern":"1","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","article_processing_charge":"No","_id":"4016","author":[{"first_name":"Herbert","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"full_name":"Facello, Michael","first_name":"Michael","last_name":"Facello"},{"last_name":"Fu","full_name":"Fu, Ping","first_name":"Ping"},{"first_name":"Jiang","full_name":"Qian, Jiang","last_name":"Qian"},{"last_name":"Nekhayev","full_name":"Nekhayev, Dmitry","first_name":"Dmitry"}],"abstract":[{"lang":"eng","text":"Geomagic Wrap™ is a commercially available software for reconstructing shapes and surfaces from 3D scanning data. The data can be any arbitrary finite point set in 3D, and there are no requirements on local density or organization in slices etc. The software contains components for surface reconstruction, improvement, and analysis, and it supports a variety of input and output formats that make it compatible with scanning hardware and CAD and graphics software."}],"day":"01","publication_status":"published","oa_version":"None","date_published":"1998-01-01T00:00:00Z","page":"148 - 158","year":"1998","publisher":"SPIE","date_updated":"2022-08-25T12:37:01Z","doi":"10.1117/12.302448","language":[{"iso":"eng"}],"type":"conference","status":"public"},{"date_published":"1998-09-01T00:00:00Z","oa":1,"_id":"4017","author":[{"first_name":"Jie","full_name":"Liang, Jie","last_name":"Liang"},{"first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Woodward, Clare","first_name":"Clare","last_name":"Woodward"}],"type":"journal_article","publisher":"Wiley-Blackwell","year":"1998","language":[{"iso":"eng"}],"doi":"10.1002/pro.5560070905","volume":7,"article_type":"original","quality_controlled":"1","publist_id":"2111","publication_identifier":{"issn":["0961-8368"]},"month":"09","intvolume":"         7","article_processing_charge":"No","extern":"1","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","pmid":1,"date_created":"2018-12-11T12:06:27Z","abstract":[{"text":"Identification and size characterization of surface pockets and occluded cavities are initial steps in protein structure-based ligand design. A new program, CAST, for automatically locating and measuring protein pockets and cavities, is based on precise computational geometry methods, including alpha shape and discrete flow theory. CAST identifies and measures pockets and pocket mouth openings, as well as cavities. The program specifies the atoms lining pockets, pocket openings. and buried cavities; the volume and area of pockets and cavities; and the area and circumference of mouth openings. CAST analysis of over 100 proteins has been carried out; proteins examined include a set of 51 monomeric enzyme-ligand structures, several elastase-inhibitor complexes, the FK506 binding protein, 30 HIV-1 protease-inhibitor complexes, and a number of small and large protein inhibitors, Medium-sized globular proteins typically have 10-20 pockets/cavities. Most often, binding sites are pockets with 1-2 mouth openings; much less frequently they are cavities. Ligand binding pockets vary widely in size, most within the range 10(2)-10(3) Angstrom(3). Statistical analysis reveals that the number of pockets and cavities is correlated with protein size, but there is no correlation between the size of the protein and the size of binding sites. Most frequently, the largest pocket/cavity is thp active site, but there are a number of instructive exceptions. Ligand volume and binding site volume are somewhat correlated when binding site volume is less than or equal to 700 Angstrom(3), but the ligand seldom occupies the entire site. Auxiliary pockets near the active site have been suggested as additional binding surface for designed ligands (Mattos C ct al., 1993, Nat Struct Biol 1:55-58). Analysis of elastase-inhibitor complexes suggests that CAST can identify ancillary pockets, suitable for recruitment in ligand design strategies. Analysis of the FK506 binding protein, and of compounds developed in SAR by NMR (Shuker SE et al.. 1996, Science 274:1531-1534), indicates that CAST pocket computation may provide a priori identification of target