[{"month":"01","title":"Reactive modules","oa_version":"None","publication_status":"published","article_processing_charge":"No","date_created":"2018-12-11T12:09:37Z","author":[{"first_name":"Rajeev","last_name":"Alur","full_name":"Alur, Rajeev"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"_id":"4588","publication":"Proceedings 11th Annual IEEE Symposium on Logic in Computer Science","scopus_import":"1","conference":{"start_date":"1996-07-27","name":"LICS: Logic in Computer Science","end_date":"1996-07-30","location":"New Brunswick, NJ, USA"},"publisher":"IEEE","language":[{"iso":"eng"}],"page":"207 - 218","quality_controlled":"1","abstract":[{"text":"We present a formal model for concurrent systems. The model represents synchronous and asynchronous components in a uniform framework that supports compositional (assume-guarantee) and hierarchical (stepwise refinement) reasoning. While synchronous models are based on a notion of atomic computation step, and asynchronous models remove that notion by introducing stuttering, our model is based on a flexible notion of what constitutes a computation step: by applying an abstraction operator to a system, arbitrarily many consecutive steps can be collapsed into a single step. The abstraction operator, which may turn an asynchronous system into a synchronous one, allows us to describe systems at various levels of temporal detail. For describing systems at various levels of spatial detail, we use a hiding operator that may turn a synchronous system into an asynchronous one. We illustrate the model with diverse examples from synchronous circuits, asynchronous shared-memory programs, and synchronous message passing","lang":"eng"}],"publist_id":"121","doi":"10.1109/LICS.1996.561320","publication_identifier":{"issn":["0018-9162"]},"day":"01","date_published":"1996-01-01T00:00:00Z","type":"conference","date_updated":"2022-07-04T14:51:40Z","citation":{"ista":"Alur R, Henzinger TA. 1996. Reactive modules. Proceedings 11th Annual IEEE Symposium on Logic in Computer Science. LICS: Logic in Computer Science, 207–218.","mla":"Alur, Rajeev, and Thomas A. Henzinger. “Reactive Modules.” <i>Proceedings 11th Annual IEEE Symposium on Logic in Computer Science</i>, IEEE, 1996, pp. 207–18, doi:<a href=\"https://doi.org/10.1109/LICS.1996.561320\">10.1109/LICS.1996.561320</a>.","short":"R. Alur, T.A. Henzinger, in:, Proceedings 11th Annual IEEE Symposium on Logic in Computer Science, IEEE, 1996, pp. 207–218.","ieee":"R. Alur and T. A. Henzinger, “Reactive modules,” in <i>Proceedings 11th Annual IEEE Symposium on Logic in Computer Science</i>, New Brunswick, NJ, USA, 1996, pp. 207–218.","chicago":"Alur, Rajeev, and Thomas A Henzinger. “Reactive Modules.” In <i>Proceedings 11th Annual IEEE Symposium on Logic in Computer Science</i>, 207–18. IEEE, 1996. <a href=\"https://doi.org/10.1109/LICS.1996.561320\">https://doi.org/10.1109/LICS.1996.561320</a>.","apa":"Alur, R., &#38; Henzinger, T. A. (1996). Reactive modules. In <i>Proceedings 11th Annual IEEE Symposium on Logic in Computer Science</i> (pp. 207–218). New Brunswick, NJ, USA: IEEE. <a href=\"https://doi.org/10.1109/LICS.1996.561320\">https://doi.org/10.1109/LICS.1996.561320</a>","ama":"Alur R, Henzinger TA. Reactive modules. In: <i>Proceedings 11th Annual IEEE Symposium on Logic in Computer Science</i>. IEEE; 1996:207-218. doi:<a href=\"https://doi.org/10.1109/LICS.1996.561320\">10.1109/LICS.1996.561320</a>"},"year":"1996","extern":"1","status":"public","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","main_file_link":[{"url":"https://ieeexplore.ieee.org/document/561320"}]},{"publist_id":"95","publication_identifier":{"issn":["0004-5411"]},"type":"journal_article","date_published":"1996-01-01T00:00:00Z","status":"public","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","main_file_link":[{"url":"https://dl.acm.org/doi/10.1145/227595.227602"}],"month":"01","oa_version":"None","publication":"Journal of the ACM","language":[{"iso":"eng"}],"abstract":[{"text":"The most natural, compositional, way of modeling real-time systems uses a dense domain for time. The satisfiability of timing constraints that are capable of expressing punctuality in this model, however, is known to be undecidable. We introduce a temporal language that can constrain the time difference between events only with finite, yet arbitrary, precision and show the resulting logic to be EXPSPACE-complete. This result allows us to develop an algorithm for the verification of timing properties of real-time systems with a dense semantics.","lang":"eng"}],"day":"01","doi":"10.1145/227595.227602","year":"1996","citation":{"ama":"Alur R, Feder T, Henzinger TA. The benefits of relaxing punctuality. <i>Journal of the ACM</i>. 1996;43(1):116-146. doi:<a href=\"https://doi.org/10.1145/227595.227602\">10.1145/227595.227602</a>","apa":"Alur, R., Feder, T., &#38; Henzinger, T. A. (1996). The benefits of relaxing punctuality. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/227595.227602\">https://doi.org/10.1145/227595.227602</a>","chicago":"Alur, Rajeev, Tomás Feder, and Thomas A Henzinger. “The Benefits of Relaxing Punctuality.” <i>Journal of the ACM</i>. ACM, 1996. <a href=\"https://doi.org/10.1145/227595.227602\">https://doi.org/10.1145/227595.227602</a>.","ieee":"R. Alur, T. Feder, and T. A. Henzinger, “The benefits of relaxing punctuality,” <i>Journal of the ACM</i>, vol. 43, no. 1. ACM, pp. 116–146, 1996.","short":"R. Alur, T. Feder, T.A. Henzinger, Journal of the ACM 43 (1996) 116–146.","mla":"Alur, Rajeev, et al. “The Benefits of Relaxing Punctuality.” <i>Journal of the ACM</i>, vol. 43, no. 1, ACM, 1996, pp. 116–46, doi:<a href=\"https://doi.org/10.1145/227595.227602\">10.1145/227595.227602</a>.","ista":"Alur R, Feder T, Henzinger TA. 1996. The benefits of relaxing punctuality. Journal of the ACM. 43(1), 116–146."},"date_updated":"2022-07-04T12:38:01Z","extern":"1","volume":43,"acknowledgement":"We wish to thank an anonymous referee for pointing out the PSPACE-fragment of Section 4.5. ","intvolume":"        43","title":"The benefits of relaxing punctuality","article_processing_charge":"No","date_created":"2018-12-11T12:09:44Z","publication_status":"published","issue":"1","author":[{"full_name":"Alur, Rajeev","last_name":"Alur","first_name":"Rajeev"},{"last_name":"Feder","first_name":"Tomás","full_name":"Feder, Tomás"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","_id":"4610","article_type":"original","publisher":"ACM","quality_controlled":"1","page":"116 - 146"},{"acknowledgement":"We thank Costas Courcoubetis, Nicolas Halbwachs, Peter Kopke, Joseph Sifakis, and Howard Wong-Toi for helpful\r\ndiscussions and valuable comments. Thomas A. Henzinger's research was supported in part by the U.S. Office of Naval Research Young Investigator award N00014-95-1-0520, by the National Science Foundation CAREER award CCR-9501708, by National Science Foundation grants CCR-9200794 and CCR-9504469, by U.S. Air Force Office of Scientific Research contract F49620-93-1- 0056, and by Advanced Research Projects Agency grant NAG2-892. ","volume":22,"extern":"1","doi":"10.1109/32.489079","day":"01","abstract":[{"text":"Presents a model-checking procedure and its implementation for the automatic verification of embedded systems. The system components are described as hybrid automata-communicating machines with finite control and real-valued variables that represent continuous environment parameters such as time, pressure and temperature. The system requirements are specified in a temporal logic with stop-watches, and verified by symbolic fixpoint computation. The verification procedure-implemented in the Cornell Hybrid Technology tool, HyTech-applies to hybrid automata whose continuous dynamics is governed by linear constraints on the variables and their derivatives. We illustrate the method and the tool by checking safety, liveness, time-bounded and duration requirements of digital controllers, schedulers and distributed algorithms","lang":"eng"}],"date_updated":"2022-07-04T12:47:05Z","citation":{"short":"R. Alur, T.A. Henzinger, P. Ho, IEEE Transactions on Software Engineering 22 (1996) 181–201.","mla":"Alur, Rajeev, et al. “Automatic Symbolic Verification of Embedded Systems.” <i>IEEE Transactions on Software Engineering</i>, vol. 22, no. 3, IEEE, 1996, pp. 181–201, doi:<a href=\"https://doi.org/10.1109/32.489079\">10.1109/32.489079</a>.","ista":"Alur R, Henzinger TA, Ho P. 1996. Automatic symbolic verification of embedded systems. IEEE Transactions on Software Engineering. 22(3), 181–201.","apa":"Alur, R., Henzinger, T. A., &#38; Ho, P. (1996). Automatic symbolic verification of embedded systems. <i>IEEE Transactions on Software Engineering</i>. IEEE. <a href=\"https://doi.org/10.1109/32.489079\">https://doi.org/10.1109/32.489079</a>","ama":"Alur R, Henzinger TA, Ho P. Automatic symbolic verification of embedded systems. <i>IEEE Transactions on Software Engineering</i>. 1996;22(3):181-201. doi:<a href=\"https://doi.org/10.1109/32.489079\">10.1109/32.489079</a>","chicago":"Alur, Rajeev, Thomas A Henzinger, and Pei Ho. “Automatic Symbolic Verification of Embedded Systems.” <i>IEEE Transactions on Software Engineering</i>. IEEE, 1996. <a href=\"https://doi.org/10.1109/32.489079\">https://doi.org/10.1109/32.489079</a>.","ieee":"R. Alur, T. A. Henzinger, and P. Ho, “Automatic symbolic verification of embedded systems,” <i>IEEE Transactions on Software Engineering</i>, vol. 22, no. 3. IEEE, pp. 181–201, 1996."