--- _id: '3584' abstract: - lang: eng text: We develop fast algorithms for computing the linking number of a simplicial complex within a filtration.We give experimental results in applying our work toward the detection of non-trivial tangling in biomolecules, modeled as alpha complexes. author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Afra full_name: Zomorodian, Afra last_name: Zomorodian citation: ama: Edelsbrunner H, Zomorodian A. Computing linking numbers of a filtration. Homology, Homotopy and Applications. 2003;5(2):19-37. apa: Edelsbrunner, H., & Zomorodian, A. (2003). Computing linking numbers of a filtration. Homology, Homotopy and Applications. International Press. chicago: Edelsbrunner, Herbert, and Afra Zomorodian. “Computing Linking Numbers of a Filtration.” Homology, Homotopy and Applications. International Press, 2003. ieee: H. Edelsbrunner and A. Zomorodian, “Computing linking numbers of a filtration,” Homology, Homotopy and Applications, vol. 5, no. 2. International Press, pp. 19–37, 2003. ista: Edelsbrunner H, Zomorodian A. 2003. Computing linking numbers of a filtration. Homology, Homotopy and Applications. 5(2), 19–37. mla: Edelsbrunner, Herbert, and Afra Zomorodian. “Computing Linking Numbers of a Filtration.” Homology, Homotopy and Applications, vol. 5, no. 2, International Press, 2003, pp. 19–37. short: H. Edelsbrunner, A. Zomorodian, Homology, Homotopy and Applications 5 (2003) 19–37. date_created: 2018-12-11T12:04:05Z date_published: 2003-04-22T00:00:00Z date_updated: 2021-01-12T07:44:28Z day: '22' extern: '1' intvolume: ' 5' issue: '2' language: - iso: eng main_file_link: - url: http://projecteuclid.org/euclid.hha/1088453320 month: '04' oa_version: None page: 19 - 37 publication: Homology, Homotopy and Applications publication_status: published publisher: International Press publist_id: '2801' quality_controlled: '1' status: public title: Computing linking numbers of a filtration type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2003' ... --- _id: '3620' abstract: - lang: eng text: 'Stable hybrid zones in which ecologically divergent taxa give rise to a range of recombinants are natural laboratories in which the genetic basis of adaptation and reproductive isolation can be unraveled. One such hybrid zone is formed by the fire-bellied toads Bombina bombina and B. variegata (Anura: Discoglossidae). Adaptations to permanent and ephemeral breeding habitats, respectively, have shaped numerous phenotypic differences between the taxa. All of these are, in principle, candidates for a genetic dissection via QTL mapping. We present here a linkage map of 28 codominant and 10 dominant markers in the Bombina genome. In an F2 cross, markers that were mainly microsatellites, SSCPs or allozymes were mapped to 20 linkage groups. Among the 40 isolated CA microsatellites, we noted a preponderance of compound and frequently interleaved CA-TA repeats as well as a striking polarity at the 5′ end of the repeats.' author: - first_name: Beate full_name: Nürnberger, Beate last_name: Nürnberger - first_name: Sebastian full_name: Hofman, Sebastian last_name: Hofman - first_name: Bqruni full_name: Förg-Brey, Bqruni last_name: Förg Brey - first_name: Gabriele full_name: Praetzel, Gabriele last_name: Praetzel - first_name: Alan full_name: Maclean, Alan W last_name: Maclean - first_name: Jacek full_name: Szymura, Jacek M last_name: Szymura - first_name: Catherine full_name: Abbott, Catherine M last_name: Abbott - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Nürnberger B, Hofman S, Förg Brey B, et al. A linkage map for the hybridising toads Bombina bombina and B. variegata (Anura: Discoglossidae). Heredity. 2003;91(2):136-142. doi:10.1038/sj.hdy.6800291' apa: 'Nürnberger, B., Hofman, S., Förg Brey, B., Praetzel, G., Maclean, A., Szymura, J., … Barton, N. H. (2003). A linkage map for the hybridising toads Bombina bombina and B. variegata (Anura: Discoglossidae). Heredity. Nature Publishing Group. https://doi.org/10.1038/sj.hdy.6800291' chicago: 'Nürnberger, Beate, Sebastian Hofman, Bqruni Förg Brey, Gabriele Praetzel, Alan Maclean, Jacek Szymura, Catherine Abbott, and Nicholas H Barton. “A Linkage Map for the Hybridising Toads Bombina Bombina and B. Variegata (Anura: Discoglossidae).” Heredity. Nature Publishing Group, 2003. https://doi.org/10.1038/sj.hdy.6800291.' ieee: 'B. Nürnberger et al., “A linkage map for the hybridising toads Bombina bombina and B. variegata (Anura: Discoglossidae),” Heredity, vol. 91, no. 2. Nature Publishing Group, pp. 136–142, 2003.' ista: 'Nürnberger B, Hofman S, Förg Brey B, Praetzel G, Maclean A, Szymura J, Abbott C, Barton NH. 2003. A linkage map for the hybridising toads Bombina bombina and B. variegata (Anura: Discoglossidae). Heredity. 