[{"abstract":[{"text":"We address the problem of localizing homology classes, namely, finding the cycle representing a given class with the most concise geometric measure. We focus on the volume measure, that is, the 1-norm of a cycle. Two main results are presented. First, we prove the problem is NP-hard to approximate within any constant factor. Second, we prove that for homology of dimension two or higher, the problem is NP-hard to approximate even when the Betti number is O(1). A side effect is the inapproximability of the problem of computing the nonbounding cycle with the smallest volume, and computing cycles representing a homology basis with the minimal total volume. We also discuss other geometric measures (diameter and radius) and show their disadvantages in homology localization. Our work is restricted to homology over the ℤ2 field.","lang":"eng"}],"publisher":"Society for Industrial and Applied Mathematics","author":[{"first_name":"Chao","last_name":"Chen","full_name":"Chen, Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Freedman, Daniel","last_name":"Freedman","first_name":"Daniel"}],"conference":{"start_date":"2010-01-17","end_date":"2010-01-19","location":"Austin, TX, United States","name":"SODA: Symposium on Discrete Algorithms"},"publication_identifier":{"eisbn":["9781611973075"]},"scopus_import":"1","citation":{"ieee":"C. Chen and D. Freedman, “Hardness results for homology localization,” in <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Austin, TX, United States, 2010, pp. 1594–1604.","short":"C. Chen, D. Freedman, in:, Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2010, pp. 1594–1604.","ama":"Chen C, Freedman D. Hardness results for homology localization. In: <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Society for Industrial and Applied Mathematics; 2010:1594-1604. doi:<a href=\"https://doi.org/10.1137/1.9781611973075.129\">10.1137/1.9781611973075.129</a>","ista":"Chen C, Freedman D. 2010. Hardness results for homology localization. Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1594–1604.","chicago":"Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” In <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 1594–1604. Society for Industrial and Applied Mathematics, 2010. <a href=\"https://doi.org/10.1137/1.9781611973075.129\">https://doi.org/10.1137/1.9781611973075.129</a>.","apa":"Chen, C., &#38; Freedman, D. (2010). Hardness results for homology localization. In <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i> (pp. 1594–1604). Austin, TX, United States: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611973075.129\">https://doi.org/10.1137/1.9781611973075.129</a>","mla":"Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Society for Industrial and Applied Mathematics, 2010, pp. 1594–604, doi:<a href=\"https://doi.org/10.1137/1.9781611973075.129\">10.1137/1.9781611973075.129</a>."},"page":"1594-1604","publication":"Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","acknowledgement":"Partially supported by the Austrian Science Fund under grantFSP-S9103-N04 and P20134-N13.","quality_controlled":"1","doi":"10.1137/1.9781611973075.129","year":"2010","date_published":"2010-02-01T00:00:00Z","month":"02","related_material":{"record":[{"status":"public","relation":"later_version","id":"3267"}]},"title":"Hardness results for homology localization","date_created":"2022-03-21T08:24:07Z","type":"conference","date_updated":"2023-02-23T11:19:46Z","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"publication_status":"published","article_processing_charge":"No","oa_version":"None","day":"01","_id":"10909"},{"volume":5,"doi":"10.1186/1748-7188-5-37","quality_controlled":"1","ddc":["576"],"status":"public","acknowledgement":"Financial support from the Wiener Wissenschafts-, Forschungs- and Technologiefonds (WWTF) is greatly appreciated. A.v.H. acknowledges support from the German Research