},"year":"1996","publisher":"IEEE","article_type":"original","page":"181 - 201","quality_controlled":"1","publication_status":"published","article_processing_charge":"No","date_created":"2018-12-11T12:09:45Z","title":"Automatic symbolic verification of embedded systems","intvolume":"        22","_id":"4611","scopus_import":"1","author":[{"last_name":"Alur","first_name":"Rajeev","full_name":"Alur, Rajeev"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ho","first_name":"Pei","full_name":"Ho, Pei"}],"issue":"3","main_file_link":[{"url":"https://ecommons.cornell.edu/handle/1813/7170","open_access":"1"}],"status":"public","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","publication_identifier":{"issn":["0018-9162"]},"publist_id":"96","oa":1,"date_published":"1996-03-01T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"oa_version":"Published Version","month":"03","publication":"IEEE Transactions on Software Engineering"},{"citation":{"ista":"Alur R, Henzinger TA, Sontag ED eds. 1996. Hybrid Systems III: Verification and Control, Berlin ; Heidelberg: Springer, IX, 619p.","mla":"Alur, Rajeev, et al., editors. <i>Hybrid Systems III: Verification and Control</i>. Vol. 1066, Springer, 1996, doi:<a href=\"https://doi.org/10.1007/BFb0020931\">10.1007/BFb0020931</a>.","short":"R. Alur, T.A. Henzinger, E.D. Sontag, eds., Hybrid Systems III: Verification and Control, Springer, Berlin ; Heidelberg, 1996.","ieee":"R. Alur, T. A. Henzinger, and E. D. Sontag, Eds., <i>Hybrid Systems III: Verification and Control</i>, vol. 1066. Berlin ; Heidelberg: Springer, 1996.","chicago":"Alur, Rajeev, Thomas A Henzinger, and Eduardo D Sontag, eds. <i>Hybrid Systems III: Verification and Control</i>. Vol. 1066. Lecture Notes in Computer Science. Berlin ; Heidelberg: Springer, 1996. <a href=\"https://doi.org/10.1007/BFb0020931\">https://doi.org/10.1007/BFb0020931</a>.","apa":"Alur, R., Henzinger, T. A., &#38; Sontag, E. D. (Eds.). (1996). <i>Hybrid Systems III: Verification and Control</i> (Vol. 1066). Berlin ; Heidelberg: Springer. <a href=\"https://doi.org/10.1007/BFb0020931\">https://doi.org/10.1007/BFb0020931</a>","ama":"Alur R, Henzinger TA, Sontag ED, eds. <i>Hybrid Systems III: Verification and Control</i>. Vol 1066. Berlin ; Heidelberg: Springer; 1996. doi:<a href=\"https://doi.org/10.1007/BFb0020931\">10.1007/BFb0020931</a>"},"year":"1996","date_updated":"2021-12-22T13:57:33Z","type":"book_editor","date_published":"1996-01-01T00:00:00Z","publication_identifier":{"issn":["0302-9743"],"isbn":["978-3-540-61155-4"]},"day":"01","doi":"10.1007/BFb0020931","publist_id":"97","place":"Berlin ; Heidelberg","volume":1066,"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","_id":"4612","date_created":"2018-12-11T12:09:45Z","article_processing_charge":"No","publication_status":"published","oa_version":"None","intvolume":"      1066","alternative_title":["LNCS"],"month":"01","title":"Hybrid Systems III: Verification and Control","quality_controlled":"1","series_title":"Lecture Notes in Computer Science","page":"IX, 619","language":[{"iso":"eng"}],"editor":[{"last_name":"Alur","first_name":"Rajeev","full_name":"Alur, Rajeev"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Eduardo D","last_name":"Sontag","full_name":"Sontag, Eduardo D"}],"publisher":"Springer"},{"date_updated":"2021-01-12T08:06:28Z","citation":{"apa":"de Bono, M., &#38; Hodgkin, J. (1996). Evolution of sex determination in Caenorhabditis: Unusually high divergence of tra-1 and its functional consequences. <i>Genetics</i>. Genetics Society of America.","ama":"de Bono M, Hodgkin J. Evolution of sex determination in Caenorhabditis: Unusually high divergence of tra-1 and its functional consequences. <i>Genetics</i>. 1996;144(2):587-595.","ieee":"M. de Bono and J. Hodgkin, “Evolution of sex determination in Caenorhabditis: Unusually high divergence of tra-1 and its functional consequences,” <i>Genetics</i>, vol. 144, no. 2. Genetics Society of America, pp. 587–595, 1996.","chicago":"Bono, Mario de, and J. Hodgkin. “Evolution of Sex Determination in Caenorhabditis: Unusually High Divergence of Tra-1 and Its Functional Consequences.” <i>Genetics</i>. Genetics Society of America, 1996.","mla":"de Bono, Mario, and J. Hodgkin. “Evolution of Sex Determination in Caenorhabditis: Unusually High Divergence of Tra-1 and Its Functional Consequences.” <i>Genetics</i>, vol. 144, no. 2, Genetics Society of America, 1996, pp. 587–95.","short":"M. de Bono, J. Hodgkin, Genetics 144 (1996) 587–595.","ista":"de Bono M, Hodgkin J. 1996. Evolution of sex determination in Caenorhabditis: Unusually high divergence of tra-1 and its functional consequences. Genetics. 144(2), 587–595."},"year":"1996","external_id":{"pmid":["8889522"]},"day":"01","abstract":[{"text":"The tra-1 gene is a terminal regulator of somatic sex in Caenorhabditis elegans: high tra-1 activity elicits female development, low tra-1 activity elicits male development. To investigate the function and evolution of tra- 1, we examined the tra-1 gene from the closely related nematode C. briggsae. Ce-tra-1 and Cb-tra-1 are unusually divergent. Each gene generates two transcripts, but only one of these is present in both species. This common transcript encodes TRA-1A, which shows only 44% amino acid identity between the species, a figure much lower than that for previously compared genes. A Cb-tra-1 transgene rescues many tissues of tra-1(null) mutants of C. elegans but not the somatic gonad or germ line. This transgene also causes nongonadal feminization of XO animals, indicating incorrect sexual regulation. Alignment of Ce-TRA-1A and Cb-TRA-1A defined several conserved regions likely to be important for tra-1 function. The phenotype differences between Ce-tra- 1(null) mutants rescued by Cb-tra-1 transgenes and wild-type C. elegans indicate significant divergence of regulatory regions. These molecular and functional studies suggest that evolution of sex determination in nematodes is rapid and genetically complex.","lang":"eng"}],"volume":144,"extern":"1","pmid":1,"_id":"6161","author":[{"full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","last_name":"de Bono","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hodgkin, J.","last_name":"Hodgkin","first_name":"J."}],"issue":"2","publication_status":"published","date_created":"2019-03-21T11:50:37Z","title":"Evolution of sex determination in Caenorhabditis: Unusually high divergence of tra-1 and its functional consequences","intvolume":"       144","page":"587-595","quality_controlled":"1","publisher":"Genetics Society of America","date_published":"1996-10-01T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["00166731"]},"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1207552/","open_access":"1"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","publication":"Genetics","oa_version":"Published Version","month":"10","language":[{"iso":"eng"}],"keyword":["amino acid sequence","article","caenorhabditis elegans","evolution","genetic variability","nonhuman","priority journal","sex determination","Amino Acid Sequence","Animals","Animals","Genetically Modified","Base Sequence","Caenorhabditis","Caenorhabditis elegans","Caenorhabditis elegans Proteins","DNA","Helminth","DNA-Binding Proteins","Evolution","Molecular","Female","Helminth Proteins","Membrane Proteins","Molecular Sequence Data","Mutagenesis","RNA","Messenger","Sequence Homology","Amino Acid","Sex Determination (Analysis)","Transcription Factors","Transgenes","Turner Syndrome","Animalia","Caenorhabditis","Caenorhabditis briggsae","Caenorhabditis elegans","Nematoda"]},{"publication":"5th Scandinavian Workshop on Algorithm Theory","_id":"11804","scopus_import":"1","author":[{"first_name":"Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Telle, Jan Arne","first_name":"Jan Arne","last_name":"Telle"}],"publication_status":"published","oa_version":"None","article_processing_charge":"No","date_created":"2022-08-11T13:42:42Z","month":"07","alternative_title":["LNCS"],"title":"Faster algorithms for the nonemptiness of streett automata and for communication protocol pruning","intvolume":"      1097","page":"16–27","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Springer Nature","conference":{"name":"SWAT: Scandinavian Workshop on Algorithm Theory","start_date":"1996-07-03","location":"Reykjavik, Iceland","end_date":"1996-07-05"},"date_updated":"2023-02-14T07:52:17Z","citation":{"mla":"Henzinger, Monika H., and Jan Arne Telle. “Faster Algorithms for the Nonemptiness of Streett Automata and for Communication Protocol Pruning.” <i>5th Scandinavian Workshop on Algorithm Theory</i>, vol. 1097, Springer Nature, 1996, pp. 16–27, doi:<a href=\"https://doi.org/10.1007/3-540-61422-2_117\">10.1007/3-540-61422-2_117</a>.","short":"M.H. Henzinger, J.A. Telle, in:, 5th Scandinavian Workshop on Algorithm Theory, Springer Nature, 1996, pp. 16–27.","ista":"Henzinger MH, Telle JA. 1996. Faster algorithms for the nonemptiness of streett automata and for communication protocol pruning. 