[{"author":[{"full_name":"Cheng, Siu","first_name":"Siu","last_name":"Cheng"},{"first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fu","first_name":"Ping","full_name":"Fu, Ping"},{"first_name":"Ka","last_name":"Lam","full_name":"Lam, Ka"}],"extern":"1","quality_controlled":"1","citation":{"ieee":"S. Cheng, H. Edelsbrunner, P. Fu, and K. Lam, “Design and analysis of planar shape deformation,” <i>Computational Geometry: Theory and Applications</i>, vol. 19, no. 2–3. Elsevier, pp. 205–218, 2001.","ama":"Cheng S, Edelsbrunner H, Fu P, Lam K. Design and analysis of planar shape deformation. <i>Computational Geometry: Theory and Applications</i>. 2001;19(2-3):205-218. doi:<a href=\"https://doi.org/10.1016/S0925-7721(01)00020-7\">10.1016/S0925-7721(01)00020-7</a>","chicago":"Cheng, Siu, Herbert Edelsbrunner, Ping Fu, and Ka Lam. “Design and Analysis of Planar Shape Deformation.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2001. <a href=\"https://doi.org/10.1016/S0925-7721(01)00020-7\">https://doi.org/10.1016/S0925-7721(01)00020-7</a>.","short":"S. Cheng, H. Edelsbrunner, P. Fu, K. Lam, Computational Geometry: Theory and Applications 19 (2001) 205–218.","ista":"Cheng S, Edelsbrunner H, Fu P, Lam K. 2001. Design and analysis of planar shape deformation. Computational Geometry: Theory and Applications. 19(2–3), 205–218.","apa":"Cheng, S., Edelsbrunner, H., Fu, P., &#38; Lam, K. (2001). Design and analysis of planar shape deformation. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/S0925-7721(01)00020-7\">https://doi.org/10.1016/S0925-7721(01)00020-7</a>","mla":"Cheng, Siu, et al. “Design and Analysis of Planar Shape Deformation.” <i>Computational Geometry: Theory and Applications</i>, vol. 19, no. 2–3, Elsevier, 2001, pp. 205–18, doi:<a href=\"https://doi.org/10.1016/S0925-7721(01)00020-7\">10.1016/S0925-7721(01)00020-7</a>."},"year":"2001","_id":"4002","publication":"Computational Geometry: Theory and Applications","title":"Design and analysis of planar shape deformation","abstract":[{"lang":"eng","text":"Shape deformation refers to the continuous change of one geometric object to another. We develop a software tool for planning, analyzing and visualizing deformations between two shapes in R-2. The deformation is generated automatically without any user intervention or specification of feature correspondences. A unique property of the tool is the explicit availability of a two-dimensional shape space, which can be used for designing the deformation either automatically by following constraints and objectives or manually by drawing deformation paths."}],"publication_status":"published","issue":"2-3","volume":19,"publisher":"Elsevier","article_type":"original","publist_id":"2124","intvolume":"        19","status":"public","month":"07","date_created":"2018-12-11T12:06:22Z","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","article_processing_charge":"No","day":"01","oa_version":"None","type":"journal_article","date_updated":"2023-05-10T14:21:31Z","language":[{"iso":"eng"}],"doi":"10.1016/S0925-7721(01)00020-7","acknowledgement":"NSF under grants CCR-96-19542 and CCR-97-12088.","page":"205 - 218","date_published":"2001-07-01T00:00:00Z","scopus_import":"1","publication_identifier":{"issn":["0925-7721"]}},{"date_created":"2018-12-11T12:06:23Z","conference":{"name":"SODA: Symposium on Discrete Algorithms","end_date":"2001-01-09","start_date":"2001-01-07","location":"Washington, DC, USA "},"month":"01","status":"public","publist_id":"2120","publication_identifier":{"isbn":["9780898714906"]},"publisher":"SIAM","date_published":"2001-01-09T00:00:00Z","page":"47 - 56","publication_status":"published","abstract":[{"lang":"eng","text":"This paper describes an algorithm for maintaining an approximating triangulation of a deforming surface in R-3. The triangulation adapts dynamically to changing shape, curvature, and topology of the surface."}],"title":"Dynamic skin triangulation","publication":"Proceedings of the 12th annual ACM-SIAM symposium on Discrete algorithms","language":[{"iso":"eng"}],"_id":"4005","type":"conference","date_updated":"2023-05-10T12:35:44Z","oa_version":"None","day":"09","year":"2001","citation":{"apa":"Cheng, H., Dey, T., Edelsbrunner, H., &#38; Sullivan, J. (2001). Dynamic skin triangulation. In <i>Proceedings of the 12th annual ACM-SIAM symposium on Discrete algorithms</i> (pp. 47–56). Washington, DC, USA : SIAM.","mla":"Cheng, Ho, et al. “Dynamic Skin Triangulation.” <i>Proceedings of the 12th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, SIAM, 2001, pp. 47–56.","short":"H. Cheng, T. Dey, H. Edelsbrunner, J. Sullivan, in:, Proceedings of the 12th Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2001, pp. 47–56.","chicago":"Cheng, Ho, Tamal Dey, Herbert Edelsbrunner, and John Sullivan. “Dynamic Skin Triangulation.” In <i>Proceedings of the 12th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 47–56. SIAM, 2001.","ista":"Cheng H, Dey T, Edelsbrunner H, Sullivan J. 2001. Dynamic skin triangulation. Proceedings of the 12th annual ACM-SIAM symposium on Discrete algorithms. SODA: Symposium on Discrete Algorithms, 47–56.","ama":"Cheng H, Dey T, Edelsbrunner H, Sullivan J. Dynamic skin triangulation. In: <i>Proceedings of the 12th Annual ACM-SIAM Symposium on Discrete Algorithms</i>. SIAM; 2001:47-56.","ieee":"H. Cheng, T. Dey, H. Edelsbrunner, and J. Sullivan, “Dynamic skin triangulation,” in <i>Proceedings of the 12th annual ACM-SIAM symposium on Discrete algorithms</i>, Washington, DC, USA , 2001, pp. 47–56."},"main_file_link":[{"url":"https://dl.acm.org/doi/10.5555/365411.365418"}],"extern":"1","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","author":[{"full_name":"Cheng, Ho","first_name":"Ho","last_name":"Cheng"},{"full_name":"Dey, Tamal","last_name":"Dey","first_name":"Tamal"},{"last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"John","last_name":"Sullivan","full_name":"Sullivan, John"}],"quality_controlled":"1","article_processing_charge":"No"},{"issue":"5","page":"379 - 399","volume":7,"date_published":"2001-05-28T00:00:00Z","publisher":"Springer","article_type":"original","publication_identifier":{"issn":["0948-695X"]},"publist_id":"2121","intvolume":"         7","status":"public","date_created":"2018-12-11T12:06:24Z","month":"05","extern":"1","quality_controlled":"1","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert"}],"article_processing_charge":"No","citation":{"apa":"Edelsbrunner, H. (2001). 180 wrapped tubes. <i>Journal of Universal Computer Science</i>. Springer. <a href=\"https://doi.org/10.3217/jucs-007-05-0379\">https://doi.org/10.3217/jucs-007-05-0379</a>","mla":"Edelsbrunner, Herbert. “180 Wrapped Tubes.” <i>Journal of Universal Computer Science</i>, vol. 7, no. 5, Springer, 2001, pp. 379–99, doi:<a href=\"https://doi.org/10.3217/jucs-007-05-0379\">10.3217/jucs-007-05-0379</a>.","chicago":"Edelsbrunner, Herbert. “180 Wrapped Tubes.” <i>Journal of Universal Computer Science</i>. Springer, 2001. <a href=\"https://doi.org/10.3217/jucs-007-05-0379\">https://doi.org/10.3217/jucs-007-05-0379</a>.","short":"H. Edelsbrunner, Journal of Universal Computer Science 7 (2001) 379–399.","ista":"Edelsbrunner H. 2001. 180 wrapped tubes. Journal of Universal Computer Science. 7(5), 379–399.","ama":"Edelsbrunner H. 180 wrapped tubes. <i>Journal of Universal Computer Science</i>. 2001;7(5):379-399. doi:<a href=\"https://doi.org/10.3217/jucs-007-05-0379\">10.3217/jucs-007-05-0379</a>","ieee":"H. Edelsbrunner, “180 wrapped tubes,” <i>Journal of Universal Computer Science</i>, vol. 7, no. 5. Springer, pp. 379–399, 2001."},"day":"28","year":"2001","date_updated":"2023-05-10T12:39:54Z","type":"journal_article","oa_version":"None","doi":"10.3217/jucs-007-05-0379","language":[{"iso":"eng"}],"_id":"4006","title":"180 wrapped tubes","publication":"Journal of Universal Computer Science","publication_status":"published","abstract":[{"text":"The 180 models collected in this paper are produced by sampling and wrapping point sets on tubes. The surfaces are represented as triangulated 2-manifolds and available as st1-files from the author's web site at www.cs.duke.edu/similar toedels. Each tube is obtained by thickening a circle or a smooth torus knot, and for some we use the degrees of freedom in the thickening process to encode meaningful information, such as curvature or torsion.","lang":"eng"}]},{"scopus_import":"1","publication_identifier":{"issn":["0179-5376"]},"page":"525 - 568","date_published":"2001-04-04T00:00:00Z","doi":"10.1007/s00454-001-0007-1","language":[{"iso":"eng"}],"acknowledgement":"NSF under grant DMS- 98-73945, ARO under grant DAAG55-98-1-0177, NSF under grants CCR-96- 19542 and CCR-97-12088.","article_processing_charge":"No","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","day":"04","oa_version":"None","date_updated":"2023-05-10T12:45:59Z","type":"journal_article","publist_id":"2122","intvolume":"        25","status":"public","month":"04","date_created":"2018-12-11T12:06:24Z","volume":25,"issue":"4","publisher":"Springer","article_type":"original","_id":"4007","title":"Dynamic skin triangulation","publication":"Discrete & Computational Geometry","abstract":[{"lang":"eng","text":"This paper describes an algorithm for maintaining an approximating triangulation of a deforming surface in R 3 . The surface is the envelope of an infinite family of spheres defined and controlled by a finite collection of weighted points. The triangulation adapts dynamically to changing shape, curvature, and topology of the surface. "}],"publication_status":"published","extern":"1","author":[{"full_name":"Cheng, Ho","first_name":"Ho","last_name":"Cheng"},{"full_name":"Dey, Tamal","last_name":"Dey","first_name":"Tamal"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert"},{"last_name":"Sullivan","first_name":"John","full_name":"Sullivan, John"}],"quality_controlled":"1","citation":{"mla":"Cheng, Ho, et al. “Dynamic Skin Triangulation.” <i>Discrete &#38; Computational Geometry</i>, vol. 25, no. 4, Springer, 2001, pp. 525–68, doi:<a href=\"https://doi.org/10.1007/s00454-001-0007-1\">10.1007/s00454-001-0007-1</a>.","apa":"Cheng, H., Dey, T., Edelsbrunner, H., &#38; Sullivan, J. (2001). Dynamic skin triangulation. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-001-0007-1\">https://doi.org/10.1007/s00454-001-0007-1</a>","ieee":"H. Cheng, T. Dey, H. Edelsbrunner, and J. Sullivan, “Dynamic skin triangulation,” <i>Discrete &#38; Computational Geometry</i>, vol. 25, no. 4. Springer, pp. 525–568, 2001.","ama":"Cheng H, Dey T, Edelsbrunner H, Sullivan J. Dynamic skin triangulation. <i>Discrete &#38; Computational Geometry</i>. 2001;25(4):525-568. doi:<a href=\"https://doi.org/10.1007/s00454-001-0007-1\">10.1007/s00454-001-0007-1</a>","ista":"Cheng H, Dey T, Edelsbrunner H, Sullivan J. 2001. Dynamic skin triangulation. Discrete &#38; Computational Geometry. 25(4), 525–568.","short":"H. Cheng, T. Dey, H. Edelsbrunner, J. Sullivan, Discrete &#38; Computational Geometry 25 (2001) 525–568.","chicago":"Cheng, Ho, Tamal Dey, Herbert Edelsbrunner, and John Sullivan. “Dynamic Skin Triangulation.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2001. <a href=\"https://doi.org/10.1007/s00454-001-0007-1\">https://doi.org/10.1007/s00454-001-0007-1</a>."},"year":"2001"},{"publication_identifier":{"issn":["0890-9369"]},"page":"1427 - 1434","external_id":{"pmid":["11390362"]},"date_published":"2001-06-01T00:00:00Z","acknowledgement":"We thank many colleagues who provided reagents that enabled us to test axin1 and several other genes as candidates for the mbl mutation. In particular, we are indebted to Masahiko Hibi, Ken Irvine, Antonio Jacinto, Yun-Jin Jiang, Julian Lewis, and Tom Vogt for help and advice. We thank Ajay Chitnis and Dana Zivkovic for providing information prior to publication. This study was supported primarily by grants from the EMBO and EC to C.P.H., Wellcome Trust and EC to S.W.W., from the MRC to D.S., from Naito to M.T., from the DHGP to G.J.R. and R.G., and from the CRC/ICR to T.D. P.C. was supported by a PhD studentship from Fundação para a Ciência e Tecnologia, Programa PRAXIS XXI. S.W.W. is a Wellcome Trust Senior Research Fellow.\r\n\r\nThe publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 USC section 1734 solely to indicate this fact.","doi":"10.1101/gad.194301","language":[{"iso":"eng"}],"day":"01","oa_version":"Published Version","type":"journal_article","date_updated":"2023-05-10T12:27:02Z","article_processing_charge":"No","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","status":"public","month":"06","date_created":"2018-12-11T12:07:33Z","publist_id":"1916","intvolume":"        15","publisher":"Cold Spring Harbor Laboratory Press","article_type":"original","issue":"11","volume":15,"abstract":[{"text":"Zebrafish embryos homozygous for the masterblind (mb1) mutation exhibit a striking phenotype in which the eyes and telencephalon are reduced or absent and diencephalic fates expand to the front of the brain. Here we show that mb1(-/-) embryos carry an amino-acid change at a conserved site in the Wnt pathway scaffolding protein, Axin1. The amino-acid substitution present in the mbl allele abolishes the binding of Axin to Gsk3 and affects Tcf-dependent transcription. Therefore, Gsk3 activity may be decreased in mbl(-/-) embryos and in support of this possibility, overexpression of either wild-type Axin1 or Gsk3 beta can restore eye and telencephalic fates to mb1(-/-) embryos. Our data reveal a crucial role for Axin1-dependent inhibition of the Wnt pathway in the early regional subdivision of the anterior neural plate into telencephalic, diencephalic, and eye-forming territories.","lang":"eng"}],"publication_status":"published","_id":"4200","oa":1,"pmid":1,"title":"A mutation in the Gsk3-binding domain of zebrafish Masterblind/Axin1 leads to a fate transformation of telencephalon and eyes to diencephalon","publication":"Genes and Development","year":"2001","extern":"1","quality_controlled":"1","author":[{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"},{"full_name":"Houart, Corinne","last_name":"Houart","first_name":"Corinne"},{"full_name":"Take Uchi, Masaya","first_name":"Masaya","last_name":"Take Uchi"},{"full_name":"Rauch, Gerd","first_name":"Gerd","last_name":"Rauch"},{"first_name":"Neville","last_name":"Young","full_name":"Young, Neville"},{"full_name":"Coutinho, Pedro","last_name":"Coutinho","first_name":"Pedro"},{"full_name":"Masai, Ichiro","last_name":"Masai","first_name":"Ichiro"},{"first_name":"Luca","last_name":"Caneparo","full_name":"Caneparo, Luca"},{"full_name":"Concha, Miguel","first_name":"Miguel","last_name":"Concha"},{"last_name":"Geisler","first_name":"Robert","full_name":"Geisler, Robert"},{"full_name":"Dale, Trevor","last_name":"Dale","first_name":"Trevor"},{"full_name":"Wilson, Stephen","last_name":"Wilson","first_name":"Stephen"},{"full_name":"Stemple, Derek","first_name":"Derek","last_name":"Stemple"}],"citation":{"ista":"Heisenberg C-PJ, Houart C, Take Uchi M, Rauch G, Young N, Coutinho P, Masai I, Caneparo L, Concha M, Geisler R, Dale T, Wilson S, Stemple D. 2001. A mutation in the Gsk3-binding domain of zebrafish Masterblind/Axin1 leads to a fate transformation of telencephalon and eyes to diencephalon. Genes and Development. 15(11), 1427–1434.","chicago":"Heisenberg, Carl-Philipp J, Corinne Houart, Masaya Take Uchi, Gerd Rauch, Neville Young, Pedro Coutinho, Ichiro Masai, et al. “A Mutation in the Gsk3-Binding Domain of Zebrafish Masterblind/Axin1 Leads to a Fate Transformation of Telencephalon and Eyes to Diencephalon.” <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press, 2001. <a href=\"https://doi.org/10.1101/gad.194301\">https://doi.org/10.1101/gad.194301</a>.","short":"C.-P.J. Heisenberg, C. Houart, M. Take Uchi, G. Rauch, N. Young, P. Coutinho, I. Masai, L. Caneparo, M. Concha, R. Geisler, T. Dale, S. Wilson, D. Stemple, Genes and Development 15 (2001) 1427–1434.","ieee":"C.-P. J. Heisenberg <i>et al.</i>, “A mutation in the Gsk3-binding domain of zebrafish Masterblind/Axin1 leads to a fate transformation of telencephalon and eyes to diencephalon,” <i>Genes and Development</i>, vol. 15, no. 11. Cold Spring Harbor Laboratory Press, pp. 1427–1434, 2001.","ama":"Heisenberg C-PJ, Houart C, Take Uchi M, et al. A mutation in the Gsk3-binding domain of zebrafish Masterblind/Axin1 leads to a fate transformation of telencephalon and eyes to diencephalon. <i>Genes and Development</i>. 2001;15(11):1427-1434. doi:<a href=\"https://doi.org/10.1101/gad.194301\">10.1101/gad.194301</a>","apa":"Heisenberg, C.-P. J., Houart, C., Take Uchi, M., Rauch, G., Young, N., Coutinho, P., … Stemple, D. (2001). A mutation in the Gsk3-binding domain of zebrafish Masterblind/Axin1 leads to a fate transformation of telencephalon and eyes to diencephalon. <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gad.194301\">https://doi.org/10.1101/gad.194301</a>","mla":"Heisenberg, Carl-Philipp J., et al. “A Mutation in the Gsk3-Binding Domain of Zebrafish Masterblind/Axin1 Leads to a Fate Transformation of Telencephalon and Eyes to Diencephalon.” <i>Genes and Development</i>, vol. 15, no. 11, Cold Spring Harbor Laboratory Press, 2001, pp. 1427–34, doi:<a href=\"https://doi.org/10.1101/gad.194301\">10.1101/gad.194301</a>."},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC312705/","open_access":"1"}]},{"page":"117 - 128","external_id":{"pmid":["11231891"]},"date_published":"2001-02-01T00:00:00Z","publication_identifier":{"issn":["0022-2844"]},"day":"01","oa_version":"None","date_updated":"2023-05-10T12:23:49Z","type":"journal_article","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","article_processing_charge":"No","acknowledgement":"We thank Kenneth G. Karol, Andrea J. Betancourt, Daven C. Presgraves, and Bret Larget for helpful comments and\r\nsuggestions. This work was supported by funding from the National Science Foundation (MCB-0075404 and DEB-0075406) to J.P.H.","doi":"10.1007/s002390010140","language":[{"iso":"eng"}],"article_type":"original","publisher":"Springer","issue":"2","volume":52,"status":"public","month":"02","date_created":"2018-12-11T12:07:43Z","publist_id":"1886","intvolume":"        52","year":"2001","extern":"1","author":[{"first_name":"Jonathan P","last_name":"Bollback","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Huelsenbeck, John","first_name":"John","last_name":"Huelsenbeck"}],"quality_controlled":"1","citation":{"mla":"Bollback, Jonathan P., and John Huelsenbeck. “Phylogeny, Genome Evolution, and Host Specificity of Single-Stranded RNA Bacteriophage (Family Leviviridae).” <i>Journal of Molecular Evolution</i>, vol. 52, no. 2, Springer, 2001, pp. 117–28, doi:<a href=\"https://doi.org/10.1007/s002390010140\">10.1007/s002390010140</a>.","apa":"Bollback, J. P., &#38; Huelsenbeck, J. (2001). Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (Family Leviviridae). <i>Journal of Molecular Evolution</i>. Springer. <a href=\"https://doi.org/10.1007/s002390010140\">https://doi.org/10.1007/s002390010140</a>","ista":"Bollback JP, Huelsenbeck J. 2001. Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (Family Leviviridae). Journal of Molecular Evolution. 