Foundation (DFG, SPP-1174).","scopus_import":1,"abstract":[{"lang":"eng","text":"Background: The availability of many gene alignments with overlapping taxon sets raises the question of which strategy is the best to infer species phylogenies from multiple gene information. Methods and programs abound that use the gene alignment in different ways to reconstruct the species tree. In particular, different methods combine the original data at different points along the way from the underlying sequences to the final tree. Accordingly, they are classified into superalignment, supertree and medium-level approaches. Here, we present a simulation study to compare different methods from each of these three approaches.\r\n\r\nResults: We observe that superalignment methods usually outperform the other approaches over a wide range of parameters including sparse data and gene-specific evolutionary parameters. In the presence of high incongruency among gene trees, however, other combination methods show better performance than the superalignment approach. Surprisingly, some supertree and medium-level methods exhibit, on average, worse results than a single gene phylogeny with complete taxon information.\r\n\r\nConclusions: For some methods, using the reconstructed gene tree as an estimation of the species tree is superior to the combination of incomplete information. Superalignment usually performs best since it is less susceptible to stochastic error. Supertree methods can outperform superalignment in the presence of gene-tree conflict."}],"article_number":"37","author":[{"first_name":"Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Kupczok","full_name":"Kupczok, Anne"},{"first_name":"Heiko","full_name":"Schmidt, Heiko","last_name":"Schmidt"},{"last_name":"Von Haeseler","full_name":"Von Haeseler, Arndt","first_name":"Arndt"}],"publisher":"BioMed Central","oa_version":"Published Version","type":"journal_article","license":"https://creativecommons.org/licenses/by/4.0/","publication_status":"published","pubrep_id":"939","date_created":"2018-12-11T11:57:30Z","has_accepted_license":"1","title":"Accuracy of phylogeny reconstruction methods combining overlapping gene data sets ","year":"2010","month":"12","issue":"1","intvolume":"         5","publication":"Algorithms for Molecular Biology","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"4517","file_date_updated":"2020-07-14T12:45:40Z","oa":1,"citation":{"ieee":"A. Kupczok, H. Schmidt, and A. Von Haeseler, “Accuracy of phylogeny reconstruction methods combining overlapping gene data sets ,” <i>Algorithms for Molecular Biology</i>, vol. 5, no. 1. BioMed Central, 2010.","short":"A. Kupczok, H. Schmidt, A. Von Haeseler, Algorithms for Molecular Biology 5 (2010).","ista":"Kupczok A, Schmidt H, Von Haeseler A. 2010. Accuracy of phylogeny reconstruction methods combining overlapping gene data sets . Algorithms for Molecular Biology. 5(1), 37.","ama":"Kupczok A, Schmidt H, Von Haeseler A. Accuracy of phylogeny reconstruction methods combining overlapping gene data sets . <i>Algorithms for Molecular Biology</i>. 2010;5(1). doi:<a href=\"https://doi.org/10.1186/1748-7188-5-37\">10.1186/1748-7188-5-37</a>","chicago":"Kupczok, Anne, Heiko Schmidt, and Arndt Von Haeseler. “Accuracy of Phylogeny Reconstruction Methods Combining Overlapping Gene Data Sets .” <i>Algorithms for Molecular Biology</i>. BioMed Central, 2010. <a href=\"https://doi.org/10.1186/1748-7188-5-37\">https://doi.org/10.1186/1748-7188-5-37</a>.","apa":"Kupczok, A., Schmidt, H., &#38; Von Haeseler, A. (2010). Accuracy of phylogeny reconstruction methods combining overlapping gene data sets . <i>Algorithms for Molecular Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1748-7188-5-37\">https://doi.org/10.1186/1748-7188-5-37</a>","mla":"Kupczok, Anne, et al. “Accuracy of Phylogeny Reconstruction Methods Combining Overlapping Gene Data Sets .” <i>Algorithms for Molecular Biology</i>, vol. 5, no. 1, 37, BioMed Central, 2010, doi:<a href=\"https://doi.org/10.1186/1748-7188-5-37\">10.1186/1748-7188-5-37</a>."