proteins for Linked-fragment design. CAST analysis of 30 HIV-1 protease-inhibitor complexes shows that the flexible active site pocket can vary over a range of 853-1,566 Angstrom(3), and that there are two pockets near or adjoining the active site that may be recruited for ligand design.","lang":"eng"}],"page":"1884 - 1897","oa_version":"Published Version","publication_status":"published","day":"01","status":"public","date_updated":"2022-08-25T12:49:41Z","external_id":{"pmid":["9761470 "]},"title":"Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design","publication":"Protein Science","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2144175/"}],"issue":"9","scopus_import":"1","citation":{"ama":"Liang J, Edelsbrunner H, Woodward C. Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design. <i>Protein Science</i>. 1998;7(9):1884-1897. doi:<a href=\"https://doi.org/10.1002/pro.5560070905\">10.1002/pro.5560070905</a>","apa":"Liang, J., Edelsbrunner, H., &#38; Woodward, C. (1998). Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design. <i>Protein Science</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/pro.5560070905\">https://doi.org/10.1002/pro.5560070905</a>","ista":"Liang J, Edelsbrunner H, Woodward C. 1998. Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design. Protein Science. 7(9), 1884–1897.","mla":"Liang, Jie, et al. “Anatomy of Protein Pockets and Cavities: Measurement of Binding Site Geometry and Implications for Ligand Design.” <i>Protein Science</i>, vol. 7, no. 9, Wiley-Blackwell, 1998, pp. 1884–97, doi:<a href=\"https://doi.org/10.1002/pro.5560070905\">10.1002/pro.5560070905</a>.","short":"J. Liang, H. Edelsbrunner, C. Woodward, Protein Science 7 (1998) 1884–1897.","ieee":"J. Liang, H. Edelsbrunner, and C. Woodward, “Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design,” <i>Protein Science</i>, vol. 7, no. 9. Wiley-Blackwell, pp. 1884–1897, 1998.","chicago":"Liang, Jie, Herbert Edelsbrunner, and Clare Woodward. “Anatomy of Protein Pockets and Cavities: Measurement of Binding Site Geometry and Implications for Ligand Design.” <i>Protein Science</i>. Wiley-Blackwell, 1998. <a href=\"https://doi.org/10.1002/pro.5560070905\">https://doi.org/10.1002/pro.5560070905</a>."}},{"day":"01","oa_version":"None","publication_status":"published","date_published":"1998-10-01T00:00:00Z","page":"104 - 113","abstract":[{"text":"The construction of shape spaces is studied from a mathematical and a computational viewpoint. A program is outlined reducing the problem to four tasks: the representation of geometry, the canonical deformation of geometry, the measuring of distance in shape space, and the selection of base shapes. The technical part of this paper focuses on the second task: the specification of a deformation mixing two or more shapes in continuously, changing proportions.","lang":"eng"}],"author":[{"first_name":"Ho","full_name":"Cheng, Ho","last_name":"Cheng"},{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","first_name":"Herbert"},{"full_name":"Fu, Ping","first_name":"Ping","last_name":"Fu"}],"_id":"4019","status":"public","type":"conference","doi":"10.1109/PCCGA.1998.732056","language":[{"iso":"eng"}],"year":"1998","publisher":"IEEE","date_updated":"2022-08-25T12:06:20Z","publication":"Proceedings of the 6th Pacific Conference on Computer Graphics and Applications","title":"Shape space from deformation","month":"10","publist_id":"2107","publication_identifier":{"isbn":["0818686200"]},"quality_controlled":"1","conference":{"end_date":"1998-10-29","start_date":"1998-10-26","name":"CGA: Conference on Computer Graphics and Applications ","location":"Singapore"},"article_processing_charge":"No","extern":"1","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","date_created":"2018-12-11T12:06:28Z","acknowledgement":"This research is partially supported by the National Science Foundation under grants CCR-96-19542 and CCR-97-12088, and by the Army Research O*ce under grant DAAG55-98-1-0177.","citation":{"ieee":"H. Cheng, H. Edelsbrunner, and P. Fu, “Shape space from deformation,” in <i>Proceedings of the 6th Pacific Conference on Computer