5th Scandinavian Workshop on Algorithm Theory. SWAT: Scandinavian Workshop on Algorithm Theory, LNCS, vol. 1097, 16–27.","apa":"Henzinger, M. H., &#38; Telle, J. A. (1996). Faster algorithms for the nonemptiness of streett automata and for communication protocol pruning. In <i>5th Scandinavian Workshop on Algorithm Theory</i> (Vol. 1097, pp. 16–27). Reykjavik, Iceland: Springer Nature. <a href=\"https://doi.org/10.1007/3-540-61422-2_117\">https://doi.org/10.1007/3-540-61422-2_117</a>","ama":"Henzinger MH, Telle JA. Faster algorithms for the nonemptiness of streett automata and for communication protocol pruning. In: <i>5th Scandinavian Workshop on Algorithm Theory</i>. Vol 1097. Springer Nature; 1996:16–27. doi:<a href=\"https://doi.org/10.1007/3-540-61422-2_117\">10.1007/3-540-61422-2_117</a>","chicago":"Henzinger, Monika H, and Jan Arne Telle. “Faster Algorithms for the Nonemptiness of Streett Automata and for Communication Protocol Pruning.” In <i>5th Scandinavian Workshop on Algorithm Theory</i>, 1097:16–27. Springer Nature, 1996. <a href=\"https://doi.org/10.1007/3-540-61422-2_117\">https://doi.org/10.1007/3-540-61422-2_117</a>.","ieee":"M. H. Henzinger and J. A. Telle, “Faster algorithms for the nonemptiness of streett automata and for communication protocol pruning,” in <i>5th Scandinavian Workshop on Algorithm Theory</i>, Reykjavik, Iceland, 1996, vol. 1097, pp. 16–27."},"year":"1996","date_published":"1996-07-01T00:00:00Z","type":"conference","doi":"10.1007/3-540-61422-2_117","day":"01","publication_identifier":{"isbn":["9783540614227"],"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["9783540685296"]},"abstract":[{"text":"This paper shows how a general technique, called lock-step search, used in dynamic graph algorithms, can be used to improve the running time of two problems arising in program verification and communication protocol design.\r\n(1)We consider the nonemptiness problem for Streett automata: We are given a directed graph G = (V, E) with n = ¦V¦ and m = ¦E¦, and a collection of pairs of subsets of vertices, called Streett pairs,〈L i , U i 〉, i = 1.k. The question is whether G has a cycle (not necessarily simple) which, for each 1 ≤ i ≤ k, if it contains a vertex from L i then it also contains a vertex of U i . Let b=Σ i=1..k |L i |+|U i |. The previously best algorithm takes time O((m + b) min{n, k}). We present an algorithm that takes time 𝑂(𝑚min{𝑚𝑙𝑜𝑔𝑛,‾‾‾‾‾‾√𝑘,𝑛}+𝑏𝑚𝑖𝑛{𝑙𝑜𝑔𝑛,𝑘}).\r\n(2)In communication protocol pruning we are given a directed graph G = (V, E) with l special vertices. The problem is to efficiently maintain the strongly-connected components of the special vertices on a restricted set of edge deletions. Let m i be the number of edges in the strongly connected component of the ith special vertex. The previously best algorithm repeatedly recomputes the strongly-connected components which leads to a running time of O(Σ i m 2i). We present an algorithm with time 𝑂(𝑙√∑𝑖𝑚1.5𝑖).","lang":"eng"}],"volume":1097,"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public"},{"volume":1099,"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_updated":"2023-02-14T07:57:14Z","citation":{"short":"M.H. Henzinger, M. Thorup, in:, 23rd International Colloquium on Automata, Languages, and Programming, Springer Nature, 1996, pp. 290–299.","mla":"Henzinger, Monika H., and Mikkel Thorup. “Improved Sampling with Applications to Dynamic Graph Algorithms.” <i>23rd International Colloquium on Automata, Languages, and Programming</i>, vol. 1099, Springer Nature, 1996, pp. 290–99, doi:<a href=\"https://doi.org/10.1007/3-540-61440-0_136\">10.1007/3-540-61440-0_136</a>.","ista":"Henzinger MH, Thorup M. 1996. Improved sampling with applications to dynamic graph algorithms. 23rd International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LNCS, vol. 1099, 290–299.","ama":"Henzinger MH, Thorup M. Improved sampling with applications to dynamic graph algorithms. In: <i>23rd International Colloquium on Automata, Languages, and Programming</i>. Vol 1099. Springer Nature; 1996:290-299. doi:<a href=\"https://doi.org/10.1007/3-540-61440-0_136\">10.1007/3-540-61440-0_136</a>","apa":"Henzinger, M. H., &#38; Thorup, M. (1996). Improved sampling with applications to dynamic graph algorithms. In <i>23rd International Colloquium on Automata, Languages, and Programming</i> (Vol. 1099, pp. 290–299). Paderborn, Germany: Springer Nature. <a href=\"https://doi.org/10.1007/3-540-61440-0_136\">https://doi.org/10.1007/3-540-61440-0_136</a>","ieee":"M. H. Henzinger and M. Thorup, “Improved sampling with applications to dynamic graph algorithms,” in <i>23rd International Colloquium on Automata, Languages, and Programming</i>, Paderborn, Germany, 1996, vol. 1099, pp. 290–299.","chicago":"Henzinger, Monika H, and Mikkel Thorup. “Improved Sampling with Applications to Dynamic Graph Algorithms.” In <i>23rd International Colloquium on Automata, Languages, and Programming</i>, 1099:290–99. Springer Nature, 1996. <a href=\"https://doi.org/10.1007/3-540-61440-0_136\">https://doi.org/10.1007/3-540-61440-0_136</a>."},"year":"1996","date_published":"1996-07-01T00:00:00Z","type":"conference","doi":"10.1007/3-540-61440-0_136","day":"01","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"eisbn":["9783540685807"],"isbn":["9783540614401"]},"abstract":[{"text":"We state a new sampling lemma and use it to improve the running time of dynamic graph algorithms.\r\n\r\nFor the dynamic connectivity problem the previously best randomized algorithm takes expected time O(log3 n) per update, amortized over Ω(m) updates. Using the new sampling lemma, we improve its running time to O(log2 n). There exists a lower bound in the cell probe model for the time per operation of Ω(log n/ log log n) for this problem.\r\n\r\nSimilarly improved running times are achieved for 2-edge connectivity, k-weight minimum spanning tree, and bipartiteness.","lang":"eng"}],"page":"290-299","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Springer Nature","conference":{"end_date":"1996-07-12","location":"Paderborn, Germany","start_date":"1996-07-08","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"_id":"11910","publication":"23rd International Colloquium on Automata, Languages, and Programming","scopus_import":"1","author":[{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","first_name":"Monika H"},{"first_name":"Mikkel","last_name":"Thorup","full_name":"Thorup, Mikkel"}],"publication_status":"published","oa_version":"None","date_created":"2022-08-18T06:42:24Z","article_processing_charge":"No","alternative_title":["LNCS"],"title":"Improved sampling with applications to dynamic graph algorithms","month":"07","intvolume":"      1099"},{"type":"conference","date_published":"1996-01-28T00:00:00Z","citation":{"chicago":"Henzinger, Monika H, Valerie King, and Tandy Warnow. “Constructing a Tree from Homeomorphic Subtrees, with Applications to Computational Evolutionary Biology.” In <i>7th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 333–40. Society for Industrial and Applied Mathematics, 1996.","ieee":"M. H. Henzinger, V. King, and T. Warnow, “Constructing a tree from homeomorphic subtrees, with applications to computational evolutionary biology,” in <i>7th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Atlanta, GA, United States, 1996, pp. 333–340.","apa":"Henzinger, M. H., King, V., &#38; Warnow, T. (1996). Constructing a tree from homeomorphic subtrees, with applications to computational evolutionary biology. In <i>7th Annual ACM-SIAM Symposium on Discrete Algorithms</i> (pp. 333–340). Atlanta, GA, United States: Society for Industrial and Applied Mathematics.","ama":"Henzinger MH, King V, Warnow T. Constructing a tree from homeomorphic subtrees, with applications to computational evolutionary biology. In: <i>7th Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Society for Industrial and Applied Mathematics; 1996:333-340.","ista":"Henzinger MH, King V, Warnow T. 1996. Constructing a tree from homeomorphic subtrees, with applications to computational evolutionary biology. 7th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 333–340.","mla":"Henzinger, Monika H., et al. “Constructing a Tree from Homeomorphic Subtrees, with Applications to Computational Evolutionary Biology.” <i>7th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Society for Industrial and Applied Mathematics, 1996, pp. 333–40.","short":"M.H. Henzinger, V. King, T. Warnow, in:, 7th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 1996, pp. 333–340."},"year":"1996","date_updated":"2023-02-21T16:24:53Z","oa":1,"abstract":[{"text":"We are given a set 7 = {Tl , Tz, . . . , Tk} of rooted binary trees, each Ti leaf-labeled by a subset L(x) c {1,2 )...) n}. IfT is a tree on {1,2, . . , n}, we let T]L denote the subtree of T induced by the nodes of L and all their ancestors. The consensus tree problem asks whether there exists a tree T* such that for every I, T’ IC(Ti) is homeomorphic to Ti. We present algorithms which test if a given set of trees has a consensus tree and if so, construct one. The deterministic algorithm takes time min{O(mn’/‘), O(m + n2 logn)}, where m = Ci IZl and uses linear space. The randomized algorithm takes\r\ntime O(m log3 n) and uses linear space. The previous best for this problem was an 1981 O(mn) algorithm by Aho et al. Our faster deterministic algorithm uses a new efficient algorithm for the following interesting dynamic graph problem: Given a graph G with n nodes and m edges and a sequence of b batches of one or more edge deletions, then after each batch, either find a new component that has just been created or determine that there is no such component. For this\r\nproblem, we have a simple algorithm with running time O(n2 log n + be min{ n2, m log n}), where be is the number of batches which do not result in a new component. For our particular application, bc 5 1. If all edges are deleted, then the best previously known deterministic algorithm requires time O(mJ;ii) to solve this problem. computational evolutionary biology. The first application is in the problem of inferring consensus of trees when there can be disagreement[l6]. There have, been several models suggested for this problem[2, 3, 4, 8, ?, 11, 17, 181, of which one is called the Local Consensus Tree[l5]. The local consensus tree model presumes that the user provides a local consensus rule which determines the form of the output tree on (perhaps) each triple of leaves, and the objective is to determine whether a tree exists which is consistent with each of the constraints. We will show that we can construct the local consensus tree of k trees on n species in O(kn3) time, improving on the O(lcn3 + n”) running time if we use the Aho et al algorithm. The second application is a\r\nheuristic for constructing the maximum likelihood tree based upon combining solutions to small subproblems.