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"06","_id":"2409","date_updated":"2021-01-12T06:57:18Z","department":[{"_id":"JoBo"}],"language":[{"iso":"eng"}],"file":[{"relation":"main_file","date_updated":"2020-07-14T12:45:40Z","file_size":723929,"checksum":"e2497285388bc4da629bafb46662eb43","date_created":"2018-12-12T10:09:16Z","access_level":"open_access","creator":"system","file_id":"4739","file_name":"IST-2018-939-v1+1_2010_Kupczok_Accuracy_of.pdf","content_type":"application/pdf"}],"date_published":"2010-12-06T00:00:00Z"},{"intvolume":"       186","publication":"Genetics","publist_id":"3337","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"4","oa":1,"citation":{"ista":"Weissman D, Feldman M, Fisher D. 2010. The rate of fitness-valley crossing in sexual populations. Genetics. 186(4), 1389–1410.","ama":"Weissman D, Feldman M, Fisher D. The rate of fitness-valley crossing in sexual populations. <i>Genetics</i>. 2010;186(4):1389-1410. doi:<a href=\"https://doi.org/10.1534/genetics.110.123240\">10.1534/genetics.110.123240</a>","ieee":"D. Weissman, M. Feldman, and D. Fisher, “The rate of fitness-valley crossing in sexual populations,” <i>Genetics</i>, vol. 186, no. 4. Genetics Society of America, pp. 1389–1410, 2010.","short":"D. Weissman, M. Feldman, D. Fisher, Genetics 186 (2010) 1389–1410.","mla":"Weissman, Daniel, et al. “The Rate of Fitness-Valley Crossing in Sexual Populations.” <i>Genetics</i>, vol. 186, no. 4, Genetics Society of America, 2010, pp. 1389–410, doi:<a href=\"https://doi.org/10.1534/genetics.110.123240\">10.1534/genetics.110.123240</a>.","apa":"Weissman, D., Feldman, M., &#38; Fisher, D. (2010). The rate of fitness-valley crossing in sexual populations. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.110.123240\">https://doi.org/10.1534/genetics.110.123240</a>","chicago":"Weissman, Daniel, Marcus Feldman, and Daniel Fisher. “The Rate of Fitness-Valley Crossing in Sexual Populations.” <i>Genetics</i>. Genetics Society of America, 2010. <a href=\"https://doi.org/10.1534/genetics.110.123240\">https://doi.org/10.1534/genetics.110.123240</a>."},"page":"1389 - 1410","date_updated":"2021-01-12T07:42:31Z","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"_id":"3303","day":"01","date_published":"2010-12-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998319/"}],"status":"public","acknowledgement":"This work was supported in part by a Robert N. Noyce Stanford Graduate Fellowship and European Research Council grant 250152 (to D.B.W.) and by National Institutes of Health grant GM 28016 (to M.W.F.).\r\nWe thank Michael Desai for many ideas and discussions and are grateful to Joanna Masel and an anonymous reviewer for their helpful suggestions. ","ec_funded":1,"quality_controlled":"1","doi":"10.1534/genetics.110.123240","volume":186,"publisher":"Genetics Society of America","author":[{"id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","full_name":"Weissman, Daniel","last_name":"Weissman","first_name":"Daniel"},{"last_name":"Feldman","full_name":"Feldman, Marcus","first_name":"Marcus"},{"last_name":"Fisher","full_name":"Fisher, Daniel","first_name":"Daniel"}],"abstract":[{"lang":"eng","text":"Biological traits result in part from interactions between different genetic loci. This can lead to sign epistasis, in which a beneficial adaptation involves a combination of individually deleterious or neutral mutations; in this case, a population must cross a “fitness valley” to adapt. Recombination can assist this process by combining mutations from different individuals or retard it by breaking up the adaptive combination. Here, we analyze the simplest fitness valley, in which an adaptation requires one mutation at each of two loci to provide a fitness benefit. We present a