Graphics and Applications</i>, Singapore, 1998, pp. 104–113.","chicago":"Cheng, Ho, Herbert Edelsbrunner, and Ping Fu. “Shape Space from Deformation.” In <i>Proceedings of the 6th Pacific Conference on Computer Graphics and Applications</i>, 104–13. IEEE, 1998. <a href=\"https://doi.org/10.1109/PCCGA.1998.732056\">https://doi.org/10.1109/PCCGA.1998.732056</a>.","ama":"Cheng H, Edelsbrunner H, Fu P. Shape space from deformation. In: <i>Proceedings of the 6th Pacific Conference on Computer Graphics and Applications</i>. IEEE; 1998:104-113. doi:<a href=\"https://doi.org/10.1109/PCCGA.1998.732056\">10.1109/PCCGA.1998.732056</a>","mla":"Cheng, Ho, et al. “Shape Space from Deformation.” <i>Proceedings of the 6th Pacific Conference on Computer Graphics and Applications</i>, IEEE, 1998, pp. 104–13, doi:<a href=\"https://doi.org/10.1109/PCCGA.1998.732056\">10.1109/PCCGA.1998.732056</a>.","ista":"Cheng H, Edelsbrunner H, Fu P. 1998. Shape space from deformation. Proceedings of the 6th Pacific Conference on Computer Graphics and Applications. CGA: Conference on Computer Graphics and Applications , 104–113.","short":"H. Cheng, H. Edelsbrunner, P. Fu, in:, Proceedings of the 6th Pacific Conference on Computer Graphics and Applications, IEEE, 1998, pp. 104–113.","apa":"Cheng, H., Edelsbrunner, H., &#38; Fu, P. (1998). Shape space from deformation. In <i>Proceedings of the 6th Pacific Conference on Computer Graphics and Applications</i> (pp. 104–113). Singapore: IEEE. <a href=\"https://doi.org/10.1109/PCCGA.1998.732056\">https://doi.org/10.1109/PCCGA.1998.732056</a>"}},{"quality_controlled":"1","publist_id":"2108","publication_identifier":{"isbn":["9781568810812"]},"month":"10","title":"Geometry for modeling biomolecules","publication":"Robotics: The Algorithmic Perspective","citation":{"ista":"Edelsbrunner H. 1998.Geometry for modeling biomolecules. In: Robotics: The Algorithmic Perspective. , 265–277.","apa":"Edelsbrunner, H. (1998). Geometry for modeling biomolecules. In <i>Robotics: The Algorithmic Perspective</i> (pp. 265–277). AK Peters.","short":"H. Edelsbrunner, in:, Robotics: The Algorithmic Perspective, AK Peters, 1998, pp. 265–277.","mla":"Edelsbrunner, Herbert. “Geometry for Modeling Biomolecules.” <i>Robotics: The Algorithmic Perspective</i>, AK Peters, 1998, pp. 265–77.","ama":"Edelsbrunner H. Geometry for modeling biomolecules. In: <i>Robotics: The Algorithmic Perspective</i>. AK Peters; 1998:265-277.","chicago":"Edelsbrunner, Herbert. “Geometry for Modeling Biomolecules.” In <i>Robotics: The Algorithmic Perspective</i>, 265–77. AK Peters, 1998.","ieee":"H. Edelsbrunner, “Geometry for modeling biomolecules,” in <i>Robotics: The Algorithmic Perspective</i>, AK Peters, 1998, pp. 265–277."},"date_created":"2018-12-11T12:06:28Z","extern":"1","article_processing_charge":"No","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","_id":"4020","author":[{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"}],"abstract":[{"text":"Space Filing diagrams are geometric models of molecular conformations in three-dimensional space. Each atom is a location is space and a quantitative expression of influence on the immediate surrounding. This paper surveys the basic types of space filling diagrams with a focus on the dual alpha shape. Properties of those diagrams that relate to questions of connectivity, size, shape and symmetry, and metamorphosis are discussed.","lang":"eng"}],"oa_version":"None","publication_status":"published","page":"265 - 277","date_published":"1998-10-01T00:00:00Z","day":"01","publisher":"AK Peters","date_updated":"2022-08-25T12:12:04Z","year":"1998","language":[{"iso":"eng"}],"type":"book_chapter","status":"public"},{"date_published":"1998-07-01T00:00:00Z","_id":"4280","author":[{"first_name":"Mike","full_name":"Ritchie, Mike","last_name":"Ritchie"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"type":"journal_article","year":"1998","publisher":"Cell Press","doi":"10.1016/S0169-5347(98)01396-2","language":[{"iso":"eng"}],"article_type":"original","volume":13,"publist_id":"1806","publication_identifier":{"issn":["0169-5347"]},"quality_controlled":"1","month":"07","intvolume":"        