\r\nThis is a simple and yet potentially significantly interesting approach to the evolutionary tree construction\r\nproblem. ","lang":"eng"}],"day":"28","publication_identifier":{"isbn":["0898713668"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","related_material":{"record":[{"status":"public","relation":"later_version","id":"11679"}]},"extern":"1","main_file_link":[{"url":"https://dl.acm.org/doi/10.5555/313852.314080","open_access":"1"}],"author":[{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","first_name":"Monika H"},{"last_name":"King","first_name":"Valerie","full_name":"King, Valerie"},{"last_name":"Warnow","first_name":"Tandy","full_name":"Warnow, Tandy"}],"scopus_import":"1","_id":"11927","publication":"7th Annual ACM-SIAM Symposium on Discrete Algorithms","month":"01","title":"Constructing a tree from homeomorphic subtrees, with applications to computational evolutionary biology","article_processing_charge":"No","date_created":"2022-08-19T06:57:47Z","publication_status":"published","oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","page":"333 -340","conference":{"location":"Atlanta, GA, United States","end_date":"1996-01-30","start_date":"1996-01-28","name":"SODA: Symposium on Discrete Algorithms"},"publisher":"Society for Industrial and Applied Mathematics"},{"publisher":"Elsevier","article_type":"original","page":"141 - 144","quality_controlled":"1","publication_status":"published","date_created":"2018-12-11T12:03:27Z","article_processing_charge":"No","title":"Analysis of molecular determinants in native AMPA receptors","intvolume":"        28","pmid":1,"_id":"3462","scopus_import":"1","author":[{"first_name":"Thorsten","last_name":"Melcher","full_name":"Melcher, Thorsten"},{"first_name":"Jörg","last_name":"Geiger","full_name":"Geiger, Jörg"},{"first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Monyer, Hannah","first_name":"Hannah","last_name":"Monyer"}],"issue":"2","volume":28,"extern":"1","doi":"10.1016/0197-0186(95)00077-1","day":"01","date_updated":"2022-08-11T09:42:29Z","citation":{"ista":"Melcher T, Geiger J, Jonas PM, Monyer H. 1996. Analysis of molecular determinants in native AMPA receptors. Neurochemistry International. 28(2), 141–144.","mla":"Melcher, Thorsten, et al. “Analysis of Molecular Determinants in Native AMPA Receptors.” <i>Neurochemistry International</i>, vol. 28, no. 2, Elsevier, 1996, pp. 141–44, doi:<a href=\"https://doi.org/10.1016/0197-0186(95)00077-1\">10.1016/0197-0186(95)00077-1</a>.","short":"T. Melcher, J. Geiger, P.M. Jonas, H. Monyer, Neurochemistry International 28 (1996) 141–144.","ieee":"T. Melcher, J. Geiger, P. M. Jonas, and H. Monyer, “Analysis of molecular determinants in native AMPA receptors,” <i>Neurochemistry International</i>, vol. 28, no. 2. Elsevier, pp. 141–144, 1996.","chicago":"Melcher, Thorsten, Jörg Geiger, Peter M Jonas, and Hannah Monyer. “Analysis of Molecular Determinants in Native AMPA Receptors.” <i>Neurochemistry International</i>. Elsevier, 1996. <a href=\"https://doi.org/10.1016/0197-0186(95)00077-1\">https://doi.org/10.1016/0197-0186(95)00077-1</a>.","apa":"Melcher, T., Geiger, J., Jonas, P. M., &#38; Monyer, H. (1996). Analysis of molecular determinants in native AMPA receptors. <i>Neurochemistry International</i>. Elsevier. <a href=\"https://doi.org/10.1016/0197-0186(95)00077-1\">https://doi.org/10.1016/0197-0186(95)00077-1</a>","ama":"Melcher T, Geiger J, Jonas PM, Monyer H. Analysis of molecular determinants in native AMPA receptors. <i>Neurochemistry International</i>. 1996;28(2):141-144. doi:<a href=\"https://doi.org/10.1016/0197-0186(95)00077-1\">10.1016/0197-0186(95)00077-1</a>"},"year":"1996","external_id":{"pmid":["8719701 "]},"language":[{"iso":"eng"}],"oa_version":"None","month":"02","publication":"Neurochemistry International","status":"public","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","publication_identifier":{"issn":["0197-0186"]},"publist_id":"2925","date_published":"1996-02-01T00:00:00Z","type":"journal_article"},{"page":"35-41 and - 193-194","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"ACM","conference":{"name":"VRST: Symposium on Virtual Reality Software and Technology","start_date":"1996-07-01","end_date":"1996-07-04","location":"Hong Kong"},"publication":"Proceedings of the ACM Symposium on Virtual Reality Software and Technology","_id":"3553","author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fu, Ping","last_name":"Fu","first_name":"Ping"},{"full_name":"Quian, Jiang","last_name":"Quian","first_name":"Jiang"}],"oa_version":"None","publication_status":"published","date_created":"2018-12-11T12:03:56Z","article_processing_charge":"No","title":"Geometric modeling in CAVE","month":"07","acknowledgement":"We thank Ernst Miicke and Michael Facello for their work on the Alpha shape library, and Nataraj Akkiraju for his work on the surface triangulation library. We thank NCSA for providing access to the CAVE.","extern":"1","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","status":"public","date_updated":"2022-08-10T13:42:02Z","citation":{"mla":"Edelsbrunner, Herbert, et al. “Geometric Modeling in CAVE.” <i>Proceedings of the ACM Symposium on Virtual Reality Software and Technology</i>, ACM, 1996, pp. 35-41 and-193–94, doi:<a href=\"https://doi.org/10.1145/3304181.3304190\">10.1145/3304181.3304190</a>.","short":"H. Edelsbrunner, P. Fu, J. Quian, in:, Proceedings of the ACM Symposium on Virtual Reality Software and Technology, ACM, 1996, pp. 35-41 and-193–194.","ista":"Edelsbrunner H, Fu P, Quian J. 1996. Geometric modeling in CAVE. Proceedings of the ACM Symposium on Virtual Reality Software and Technology. VRST: Symposium on Virtual Reality Software and Technology, 35-41 and-193–194.","ama":"Edelsbrunner H, Fu P, Quian J. Geometric modeling in CAVE. In: <i>Proceedings of the ACM Symposium on Virtual Reality Software and Technology</i>. ACM; 1996:35-41 and-193-194. doi:<a href=\"https://doi.org/10.1145/3304181.3304190\">10.1145/3304181.3304190</a>","apa":"Edelsbrunner, H., Fu, P., &#38; Quian, J. (1996). Geometric modeling in CAVE. In <i>Proceedings of the ACM Symposium on Virtual Reality Software and Technology</i> (pp. 35-41 and-193–194). Hong Kong: ACM. <a href=\"https://doi.org/10.1145/3304181.3304190\">https://doi.org/10.1145/3304181.3304190</a>","chicago":"Edelsbrunner, Herbert, Ping Fu, and Jiang Quian. “Geometric Modeling in CAVE.” In <i>Proceedings of the ACM Symposium on Virtual Reality Software and Technology</i>, 35-41 and-193–94. ACM, 1996. <a href=\"https://doi.org/10.1145/3304181.3304190\">https://doi.org/10.1145/3304181.3304190</a>.","ieee":"H. Edelsbrunner, P. Fu, and J. Quian, “Geometric modeling in CAVE,” in <i>Proceedings of the ACM Symposium on Virtual Reality Software and Technology</i>, Hong Kong, 1996, pp. 35-41 and-193–194."},"year":"1996","date_published":"1996-07-01T00:00:00Z","type":"conference","doi":"10.1145/3304181.3304190","publication_identifier":{"isbn":["9780897918251"]},"day":"01","abstract":[{"text":"Virtual environments open up new opportunities and challenges for geometric modeling systems. A general approach to geometric modeling suitable for the Cave Automatic Virtual Environment is described. The approach is based on alpha complexes, and some of its capabilities are demonstrated by applying it to the study of biomolecules.","lang":"eng"}],"publist_id":"2832"},{"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","month":"06","oa_version":"None","language":[{"iso":"eng"}],"type":"journal_article","date_published":"1996-06-29T00:00:00Z","publist_id":"2749","publication_identifier":{"issn":["0962-8436"]},"status":"public","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","issue":"1341","author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mallet","first_name":"James","full_name":"Mallet, James"}],"scopus_import":"1","pmid":1,"_id":"3634","intvolume":"       351","title":"Natural selection and random genetic drift as causes of evolution on islands","article_processing_charge":"No","date_created":"2018-12-11T12:04:21Z","publication_status":"published","quality_controlled":"1","page":"785 - 795","article_type":"original","publisher":"Royal Society of London","external_id":{"pmid":["8693020"]},"year":"1996","citation":{"ista":"Barton NH, Mallet J. 1996. Natural selection and random genetic drift as causes of evolution on islands. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 351(1341), 785–795.","short":"N.H. Barton, J. Mallet, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 351 (1996) 785–795.","mla":"Barton, Nicholas H., and James Mallet. “Natural Selection and Random Genetic Drift as Causes of Evolution on Islands.