theoretical analysis of the effect of recombination on the valley-crossing process across the full spectrum of possible parameter regimes. We find that low recombination rates can speed up valley crossing relative to the asexual case, while higher recombination rates slow down valley crossing, with the transition between the two regimes occurring when the recombination rate between the loci is approximately equal to the selective advantage provided by the adaptation. In large populations, if the recombination rate is high and selection against single mutants is substantial, the time to cross the valley grows exponentially with population size, effectively meaning that the population cannot acquire the adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing time by up to several orders of magnitude relative to that in an asexual population. "}],"scopus_import":1,"publication_status":"published","type":"journal_article","oa_version":"Submitted Version","month":"12","year":"2010","title":"The rate of fitness-valley crossing in sexual populations","date_created":"2018-12-11T12:02:33Z"},{"oa_version":"None","_id":"3604","day":"01","publication_status":"published","type":"journal_article","date_updated":"2021-01-12T07:44:36Z","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T12:04:12Z","title":"Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland","date_published":"2010-03-01T00:00:00Z","month":"03","year":"2010","issue":"5","quality_controlled":"1","doi":"10.1111/j.1365-294X.2009.04497.x","volume":19,"status":"public","intvolume":"        19","publication":"Molecular Ecology","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"2779","scopus_import":1,"page":"910 - 924","citation":{"chicago":"Senn, Helen, Simon Goodman, Graeme Swanson, Nicholas H Barton, and Josephine Pemberton. “Investigating Temporal Changes in Hybridisation and Introgression between Invasive Sika (Cervus Nippon) and Native Red Deer (Cervus Elaphus) on the Kintyre Peninsula, Scotland.” <i>Molecular Ecology</i>. Wiley-Blackwell, 2010. <a href=\"https://doi.org/10.1111/j.1365-294X.2009.04497.x\">https://doi.org/10.1111/j.1365-294X.2009.04497.x</a>.","mla":"Senn, Helen, et al. “Investigating Temporal Changes in Hybridisation and Introgression between Invasive Sika (Cervus Nippon) and Native Red Deer (Cervus Elaphus) on the Kintyre Peninsula, Scotland.” <i>Molecular Ecology</i>, vol. 19, no. 5, Wiley-Blackwell, 2010, pp. 910–24, doi:<a href=\"https://doi.org/10.1111/j.1365-294X.2009.04497.x\">10.1111/j.1365-294X.2009.04497.x</a>.","apa":"Senn, H., Goodman, S., Swanson, G., Barton, N. H., &#38; Pemberton, J. (2010). Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. <i>Molecular Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1365-294X.2009.04497.x\">https://doi.org/10.1111/j.1365-294X.2009.04497.x</a>","short":"H. Senn, S. Goodman, G. Swanson, N.H. Barton, J. Pemberton, Molecular Ecology 19 (2010) 910–924.","ieee":"H. Senn, S. Goodman, G. Swanson, N. H. Barton, and J. Pemberton, “Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland,” <i>Molecular Ecology</i>, vol. 19, no. 5. Wiley-Blackwell, pp. 910–924, 2010.","ista":"Senn H, Goodman S, Swanson G, Barton NH, Pemberton J. 2010. Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. Molecular Ecology. 19(5), 910–924.","ama":"Senn H, Goodman S, Swanson G, Barton NH, Pemberton J. Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. <i>Molecular Ecology</i>. 