13","article_processing_charge":"No","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","extern":"1","pmid":1,"date_created":"2018-12-11T12:08:01Z","day":"01","publication_status":"published","oa_version":"None","page":"282 - 283","status":"public","date_updated":"2022-08-25T11:56:08Z","title":"Hybrids and hybrid zones: Reply from M.G. Ritchie and N.H. Barton","external_id":{"pmid":["21238302"]},"publication":"Trends in Ecology and Evolution","issue":"7","citation":{"ama":"Ritchie M, Barton NH. Hybrids and hybrid zones: Reply from M.G. Ritchie and N.H. Barton. <i>Trends in Ecology and Evolution</i>. 1998;13(7):282-283. doi:<a href=\"https://doi.org/10.1016/S0169-5347(98)01396-2\">10.1016/S0169-5347(98)01396-2</a>","short":"M. Ritchie, N.H. Barton, Trends in Ecology and Evolution 13 (1998) 282–283.","apa":"Ritchie, M., &#38; Barton, N. H. (1998). Hybrids and hybrid zones: Reply from M.G. Ritchie and N.H. Barton. <i>Trends in Ecology and Evolution</i>. Cell Press. <a href=\"https://doi.org/10.1016/S0169-5347(98)01396-2\">https://doi.org/10.1016/S0169-5347(98)01396-2</a>","ista":"Ritchie M, Barton NH. 1998. Hybrids and hybrid zones: Reply from M.G. Ritchie and N.H. Barton. Trends in Ecology and Evolution. 13(7), 282–283.","mla":"Ritchie, Mike, and Nicholas H. Barton. “Hybrids and Hybrid Zones: Reply from M.G. Ritchie and N.H. Barton.” <i>Trends in Ecology and Evolution</i>, vol. 13, no. 7, Cell Press, 1998, pp. 282–83, doi:<a href=\"https://doi.org/10.1016/S0169-5347(98)01396-2\">10.1016/S0169-5347(98)01396-2</a>.","ieee":"M. Ritchie and N. H. Barton, “Hybrids and hybrid zones: Reply from M.G. Ritchie and N.H. Barton,” <i>Trends in Ecology and Evolution</i>, vol. 13, no. 7. Cell Press, pp. 282–283, 1998.","chicago":"Ritchie, Mike, and Nicholas H Barton. “Hybrids and Hybrid Zones: Reply from M.G. Ritchie and N.H. Barton.” <i>Trends in Ecology and Evolution</i>. Cell Press, 1998. <a href=\"https://doi.org/10.1016/S0169-5347(98)01396-2\">https://doi.org/10.1016/S0169-5347(98)01396-2</a>."}},{"type":"journal_article","year":"1998","publisher":"American Association for the Advancement of Science","doi":"10.1126/science.281.5385.1986","language":[{"iso":"eng"}],"date_published":"1998-09-25T00:00:00Z","_id":"4281","author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Charlesworth","first_name":"Brian","full_name":"Charlesworth, Brian"}],"intvolume":"       281","extern":"1","article_processing_charge":"No","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","pmid":1,"date_created":"2018-12-11T12:08:01Z","volume":281,"article_type":"original","publist_id":"1804","publication_identifier":{"issn":["0036-8075"]},"quality_controlled":"1","month":"09","status":"public","date_updated":"2022-08-25T11:53:29Z","abstract":[{"lang":"eng","text":"Most higher organisms reproduce sexually, despite the automatic reproductive advantage experienced by asexual variants. This implies the operation of selective forces that confer an advantage to sexuality and genetic recombination, at either the population or individual level. The effect of sex and recombination in breaking down negative correlations between favorable variants at different genetic loci, which increases the efficiency of natural selection, is likely to be a major factor favoring their evolution and maintenance. Various processes that can cause such an effect have been studied theoretically. It has, however, so far proved hard to discriminate among them empirically. "}],"day":"25","oa_version":"None","publication_status":"published","page":"1986 - 1990","scopus_import":"1","issue":"5385","citation":{"ista":"Barton NH, Charlesworth B. 1998. Why sex and recombination? Science. 281(5385), 1986–1990.","apa":"Barton, N. H., &#38; Charlesworth, B. (1998). Why sex and recombination? <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.281.5385.1986\">https://doi.org/10.1126/science.281.5385.1986</a>","short":"N.H. Barton, B. Charlesworth, Science 281 (1998) 1986–1990.","mla":"Barton, Nicholas H., and Brian Charlesworth. “Why Sex and Recombination?” <i>Science</i>, vol. 281, no. 5385, American Association for the Advancement of Science, 1998, pp. 1986–90, doi:<a href=\"https://doi.org/10.1126/science.281.5385.1986\">10.1126/science.281.5385.1986</a>.","ama":"Barton NH, Charlesworth B. Why sex and recombination? <i>Science</i>. 