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 351, no. 1341, Royal Society of London, 1996, pp. 785–95, doi:<a href=\"https://doi.org/10.1098/rstb.1996.0073\">10.1098/rstb.1996.0073</a>.","ieee":"N. H. Barton and J. Mallet, “Natural selection and random genetic drift as causes of evolution on islands,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 351, no. 1341. Royal Society of London, pp. 785–795, 1996.","chicago":"Barton, Nicholas H, and James Mallet. “Natural Selection and Random Genetic Drift as Causes of Evolution on Islands.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society of London, 1996. <a href=\"https://doi.org/10.1098/rstb.1996.0073\">https://doi.org/10.1098/rstb.1996.0073</a>.","apa":"Barton, N. H., &#38; Mallet, J. (1996). Natural selection and random genetic drift as causes of evolution on islands. <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rstb.1996.0073\">https://doi.org/10.1098/rstb.1996.0073</a>","ama":"Barton NH, Mallet J. Natural selection and random genetic drift as causes of evolution on islands. <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 1996;351(1341):785-795. doi:<a href=\"https://doi.org/10.1098/rstb.1996.0073\">10.1098/rstb.1996.0073</a>"},"date_updated":"2022-08-10T12:57:10Z","abstract":[{"text":"The evolutionary processes responsible for adaptation and speciation on islands differ in several ways from those on the mainland. Most attention has been given to the random genetic drift that arises when a population is founded from just a few colonizing genomes. Theoretical obstacles to 'founder effect speciation' are discussed, together with recent proposals for avoiding them. It is argued that although certain kinds of epistasis can facilitate the evolution of strong reproductive isolation, this favours divergence by selection as much as by random drift.","lang":"eng"}],"day":"29","doi":"10.1098/rstb.1996.0073","extern":"1","volume":351},{"user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","status":"public","date_published":"1996-02-01T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["0016-6723"]},"publist_id":"2748","language":[{"iso":"eng"}],"publication":"Genetical Research","oa_version":"None","month":"02","volume":67,"extern":"1","date_updated":"2022-08-10T12:38:51Z","citation":{"ieee":"B. Charlesworth and N. H. Barton, “Recombination load associated with selection for increased recombination,” <i>Genetical Research</i>, vol. 67, no. 1. Cambridge University Press, pp. 27–41, 1996.","chicago":"Charlesworth, Brian, and Nicholas H Barton. “Recombination Load Associated with Selection for Increased Recombination.” <i>Genetical Research</i>. Cambridge University Press, 1996. <a href=\"https://doi.org/10.1017/S0016672300033450\">https://doi.org/10.1017/S0016672300033450</a>.","apa":"Charlesworth, B., &#38; Barton, N. H. (1996). Recombination load associated with selection for increased recombination. <i>Genetical Research</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/S0016672300033450\">https://doi.org/10.1017/S0016672300033450</a>","ama":"Charlesworth B, Barton NH. Recombination load associated with selection for increased recombination. <i>Genetical Research</i>. 1996;67(1):27-41. doi:<a href=\"https://doi.org/10.1017/S0016672300033450\">10.1017/S0016672300033450</a>","ista":"Charlesworth B, Barton NH. 1996. Recombination load associated with selection for increased recombination. Genetical Research. 67(1), 27–41.","short":"B. Charlesworth, N.H. Barton, Genetical Research 67 (1996) 27–41.","mla":"Charlesworth, Brian, and Nicholas H. Barton. “Recombination Load Associated with Selection for Increased Recombination.” <i>Genetical Research</i>, vol. 67, no. 1, Cambridge University Press, 1996, pp. 27–41, doi:<a href=\"https://doi.org/10.1017/S0016672300033450\">10.1017/S0016672300033450</a>."},"year":"1996","external_id":{"pmid":["8919888 "]},"doi":"10.1017/S0016672300033450","day":"01","abstract":[{"text":"Experiments on Drosophila suggest that genetic recombination may result in lowered fitness of progeny (a 'recombination load'). This has been interpreted as evidence either for a direct effect of recombination on fitness, or for the maintenance of linkage disequilibria by epistatic selection. Here we show that such a recombination load is to be expected even if selection favours increased genetic recombination. This is because of the fact that, although a modifier may suffer an immediate loss of fitness if it increases recombination, it eventually becomes associated with a higher additive genetic variance in fitness, which allows a faster response to direction selection. This argument applies to mutation-selection balance with synergistic epistasis, directional selection on quantitative traits, and ectopic exchange among transposable elements. Further experiments are needed to determine whether the selection against recombination due to the immediate load is outweighed by the increased additive variance in fitness produced by recombination.","lang":"eng"}],"page":"27 - 41","quality_controlled":"1","publisher":"Cambridge University Press","article_type":"original","_id":"3635","pmid":1,"scopus_import":"1","author":[{"full_name":"Charlesworth, Brian","last_name":"Charlesworth","first_name":"Brian"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"}],"issue":"1","publication_status":"published","date_created":"2018-12-11T12:04:21Z","article_processing_charge":"No","title":"Recombination load associated with selection for increased recombination","intvolume":"        67"},{"date_updated":"2022-08-09T14:20:13Z","year":"1996","citation":{"ista":"Dogterom M, Felix M, Guet CC, Leibler S. 1996. Influence of M-phase chromatin on the anisotropy of microtubule asters. Journal of Cell Biology. 133(1), 125–140.","mla":"Dogterom, Marileen, et al. “Influence of M-Phase Chromatin on the Anisotropy of Microtubule Asters.” <i>Journal of Cell Biology</i>, vol. 133, no. 1, Rockefeller University Press, 1996, pp. 125–40, doi:<a href=\"https://doi.org/doi: 10.1083/jcb.133.1.125 \">doi: 10.1083/jcb.133.1.125 </a>.","short":"M. Dogterom, M. Felix, C.C. Guet, S. Leibler, Journal of Cell Biology 133 (1996) 125–140.","chicago":"Dogterom, Marileen, M. Felix, Calin C Guet, and Stanislas Leibler. “Influence of M-Phase Chromatin on the Anisotropy of Microtubule Asters.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 1996. <a href=\"https://doi.org/doi: 10.1083/jcb.133.1.125 \">https://doi.org/doi: 10.1083/jcb.133.1.125 </a>.","ieee":"M. Dogterom, M. Felix, C. C. Guet, and S. Leibler, “Influence of M-phase chromatin on the anisotropy of microtubule asters,” <i>Journal of Cell Biology</i>, vol. 133, no. 1. Rockefeller University Press, pp. 125–140, 1996.","ama":"Dogterom M, Felix M, Guet CC, Leibler S. Influence of M-phase chromatin on the anisotropy of microtubule asters. <i>Journal of Cell Biology</i>. 1996;133(1):125-140. doi:<a href=\"https://doi.org/doi: 10.1083/jcb.133.1.125 \">doi: 10.1083/jcb.133.1.125 </a>","apa":"Dogterom, M., Felix, M., Guet, C. C., &#38; Leibler, S. (1996). Influence of M-phase chromatin on the anisotropy of microtubule asters. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/doi: 10.1083/jcb.133.1.125 \">https://doi.org/doi: 10.1083/jcb.133.1.125 </a>"},"external_id":{"pmid":["8601601"]},"doi":"doi: 10.1083/jcb.133.1.125 ","day":"01","abstract":[{"text":"In many eukaryotic cells going through M-phase, a bipolar spindle is formed by microtubules nucleated from centrosomes. These microtubules, in addition to being `'captured” by kinetochores, may be stabilized by chromatin in two different ways: short-range stabilization effects may affect microtubules in close contact with the chromatin, while long-range stabilization effects may `'guide” microtubule growth towards the chromatin (e.g., by introducing a diffusive gradient of an enzymatic activity that affects microtubule assembly). Here, we use both meiotic and mitotic extracts from Xenopus laevis eggs to study microtubule aster formation and microtubule dynamics in the presence of chromatin. In `'low-speed” meiotic extracts, in the presence of salmon sperm chromatin, we find that short-range stabilization effects lead to a strong anisotropy of the microtubule asters. Analysis of the dynamic parameters of microtubule growth shows that this anisotropy arises from a decrease in the catastrophe frequency, an increase in the rescue frequency and a decrease in the growth velocity. In this system we also find evidence for long-range `'guidance” effects, which lead to a weak anisotropy of the asters. Statistically relevant results on these long-range effects are obtained in `'high-speed” mitotic extracts in the presence of artificially constructed chromatin stripes. We find that aster anisotropy is biased in the direction of the chromatin and that the catastrophe frequency is reduced in its vicinity. In this system we also find a surprising dependence of the catastrophe and the rescue frequencies on the length of microtubules nucleated from centrosomes: the catastrophe frequency increases and the rescue frequency decreases with microtubule length.","lang":"eng"}],"acknowledgement":"We would like to thank T. Holy and T. Mitchison for providing us with centrosomes; M. Glotzer and T. Mitchison for giving us the plasmid for A90 cyclin B; J. Stock and members of his laboratory for help with biochemical preparations; R. Zimmerman for help with the biotinylation of DNA; J. Shepard for help with the patterning of surfaces; D. Tsui for use\r\nof his clean room facility, and D. Fygenson, T. Holy, E. Karsenti, E. Kennedy, A. Levine, T. Mitchison, and G. Waters for valuable discussions, constant encouragement and technical help. This work was partially supported by the National Institutes of Health (Grant No. GM-50712) and the Human Frontier Science Program.","volume":133,"extern":"1","pmid":1,"_id":"3756","scopus_import":"1","author":[{"first_name":"Marileen","last_name":"Dogterom","full_name":"Dogterom, Marileen"},{"last_name":"Felix","first_name":"M.","full_name":"Felix, M."