2010;19(5):910-924. doi:<a href=\"https://doi.org/10.1111/j.1365-294X.2009.04497.x\">10.1111/j.1365-294X.2009.04497.x</a>"},"publisher":"Wiley-Blackwell","author":[{"full_name":"Senn, Helen","last_name":"Senn","first_name":"Helen"},{"full_name":"Goodman, Simon","last_name":"Goodman","first_name":"Simon"},{"full_name":"Swanson, Graeme","last_name":"Swanson","first_name":"Graeme"},{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H"},{"full_name":"Pemberton, Josephine","last_name":"Pemberton","first_name":"Josephine"}],"abstract":[{"lang":"eng","text":"We investigated temporal changes in hybridization and introgression between native red deer (Cervus elaphus) and invasive Japanese sika (Cervus nippon) on the Kintyre Peninsula, Scotland, over 15 years, through analysis of 1513 samples of deer at 20 microsatellite loci and a mtDNA marker. We found no evidence that either the proportion of recent hybrids, or the levels of introgression had changed over the study period. Nevertheless, in one population where the two species have been in contact since ∼1970, 44% of individuals sampled during the study were hybrids. This suggests that hybridization between these species can proceed fairly rapidly. By analysing the number of alleles that have introgressed from polymorphic red deer into the genetically homogenous sika population, we reconstructed the haplotypes of red deer alleles introduced by backcrossing. Five separate hybridization events could account for all the recently hybridized sika-like individuals found across a large section of the Peninsula. Although we demonstrate that low rates of F1 hybridization can lead to substantial introgression, the progress of hybridization and introgression appears to be unpredictable over the short timescales."}]},{"oa_version":"None","_id":"3718","day":"01","type":"journal_article","date_updated":"2021-01-12T07:51:42Z","department":[{"_id":"PeJo"}],"language":[{"iso":"eng"}],"publication_status":"published","title":"P2Y1 receptors inhibit long-term depression in the prefrontal cortex.","date_created":"2018-12-11T12:04:47Z","year":"2010","date_published":"2010-11-01T00:00:00Z","month":"11","quality_controlled":"1","doi":"10.1016/j.neuropharm.2010.05.013","volume":59,"issue":"6","publication":"Neuropharmacology","intvolume":"        59","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"2512","status":"public","acknowledgement":" The financial support of the Deutsche Forschungsgemeinschaft (IL 20/12-1, KI 677/2-4) is gratefully acknowledged.\r\nWe thank B. H. Koller (Department of Genetics and Molecular Biology, University of North Carolina at Chapel Hill, NC, USA) for the generous supply of P2Y1−/− and P2Y2−/− mice. We are grateful to Dr. A. Schulz for reanalysing the genotype of the P2Y1−/− mice. The authors thank P. Jonas and U. Heinemann for many helpful comments and A-K. Krause, L Feige and M. Eberts for their excellent technical support.","scopus_import":1,"citation":{"apa":"Guzmán, J., Schmidt, H., Franke, H., Krügel, U., Eilers, J., Illes, P., &#38; Gerevich, Z. (2010). P2Y1 receptors inhibit long-term depression in the prefrontal cortex. <i>Neuropharmacology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuropharm.2010.05.013\">https://doi.org/10.1016/j.neuropharm.2010.05.013</a>","mla":"Guzmán, José, et al. “P2Y1 Receptors Inhibit Long-Term Depression in the Prefrontal Cortex.” <i>Neuropharmacology</i>, vol. 59, no. 6, Elsevier, 2010, pp. 406–15, doi:<a href=\"https://doi.org/10.1016/j.neuropharm.2010.05.013\">10.1016/j.neuropharm.2010.05.013</a>.","chicago":"Guzmán, José, Hartmut Schmidt, Heike Franke, Ute Krügel, Jens Eilers, Peter Illes, and Zoltan Gerevich. “P2Y1 Receptors Inhibit Long-Term Depression in the Prefrontal Cortex.” <i>Neuropharmacology</i>. Elsevier, 2010. <a href=\"https://doi.org/10.1016/j.neuropharm.2010.05.013\">https://doi.org/10.1016/j.neuropharm.2010.05.013</a>.","ista":"Guzmán J, Schmidt H, Franke H, Krügel U, Eilers J, Illes P, Gerevich Z. 2010. P2Y1 receptors inhibit long-term depression in the prefrontal cortex. Neuropharmacology. 59(6), 406–415.","ama":"Guzmán J, Schmidt H, Franke H, et al. P2Y1 receptors inhibit long-term depression in the prefrontal cortex. <i>Neuropharmacology</i>. 2010;59(6):406-415. doi:<a href=\"https://doi.org/10.1016/j.neuropharm.2010.05.013\">10.1016/j.neuropharm.2010.05.013</a>","ieee":"J. Guzmán <i>et al.