1998;281(5385):1986-1990. doi:<a href=\"https://doi.org/10.1126/science.281.5385.1986\">10.1126/science.281.5385.1986</a>","chicago":"Barton, Nicholas H, and Brian Charlesworth. “Why Sex and Recombination?” <i>Science</i>. American Association for the Advancement of Science, 1998. <a href=\"https://doi.org/10.1126/science.281.5385.1986\">https://doi.org/10.1126/science.281.5385.1986</a>.","ieee":"N. H. Barton and B. Charlesworth, “Why sex and recombination?,” <i>Science</i>, vol. 281, no. 5385. American Association for the Advancement of Science, pp. 1986–1990, 1998."},"title":"Why sex and recombination?","external_id":{"pmid":["9748151"]},"publication":"Science"},{"citation":{"apa":"Barton, N. H. (1998). Genetics and analysis of quantitative traits. <i>Genetical Research</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/S0016672398219732\">https://doi.org/10.1017/S0016672398219732</a>","mla":"Barton, Nicholas H. “Genetics and Analysis of Quantitative Traits.” <i>Genetical Research</i>, vol. 72, no. 1, Cambridge University Press, 1998, pp. 73–73, doi:<a href=\"https://doi.org/10.1017/S0016672398219732\">10.1017/S0016672398219732</a>.","short":"N.H. Barton, Genetical Research 72 (1998) 73–73.","ista":"Barton NH. 1998. Genetics and analysis of quantitative traits. Genetical Research. 72(1), 73–73.","ama":"Barton NH. Genetics and analysis of quantitative traits. <i>Genetical Research</i>. 1998;72(1):73-73. doi:<a href=\"https://doi.org/10.1017/S0016672398219732\">10.1017/S0016672398219732</a>","chicago":"Barton, Nicholas H. “Genetics and Analysis of Quantitative Traits.” <i>Genetical Research</i>. Cambridge University Press, 1998. <a href=\"https://doi.org/10.1017/S0016672398219732\">https://doi.org/10.1017/S0016672398219732</a>.","ieee":"N. H. Barton, “Genetics and analysis of quantitative traits,” <i>Genetical Research</i>, vol. 72, no. 1. Cambridge University Press, pp. 73–73, 1998."},"date_created":"2018-12-11T12:08:01Z","intvolume":"        72","issue":"1","extern":"1","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","article_processing_charge":"No","publication_identifier":{"issn":["0016-6723"]},"publist_id":"1801","month":"08","title":"Genetics and analysis of quantitative traits","volume":72,"publication":"Genetical Research","year":"1998","date_updated":"2022-08-24T13:36:46Z","publisher":"Cambridge University Press","doi":"10.1017/S0016672398219732","language":[{"iso":"eng"}],"type":"review","status":"public","_id":"4282","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}],"day":"01","publication_status":"published","oa_version":"None","page":"73 - 73","date_published":"1998-08-01T00:00:00Z"},{"citation":{"ama":"Barton NH. 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Nature Publishing Group, 1998. <a href=\"https://doi.org/10.1038/27338\">https://doi.org/10.1038/27338</a>."},"date_created":"2018-12-11T12:08:02Z","intvolume":"       395","article_processing_charge":"No","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","issue":"6704","extern":"1","scopus_import":"1","quality_controlled":"1","publist_id":"1802","publication_identifier":{"issn":["0028-0836"]},"month":"10","volume":395,"title":"The geometry of adaptation","publication":"Nature","date_updated":"2022-08-24T13:50:49Z","publisher":"Nature Publishing Group","year":"1998","language":[{"iso":"eng"}],"doi":"10.1038/27338","type":"review","status":"public","_id":"4283","author":[{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"publication_status":"published","page":"751 - 752","date_published":"1998-10-01T00:00:00Z","oa_version":"None","day":"01"},{"type":"conference","doi":"10.1007/BFb0055625","language":[{"iso":"eng"}],"year":"1998","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_published":"1998-01-01T00:00:00Z","author":[{"first_name":"Jean","full_name":"Raskin, Jean","last_name":"Raskin"},{"last_name":"Schobbens","first_name":"Pierre","full_name":"Schobbens, Pierre"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"_id":"4408","conference":{"name":"CONCUR: Concurrency Theory","end_date":"1998-09-11","start_date":"1998-09-08","location":"Nice, France"},"user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","article_processing_charge":"No","extern":"1","intvolume":"      1466","date_created":"2018-12-11T12:08:42Z","acknowledgement":"This work is supported in part by the ONR YIP award N00014-95-1-0520, by the NSF CAREER award CCR-9501708, by the NSF grant CCR-9504469, by the DARPA/NASA grant NAG2-1214, by the ARO MURI grant DAAH-04-96-1-0341, by the SRC contract 97-DC-324.041, the Belgian National Fund for Scientific Research (FNRS), the European Commission under WGs Aspire and Fireworks, the Portuguese FCT, and by Belgacom.","volume":1466,"month":"01","publist_id":"323","publication_identifier":{"isbn":["9783540648963"]},"quality_controlled":"1","status":"public","date_updated":"2022-08-24T12:15:17Z","day":"01","oa_version":"None","publication_status":"published","page":"219 - 236","abstract":[{"lang":"eng","text":"This paper presents a complete axiomatization of fully decidable propositional real-time linear temporal logics with past: the Event Clock Logic (ECL) and the Metric Interval Temporal Logic with past (MITL). The completeness proof consists of an effective proof building procedure for ECL. From this result we obtain a complete axiomatization of MITL by providing axioms translating MITL formulae into ECL formulae, the two logics being equally expressive. Our proof is structured to yield a similar axiomatization and procedure for interesting fragments of these logics, such as the linear temporal logic of the real numbers (LTR)."}],"scopus_import":"1","alternative_title":["LNCS"],"citation":{"mla":"Raskin, Jean, et al. “Axioms for Real-Time Logics.” <i>Proceedings of the 9th Interantional Conference on Concurrency Theory</i>, vol. 1466, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 1998, pp. 219–36, doi:<a href=\"https://doi.org/10.1007/BFb0055625\">10.1007/BFb0055625</a>.","apa":"Raskin, J., Schobbens, P., &#38; Henzinger, T. A. (1998). Axioms for real-time logics. In <i>Proceedings of the 9th Interantional Conference on Concurrency Theory</i> (Vol. 1466, pp. 219–236). Nice, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.1007/BFb0055625\">https://doi.org/10.1007/BFb0055625</a>","short":"J. Raskin, P. Schobbens, T.A. Henzinger, in:, Proceedings of the 9th Interantional Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 1998, pp. 219–236.","ista":"Raskin J, Schobbens P, Henzinger TA. 1998. Axioms for real-time logics. Proceedings of the 9th Interantional Conference on Concurrency Theory. CONCUR: Concurrency Theory, LNCS, vol. 1466, 219–236.","ama":"Raskin J, Schobbens P, Henzinger TA. Axioms for real-time logics. In: <i>Proceedings of the 9th Interantional Conference on Concurrency Theory</i>. Vol 1466. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 1998:219-236. doi:<a href=\"https://doi.org/10.1007/BFb0055625\">10.1007/BFb0055625</a>","chicago":"Raskin, Jean, Pierre Schobbens, and Thomas A Henzinger. “Axioms for Real-Time Logics.” In <i>Proceedings of the 9th Interantional Conference on Concurrency Theory</i>, 1466:219–36. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 1998. <a href=\"https://doi.org/10.1007/BFb0055625\">https://doi.org/10.1007/BFb0055625</a>.","ieee":"J. Raskin, P. Schobbens, and T. A. Henzinger, “Axioms for real-time logics,” in <i>Proceedings of the 9th Interantional Conference on Concurrency Theory</i>, Nice, France, 1998, vol. 1466, pp. 219–236."