},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"},{"first_name":"Stanislas","last_name":"Leibler","full_name":"Leibler, Stanislas"}],"issue":"1","publication_status":"published","article_processing_charge":"No","date_created":"2018-12-11T12:05:00Z","title":"Influence of M-phase chromatin on the anisotropy of microtubule asters","intvolume":"       133","page":"125 - 140","quality_controlled":"1","publisher":"Rockefeller University Press","article_type":"original","date_published":"1996-01-01T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["0021-9525"]},"publist_id":"2473","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2120784/"}],"status":"public","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","publication":"Journal of Cell Biology","oa_version":"Published Version","month":"01","language":[{"iso":"eng"}]},{"volume":16,"extern":"1","date_updated":"2022-08-09T13:32:21Z","citation":{"short":"N. Akkiraju, H. Edelsbrunner, P. Fu, J. Qian, IEEE Computer Graphics and Applications 16 (1996) 58–61.","mla":"Akkiraju, Nataraj, et al. “Viewing Geometric Protein Structures from inside a CAVE.” <i>IEEE Computer Graphics and Applications</i>, vol. 16, no. 4, IEEE, 1996, pp. 58–61, doi:<a href=\"https://doi.org/10.1109/38.511855\">10.1109/38.511855</a>.","ista":"Akkiraju N, Edelsbrunner H, Fu P, Qian J. 1996. Viewing geometric protein structures from inside a CAVE. IEEE Computer Graphics and Applications. 16(4), 58–61.","apa":"Akkiraju, N., Edelsbrunner, H., Fu, P., &#38; Qian, J. (1996). Viewing geometric protein structures from inside a CAVE. <i>IEEE Computer Graphics and Applications</i>. IEEE. <a href=\"https://doi.org/10.1109/38.511855\">https://doi.org/10.1109/38.511855</a>","ama":"Akkiraju N, Edelsbrunner H, Fu P, Qian J. Viewing geometric protein structures from inside a CAVE. <i>IEEE Computer Graphics and Applications</i>. 1996;16(4):58-61. doi:<a href=\"https://doi.org/10.1109/38.511855\">10.1109/38.511855</a>","ieee":"N. Akkiraju, H. Edelsbrunner, P. Fu, and J. Qian, “Viewing geometric protein structures from inside a CAVE,” <i>IEEE Computer Graphics and Applications</i>, vol. 16, no. 4. IEEE, pp. 58–61, 1996.","chicago":"Akkiraju, Nataraj, Herbert Edelsbrunner, Ping Fu, and Jiang Qian. “Viewing Geometric Protein Structures from inside a CAVE.” <i>IEEE Computer Graphics and Applications</i>. IEEE, 1996. <a href=\"https://doi.org/10.1109/38.511855\">https://doi.org/10.1109/38.511855</a>."},"year":"1996","doi":"10.1109/38.511855","day":"01","abstract":[{"text":"We have developed general modeling software for a Cave Automatic Virtual Environment (CAVE); one of its applications is modeling 3D protein structures, generating both outside-in and inside-out views of geometric models. An advantage of the CAVE over other virtual environments is that multiple viewers can observe the same scene at the same time and place. Our software is scalable-from high-end virtual environments such as the CAVE, to mid-range immersive desktop systems, down to low-end graphics workstations. In the current configuration, a parallel Silicon Graphics Power Challenge supercomputer architecture performs the computationally intensive construction of surface patches remotely, and sends the results through the I-WAY (Information Wide Area Year) using VBNS (Very-high-Bandwidth Network Systems) to the graphics machines that drive the CAVE and our graphics visualization software, Valvis (Virtual ALpha shapes VISualizer).","lang":"eng"}],"page":"58 - 61","quality_controlled":"1","publisher":"IEEE","article_type":"original","_id":"4024","scopus_import":"1","author":[{"full_name":"Akkiraju, Nataraj","last_name":"Akkiraju","first_name":"Nataraj"},{"last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fu, Ping","first_name":"Ping","last_name":"Fu"},{"full_name":"Qian, Jiang","last_name":"Qian","first_name":"Jiang"}],"issue":"4","publication_status":"published","article_processing_charge":"No","date_created":"2018-12-11T12:06:30Z","title":"Viewing geometric protein structures from inside a CAVE","intvolume":"        16","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","status":"public","date_published":"1996-07-01T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["0018-9162"]},"publist_id":"2101","language":[{"iso":"eng"}],"publication":"IEEE Computer Graphics and Applications","oa_version":"None","month":"07"},{"extern":"1","volume":71,"acknowledgement":"The research of both authors is partially supported by the Office of Naval Research. Herbert Edelsbrunner is also supported through the Alan T. Waterman award, grant CCR-9118874. ","abstract":[{"text":"Questions of chemical reactivity can often be cast as questions of molecular geometry. Common geometric models for proteins and other molecules are the space-filling diagram, the solvent accessible surface and the molecular surface. In this paper we present a new approach to triangulating the surface of a molecule under the three models, which is fast, robust, and results in topologically correct triangulations. Our computations are based on a simplicial complex dual to the molecule models. All proposed algorithms are parallelizable.","lang":"eng"}],"day":"05","doi":"10.1016/S0166-218X(96)00054-6","year":"1996","citation":{"ieee":"N. Akkiraju and H. Edelsbrunner, “Triangulating the surface of a molecule,” <i>Discrete Applied Mathematics</i>, vol. 71, no. 1–3. Elsevier, pp. 5–22, 1996.","chicago":"Akkiraju, Nataraj, and Herbert Edelsbrunner. “Triangulating the Surface of a Molecule.” <i>Discrete Applied Mathematics</i>. Elsevier, 1996. <a href=\"https://doi.org/10.1016/S0166-218X(96)00054-6\">https://doi.org/10.1016/S0166-218X(96)00054-6</a>.","apa":"Akkiraju, N., &#38; Edelsbrunner, H. (1996). Triangulating the surface of a molecule. <i>Discrete Applied Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/S0166-218X(96)00054-6\">https://doi.org/10.1016/S0166-218X(96)00054-6</a>","ama":"Akkiraju N, Edelsbrunner H. Triangulating the surface of a molecule. <i>Discrete Applied Mathematics</i>. 1996;71(1-3):5-22. doi:<a href=\"https://doi.org/10.1016/S0166-218X(96)00054-6\">10.1016/S0166-218X(96)00054-6</a>","ista":"Akkiraju N, Edelsbrunner H. 1996. Triangulating the surface of a molecule. Discrete Applied Mathematics. 71(1–3), 5–22.","short":"N. Akkiraju, H. Edelsbrunner, Discrete Applied Mathematics 71 (1996) 5–22.","mla":"Akkiraju, Nataraj, and Herbert Edelsbrunner. “Triangulating the Surface of a Molecule.” <i>Discrete Applied Mathematics</i>, vol. 71, no. 1–3, Elsevier, 1996, pp. 5–22, doi:<a href=\"https://doi.org/10.1016/S0166-218X(96)00054-6\">10.1016/S0166-218X(96)00054-6</a>."},"date_updated":"2022-08-09T14:06:12Z","article_type":"original","publisher":"Elsevier","quality_controlled":"1","page":"5 - 22","intvolume":"        71","title":"Triangulating the surface of a molecule","date_created":"2018-12-11T12:06:30Z","article_processing_charge":"No","publication_status":"published","issue":"1-3","author":[{"full_name":"Akkiraju, Nataraj","first_name":"Nataraj","last_name":"Akkiraju"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"scopus_import":"1","_id":"4025","status":"public","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","main_file_link":[{"open_access":"1","url":"https://www.sciencedirect.com/science/article/pii/S0166218X96000546?via%3Dihub"}],"oa":1,"publist_id":"2102","publication_identifier":{"issn":["0166-218X"]},"type":"journal_article","date_published":"1996-12-05T00:00:00Z","language":[{"iso":"eng"}],"month":"12","oa_version":"Published Version","publication":"Discrete Applied Mathematics"},{"language":[{"iso":"eng"}],"month":"03","oa_version":"None","publication":"Algorithmica","status":"public","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","publist_id":"2099","publication_identifier":{"issn":["0178-4617"]},"type":"journal_article","date_published":"1996-03-01T00:00:00Z","article_type":"original","publisher":"Springer","quality_controlled":"1","page":"223 - 241","intvolume":"        15","title":"Incremental topological flipping works for regular triangulations","date_created":"2018-12-11T12:06:31Z","article_processing_charge":"No","publication_status":"published","issue":"3","author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Shah","first_name":"Nimish","full_name":"Shah, Nimish"}],"scopus_import":"1","_id":"4026","extern":"1","acknowledgement":"National Science Foundation under Grant CCR-8921421, Alan T. Waterman award, Grant CCR-9118874.","volume":15,"abstract":[{"lang":"eng","text":"A set of n weighted points in general position in R(d) defines a unique regular triangulation. This paper proves that if the points are added one by one, then flipping in a topological order will succeed in constructing this triangulation. If, in addition, the points are added in a random sequence and the history of the flips is used for locating the next point, then the algorithm takes expected time at most O(n log n + n(inverted left perpendicular d/2 inverted right perpendicular)). Under the assumption that the points and weights are independently and identically distributed, the expected running time is between proportional to and a factor log n more than the expected size of the regular triangulation. The expectation is over choosing the points and over independent coin-flips performed by the algorithm."