91(2), 136–142.' mla: 'Nürnberger, Beate, et al. “A Linkage Map for the Hybridising Toads Bombina Bombina and B. Variegata (Anura: Discoglossidae).” Heredity, vol. 91, no. 2, Nature Publishing Group, 2003, pp. 136–42, doi:10.1038/sj.hdy.6800291.' short: B. Nürnberger, S. Hofman, B. Förg Brey, G. Praetzel, A. Maclean, J. Szymura, C. Abbott, N.H. Barton, Heredity 91 (2003) 136–142. date_created: 2018-12-11T12:04:17Z date_published: 2003-08-01T00:00:00Z date_updated: 2021-01-12T07:44:43Z day: '01' doi: 10.1038/sj.hdy.6800291 extern: 1 intvolume: ' 91' issue: '2' month: '08' page: 136 - 142 publication: Heredity publication_status: published publisher: Nature Publishing Group publist_id: '2763' quality_controlled: 0 status: public title: 'A linkage map for the hybridising toads Bombina bombina and B. variegata (Anura: Discoglossidae)' type: journal_article volume: 91 year: '2003' ... --- _id: '3619' abstract: - lang: eng text: What is the chance that some part of a stretch of genome will survive? In a population of constant size, and with no selection, the probability of survival of some part of a stretch of map length y<1 approaches View the MathML source for View the MathML source. Thus, the whole genome is certain to be lost, but the rate of loss is extremely slow. This solution extends to give the whole distribution of surviving block sizes as a function of time. We show that the expected number of blocks at time t is 1+yt and give expressions for the moments of the number of blocks and the total amount of genome that survives for a given time. The solution is based on a branching process and assumes complete interference between crossovers, so that each descendant carries only a single block of ancestral material. We consider cases where most individuals carry multiple blocks, either because there are multiple crossovers in a long genetic map, or because enough time has passed that most individuals in the population are related to each other. For species such as ours, which have a long genetic map, the genome of any individual which leaves descendants (∼80% of the population for a Poisson offspring number with mean two) is likely to persist for an extremely long time, in the form of a few short blocks of genome. author: - first_name: Stuart full_name: Baird, Stuart J last_name: Baird - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Alison full_name: Etheridge, Alison M last_name: Etheridge citation: ama: Baird S, Barton NH, Etheridge A. The distribution of surviving blocks of an ancestral genome. Theoretical Population Biology. 2003;64(4):451-471. doi:10.1016/S0040-5809(03)00098-4 apa: Baird, S., Barton, N. H., & Etheridge, A. (2003). The distribution of surviving blocks of an ancestral genome. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/S0040-5809(03)00098-4 chicago: Baird, Stuart, Nicholas H Barton, and Alison Etheridge. “The Distribution of Surviving Blocks of an Ancestral Genome.” Theoretical Population Biology. Academic Press, 2003. https://doi.org/10.1016/S0040-5809(03)00098-4. ieee: S. Baird, N. H. Barton, and A. Etheridge, “The distribution of surviving blocks of an ancestral genome,” Theoretical Population Biology, vol. 64, no. 4. Academic Press, pp. 451–471, 2003. ista: Baird S, Barton NH, Etheridge A. 2003. The distribution of surviving blocks of an ancestral genome. Theoretical Population Biology. 64(4), 451–471. mla: Baird, Stuart, et al. “The Distribution of Surviving Blocks of an Ancestral Genome.” Theoretical Population Biology, vol. 64, no. 4, Academic Press, 2003, pp. 451–71, doi:10.1016/S0040-5809(03)00098-4. short: S. Baird, N.H. Barton, A. Etheridge, Theoretical Population Biology 64 (2003) 451–471. date_created: 2018-12-11T12:04:17Z date_published: 2003-12-01T00:00:00Z date_updated: 2021-01-12T07:44:42Z day: '01' doi: 10.1016/S0040-5809(03)00098-4 extern: 1 intvolume: ' 64' issue: '4' month: '12' page: 451 - 471 publication: Theoretical Population Biology publication_status: published publisher: Academic Press publist_id: '2764' quality_controlled: 0 status: public title: The distribution of surviving blocks of an ancestral genome type: journal_article volume: 64 year: '2003' ... --- _id: '3618' abstract: - lang: eng text: There are several analyses in evolutionary ecology which assume that a family of offspring has come from only two parents. Here, we present a simple test for detecting when a batch involves two or more subfamilies. It is based on the fact that the mixing of families generates associations amongst unlinked marker loci. We also present simulations illustrating the power of our method for varying numbers of loci, alleles per locus and genotyped individuals. author: - first_name: Timothy full_name: Vines, Timothy H last_name: Vines - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Vines T, Barton NH. A new approach to detecting mixed families. Molecular Ecology. 2003;12(7):1999-2002. doi:10.1046/j.1365-294X.2003.01867.x apa: Vines, T., & Barton, N. H. (2003). A new approach to detecting mixed families. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1046/j.1365-294X.2003.01867.x chicago: Vines, Timothy, and Nicholas H Barton. “A New Approach to Detecting Mixed Families.” Molecular Ecology. Wiley-Blackwell, 2003. https://doi.org/10.1046/j.1365-294X.2003.01867.x. ieee: T. Vines and N. H. Barton, “A new approach to detecting mixed families,” Molecular Ecology, vol. 12, no. 7. Wiley-Blackwell, pp. 1999–2002, 2003. ista: Vines T, Barton NH. 2003. A new approach to detecting mixed families. Molecular Ecology. 12(7), 1999–2002. mla: Vines, Timothy, and Nicholas H. Barton. “A New Approach to Detecting Mixed Families.” Molecular Ecology, vol. 12, no. 7, Wiley-Blackwell, 2003, pp. 1999–2002, doi:10.1046/j.1365-294X.2003.01867.x. short: T. Vines, N.H. Barton, Molecular Ecology 12 (2003) 1999–2002. date_created: 2018-12-11T12:04:16Z date_published: 2003-07-01T00:00:00Z date_updated: 2021-01-12T07:44:42Z day: '01' doi: 10.1046/j.1365-294X.2003.01867.x extern: 1 intvolume: ' 12' issue: '7' month: '07' page: 1999 - 2002 publication: Molecular Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '2765' quality_controlled: 0 status: public title: A new approach to detecting mixed families type: journal_article volume: 12 year: '2003' ... --- _id: '3752' abstract: - lang: eng text: We use the lac operon in Escherichia coli as a prototype system to illustrate the current state, applicability, and limitations of modeling the dynamics of cellular networks. We integrate three different levels of description (molecular, cellular, and that of cell population) into a single model, which seems to capture many experimental aspects of the system. author: - first_name: Jose full_name: Vilar,Jose M last_name: Vilar - first_name: Calin C full_name: Calin Guet id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Stanislas full_name: Leibler, Stanislas last_name: Leibler citation: ama: 'Vilar J, Guet CC, Leibler S. Modeling network dynamics: the lac operon, a case study. Journal of Cell Biology. 2003;161(3):471-476. doi:10.1083/jcb.200301125' apa: 'Vilar, J., Guet, C. C., & Leibler, S. (2003). Modeling network dynamics: the lac operon, a case study. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.200301125' chicago: 'Vilar, Jose, Calin C Guet, and Stanislas Leibler. “Modeling Network Dynamics: The Lac Operon, a Case Study.” Journal of Cell Biology. Rockefeller University Press, 2003. https://doi.org/10.1083/jcb.200301125.' ieee: 'J. Vilar, C. C. Guet, and S. Leibler, “Modeling network dynamics: the lac operon, a case study,” Journal of Cell Biology, vol. 161, no. 3. Rockefeller University Press, pp. 471–476, 2003.' ista: 'Vilar J, Guet CC, Leibler S. 2003. Modeling network dynamics: the lac operon, a case study. Journal of Cell Biology. 161(3), 471–476.' mla: 'Vilar, Jose, et al. “Modeling Network Dynamics: The Lac Operon, a Case Study.” Journal of Cell Biology, vol. 161, no. 3, Rockefeller University Press, 2003, pp. 471–76, doi:10.1083/jcb.200301125.' short: J. Vilar, C.C. Guet, S. Leibler, Journal of Cell Biology 161 (2003) 471–476. date_created: 2018-12-11T12:04:58Z date_published: 2003-01-12T00:00:00Z date_updated: 2021-01-12T07:51:57Z day: '12' doi: 10.1083/jcb.200301125 extern: 1 intvolume: ' 161' issue: '3' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2172934/?tool=pubmed month: '01' oa: 1 page: 471 - 476 publication: Journal of Cell Biology publication_status: published publisher: Rockefeller University Press publist_id: '2475' quality_controlled: 0 status: public title: 'Modeling network dynamics: the lac operon, a case study' type: journal_article volume: 161 year: '2003' ...