},"publication":"Proceedings of the 9th Interantional Conference on Concurrency Theory","title":"Axioms for real-time logics"},{"acknowledgement":"This research was supported in part by the ONR YIP award N00014-95-1-0520, by the NSF CAREER award CCR-9501708, by the NSF grant CCR-9504469, by the DARPA/NASA grant NAG2-1214, by the ARO MURI grant DAAH-04-96-1-0341, and by the SRC contract 97-DC-324.041.","date_created":"2018-12-11T12:08:43Z","intvolume":"      1486","article_processing_charge":"No","extern":"1","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","conference":{"end_date":"1998-09-18","start_date":"1998-09-14","name":"FTRTFT: Formal Techniques in Real-Time and Fault-Tolerant Systems","location":"Lyngby, Denmark"},"quality_controlled":"1","publist_id":"320","publication_identifier":{"isbn":["9783540650034"]},"month":"01","volume":1486,"publisher":"Springer","year":"1998","language":[{"iso":"eng"}],"doi":"10.1007/BFb0055350","type":"conference","_id":"4410","author":[{"full_name":"Preußig, Jörg","first_name":"Jörg","last_name":"Preußig"},{"last_name":"Kowalewski","full_name":"Kowalewski, Stefan","first_name":"Stefan"},{"last_name":"Wong Toi","full_name":"Wong Toi, Howard","first_name":"Howard"},{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"date_published":"1998-01-01T00:00:00Z","citation":{"chicago":"Preußig, Jörg, Stefan Kowalewski, Howard Wong Toi, and Thomas A Henzinger. “An Algorithm for the Approximative Analysis of Rectangular Automata.” In <i>Proceedings of the 5th International Symposium on Formal Techniques in Real-Time and Fault-Tolerant Systems</i>, 1486:228–40. Springer, 1998. <a href=\"https://doi.org/10.1007/BFb0055350\">https://doi.org/10.1007/BFb0055350</a>.","ieee":"J. Preußig, S. Kowalewski, H. Wong Toi, and T. A. Henzinger, “An algorithm for the approximative analysis of rectangular automata,” in <i>Proceedings of the 5th International Symposium on Formal Techniques in Real-Time and Fault-Tolerant Systems</i>, Lyngby, Denmark, 1998, vol. 1486, pp. 228–240.","apa":"Preußig, J., Kowalewski, S., Wong Toi, H., &#38; Henzinger, T. A. (1998). An algorithm for the approximative analysis of rectangular automata. In <i>Proceedings of the 5th International Symposium on Formal Techniques in Real-Time and Fault-Tolerant Systems</i> (Vol. 1486, pp. 228–240). Lyngby, Denmark: Springer. <a href=\"https://doi.org/10.1007/BFb0055350\">https://doi.org/10.1007/BFb0055350</a>","ista":"Preußig J, Kowalewski S, Wong Toi H, Henzinger TA. 1998. An algorithm for the approximative analysis of rectangular automata. Proceedings of the 5th International Symposium on Formal Techniques in Real-Time and Fault-Tolerant Systems. FTRTFT: Formal Techniques in Real-Time and Fault-Tolerant Systems, LNCS, vol. 1486, 228–240.","short":"J. Preußig, S. Kowalewski, H. Wong Toi, T.A. Henzinger, in:, Proceedings of the 5th International Symposium on Formal Techniques in Real-Time and Fault-Tolerant Systems, Springer, 1998, pp. 228–240.","mla":"Preußig, Jörg, et al. “An Algorithm for the Approximative Analysis of Rectangular Automata.” <i>Proceedings of the 5th International Symposium on Formal Techniques in Real-Time and Fault-Tolerant Systems</i>, vol. 1486, Springer, 1998, pp. 228–40, doi:<a href=\"https://doi.org/10.1007/BFb0055350\">10.1007/BFb0055350</a>.","ama":"Preußig J, Kowalewski S, Wong Toi H, Henzinger TA. An algorithm for the approximative analysis of rectangular automata. In: <i>Proceedings of the 5th International Symposium on Formal Techniques in Real-Time and Fault-Tolerant Systems</i>. Vol 1486. Springer; 1998:228-240. doi:<a href=\"https://doi.org/10.1007/BFb0055350\">10.1007/BFb0055350</a>"},"alternative_title":["LNCS"],"scopus_import":"1","title":"An algorithm for the approximative analysis of rectangular automata","publication":"Proceedings of the 5th International Symposium on Formal Techniques in Real-Time and Fault-Tolerant Systems","date_updated":"2022-08-24T12:01:57Z","status":"public","abstract":[{"lang":"eng","text":"Rectangular automata are well suited for approximate modeling of continuous-discrete systems. The exact analysis of these automata is feasible for small examples but can encounter severe numerical problems for even medium-sized systems. This paper presents an analysis algorithm that uses conservative overapproximation to avoid these numerical problems. The algorithm is demonstrated on a simple benchmark system consisting of two connected tanks.\r\nSupported by the German Research Council (DFG) under grant Ko1430/3 in the special program KONDISK (‘Continuous-discrete dynamics of technical systems’)."