}],"day":"01","doi":"10.1007/BF01975867","year":"1996","citation":{"ama":"Edelsbrunner H, Shah N. Incremental topological flipping works for regular triangulations. <i>Algorithmica</i>. 1996;15(3):223-241. doi:<a href=\"https://doi.org/10.1007/BF01975867\">10.1007/BF01975867</a>","apa":"Edelsbrunner, H., &#38; Shah, N. (1996). Incremental topological flipping works for regular triangulations. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/BF01975867\">https://doi.org/10.1007/BF01975867</a>","chicago":"Edelsbrunner, Herbert, and Nimish Shah. “Incremental Topological Flipping Works for Regular Triangulations.” <i>Algorithmica</i>. Springer, 1996. <a href=\"https://doi.org/10.1007/BF01975867\">https://doi.org/10.1007/BF01975867</a>.","ieee":"H. Edelsbrunner and N. Shah, “Incremental topological flipping works for regular triangulations,” <i>Algorithmica</i>, vol. 15, no. 3. Springer, pp. 223–241, 1996.","short":"H. Edelsbrunner, N. Shah, Algorithmica 15 (1996) 223–241.","mla":"Edelsbrunner, Herbert, and Nimish Shah. “Incremental Topological Flipping Works for Regular Triangulations.” <i>Algorithmica</i>, vol. 15, no. 3, Springer, 1996, pp. 223–41, doi:<a href=\"https://doi.org/10.1007/BF01975867\">10.1007/BF01975867</a>.","ista":"Edelsbrunner H, Shah N. 1996. Incremental topological flipping works for regular triangulations. Algorithmica. 15(3), 223–241."},"date_updated":"2022-08-09T09:46:07Z"},{"year":"1996","citation":{"ista":"Chazelle B, Edelsbrunner H, Guibas L, Sharir M, Stolfi J. 1996. Lines in space: Combinatorics and algorithms. Algorithmica. 15(5), 428–447.","mla":"Chazelle, Bernard, et al. “Lines in Space: Combinatorics and Algorithms.” <i>Algorithmica</i>, vol. 15, no. 5, Springer, 1996, pp. 428–47, doi:<a href=\"https://doi.org/10.1007/BF01955043\">10.1007/BF01955043</a>.","short":"B. Chazelle, H. Edelsbrunner, L. Guibas, M. Sharir, J. Stolfi, Algorithmica 15 (1996) 428–447.","ieee":"B. Chazelle, H. Edelsbrunner, L. Guibas, M. Sharir, and J. Stolfi, “Lines in space: Combinatorics and algorithms,” <i>Algorithmica</i>, vol. 15, no. 5. Springer, pp. 428–447, 1996.","chicago":"Chazelle, Bernard, Herbert Edelsbrunner, Leonidas Guibas, Micha Sharir, and Jorge Stolfi. “Lines in Space: Combinatorics and Algorithms.” <i>Algorithmica</i>. Springer, 1996. <a href=\"https://doi.org/10.1007/BF01955043\">https://doi.org/10.1007/BF01955043</a>.","ama":"Chazelle B, Edelsbrunner H, Guibas L, Sharir M, Stolfi J. Lines in space: Combinatorics and algorithms. <i>Algorithmica</i>. 1996;15(5):428-447. doi:<a href=\"https://doi.org/10.1007/BF01955043\">10.1007/BF01955043</a>","apa":"Chazelle, B., Edelsbrunner, H., Guibas, L., Sharir, M., &#38; Stolfi, J. (1996). Lines in space: Combinatorics and algorithms. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/BF01955043\">https://doi.org/10.1007/BF01955043</a>"},"date_updated":"2022-08-09T09:55:46Z","day":"01","doi":"10.1007/BF01955043","abstract":[{"text":"Questions about lines in space arise frequently as subproblems in three-dimensional computational geometry. In this paper we study a number of fundamental combinatorial and algorithmic problems involving arrangements of n lines in three-dimensional space. Our main results include: 1. A tight Θ(n2) bound on the maximum combinatorial description complexity of the set of all oriented lines that have specified orientations relative to the n given lines. 2. A similar bound of Θ(n3) for the complexity of the set of all lines passing above the n given lines. 3. A preprocessing procedure using O(n2+ε) time and storage, for any ε &gt; 0, that builds a structure supporting O(logn)-time queries for testing if a line lies above all the given lines. 4. An algorithm that tests the &quot;towering property&quot; in O(n4/3+ε) time, for any ε &gt; 0: do n given red lines lie all above n given blue lines? The tools used to obtain these and other results include Plücker coordinates for lines in space and ε-nets for various geometric range spaces.","lang":"eng"}],"volume":15,"acknowledgement":"Work on this paper by Bernard Chazelle has been supported by NSF Grant CCR-87-00917. Work on this paper by Herbert Edelsbrunner has been supported by NSF Grant CCR-87-14565. Work on this paper by Leonidas Guibas has been supported by grants from the Mitsubishi and Toshiba Corporations. Work on this paper by Micha Sharir has been supported by ONR Grant N00014-87-K-0129, by NSF Grants DCR-83-20085 and CCR-89-01484, and by grants from the U.S.-Israeli Binational Science Foundation, the NCRD — the Israeli National Council for Research and Development, and the EMET Fund of the Israeli Academy of Sciences.","extern":"1","scopus_import":"1","_id":"4027","issue":"5","author":[{"full_name":"Chazelle, Bernard","first_name":"Bernard","last_name":"Chazelle"},{"last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Guibas, Leonidas","first_name":"Leonidas","last_name":"Guibas"},{"full_name":"Sharir, Micha","last_name":"Sharir","first_name":"Micha"},{"full_name":"Stolfi, Jorge","first_name":"Jorge","last_name":"Stolfi"}],"date_created":"2018-12-11T12:06:31Z","article_processing_charge":"No","publication_status":"published","intvolume":"        15","title":"Lines in space: Combinatorics and algorithms","quality_controlled":"1","page":"428 - 447","publisher":"Springer","article_type":"original","type":"journal_article","date_published":"1996-05-01T00:00:00Z","publication_identifier":{"issn":["0178-4617"]},"publist_id":"2100","status":"public","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","publication":"Algorithmica","oa_version":"None","month":"05","language":[{"iso":"eng"}]},{"citation":{"ama":"Liang J, Edelsbrunner H, Subramaniam S. <i>Effects of Molecular Shape Representations on Boundary Element Method for Protein Electrostatics Computations</i>. Vol 70. Cell Press; 1996:A224-A224. doi:<a href=\"https://doi.org/10.1016/S0006-3495(96)79664-9\">10.1016/S0006-3495(96)79664-9</a>","apa":"Liang, J., Edelsbrunner, H., &#38; Subramaniam, S. (1996). <i>Effects of molecular shape representations on boundary element method for protein electrostatics computations</i>. <i>Fortieth Annual Meeting</i> (Vol. 70, pp. A224–A224). Cell Press. <a href=\"https://doi.org/10.1016/S0006-3495(96)79664-9\">https://doi.org/10.1016/S0006-3495(96)79664-9</a>","chicago":"Liang, Jie, Herbert Edelsbrunner, and Shankar Subramaniam. <i>Effects of Molecular Shape Representations on Boundary Element Method for Protein Electrostatics Computations</i>. <i>Fortieth Annual Meeting</i>. Vol. 70. Cell Press, 1996. <a href=\"https://doi.org/10.1016/S0006-3495(96)79664-9\">https://doi.org/10.1016/S0006-3495(96)79664-9</a>.","ieee":"J. Liang, H. Edelsbrunner, and S. Subramaniam, <i>Effects of molecular shape representations on boundary element method for protein electrostatics computations</i>, vol. 70, no. 2, Part 2. Cell Press, 1996, pp. A224–A224.","mla":"Liang, Jie, et al. “Effects of Molecular Shape Representations on Boundary Element Method for Protein Electrostatics Computations.” <i>Fortieth Annual Meeting</i>, vol. 70, no. 2, Part 2, Cell Press, 1996, pp. A224–A224, doi:<a href=\"https://doi.org/10.1016/S0006-3495(96)79664-9\">10.1016/S0006-3495(96)79664-9</a>.","short":"J. Liang, H. Edelsbrunner, S. Subramaniam, Effects of Molecular Shape Representations on Boundary Element Method for Protein Electrostatics Computations, Cell Press, 1996.","ista":"Liang J, Edelsbrunner H, Subramaniam S. 1996. Effects of molecular shape representations on boundary element method for protein electrostatics computations, Cell Press,p."},"year":"1996","date_updated":"2022-08-08T10:22:38Z","type":"conference_poster","date_published":"1996-02-19T00:00:00Z","day":"19","doi":"10.1016/S0006-3495(96)79664-9","publist_id":"2097","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.sciencedirect.com/science/article/pii/S0006349596796649?via%3Dihub"}],"acknowledgement":"article M-Pos412","volume":70,"status":"public","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","extern":"1","_id":"4030","publication":"Fortieth Annual Meeting","issue":"2, Part 2","author":[{"first_name":"Jie","last_name":"Liang","full_name":"Liang, Jie"},{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Subramaniam, Shankar","first_name":"Shankar","last_name":"Subramaniam"}],"date_created":"2018-12-11T12:06:32Z","article_processing_charge":"No","publication_status":"published","oa_version":"None","intvolume":"        70","month":"02","title":"Effects of molecular shape representations on boundary element method for protein electrostatics computations","page":"A224 - A224","language":[{"iso":"eng"}],"publisher":"Cell Press"},{"issue":"2, Part 2","author":[{"last_name":"Liang","first_name":"Jie","full_name":"Liang, Jie"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner"},{"full_name":"Pamidghantam, Sudhakar","last_name":"Pamidghantam","first_name":"Sudhakar"},{"full_name":"Subramaniam, Shankar","first_name":"Shankar","last_name":"Subramaniam"}],"_id":"4031","publication":"Fortieth Annual Meeting","intvolume":"        70","month":"02","title":"Analytical method for molecular shapes: Area, volume, cavities, interface and pockets","date_created":"2018-12-11T12:06:32Z","article_processing_charge":"No","publication_status":"published","oa_version":"None","language":[{"iso":"eng"}],"page":"A377 - A377","publisher":"Cell