</i>, “P2Y1 receptors inhibit long-term depression in the prefrontal cortex.,” <i>Neuropharmacology</i>, vol. 59, no. 6. Elsevier, pp. 406–415, 2010.","short":"J. Guzmán, H. Schmidt, H. Franke, U. Krügel, J. Eilers, P. Illes, Z. Gerevich, Neuropharmacology 59 (2010) 406–415."},"page":"406 - 415","abstract":[{"text":"Long-term depression (LTD) is a form of synaptic plasticity that may contribute to information storage in the central nervous system. Here we report that LTD can be elicited in layer 5 pyramidal neurons of the rat prefrontal cortex by pairing low frequency stimulation with a modest postsynaptic depolarization. The induction of LTD required the activation of both metabotropic glutamate receptors of the mGlu1 subtype and voltage-sensitive Ca(2+) channels (VSCCs) of the T/R, P/Q and N types, leading to the stimulation of intracellular inositol trisphosphate (IP3) receptors by IP3 and Ca(2+). The subsequent release of Ca(2+) from intracellular stores activated the protein phosphatase cascade involving calcineurin and protein phosphatase 1. The activation of purinergic P2Y(1) receptors blocked LTD. This effect was prevented by P2Y(1) receptor antagonists and was absent in mice lacking P2Y(1) but not P2Y(2) receptors. We also found that activation of P2Y(1) receptors inhibits Ca(2+) transients via VSCCs in the apical dendrites and spines of pyramidal neurons. In addition, we show that the release of ATP under hypoxia is able to inhibit LTD by acting on postsynaptic P2Y(1) receptors. In conclusion, these data suggest that the reduction of Ca(2+) influx via VSCCs caused by the activation of P2Y(1) receptors by ATP is the possible mechanism for the inhibition of LTD in prefrontal cortex.","lang":"eng"}],"publisher":"Elsevier","author":[{"id":"30CC5506-F248-11E8-B48F-1D18A9856A87","full_name":"Guzmán, José","last_name":"Guzmán","first_name":"José"},{"last_name":"Schmidt","full_name":"Schmidt, Hartmut","first_name":"Hartmut"},{"full_name":"Franke, Heike","last_name":"Franke","first_name":"Heike"},{"last_name":"Krügel","full_name":"Krügel, Ute","first_name":"Ute"},{"first_name":"Jens","full_name":"Eilers, Jens","last_name":"Eilers"},{"full_name":"Illes, Peter","last_name":"Illes","first_name":"Peter"},{"full_name":"Gerevich, Zoltan","last_name":"Gerevich","first_name":"Zoltan"}]},{"alternative_title":["EPTCS"],"external_id":{"arxiv":["1011.0496"]},"intvolume":"        40","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"2511","oa":1,"page":"142-161","citation":{"ieee":"J. Feret, T. A. Henzinger, H. Koeppl, and T. Petrov, “Lumpability abstractions of rule-based systems,” presented at the MECBIC: Membrane Computing and Biologically Inspired Process Calculi, Jena, Germany, 2010, vol. 40, pp. 142–161.","short":"J. Feret, T.A. Henzinger, H. Koeppl, T. Petrov, in:, Open Publishing Association, 2010, pp. 142–161.","ama":"Feret J, Henzinger TA, Koeppl H, Petrov T. Lumpability abstractions of rule-based systems. In: Vol 40. Open Publishing Association; 2010:142-161.","ista":"Feret J, Henzinger TA, Koeppl H, Petrov T. 2010. Lumpability abstractions of rule-based systems. MECBIC: Membrane Computing and Biologically Inspired Process Calculi, EPTCS, vol. 40, 142–161.","chicago":"Feret, Jérôme, Thomas A Henzinger, Heinz Koeppl, and Tatjana Petrov. “Lumpability Abstractions of Rule-Based Systems,” 40:142–61. Open Publishing Association, 2010.","mla":"Feret, Jérôme, et al. <i>Lumpability Abstractions of Rule-Based Systems</i>. Vol. 40, Open Publishing Association, 2010, pp. 142–61.","apa":"Feret, J., Henzinger, T. A., Koeppl, H., &#38; Petrov, T. (2010). Lumpability abstractions of rule-based systems (Vol. 40, pp. 142–161). Presented at the MECBIC: Membrane Computing and Biologically Inspired Process Calculi, Jena, Germany: Open Publishing Association."