}],"oa_version":"None","publication_status":"published","page":"228 - 240","day":"01"},{"language":[{"iso":"eng"}],"doi":"10.1007/3-540-64358-3_40","publisher":"Springer","year":"1998","type":"conference","author":[{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"last_name":"Rusu","first_name":"Vlad","full_name":"Rusu, Vlad"}],"_id":"4429","date_published":"1998-01-01T00:00:00Z","date_created":"2018-12-11T12:08:48Z","acknowledgement":"This research was supported in part by the ONR YIP award N00014-95-1-0520, by the NSF CAREER award CCR-9501708, by the NSF grant CCR-9504469, by the AFOSR contract F49620-93-1-0056, by the ARO MURI grant DAAH-04-96-1-0341, by the ARPA grant NAG2-892, and by the SRC contract 95-DC-324.036.\r\nSupported by Lavoisier grant of the French Foreign Affairs Ministry and by SRI.","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","article_processing_charge":"No","extern":"1","conference":{"location":"Berkely, CA, United States of America","end_date":"1998-04-15","start_date":"1998-04-13","name":"HSCC: Hybrid Systems - Computation and Control"},"intvolume":"      1386","month":"01","quality_controlled":"1","publication_identifier":{"isbn":["9783540643586"]},"publist_id":"299","volume":1386,"date_updated":"2022-08-24T11:29:14Z","status":"public","oa_version":"None","publication_status":"published","page":"190 - 204","day":"01","abstract":[{"lang":"eng","text":"We study the reachability problem for hybrid automata. Automatic approaches, which attempt to construct the reachable region by symbolic execution, often do not terminate. In these cases, we require the user to guess the reachable region, and we use a theorem prover (Pvs) to verify the guess. We classify hybrid automata according to the theory in which their reachable region can be defined finitely. This is the theory in which the prover needs to operate in order to verify the guess. The approach is interesting, because an appropriate guess can often be deduced by extrapolating from the first few steps of symbolic execution."}],"citation":{"short":"T.A. Henzinger, V. Rusu, in:, Proceedings of the 1st International Workshop on Hybrid Systems: Computation and Control, Springer, 1998, pp. 190–204.","apa":"Henzinger, T. A., &#38; Rusu, V. (1998). Reachability verification for hybrid automata. In <i>Proceedings of the 1st International Workshop on Hybrid Systems: Computation and Control</i> (Vol. 1386, pp. 190–204). Berkely, CA, United States of America: Springer. <a href=\"https://doi.org/10.1007/3-540-64358-3_40\">https://doi.org/10.1007/3-540-64358-3_40</a>","mla":"Henzinger, Thomas A., and Vlad Rusu. “Reachability Verification for Hybrid Automata.” <i>Proceedings of the 1st International Workshop on Hybrid Systems: Computation and Control</i>, vol. 1386, Springer, 1998, pp. 190–204, doi:<a href=\"https://doi.org/10.1007/3-540-64358-3_40\">10.1007/3-540-64358-3_40</a>.","ista":"Henzinger TA, Rusu V. 1998. Reachability verification for hybrid automata. Proceedings of the 1st International Workshop on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control, LNCS, vol. 1386, 190–204.","ama":"Henzinger TA, Rusu V. Reachability verification for hybrid automata. In: <i>Proceedings of the 1st International Workshop on Hybrid Systems: Computation and Control</i>. Vol 1386. Springer; 1998:190-204. doi:<a href=\"https://doi.org/10.1007/3-540-64358-3_40\">10.1007/3-540-64358-3_40</a>","chicago":"Henzinger, Thomas A, and Vlad Rusu. “Reachability Verification for Hybrid Automata.” In <i>Proceedings of the 1st International Workshop on Hybrid Systems: Computation and Control</i>, 1386:190–204. Springer, 1998. <a href=\"https://doi.org/10.1007/3-540-64358-3_40\">https://doi.org/10.1007/3-540-64358-3_40</a>.","ieee":"T. A. Henzinger and V. Rusu, “Reachability verification for hybrid automata,” in <i>Proceedings of the 1st International Workshop on Hybrid Systems: Computation and Control</i>, Berkely, CA, United States of America, 1998, vol. 1386, pp. 190–204."},"scopus_import":"1","alternative_title":["LNCS"],"publication":"Proceedings of the 1st International Workshop on Hybrid Systems: Computation and Control","title":"Reachability verification for hybrid automata"}]