52(2), 117–128.","chicago":"Bollback, Jonathan P, and John Huelsenbeck. “Phylogeny, Genome Evolution, and Host Specificity of Single-Stranded RNA Bacteriophage (Family Leviviridae).” <i>Journal of Molecular Evolution</i>. Springer, 2001. <a href=\"https://doi.org/10.1007/s002390010140\">https://doi.org/10.1007/s002390010140</a>.","short":"J.P. Bollback, J. Huelsenbeck, Journal of Molecular Evolution 52 (2001) 117–128.","ama":"Bollback JP, Huelsenbeck J. Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (Family Leviviridae). <i>Journal of Molecular Evolution</i>. 2001;52(2):117-128. doi:<a href=\"https://doi.org/10.1007/s002390010140\">10.1007/s002390010140</a>","ieee":"J. P. Bollback and J. Huelsenbeck, “Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (Family Leviviridae),” <i>Journal of Molecular Evolution</i>, vol. 52, no. 2. Springer, pp. 117–128, 2001."},"abstract":[{"lang":"eng","text":"Bacteriophage of the family Leviviridae have played an important role in molecular biology where representative species, such as Qβ and MS2, have been studied as model systems for replication, translation, and the role of secondary structure in gene regulation. Using nucleotide sequences from the coat and replicase genes we present the first statistical estimate of phylogeny for the family Leviviridae using maximum-likelihood and Bayesian estimation. Our analyses reveal that the coliphage species are a monophyletic group consisting of two clades representing the genera Levivirus and Allolevivirus. The Pseudomonas species PP7 diverged from its common ancestor with the coliphage prior to the ancient split between these genera and their subsequent diversification. Differences in genome size, gene composition, and gene expression are shown with a high probability to have changed along the lineage leading to the Allolevivirus through gene expansion. The change in genome size of the Allolevivirus ancestor may have catalyzed subsequent changes that led to their current genome organization and gene expression."}],"publication_status":"published","_id":"4229","pmid":1,"title":"Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (Family Leviviridae)","publication":"Journal of Molecular Evolution"},{"day":"01","oa_version":"None","date_updated":"2023-05-10T12:16:55Z","type":"journal_article","article_processing_charge":"No","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","acknowledgement":"We thank D. Bolnick, B. Fitzpatrick, S. Gavrilets, R. Haygood, C.D. Jones, M. Kirkpatrick, A. Kondrashov, J.B. Mullet, S.V. Nuzhdin, H.A. Orr, T.D. Price, T. Prout, D.W. Schemske, D. Schluter, M.R. Servedio and P.S. Ward for discussion and comments. Some of these reviewers disagree with our conclusions. This work was supported by US National Science Foundation grants DEB 9527808 and DEB 0089716 to MT, grants from the Darwin Trust of Edinburgh and the Biotechnology and Biological Sciences Research Council (GRJ/76057, GR/H/09928) to NHB, and National Institutes of Health grant R01 GM58260 to JAC. ","doi":"10.1016/S0169-5347(01)02177-2","language":[{"iso":"eng"}],"page":"330 - 343","external_id":{"pmid":["11403865"]},"date_published":"2001-07-01T00:00:00Z","publication_identifier":{"issn":["0169-5347"]},"year":"2001","quality_controlled":"1","author":[{"first_name":"Michael","last_name":"Turelli","full_name":"Turelli, Michael"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"first_name":"Jerry","last_name":"Coyne","full_name":"Coyne, Jerry"}],"extern":"1","citation":{"mla":"Turelli, Michael, et al. “Theory and Speciation.” <i>Trends in Ecology and Evolution</i>, vol. 16, no. 7, Cell Press, 2001, pp. 330–43, doi:<a href=\"https://doi.org/10.1016/S0169-5347(01)02177-2\">10.1016/S0169-5347(01)02177-2</a>.","apa":"Turelli, M., Barton, N. H., &#38; Coyne, J. (2001). Theory and speciation. <i>Trends in Ecology and Evolution</i>. Cell Press. <a href=\"https://doi.org/10.1016/S0169-5347(01)02177-2\">https://doi.org/10.1016/S0169-5347(01)02177-2</a>","ama":"Turelli M, Barton NH, Coyne J. Theory and speciation. <i>Trends in Ecology and Evolution</i>. 2001;16(7):330-343. doi:<a href=\"https://doi.org/10.1016/S0169-5347(01)02177-2\">10.1016/S0169-5347(01)02177-2</a>","ieee":"M. Turelli, N. H. Barton, and J. Coyne, “Theory and speciation,” <i>Trends in Ecology and Evolution</i>, vol. 16, no. 7. Cell Press, pp. 330–343, 2001.","short":"M. Turelli, N.H. Barton, J. Coyne, Trends in Ecology and Evolution 16 (2001) 330–343.","chicago":"Turelli, Michael, Nicholas H Barton, and Jerry Coyne. “Theory and Speciation.” <i>Trends in Ecology and Evolution</i>. Cell Press, 2001. <a href=\"https://doi.org/10.1016/S0169-5347(01)02177-2\">https://doi.org/10.1016/S0169-5347(01)02177-2</a>.","ista":"Turelli M, Barton NH, Coyne J. 2001. Theory and speciation. Trends in Ecology and Evolution. 16(7), 330–343."},"abstract":[{"text":"The study of speciation has become one of the most active areas of evolutionary biology, and substantial progress has been made in documenting and understanding phenomena ranging from sympatric speciation and reinforcement to the evolutionary genetics of postzygotic isolation. This progress has been driven largely by empirical results, and most useful theoretical work has concentrated on making sense of empirical patterns. Given the complexity of speciation, mathematical theory is subordinate to verbal theory and generalizations about data. Nevertheless, mathematical theory can provide a useful classification of verbal theories; can help determine the biological plausibility of verbal theories; can determine whether alternative mechanisms of speciation are consistent with empirical patterns; and can occasionally provide predictions that go beyond empirical generalizations. We discuss recent examples of progress in each of these areas.","lang":"eng"}],"publication_status":"published","_id":"4264","pmid":1,"title":"Theory and speciation","publication":"Trends in Ecology and Evolution","publisher":"Cell Press","article_type":"original","volume":16,"issue":"7","status":"public","month":"07","date_created":"2018-12-11T12:07:55Z","publist_id":"1828","intvolume":"        16"},{"year":"2001","quality_controlled":"1","author":[{"full_name":"Otto, Sarah","last_name":"Otto","first_name":"Sarah"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"}],"extern":"1","citation":{"chicago":"Otto, Sarah, and Nicholas H Barton. “Selection for Recombination in Small Populations.” <i>Evolution; International Journal of Organic Evolution</i>. Wiley-Blackwell, 2001. <a href=\"https://doi.org/10.1111/j.0014-3820.2001.tb01310.x\">https://doi.org/10.1111/j.0014-3820.2001.tb01310.x</a>.","short":"S. Otto, N.H. Barton, Evolution; International Journal of Organic Evolution 55 (2001) 1921–1931.","ista":"Otto S, Barton NH. 2001. Selection for recombination in small populations. Evolution; International Journal of Organic Evolution. 55(10), 1921–1931.","ieee":"S. Otto and N. H. Barton, “Selection for recombination in small populations,” <i>Evolution; International Journal of Organic Evolution</i>, vol. 55, no. 10. Wiley-Blackwell, pp. 1921–1931, 2001.","ama":"Otto S, Barton NH. Selection for recombination in small populations. <i>Evolution; International Journal of Organic Evolution</i>. 2001;55(10):1921-1931. doi:<a href=\"https://doi.org/10.1111/j.0014-3820.2001.tb01310.x\">10.1111/j.0014-3820.2001.tb01310.x</a>","mla":"Otto, Sarah, and Nicholas H. Barton. “Selection for Recombination in Small Populations.” <i>Evolution; International Journal of Organic Evolution</i>, vol. 55, no. 10, Wiley-Blackwell, 2001, pp. 1921–31, doi:<a href=\"https://doi.org/10.1111/j.0014-3820.2001.tb01310.x\">10.1111/j.0014-3820.2001.tb01310.x</a>.","apa":"Otto, S., &#38; Barton, N. H. (2001). Selection for recombination in small populations. <i>Evolution; International Journal of Organic Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.0014-3820.2001.tb01310.x\">https://doi.org/10.1111/j.0014-3820.2001.tb01310.x</a>"},"abstract":[{"lang":"eng","text":"The reasons that sex and recombination are so widespread remain elusive. One popular hypothesis is that sex and recombination promote adaptation to a changing environment. The strongest evidence that increased recombination may evolve because recombination promotes adaptation comes from artificially selected populations. Recombination rates have been found to increase as a correlated response to selection on traits unrelated to recombination in several artificial selection experiments and in a comparison of domesticated and nondomesticated mammals. There are, however, several alternative explanations for the increase in recombination in such populations, including two different evolutionary explanations. The first is that the form of selection is epistatic, generating linkage disequilibria among selected loci, which can indirectly favor modifier alleles that increase recombination. The second is that random genetic drift in selected populations tends to generate disequilibria such that beneficial alleles are often found in different individuals; modifier alleles that increase recombination can bring together such favorable alleles and thus may be found in individuals with greater fitness. In this paper, we compare the evolutionary forces acting on recombination in finite populations subject to strong selection, To our surprise, we found that drift accounted for the majority of selection for increased recombination observed in simulations of small to moderately large populations, suggesting that, unless selected populations are large, epistasis plays a secondary role in the evolution of recombination."