Press","type":"conference_poster","date_published":"1996-02-21T00:00:00Z","citation":{"ama":"Liang J, Edelsbrunner H, Pamidghantam S, Subramaniam S. <i>Analytical Method for Molecular Shapes: Area, Volume, Cavities, Interface and Pockets</i>. Vol 70. Cell Press; 1996:A377-A377. doi:<a href=\"https://doi.org/10.1016/S0006-3495(96)79670-4\">10.1016/S0006-3495(96)79670-4</a>","apa":"Liang, J., Edelsbrunner, H., Pamidghantam, S., &#38; Subramaniam, S. (1996). <i>Analytical method for molecular shapes: Area, volume, cavities, interface and pockets</i>. <i>Fortieth Annual Meeting</i> (Vol. 70, pp. A377–A377). Cell Press. <a href=\"https://doi.org/10.1016/S0006-3495(96)79670-4\">https://doi.org/10.1016/S0006-3495(96)79670-4</a>","chicago":"Liang, Jie, Herbert Edelsbrunner, Sudhakar Pamidghantam, and Shankar Subramaniam. <i>Analytical Method for Molecular Shapes: Area, Volume, Cavities, Interface and Pockets</i>. <i>Fortieth Annual Meeting</i>. Vol. 70. Cell Press, 1996. <a href=\"https://doi.org/10.1016/S0006-3495(96)79670-4\">https://doi.org/10.1016/S0006-3495(96)79670-4</a>.","ieee":"J. Liang, H. Edelsbrunner, S. Pamidghantam, and S. Subramaniam, <i>Analytical method for molecular shapes: Area, volume, cavities, interface and pockets</i>, vol. 70, no. 2, Part 2. Cell Press, 1996, pp. A377–A377.","short":"J. Liang, H. Edelsbrunner, S. Pamidghantam, S. Subramaniam, Analytical Method for Molecular Shapes: Area, Volume, Cavities, Interface and Pockets, Cell Press, 1996.","mla":"Liang, Jie, et al. “Analytical Method for Molecular Shapes: Area, Volume, Cavities, Interface and Pockets.” <i>Fortieth Annual Meeting</i>, vol. 70, no. 2, Part 2, Cell Press, 1996, pp. A377–A377, doi:<a href=\"https://doi.org/10.1016/S0006-3495(96)79670-4\">10.1016/S0006-3495(96)79670-4</a>.","ista":"Liang J, Edelsbrunner H, Pamidghantam S, Subramaniam S. 1996. Analytical method for molecular shapes: Area, volume, cavities, interface and pockets, Cell Press,p."},"year":"1996","date_updated":"2022-08-08T10:21:56Z","oa":1,"publist_id":"2098","day":"21","doi":"10.1016/S0006-3495(96)79670-4","status":"public","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","extern":"1","main_file_link":[{"url":"https://www.sciencedirect.com/science/article/pii/S0006349596796704?via%3Dihub","open_access":"1"}],"acknowledgement":"article W-AM-L6","volume":70},{"intvolume":"       123","title":"Mutations affecting development of the zebrafish inner ear and lateral line","date_created":"2018-12-11T12:07:11Z","article_processing_charge":"No","publication_status":"published","author":[{"first_name":"Tanya","last_name":"Whitfield","full_name":"Whitfield, Tanya"},{"full_name":"Granato, Michael","first_name":"Michael","last_name":"Granato"},{"full_name":"Van Eeden, Fredericus","last_name":"Van Eeden","first_name":"Fredericus"},{"last_name":"Schach","first_name":"Ursula","full_name":"Schach, Ursula"},{"full_name":"Brand, Michael","last_name":"Brand","first_name":"Michael"},{"first_name":"Makoto","last_name":"Furutani Seiki","full_name":"Furutani Seiki, Makoto"},{"full_name":"Haffter, Pascal","first_name":"Pascal","last_name":"Haffter"},{"last_name":"Hammerschmidt","first_name":"Matthias","full_name":"Hammerschmidt, Matthias"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jiang","first_name":"Yunjin","full_name":"Jiang, Yunjin"},{"full_name":"Kane, Donald","first_name":"Donald","last_name":"Kane"},{"full_name":"Kelsh, Robert","last_name":"Kelsh","first_name":"Robert"},{"first_name":"Mary","last_name":"Mullins","full_name":"Mullins, Mary"},{"first_name":"Jörg","last_name":"Odenthal","full_name":"Odenthal, Jörg"},{"full_name":"Nüsslein Volhard, Christiane","first_name":"Christiane","last_name":"Nüsslein Volhard"}],"scopus_import":"1","pmid":1,"_id":"4142","article_type":"original","publisher":"Company of Biologists","quality_controlled":"1","page":"241 - 254","abstract":[{"lang":"eng","text":"Mutations giving rise to anatomical defects in the inner ear have been isolated in a large scale screen for mutations causing visible abnormalities in the zebrafish embryo (Haffter, P., Granato, M., Brand, M. et al. (1996) Development 123, 1-36). 58 mutants have been classified as having a primary ear phenotype; these fall into several phenotypic classes, affecting presence or size of the otoliths, size and shape of the otic vesicle and formation of the semicircular canals, and define at least 20 complementation groups. Mutations in seven genes cause loss of one or both otoliths, but do not appear to affect development of other structures within the ear. Mutations in seven genes affect morphology and patterning of the inner ear epithelium, including formation of the semicircular canals and, in some, development of sensory patches (maculae and cristae). Within this class, dog-eared mutants show abnormal development of semicircular canals and lack cristae within the ear, while in van gogh, semicircular canals fail to form altogether, resulting in a tiny otic vesicle containing a single sensory patch. Both these mutants show defects in the expression of homeobox genes within the otic vesicle. In a further class of mutants, ear size is affected while patterning appears to be relatively normal; mutations in three genes cause expansion of the otic vesicle, while in little ears and microtic, the ear is abnormally small, but still contains all five sensory patches, as in the wild type. Many of the ear and otolith mutants show an expected behavioural phenotype: embryos fail to balance correctly, and may swim on their sides, upside down, or in circles. Several mutants with similar balance defects have also been isolated that have no obvious structural ear defect, but that may include mutants with vestibular dysfunction of the inner ear (Granato, M., van Eeden, F. J. M., Schach, U. et al. (1996) Development, 123, 399-413,). Mutations in 19 genes causing primary defects in other structures also show an ear defect. In particular, ear phenotypes are often found in conjunction with defects of neural crest derivatives (pigment cells and/or cartilaginous elements of the jaw). At least one mutant, dog-eared, shows defects in both the ear and another placodally derived sensory system, the lateral line, while hypersensitive mutants have additional trunk lateral line organs."}],"day":"01","doi":"10.1242/dev.123.1.241","external_id":{"pmid":["9007244"]},"citation":{"ista":"Whitfield T, Granato M, Van Eeden F, Schach U, Brand M, Furutani Seiki M, Haffter P, Hammerschmidt M, Heisenberg C-PJ, Jiang Y, Kane D, Kelsh R, Mullins M, Odenthal J, Nüsslein Volhard C. 1996. Mutations affecting development of the zebrafish inner ear and lateral line. Development. 123, 241–254.","mla":"Whitfield, Tanya, et al. “Mutations Affecting Development of the Zebrafish Inner Ear and Lateral Line.” <i>Development</i>, vol. 123, Company of Biologists, 1996, pp. 241–54, doi:<a href=\"https://doi.org/10.1242/dev.123.1.241\">10.1242/dev.123.1.241</a>.","short":"T. Whitfield, M. Granato, F. Van Eeden, U. Schach, M. Brand, M. Furutani Seiki, P. Haffter, M. Hammerschmidt, C.-P.J. Heisenberg, Y. Jiang, D. Kane, R. Kelsh, M. Mullins, J. Odenthal, C. Nüsslein Volhard, Development 123 (1996) 241–254.","ieee":"T. Whitfield <i>et al.</i>, “Mutations affecting development of the zebrafish inner ear and lateral line,” <i>Development</i>, vol. 123. Company of Biologists, pp. 241–254, 1996.","chicago":"Whitfield, Tanya, Michael Granato, Fredericus Van Eeden, Ursula Schach, Michael Brand, Makoto Furutani Seiki, Pascal Haffter, et al. “Mutations Affecting Development of the Zebrafish Inner Ear and Lateral Line.” <i>Development</i>. Company of Biologists, 1996. <a href=\"https://doi.org/10.1242/dev.123.1.241\">https://doi.org/10.1242/dev.123.1.241</a>.","apa":"Whitfield, T., Granato, M., Van Eeden, F., Schach, U., Brand, M., Furutani Seiki, M., … Nüsslein Volhard, C. (1996). Mutations affecting development of the zebrafish inner ear and lateral line. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.123.1.241\">https://doi.org/10.1242/dev.123.1.241</a>","ama":"Whitfield T, Granato M, Van Eeden F, et al. Mutations affecting development of the zebrafish inner ear and lateral line. <i>Development</i>. 1996;123:241-254. doi:<a href=\"https://doi.org/10.1242/dev.123.1.241\">10.1242/dev.123.1.241</a>"},"year":"1996","date_updated":"2022-08-08T08:45:59Z","extern":"1","acknowledgement":"T. T. W. thanks all members of the Tübingen fish and fly groups for their hospitality and generosity during her visits to the laboratory. We thank Julian Lewis, in whose laboratory much of this work was carried out, for many helpful discussions and suggestions, Catherine Haddon for advice on wild-type ear development and techniques, and Stephen Massey for fish husbandry in Oxford. We are grateful to Julian Lewis, Catherine Haddon, Nick Monk and Patrick Blader for comments on the manuscript, and to Trevor Jowett, Tom Schilling,Eric Weinberg and Monte Westerfield for providing cDNAs. We also thank Jarema Malicki and Wolfgang Driever for making some of the Boston otolith mutants available before publication. T. T. W. thanks the EMBO (ASTF 7668; ASTF 7918), the Imperial Cancer Research Fund and the Wellcome Trust (03643/Z/92) for support.","volume":123,"month":"12","oa_version":"None","publication":"Development","language":[{"iso":"eng"}],"publist_id":"1979","publication_identifier":{"issn":["0950-1991"]},"type":"journal_article","date_published":"1996-12-01T00:00:00Z","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","status":"public"}]