},"file_date_updated":"2020-07-14T12:46:14Z","_id":"3719","day":"30","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"date_updated":"2023-02-23T11:15:19Z","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"3168"}]},"file":[{"content_type":"application/pdf","creator":"kschuh","file_name":"Lumpability_abstractions_of_rule-based_systems.pdf","file_id":"5904","checksum":"eaaba991a86fff37606b0eb5196878e8","date_created":"2019-01-31T12:09:09Z","access_level":"open_access","file_size":907155,"date_updated":"2020-07-14T12:46:14Z","relation":"main_file"}],"date_published":"2010-10-30T00:00:00Z","volume":40,"quality_controlled":"1","ddc":["570"],"status":"public","acknowledgement":"Jérôme Feret’s contribution was partially supported by the ABSTRACTCELL ANR-Chair of Excellence. Heinz Koeppl acknowledges the support from the Swiss National Science Foundation, grant no. 200020-117975/1. Tatjana Petrov acknowledges the support from SystemsX.ch, the Swiss Initiative in Systems Biology.","scopus_import":1,"conference":{"start_date":"2010-08-23","name":"MECBIC: Membrane Computing and Biologically Inspired Process Calculi","location":"Jena, Germany","end_date":"2010-08-23"},"author":[{"full_name":"Feret, Jérôme","last_name":"Feret","first_name":"Jérôme"},{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"full_name":"Koeppl, Heinz","last_name":"Koeppl","first_name":"Heinz"},{"first_name":"Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrov","full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905"}],"publisher":"Open Publishing Association","abstract":[{"lang":"eng","text":"The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a math- ematical model is an important challenge in systems biology. Exploiting the limited context on which most binding and modification events are conditioned, attempts have been made to reduce the com- binatorial complexity by quotienting the reachable set of molecular species, into species aggregates while preserving the deterministic semantics of the thermodynamic limit. Recently we proposed a quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics. In this paper we prove that this quotienting yields a sufficient condition for weak lumpability and that it gives rise to a backward Markov bisimulation between the original and aggregated transition system. We illustrate the framework on a case study of the EGF/insulin receptor crosstalk."}],"oa_version":"Submitted Version","publication_status":"published","type":"conference","title":"Lumpability abstractions of rule-based systems","has_accepted_license":"1","date_created":"2018-12-11T12:04:47Z","arxiv":1,"month":"10","year":"2010"},{"issue":"6","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"2454","intvolume":"         6","publication":"PLoS Genetics","citation":{"chicago":"Barton, Nicholas H. “Understanding Adaptation in Large Populations.” <i>PLoS Genetics</i>. Public Library of Science, 2010. <a href=\"https://doi.org/10.1371/journal.pgen.1000987\">https://doi.org/10.1371/journal.pgen.1000987</a>.","mla":"Barton, Nicholas H. “Understanding Adaptation in Large Populations.” <i>PLoS Genetics</i>, vol. 6, no. 6, e1000987, Public Library of Science, 2010, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1000987\">10.1371/journal.pgen.1000987</a>.","apa":"Barton, N. H. (2010). Understanding adaptation in large populations. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1000987\">https://doi.org/10.1371/journal.pgen.1000987</a>","short":"N.H. Barton, PLoS Genetics 6 (2010).","ieee":"N. H. Barton, “Understanding adaptation in large populations,” <i>PLoS Genetics</i>, vol. 6, no. 6. Public Library of Science, 2010.","ama":"Barton NH. Understanding adaptation in large populations. <i>PLoS Genetics</i>. 2010;6(6). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1000987\">10.1371/journal.pgen.1000987</a>","ista":"Barton NH. 2010. Understanding adaptation in large populations. PLoS Genetics. 6(6), e1000987."