}],"publication_status":"published","_id":"4265","pmid":1,"publication":"Evolution; International Journal of Organic Evolution","title":"Selection for recombination in small populations","publisher":"Wiley-Blackwell","article_type":"original","issue":"10","volume":55,"status":"public","month":"10","date_created":"2018-12-11T12:07:56Z","publist_id":"1827","intvolume":"        55","day":"01","oa_version":"None","type":"journal_article","date_updated":"2023-05-10T12:12:32Z","article_processing_charge":"No","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","acknowledgement":"We are grateful to P. Awadalla, T. Lenormand, A. Peters, S. West, M. Whitlock, and two anonymous reviewers for helpful comments on the manuscript. Funding was provided by the Natural Sciences and Engineering Research Council\r\n(Canada) to SPO, the Centre National de la Recherche Scientifique (France) to SPO, the Darwin Trust of Edinburgh to\r\nNHB, and the BBSRC (U.K.) to NHB. ","doi":"10.1111/j.0014-3820.2001.tb01310.x","language":[{"iso":"eng"}],"page":"1921 - 1931","external_id":{"pmid":["11761054"]},"date_published":"2001-10-01T00:00:00Z","scopus_import":"1","publication_identifier":{"issn":["0014-3820"]}},{"publist_id":"1824","intvolume":"        10","status":"public","date_created":"2018-12-11T12:07:56Z","month":"03","volume":10,"issue":"3","article_type":"original","publisher":"Wiley-Blackwell","_id":"4266","publication":"Molecular Ecology","title":"The role of hybridization in evolution","pmid":1,"publication_status":"published","abstract":[{"text":"Hybridization may influence evolution in a variety of ways. If hybrids are less fit, the geographical range of ecologically divergent populations may be limited, and prezygotic reproductive isolation may be reinforced. If some hybrid genotypes are fitter than one or both parents, at least in some environments, then hybridization could make a positive contribution. Single alleles that are at an advantage in the alternative environment and genetic background will introgress readily, although such introgression may be hard to detect. 'Hybrid speciation', in which fit combinations of alleles are established, is more problematic; its likelihood depends on how divergent populations meet, and on the structure of epistasis. These issues are illustrated using Fisher's model of stabilizing selection on multiple traits, under which reproductive isolation evolves as a side-effect of adaptation in allopatry. This confirms a priori arguments that while recombinant hybrids are less fit on average, some gene combinations may be fitter than the parents, even in the parental environment. Fisher's model does predict heterosis in diploid F1s, asymmetric incompatibility in reciprocal backcrosses, and (when dominance is included) Haldane's Rule. However, heterosis arises only when traits are additive, whereas the latter two patterns require dominance. Moreover, because adaptation is via substitutions of small effect, Fisher's model does not generate the strong effects of single chromosome regions often observed in species crosses.","lang":"eng"}],"quality_controlled":"1","extern":"1","author":[{"last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"citation":{"apa":"Barton, N. H. (2001). The role of hybridization in evolution. <i>Molecular Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1046/j.1365-294X.2001.01216.x\">https://doi.org/10.1046/j.1365-294X.2001.01216.x</a>","mla":"Barton, Nicholas H. “The Role of Hybridization in Evolution.” <i>Molecular Ecology</i>, vol. 10, no. 3, Wiley-Blackwell, 2001, pp. 551–68, doi:<a href=\"https://doi.org/10.1046/j.1365-294X.2001.01216.x\">10.1046/j.1365-294X.2001.01216.x</a>.","short":"N.H. Barton, Molecular Ecology 10 (2001) 551–568.","chicago":"Barton, Nicholas H. “The Role of Hybridization in Evolution.” <i>Molecular Ecology</i>. Wiley-Blackwell, 2001. <a href=\"https://doi.org/10.1046/j.1365-294X.2001.01216.x\">https://doi.org/10.1046/j.1365-294X.2001.01216.x</a>.","ista":"Barton NH. 2001. The role of hybridization in evolution. Molecular Ecology. 10(3), 551–568.","ama":"Barton NH. The role of hybridization in evolution. <i>Molecular Ecology</i>. 2001;10(3):551-568. doi:<a href=\"https://doi.org/10.1046/j.1365-294X.2001.01216.x\">10.1046/j.1365-294X.2001.01216.x</a>","ieee":"N. H. Barton, “The role of hybridization in evolution,” <i>Molecular Ecology</i>, vol. 10, no. 3. Wiley-Blackwell, pp. 551–568, 2001."},"year":"2001","publication_identifier":{"issn":["962-1083"]},"scopus_import":"1","page":"551 - 568","date_published":"2001-03-01T00:00:00Z","external_id":{"pmid":["11298968"]},"doi":"10.1046/j.1365-294X.2001.01216.x","language":[{"iso":"eng"}],"acknowledgement":"This work was supported by the Darwin Trust of Edinburgh and by  grant  GR3/11635  from  the  Natural  Environment  Research Council. I would like to thank Loren Rieseberg, Allen Orr, Michael Turelli, and an anonymous referee for their helpful comments","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","article_processing_charge":"No","day":"01","date_updated":"2023-05-10T11:45:07Z","type":"journal_article","oa_version":"None"},{"status":"public","date_created":"2018-12-11T12:07:57Z","month":"08","publication_identifier":{"isbn":["9780521840002"]},"publist_id":"1825","publisher":"Cambridge University Press","page":"365 - 392","date_published":"2001-08-01T00:00:00Z","publication_status":"published","abstract":[{"lang":"eng","text":"The flow of genes from the dense and well-adapted centre of a species' distribution interferes with adaptation to marginal environments, and may sharply limit a species' range. Deterministic models of a linear habitat suggest that populations could in principle adapt to very steep environmental gradients, by increasing their genetic variability. However, random fluctuations in sparse populations reduce this variance, and may be crucial in limiting the species' range."}],"language":[{"iso":"eng"}],"_id":"4267","publication":"Integrating ecology and evolution in a spatial context","title":"Adaptation at the edge of a species' range","day":"01","year":"2001","type":"book_chapter","date_updated":"2023-05-10T11:59:06Z","oa_version":"None","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"}],"article_processing_charge":"No","quality_controlled":"1","extern":"1","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","citation":{"ista":"Barton NH. 2001.Adaptation at the edge of a species’ range. In: Integrating ecology and evolution in a spatial context. , 365–392.","chicago":"Barton, Nicholas H. “Adaptation at the Edge of a Species’ Range.” In <i>Integrating Ecology and Evolution in a Spatial Context</i>, 365–92. Cambridge University Press, 2001.","short":"N.H. Barton, in:, Integrating Ecology and Evolution in a Spatial Context, Cambridge University Press, 2001, pp. 365–392.","ama":"Barton NH. Adaptation at the edge of a species’ range. In: <i>Integrating Ecology and Evolution in a Spatial Context</i>. Cambridge University Press; 2001:365-392.","ieee":"N. H. Barton, “Adaptation at the edge of a species’ range,” in <i>Integrating ecology and evolution in a spatial context</i>, Cambridge University Press, 2001, pp. 365–392.","apa":"Barton, N. H. (2001). Adaptation at the edge of a species’ range. In <i>Integrating ecology and evolution in a spatial context</i> (pp. 365–392). Cambridge University Press.","mla":"Barton, Nicholas H. “Adaptation at the Edge of a Species’ Range.” <i>Integrating Ecology and Evolution in a Spatial Context</i>, Cambridge University Press, 2001, pp. 365–92."},"main_file_link":[{"url":"https://www.cambridge.org/us/academic/subjects/life-sciences/ecology-and-conservation/integrating-ecology-and-evolution-spatial-context-14th-special-symposium-british-ecological-society?format=HB&isbn=9780521840002"}]},{"status":"public","date_created":"2018-12-11T12:08:00Z","month":"04","publist_id":"1812","publication_identifier":{"isbn":["9780198506591"]},"publisher":"Oxford University Press","date_published":"2001-04-01T00:00:00Z","publication_status":"published","abstract":[{"lang":"eng","text":"The ability of species to migrate that has interested ecologists for many years. Now that so many species and ecosystems face major environmental change, the ability of species to adapt to these changes by dispersing, migrating, or moving between different patches of habitat can be crucial to ensuring their survivial. This book provides a timely and wide-ranging overview of the study of dispersal and incorporates much of the latest research. The causes, mechanisms, and consequences of dispersal at the individual, population, species and community levels are considered. The potential of new techniques and models for studying dispersal, drawn from molecular biology and demography, is also explored. Perspectives and insights are offered from the fields of evolution, conservation biology and genetics. Throughout the book, theoretical approaches are combined with empirical data, and care has been taken to include examples from as wide a range of species as possible. "}],"language":[{"iso":"eng"}],"_id":"4278","publication":"Dispersal","title":"The evolutionary consequences of gene flow and local adaptation: Future approaches","day":"01","year":"2001","date_updated":"2023-05-10T09:57:10Z","type":"book_chapter","oa_version":"None","extern":"1","quality_controlled":"1","article_processing_charge":"No","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"citation":{"mla":"Barton, Nicholas H. “The Evolutionary Consequences of Gene Flow and Local Adaptation: Future Approaches.” <i>Dispersal</i>, Oxford University Press, 2001.","apa":"Barton, N. H. (2001). The evolutionary consequences of gene flow and local adaptation: Future approaches. In <i>Dispersal</i>. Oxford University Press.","ama":"Barton NH. The evolutionary consequences of gene flow and local adaptation: Future approaches. In: <i>Dispersal</i>. Oxford University Press; 2001.","ieee":"N. H. Barton, “The evolutionary consequences of gene flow and local adaptation: Future approaches,” in <i>Dispersal</i>, Oxford University Press, 2001.","ista":"Barton NH. 2001.The evolutionary consequences of gene flow and local adaptation: Future approaches. In: Dispersal. .","chicago":"Barton, Nicholas H. “The Evolutionary Consequences of Gene Flow and Local Adaptation: Future Approaches.” In <i>Dispersal</i>. Oxford University Press, 2001.","short":"N.H. Barton, in:, Dispersal, Oxford University Press, 2001."},"main_file_link":[{"url":"https://www.nhbs.com/dispersal-book"}]},{"publist_id":"283","publication_identifier":{"isbn":["9783540426738"]},"intvolume":"      2211","alternative_title":["LNCS"],"status":"public","date_created":"2018-12-11T12:08:54Z","conference":{"end_date":"2001-10-10","name":"EMSOFT 2001: Embedded Software","start_date":"2001-10-08","location":"Tahoe City, CA, USA"},"month":"09","volume":2211,"date_published":"2001-09-26T00:00:00Z","publisher":"ACM","editor":[{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"}],"language":[{"iso":"eng"}],"doi":"10.1007/3-540-45449-7","_id":"4449","title":"EMSOFT: Embedded Software","publication_status":"published","abstract":[{"text":"Embedded software is software that interacts with physical processes. As em- bedded systems increasingly permeate our daily lives on all levels, from micros- copic devices to international networks, the cost-efficient development of reliable embedded software is one of the grand challenges in computer science today. The purpose of the workshop is to bring together researchers in all areas of computer science that are traditionally distinct but relevant to embedded software develop- ment, and to incubate a research community in this way. The workshop aims to cover all aspects of the design and implementation of embedded software, inclu- ding operating systems and middleware, programming languages and compilers, modeling and validation, software engineering and programming methodologies, scheduling and execution time analysis, networking and fault tolerance, as well as application areas, such as embedded control, real-time signal processing, and telecommunications.","lang":"eng"}],"extern":"1","article_processing_charge":"No","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","quality_controlled":"1","citation":{"ieee":"T. A. Henzinger, Ed., <i>EMSOFT: Embedded Software</i>, vol. 2211. ACM, 2001.","ama":"Henzinger TA, ed. <i>EMSOFT: Embedded Software</i>. Vol 2211. ACM; 2001. doi:<a href=\"https://doi.org/10.1007/3-540-45449-7\">10.1007/3-540-45449-7</a>","chicago":"Henzinger, Thomas A, ed. <i>EMSOFT: Embedded Software</i>. Vol. 2211. ACM, 2001. <a href=\"https://doi.org/10.1007/3-540-45449-7\">https://doi.org/10.1007/3-540-45449-7</a>.","short":"T.A. Henzinger, ed., EMSOFT: Embedded Software, ACM, 2001.","ista":"Henzinger TA ed. 2001. EMSOFT: Embedded Software, ACM,p.","mla":"Henzinger, Thomas A., editor. <i>EMSOFT: Embedded Software</i>. Vol. 2211, ACM, 2001, doi:<a href=\"https://doi.org/10.1007/3-540-45449-7\">10.1007/3-540-45449-7</a>.","apa":"Henzinger, T. A. (Ed.). (2001). <i>EMSOFT: Embedded Software</i> (Vol. 2211). Presented at the EMSOFT 2001: Embedded Software, Tahoe City, CA, USA: ACM. <a href=\"https://doi.org/10.1007/3-540-45449-7\">https://doi.org/10.1007/3-540-45449-7</a>"},"day":"26","year":"2001","type":"conference_editor","date_updated":"2023-05-10T09:53:17Z","oa_version":"None"},{"intvolume":"         3","scopus_import":"1","publist_id":"253","publication_identifier":{"isbn":["0780370619"]},"month":"05","conference":{"start_date":"2001-12-04","location":"Orlando, FL, USA","name":"CDC: Decision and Control","end_date":"2001-12-07"},"date_created":"2018-12-11T12:09:02Z","status":"public","date_published":"2001-05-01T00:00:00Z","volume":3,"page":"2887 - 2892","publisher":"IEEE","publication":"Proceedings of the 40th IEEE Conference on Decision and Control","title":"Some lessons from the HYTECH experience","_id":"4475","language":[{"iso":"eng"}],"doi":"10.1109/.2001.980714","abstract":[{"text":"We provide an overview of the current status of HYTECH, and reflect on some of the lessons learned from our experiences with the tool. HYTECH is a symbolic model checker for mixed discrete-continuous systems that are modeled as automata with piecewise-constant polyhedral differential inclusions. The use of a formal input language and automated procedures for state-space traversal lay the foundation for formally verifying properties of hybrid dynamical systems. We describe some recent experiences analyzing three hybrid systems. We point out the successes and limitations of the tool. The analysis procedure has been extended in a number of ways to address some of the tool's shortcomings. We evaluate these extensions, and conclude with some desiderata for verification tools for hybrid systems.","lang":"eng"}],"publication_status":"published","citation":{"ama":"Henzinger TA, Preussig J, Wong Toi H. Some lessons from the HYTECH experience. In: <i>Proceedings of the 40th IEEE Conference on Decision and Control</i>. Vol 3. IEEE; 2001:2887-2892. doi:<a href=\"https://doi.org/10.1109/.2001.980714\">10.1109/.2001.980714</a>","ieee":"T. A. Henzinger, J. Preussig, and H. Wong Toi, “Some lessons from the HYTECH experience,” in <i>Proceedings of the 40th IEEE Conference on Decision and Control</i>, Orlando, FL, USA, 2001, vol. 3, pp. 2887–2892.","ista":"Henzinger TA, Preussig J, Wong Toi H. 2001. Some lessons from the HYTECH experience. Proceedings of the 40th IEEE Conference on Decision and Control. CDC: Decision and Control vol. 3, 2887–2892.","short":"T.A. Henzinger, J. Preussig, H. Wong Toi, in:, Proceedings of the 40th IEEE Conference on Decision and Control, IEEE, 2001, pp. 2887–2892.","chicago":"Henzinger, Thomas A, Joerg Preussig, and Howard Wong Toi. “Some Lessons from the HYTECH Experience.” In <i>Proceedings of the 40th IEEE Conference on Decision and Control</i>, 3:2887–92. IEEE, 2001. <a href=\"https://doi.org/10.1109/.2001.980714\">https://doi.org/10.1109/.2001.980714</a>.","mla":"Henzinger, Thomas A., et al. “Some Lessons from the HYTECH Experience.” <i>Proceedings of the 40th IEEE Conference on Decision and Control</i>, vol. 3, IEEE, 2001, pp. 2887–92, doi:<a href=\"https://doi.org/10.1109/.2001.980714\">10.1109/.2001.980714</a>.","apa":"Henzinger, T. A., Preussig, J., &#38; Wong Toi, H. (2001). Some lessons from the HYTECH experience. In <i>Proceedings of the 40th IEEE Conference on Decision and Control</i> (Vol. 3, pp. 2887–2892). Orlando, FL, USA: IEEE. <a href=\"https://doi.org/10.1109/.2001.980714\">https://doi.org/10.1109/.2001.980714</a>"},"extern":"1","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","quality_controlled":"1","article_processing_charge":"No","author":[{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"last_name":"Preussig","first_name":"Joerg","full_name":"Preussig, Joerg"},{"last_name":"Wong Toi","first_name":"Howard","full_name":"Wong Toi, Howard"}],"oa_version":"None","date_updated":"2023-05-10T09:47:20Z","type":"conference","year":"2001","day":"01"},{"date_published":"2001-03-14T00:00:00Z","page":"275 - 290","alternative_title":["LNCS"],"scopus_import":"1","publication_identifier":{"isbn":["9783540418665"]},"user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","article_processing_charge":"No","oa_version":"None","type":"conference","date_updated":"2023-05-09T14:47:37Z","day":"14","doi":"10.1007/3-540-45351-2_24","language":[{"iso":"eng"}],"acknowledgement":"Support for this research was provided in part by the AFOSR MURI grant F49620- 00-1-0327, and the DARPA SEC grant F33615-C-98-3614, the MARCO GSRC grant 98-DT-660, the NSF ITR grant CCR-0085949.","volume":2034,"publisher":"Springer","intvolume":"      2034","publist_id":"250","conference":{"location":"Rome, Italy","start_date":"2001-03-28","name":"HSCC: Hybrid Systems - Computation and Control","end_date":"2001-03-30"},"month":"03","date_created":"2018-12-11T12:09:03Z","status":"public","citation":{"ieee":"T. A. Henzinger, M. Minea, and V. Prabhu, “Assume-guarantee reasoning for hierarchical hybrid systems,” in <i>Proceedings of the 4th International Workshop on Hybrid Systems</i>, Rome, Italy, 2001, vol. 2034, pp. 275–290.","ama":"Henzinger TA, Minea M, Prabhu V. Assume-guarantee reasoning for hierarchical hybrid systems. In: <i>Proceedings of the 4th International Workshop on Hybrid Systems</i>. Vol 2034. Springer; 2001:275-290. doi:<a href=\"https://doi.org/10.1007/3-540-45351-2_24\">10.1007/3-540-45351-2_24</a>","ista":"Henzinger TA, Minea M, Prabhu V. 2001. Assume-guarantee reasoning for hierarchical hybrid systems. Proceedings of the 4th International Workshop on Hybrid Systems. HSCC: Hybrid Systems - Computation and Control, LNCS, vol. 2034, 275–290.","short":"T.A. Henzinger, M. Minea, V. Prabhu, in:, Proceedings of the 4th International Workshop on Hybrid Systems, Springer, 2001, pp. 275–290.","chicago":"Henzinger, Thomas A, Marius Minea, and Vinayak Prabhu. “Assume-Guarantee Reasoning for Hierarchical Hybrid Systems.” In <i>Proceedings of the 4th International Workshop on Hybrid Systems</i>, 2034:275–90. Springer, 2001. <a href=\"https://doi.org/10.1007/3-540-45351-2_24\">https://doi.org/10.1007/3-540-45351-2_24</a>.","apa":"Henzinger, T. A., Minea, M., &#38; Prabhu, V. (2001). Assume-guarantee reasoning for hierarchical hybrid systems. In <i>Proceedings of the 4th International Workshop on Hybrid Systems</i> (Vol. 2034, pp. 275–290). Rome, Italy: Springer. <a href=\"https://doi.org/10.1007/3-540-45351-2_24\">https://doi.org/10.1007/3-540-45351-2_24</a>","mla":"Henzinger, Thomas A., et al. “Assume-Guarantee Reasoning for Hierarchical Hybrid Systems.” <i>Proceedings of the 4th International Workshop on Hybrid Systems</i>, vol. 2034, Springer, 2001, pp. 275–90, doi:<a href=\"https://doi.org/10.1007/3-540-45351-2_24\">10.1007/3-540-45351-2_24</a>."},"author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Minea, Marius","last_name":"Minea","first_name":"Marius"},{"full_name":"Prabhu, Vinayak","last_name":"Prabhu","first_name":"Vinayak"}],"extern":"1","quality_controlled":"1","year":"2001","title":"Assume-guarantee reasoning for hierarchical hybrid systems","publication":"Proceedings of the 4th International Workshop on Hybrid Systems","_id":"4477","abstract":[{"lang":"eng","text":"The assume-guarantee paradigm is a powerful divide-and-conquer mechanism for decomposing a verification task about a system into subtasks about the individual components of the system. The key to assume-guarantee reasoning is to consider each component not in isolation, but in conjunction with assumptions about the context of the component. Assume-guarantee principles are known for purely concurrent contexts, which constrain the input data of a component, as well as for purely sequential contexts, which constrain the entry configurations of a component. We present a model for hierarchical system design which permits the arbitrary nesting of parallel as well as serial composition, and which supports an assume-guarantee principle for mixed parallel-serial contexts. Our model also supports both discrete and continuous processes, and is therefore well-suited for the modeling and analysis of embedded software systems which interact with real-world environments. Using an example of two cooperating robots, we show refinement between a high-level model which specifies continuous timing constraints and an implementation which relies on discrete sampling."}],"publication_status":"published"},{"article_processing_charge":"No","author":[{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"first_name":"Benjamin","last_name":"Horowitz","full_name":"Horowitz, Benjamin"},{"full_name":"Kirsch, Christoph","last_name":"Kirsch","first_name":"Christoph"}],"extern":"1","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","quality_controlled":"1","citation":{"short":"T.A. Henzinger, B. Horowitz, C. Kirsch, in:, Proceedings of the 2nd ACM SIGPLAN Workshop on Languages, Compilers and Tools for Embedded Systems, ACM, 2001, pp. 64–72.","chicago":"Henzinger, Thomas A, Benjamin Horowitz, and Christoph Kirsch. “Embedded Control Systems Development with Giotto.” In <i>Proceedings of the 2nd ACM SIGPLAN Workshop on Languages, Compilers and Tools for Embedded Systems</i>, 64–72. ACM, 2001. <a href=\"https://doi.org/10.1145/384197.384208\">https://doi.org/10.1145/384197.384208</a>.","ista":"Henzinger TA, Horowitz B, Kirsch C. 2001. Embedded control systems development with Giotto. Proceedings of the 2nd ACM SIGPLAN workshop on Languages, compilers and tools for embedded systems. LCTES: Languages, Compilers, and Tools for Embedded Systems, 64–72.","ama":"Henzinger TA, Horowitz B, Kirsch C. Embedded control systems development with Giotto. In: <i>Proceedings of the 2nd ACM SIGPLAN Workshop on Languages, Compilers and Tools for Embedded Systems</i>. ACM; 2001:64-72. doi:<a href=\"https://doi.org/10.1145/384197.384208\">10.1145/384197.384208</a>","ieee":"T. A. Henzinger, B. Horowitz, and C. Kirsch, “Embedded control systems development with Giotto,” in <i>Proceedings of the 2nd ACM SIGPLAN workshop on Languages, compilers and tools for embedded systems</i>, New York, NY, United States, 2001, pp. 64–72.","apa":"Henzinger, T. A., Horowitz, B., &#38; Kirsch, C. (2001). Embedded control systems development with Giotto. In <i>Proceedings of the 2nd ACM SIGPLAN workshop on Languages, compilers and tools for embedded systems</i> (pp. 64–72). New York, NY, United States: ACM. <a href=\"https://doi.org/10.1145/384197.384208\">https://doi.org/10.1145/384197.384208</a>","mla":"Henzinger, Thomas A., et al. “Embedded Control Systems Development with Giotto.” <i>Proceedings of the 2nd ACM SIGPLAN Workshop on Languages, Compilers and Tools for Embedded Systems</i>, ACM, 2001, pp. 64–72, doi:<a href=\"https://doi.org/10.1145/384197.384208\">10.1145/384197.384208</a>."},"day":"01","year":"2001","date_updated":"2023-05-10T09:37:20Z","type":"conference","oa_version":"None","language":[{"iso":"eng"}],"doi":"10.1145/384197.384208","_id":"4478","publication":"Proceedings of the 2nd ACM SIGPLAN workshop on Languages, compilers and tools for embedded systems","title":"Embedded control systems development with Giotto","publication_status":"published","abstract":[{"lang":"eng","text":"Giotto is a principled, tool-supported design methodology for implementing embedded control systems on platforms of possibly distributed sensors, actuators, CPUs, and networks. Giotto is based on the principle that time-triggered task invocations plus time-triggered mode switches can form the abstract essence of programming real-time control systems. Giotto consists of a programming language with a formal semantics, and a retargetable compiler and runtime library. Giotto supports the automation of control system design by strictly separating platform-independent functionality and timing concerns from platform-dependent scheduling and communication issues. The time-triggered predictability of Giotto makes it particularly suitable for safety-critical applications with hard real-time constraints. We illustrate the platform-independence and time-triggered execution of Giotto by coordinating a heterogeneous flock of Intel x86 robots and Lego Mindstorms robots."}],"acknowledgement":"We thank Rupak Majumdar for implementing a prototype Giotto compiler for Lego Mindstorms robots. We thank Dmitry Derevyanko and Winthrop Williams for building our Intel x86 robots. We thank Edward Lee and Xiaojun Liu for help with a Ptolemy II [4] implementation of Giotto. This research was supported in part by the DARPA SEC grant F33615-C-98-3614, the DARPA MoBIES grant F33615- 00-C-1703, the MARCO GSRC grant 98-DT-660, the AFOSR MURI grant F49620-00-1-0327, and the NSF ITR grant CCR-0085949.","page":"64 - 72","date_published":"2001-06-01T00:00:00Z","publisher":"ACM","publication_identifier":{"isbn":["9781581134254"]},"publist_id":"251","scopus_import":"1","status":"public","date_created":"2018-12-11T12:09:03Z","conference":{"location":"New York, NY, United States","name":"LCTES: Languages, Compilers, and Tools for Embedded Systems"},"month":"06"},{"acknowledgement":"This research was supported in part by the DARPA SEC grant F33615-C-98-3614 and by the MARCO GSRC grant 98-DT-660.","doi":"10.1007/3-540-45449-7_12","language":[{"iso":"eng"}],"day":"26","oa_version":"None","date_updated":"2023-05-10T09:42:10Z","type":"conference","article_processing_charge":"No","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","scopus_import":"1","publication_identifier":{"isbn":["9783540426738"]},"alternative_title":["LNCS"],"page":"166 - 184","date_published":"2001-09-26T00:00:00Z","abstract":[{"lang":"eng","text":"Giotto provides an abstract programmer’s model for the implementation of embedded control systems with hard real-time constraints. A typical control application consists of periodic software tasks together with a mode switching logic for enabling and disabling tasks. Giotto specifies time-triggered sensor readings, task invocations, and mode switches independent of any implementation platform. Giotto can be annotated with platform constraints such as task-to-host mappings, and task and communication schedules. The annotations are directives for the Giotto compiler, but they do not alter the functionality and timing of a Giotto program. By separating the platform-independent from the platform-dependent concerns, Giotto enables a great deal of flexibility in choosing control platforms as well as a great deal of automation in the validation and synthesis of control software. The time-triggered nature of Giotto achieves timing predictability, which makes Giotto particularly suitable for safety-critical applications."}],"publication_status":"published","_id":"4479","title":"Giotto: A time-triggered language for embedded programming","publication":"Proceedings of the 1st International Workshop on Embedded Software","year":"2001","extern":"1","quality_controlled":"1","author":[{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Horowitz, Benjamin","first_name":"Benjamin","last_name":"Horowitz"},{"last_name":"Kirsch","first_name":"Christoph","full_name":"Kirsch, Christoph"}],"citation":{"mla":"Henzinger, Thomas A., et al. “Giotto: A Time-Triggered Language for Embedded Programming.” <i>Proceedings of the 1st International Workshop on Embedded Software</i>, vol. 2211, ACM, 2001, pp. 166–84, doi:<a href=\"https://doi.org/10.1007/3-540-45449-7_12\">10.1007/3-540-45449-7_12</a>.","apa":"Henzinger, T. A., Horowitz, B., &#38; Kirsch, C. (2001). Giotto: A time-triggered language for embedded programming. In <i>Proceedings of the 1st International Workshop on Embedded Software</i> (Vol. 2211, pp. 166–184). Tahoe City, CA, USA: ACM. <a href=\"https://doi.org/10.1007/3-540-45449-7_12\">https://doi.org/10.1007/3-540-45449-7_12</a>","ieee":"T. A. Henzinger, B. Horowitz, and C. Kirsch, “Giotto: A time-triggered language for embedded programming,” in <i>Proceedings of the 1st International Workshop on Embedded Software</i>, Tahoe City, CA, USA, 2001, vol. 2211, pp. 166–184.","ama":"Henzinger TA, Horowitz B, Kirsch C. Giotto: A time-triggered language for embedded programming. In: <i>Proceedings of the 1st International Workshop on Embedded Software</i>. Vol 2211. ACM; 2001:166-184. doi:<a href=\"https://doi.org/10.1007/3-540-45449-7_12\">10.1007/3-540-45449-7_12</a>","ista":"Henzinger TA, Horowitz B, Kirsch C. 2001. Giotto: A time-triggered language for embedded programming. Proceedings of the 1st International Workshop on Embedded Software. EMSOFT: Embedded Software , LNCS, vol. 2211, 166–184.","short":"T.A. Henzinger, B. Horowitz, C. Kirsch, in:, Proceedings of the 1st International Workshop on Embedded Software, ACM, 2001, pp. 166–184.","chicago":"Henzinger, Thomas A, Benjamin Horowitz, and Christoph Kirsch. “Giotto: A Time-Triggered Language for Embedded Programming.” In <i>Proceedings of the 1st International Workshop on Embedded Software</i>, 2211:166–84. ACM, 2001. <a href=\"https://doi.org/10.1007/3-540-45449-7_12\">https://doi.org/10.1007/3-540-45449-7_12</a>."},"status":"public","month":"09","conference":{"start_date":"2001-10-08","location":"Tahoe City, CA, USA","name":"EMSOFT: Embedded Software ","end_date":"2001-10-10"},"date_created":"2018-12-11T12:09:04Z","publist_id":"252","intvolume":"      2211","publisher":"ACM","volume":2211},{"oa_version":"None","type":"conference","date_updated":"2023-05-09T12:23:16Z","year":"2001","day":"06","citation":{"apa":"Brown, T., Pasetti, A., Pree, W., Henzinger, T. A., &#38; Kirsch, C. (2001). A reusable and platform-independent framework for distributed control systems. In <i>Proceedings of the 20th Digital Avionics Systems Conference</i> (pp. 1–11). Daytona Beach, FL, USA: IEEE. <a href=\"https://doi.org/10.1109/DASC.2001.964169\">https://doi.org/10.1109/DASC.2001.964169</a>","mla":"Brown, Timothy, et al. “A Reusable and Platform-Independent Framework for Distributed Control Systems.” <i>Proceedings of the 20th Digital Avionics Systems Conference</i>, IEEE, 2001, pp. 1–11, doi:<a href=\"https://doi.org/10.1109/DASC.2001.964169\">10.1109/DASC.2001.964169</a>.","ieee":"T. Brown, A. Pasetti, W. Pree, T. A. Henzinger, and C. Kirsch, “A reusable and platform-independent framework for distributed control systems,” in <i>Proceedings of the 20th Digital Avionics Systems Conference</i>, Daytona Beach, FL, USA, 2001, pp. 1–11.","ama":"Brown T, Pasetti A, Pree W, Henzinger TA, Kirsch C. A reusable and platform-independent framework for distributed control systems. In: <i>Proceedings of the 20th Digital Avionics Systems Conference</i>. IEEE; 2001:1-11. doi:<a href=\"https://doi.org/10.1109/DASC.2001.964169\">10.1109/DASC.2001.964169</a>","ista":"Brown T, Pasetti A, Pree W, Henzinger TA, Kirsch C. 2001. A reusable and platform-independent framework for distributed control systems. Proceedings of the 20th Digital Avionics Systems Conference. DASC: Digital Avionics Systems Conference, 1–11.","chicago":"Brown, Timothy, Alessandro Pasetti, Wolfgang Pree, Thomas A Henzinger, and Christoph Kirsch. “A Reusable and Platform-Independent Framework for Distributed Control Systems.” In <i>Proceedings of the 20th Digital Avionics Systems Conference</i>, 1–11. IEEE, 2001. <a href=\"https://doi.org/10.1109/DASC.2001.964169\">https://doi.org/10.1109/DASC.2001.964169</a>.","short":"T. Brown, A. Pasetti, W. Pree, T.A. Henzinger, C. Kirsch, in:, Proceedings of the 20th Digital Avionics Systems Conference, IEEE, 2001, pp. 1–11."},"quality_controlled":"1","article_processing_charge":"No","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","extern":"1","author":[{"full_name":"Brown, Timothy","first_name":"Timothy","last_name":"Brown"},{"first_name":"Alessandro","last_name":"Pasetti","full_name":"Pasetti, Alessandro"},{"first_name":"Wolfgang","last_name":"Pree","full_name":"Pree, Wolfgang"},{"last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christoph","last_name":"Kirsch","full_name":"Kirsch, Christoph"}],"acknowledgement":"This research was supported in part by DARPA under grants F336 15-C-98-36 14, F33615-00-(2-1693, and F33615-00-C-1703, and by MARC0 under grant 98-DT-660. ","abstract":[{"lang":"eng","text":"This paper presents a concept for integrating the embedded programming methodology Giotto and the object-oriented AOCS Framework to create an environment for the rapid development of distributed software for safety-critical embedded control systems with hard real-time requirements of the kind typically found in aerospace applications."}],"publication_status":"published","title":"A reusable and platform-independent framework for distributed control systems","publication":"Proceedings of the 20th Digital Avionics Systems Conference","_id":"4564","doi":"10.1109/DASC.2001.964169","language":[{"iso":"eng"}],"publisher":"IEEE","date_published":"2001-08-06T00:00:00Z","page":"1 - 11","conference":{"start_date":"2001-10-14","location":"Daytona Beach, FL, USA","end_date":"2001-10-18","name":"DASC: Digital Avionics Systems Conference"},"month":"08","date_created":"2018-12-11T12:09:30Z","status":"public","scopus_import":"1","publist_id":"143","publication_identifier":{"isbn":["0780370341"]}},{"issue":"2","volume":18,"publisher":"Springer","article_type":"original","intvolume":"        18","publist_id":"108","date_created":"2018-12-11T12:09:41Z","month":"03","status":"public","citation":{"apa":"Alur, R., Brayton, R., Henzinger, T. A., Qadeer, S., &#38; Rajamani, S. (2001). Partial-order reduction in symbolic state-space exploration. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1023/A:1008767206905\">https://doi.org/10.1023/A:1008767206905</a>","mla":"Alur, Rajeev, et al. “Partial-Order Reduction in Symbolic State-Space Exploration.” <i>Formal Methods in System Design</i>, vol. 18, no. 2, Springer, 2001, pp. 97–116, doi:<a href=\"https://doi.org/10.1023/A:1008767206905\">10.1023/A:1008767206905</a>.","ista":"Alur R, Brayton R, Henzinger TA, Qadeer S, Rajamani S. 2001. Partial-order reduction in symbolic state-space exploration. Formal Methods in System Design. 18(2), 97–116.","short":"R. Alur, R. Brayton, T.A. Henzinger, S. Qadeer, S. Rajamani, Formal Methods in System Design 18 (2001) 97–116.","chicago":"Alur, Rajeev, Robert Brayton, Thomas A Henzinger, Shaz Qadeer, and Sriram Rajamani. “Partial-Order Reduction in Symbolic State-Space Exploration.” <i>Formal Methods in System Design</i>. Springer, 2001. <a href=\"https://doi.org/10.1023/A:1008767206905\">https://doi.org/10.1023/A:1008767206905</a>.","ama":"Alur R, Brayton R, Henzinger TA, Qadeer S, Rajamani S. Partial-order reduction in symbolic state-space exploration. <i>Formal Methods in System Design</i>. 2001;18(2):97-116. doi:<a href=\"https://doi.org/10.1023/A:1008767206905\">10.1023/A:1008767206905</a>","ieee":"R. Alur, R. Brayton, T. A. Henzinger, S. Qadeer, and S. Rajamani, “Partial-order reduction in symbolic state-space exploration,” <i>Formal Methods in System Design</i>, vol. 18, no. 2. Springer, pp. 97–116, 2001."},"extern":"1","author":[{"last_name":"Alur","first_name":"Rajeev","full_name":"Alur, Rajeev"},{"full_name":"Brayton, Robert","last_name":"Brayton","first_name":"Robert"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A"},{"first_name":"Shaz","last_name":"Qadeer","full_name":"Qadeer, Shaz"},{"first_name":"Sriram","last_name":"Rajamani","full_name":"Rajamani, Sriram"}],"quality_controlled":"1","year":"2001","publication":"Formal Methods in System Design","title":"Partial-order reduction in symbolic state-space exploration","_id":"4599","publication_status":"published","abstract":[{"text":"State-space explosion is a fundamental obstacle in the formal verification of designs and protocols. Several techniques for combating this problem have emerged in the past few years, among which two are significant: partial-order reduction and symbolic state-space search. In asynchronous systems, interleavings of independent concurrent events are equivalent, and only a representative interleaving needs to be explored to verify local properties. Partial-order methods exploit this redundancy and visit only a subset of the reachable states. Symbolic techniques, on the other hand, capture the transition relation of a system and the set of reachable states as boolean functions. In many cases, these functions can be represented compactly using binary decision diagrams (BDDs). Traditionally, the two techniques have been practiced by two different schools—partial-order methods with enumerative depth-first search for the analysis of asynchronous network protocols, and symbolic breadth-first search for the analysis of synchronous hardware designs. We combine both approaches and develop a method for using partial-order reduction techniques in symbolic BDD-based invariant checking. We present theoretical results to prove the correctness of the method, and experimental results to demonstrate its efficacy.","lang":"eng"}],"date_published":"2001-03-01T00:00:00Z","page":"97 - 116","publication_identifier":{"issn":["0925-9856"]},"scopus_import":"1","article_processing_charge":"No","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","date_updated":"2023-05-08T12:22:38Z","type":"journal_article","oa_version":"None","day":"01","doi":"10.1023/A:1008767206905","language":[{"iso":"eng"}],"acknowledgement":"Gerard Holzmann provided us with information on SPIN. Ken McMillan and Doron Peled contributed through discussions. The VIS group at UC Berkeley and Rajeev Ranjan in particular helped with the experiments."},{"day":"07","year":"2001","date_updated":"2023-05-08T14:06:55Z","type":"conference","oa_version":"None","author":[{"full_name":"Alur, Rajeev","first_name":"Rajeev","last_name":"Alur"},{"last_name":"De Alfaro","first_name":"Luca","full_name":"De Alfaro, Luca"},{"full_name":"Grosu, Radu","last_name":"Grosu","first_name":"Radu"},{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kang","first_name":"Myong","full_name":"Kang, Myong"},{"full_name":"Kirsch, Christoph","last_name":"Kirsch","first_name":"Christoph"},{"first_name":"Ritankar","last_name":"Majumdar","full_name":"Majumdar, Ritankar"},{"full_name":"Mang, Freddy","last_name":"Mang","first_name":"Freddy"},{"full_name":"Wang, Bow","last_name":"Wang","first_name":"Bow"}],"article_processing_charge":"No","extern":"1","quality_controlled":"1","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","citation":{"apa":"Alur, R., De Alfaro, L., Grosu, R., Henzinger, T. A., Kang, M., Kirsch, C., … Wang, B. (2001). jMocha: A model-checking tool that exploits design structure. In <i>Proceedings of the 23rd International Conference on Software Engineering</i> (pp. 835–836). IEEE. <a href=\"https://doi.org/10.1109/ICSE.2001.919196\">https://doi.org/10.1109/ICSE.2001.919196</a>","mla":"Alur, Rajeev, et al. “JMocha: A Model-Checking Tool That Exploits Design Structure.” <i>Proceedings of the 23rd International Conference on Software Engineering</i>, IEEE, 2001, pp. 835–36, doi:<a href=\"https://doi.org/10.1109/ICSE.2001.919196\">10.1109/ICSE.2001.919196</a>.","chicago":"Alur, Rajeev, Luca De Alfaro, Radu Grosu, Thomas A Henzinger, Myong Kang, Christoph Kirsch, Ritankar Majumdar, Freddy Mang, and Bow Wang. “JMocha: A Model-Checking Tool That Exploits Design Structure.” In <i>Proceedings of the 23rd International Conference on Software Engineering</i>, 835–36. IEEE, 2001. <a href=\"https://doi.org/10.1109/ICSE.2001.919196\">https://doi.org/10.1109/ICSE.2001.919196</a>.","short":"R. Alur, L. De Alfaro, R. Grosu, T.A. Henzinger, M. Kang, C. Kirsch, R. Majumdar, F. Mang, B. Wang, in:, Proceedings of the 23rd International Conference on Software Engineering, IEEE, 2001, pp. 835–836.","ista":"Alur R, De Alfaro L, Grosu R, Henzinger TA, Kang M, Kirsch C, Majumdar R, Mang F, Wang B. 2001. jMocha: A model-checking tool that exploits design structure. Proceedings of the 23rd International Conference on Software Engineering. ICSE: Software Engineering, 835–836.","ieee":"R. Alur <i>et al.</i>, “jMocha: A model-checking tool that exploits design structure,” in <i>Proceedings of the 23rd International Conference on Software Engineering</i>, 2001, pp. 835–836.","ama":"Alur R, De Alfaro L, Grosu R, et al. jMocha: A model-checking tool that exploits design structure. In: <i>Proceedings of the 23rd International Conference on Software Engineering</i>. IEEE; 2001:835-836. doi:<a href=\"https://doi.org/10.1109/ICSE.2001.919196\">10.1109/ICSE.2001.919196</a>"},"publication_status":"published","abstract":[{"lang":"eng","text":"Model checking is a practical tool for automated debugging of embedded software. In model checking, a high-level description of a system is compared against a logical correctness requirement to discover inconsistencies. Since model checking is based on exhaustive state-space exploration and the size of the state space of a design grows exponentially with the size of the description, scalability remains a challenge. We have thus developed techniques for exploiting modular design structure during model checking, and the model checker jMocha (Java MOdel-CHecking Algorithm) is based on this theme. Instead of manipulating unstructured state-transition graphs, it supports the hierarchical modeling framework of reactive modules. jMocha is a growing interactive software environment for specification, simulation and verification, and is intended as a vehicle for the development of new verification algorithms and approaches. It is written in Java and uses native C-code BDD libraries from VIS. jMocha offers: (1) a GUI that looks familiar to Windows/Java users; (2) a simulator that displays traces in a message sequence chart fashion; (3) requirements verification both by symbolic and enumerative model checking; (4) implementation verification by checking trace containment; (5) a proof manager that aids compositional and assume-guarantee reasoning; and (6) SLANG (Scripting LANGuage) for the rapid and structured development of new verification algorithms. jMocha is available publicly at ; it is a successor and extension of the original Mocha tool that was entirely written in C."}],"acknowledgement":"We thank Himyanshu Anand, Ben Horowitz, Franjo Ivancic, Michael McDougall, Marius Minea, Oliver Moeller. Shaz Qadeer, Sriram Rajamani, and Jean-Francois Raskin for their assistance in the development of JMOCHA. The MOCHA project is funded in part by the DARPA grant NAG2-1214, the NSF CAREER awards CCR95-01708 and CCR97-34115, the NSF grant CCR99-70925, the NSF ITR grant CCR0085949, the MARC0 grant 98-DT-660, and the SRC contracts 99-TJ-683.003 and 99-TJ-688. ","language":[{"iso":"eng"}],"doi":"10.1109/ICSE.2001.919196","_id":"4600","publication":"Proceedings of the 23rd International Conference on Software Engineering","title":"jMocha: A model-checking tool that exploits design structure","publisher":"IEEE","page":"835 - 836","date_published":"2001-08-07T00:00:00Z","status":"public","date_created":"2018-12-11T12:09:41Z","conference":{"name":"ICSE: Software Engineering"},"month":"08","publist_id":"109","publication_identifier":{"isbn":["0769510507"]}},{"page":"109 - 120","date_published":"2001-06-01T00:00:00Z","publisher":"ACM","scopus_import":"1","publication_identifier":{"isbn":["9781581133905"]},"publist_id":"83","status":"public","conference":{"end_date":"2001-09-14","name":"FSE: Foundations of Software Engineering","location":"Vienna, Austria","start_date":"2001-09-10"},"month":"06","date_created":"2018-12-11T12:09:48Z","author":[{"first_name":"Luca","last_name":"De Alfaro","full_name":"De Alfaro, Luca"},{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"extern":"1","article_processing_charge":"No","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","quality_controlled":"1","citation":{"apa":"De Alfaro, L., &#38; Henzinger, T. A. (2001). Interface automata. In <i>Proceedings of the 8th European software engineering conference</i> (pp. 109–120). Vienna, Austria: ACM. <a href=\"https://doi.org/10.1145/503209.503226\">https://doi.org/10.1145/503209.503226</a>","mla":"De Alfaro, Luca, and Thomas A. Henzinger. “Interface Automata.” <i>Proceedings of the 8th European Software Engineering Conference</i>, ACM, 2001, pp. 109–20, doi:<a href=\"https://doi.org/10.1145/503209.503226\">10.1145/503209.503226</a>.","ama":"De Alfaro L, Henzinger TA. Interface automata. In: <i>Proceedings of the 8th European Software Engineering Conference</i>. ACM; 2001:109-120. doi:<a href=\"https://doi.org/10.1145/503209.503226\">10.1145/503209.503226</a>","ieee":"L. De Alfaro and T. A. Henzinger, “Interface automata,” in <i>Proceedings of the 8th European software engineering conference</i>, Vienna, Austria, 2001, pp. 109–120.","ista":"De Alfaro L, Henzinger TA. 2001. Interface automata. Proceedings of the 8th European software engineering conference. FSE: Foundations of Software Engineering, 109–120.","chicago":"De Alfaro, Luca, and Thomas A Henzinger. “Interface Automata.” In <i>Proceedings of the 8th European Software Engineering Conference</i>, 109–20. ACM, 2001. <a href=\"https://doi.org/10.1145/503209.503226\">https://doi.org/10.1145/503209.503226</a>.","short":"L. De Alfaro, T.A. Henzinger, in:, Proceedings of the 8th European Software Engineering Conference, ACM, 2001, pp. 109–120."},"year":"2001","day":"01","oa_version":"None","type":"conference","date_updated":"2023-05-08T12:01:02Z","_id":"4622","language":[{"iso":"eng"}],"doi":"10.1145/503209.503226","title":"Interface automata","publication":"Proceedings of the 8th European software engineering conference","abstract":[{"lang":"eng","text":"Conventional type systems specify interfaces in terms of values and domains. We present a light-weight formalism that captures the temporal aspects of software component interfaces. Specifically, we use an automata-based language to capture both input assumptions about the order in which the methods of a component are called, and output guarantees about the order in which the component calls external methods. The formalism supports automatic compatability checks between interface models, and thus constitutes a type system for component interaction. Unlike traditional uses of automata, our formalism is based on an optimistic approach to composition, and on an alternating approach to design refinement. According to the optimistic approach, two components are compatible if there is some environment that can make them work together. According to the alternating approach, one interface refines another if it has weaker input assumptions, and stronger output guarantees. We show that these notions have game-theoretic foundations that lead to efficient algorithms for checking compatibility and refinement."}],"publication_status":"published","acknowledgement":"We thank Edward A. Lee, Xiaojun Liu, Freddy Mang, and Yuhong Xiong for fruitful discussions. This research was supported in part by the AFOSR MURI grant F49620-00-1-0327, the DARPA MoBIES grant F33615-00-C-1703, the MARCO GSRC grant 98-DT-660, the NSF Theory grant CCR-9988172, and the NSF ITR grant CCR-0085949."}]