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"file_date_updated":"2020-07-14T12:46:15Z","day":"17","_id":"3772","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T07:52:05Z","file":[{"relation":"main_file","date_updated":"2020-07-14T12:46:15Z","file_size":349965,"file_name":"IST-2016-524-v1+1_journal.pgen.1000987.PDF","file_id":"5075","creator":"system","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:14:24Z","checksum":"5c14de2680ab483cb835096c99ee734d"}],"date_published":"2010-06-17T00:00:00Z","ddc":["570","576"],"doi":"10.1371/journal.pgen.1000987","volume":6,"quality_controlled":"1","status":"public","scopus_import":1,"article_number":"e1000987","author":[{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton"}],"publisher":"Public Library of Science","oa_version":"Published Version","publication_status":"published","type":"journal_article","has_accepted_license":"1","date_created":"2018-12-11T12:05:05Z","title":"Understanding adaptation in large populations","pubrep_id":"524","month":"06","year":"2010"},{"pmid":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pubmed/20439284"}],"date_published":"2010-06-12T00:00:00Z","_id":"3773","day":"12","language":[{"iso":"eng"}],"date_updated":"2021-01-12T07:52:06Z","department":[{"_id":"NiBa"}],"page":"1825 - 1840","citation":{"mla":"Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1547, Royal Society, 2010, pp. 1825–40, doi:<a href=\"https://doi.org/10.1098/rstb.2010.0001\">10.1098/rstb.2010.0001</a>.","apa":"Barton, N. H. (2010). What role does natural selection play in speciation? <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rstb.2010.0001\">https://doi.org/10.1098/rstb.2010.0001</a>","chicago":"Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, 2010. <a href=\"https://doi.org/10.1098/rstb.2010.0001\">https://doi.org/10.1098/rstb.2010.0001</a>.","ama":"Barton NH. What role does natural selection play in speciation? <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2010;365(1547):1825-1840. doi:<a href=\"https://doi.org/10.1098/rstb.2010.0001\">10.1098/rstb.2010.0001</a>","ista":"Barton NH. 2010. What role does natural selection play in speciation? Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1547), 1825–1840.","ieee":"N. H. Barton, “What role does natural selection play in speciation?,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1547. Royal Society, pp. 1825–1840, 2010.","short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1825–1840."},"oa":1,"external_id":{"pmid":["20439284"]},"issue":"1547","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"2455","intvolume":"       365","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","date_created":"2018-12-11T12:05:05Z","title":"What role does natural selection play in speciation?","year":"2010","month":"06","oa_version":"Submitted Version","type":"journal_article","publication_status":"published","scopus_import":1,"abstract":[{"text":"If distinct biological species are to coexist in sympatry, they must be reproductively isolated and must exploit different limiting resources. A two-niche Levene model is analysed, in which habitat preference and survival depend on underlying additive traits. The population genetics of preference and viability are equivalent. However, there is a linear trade-off between the chances of settling in either niche, whereas viabilities may be constrained arbitrarily. With a convex trade-off, a sexual population evolves a single generalist genotype, whereas with a concave trade-off, disruptive selection favours maximal variance. A pure habitat preference evolves to global linkage equilibrium if mating occurs in a single pool, but remarkably, evolves to pairwise linkage equilibrium within niches if mating is within those niches--independent of the genetics. With a concave trade-off, the population shifts sharply between a unimodal distribution with high gene flow and a bimodal distribution with strong isolation, as the underlying genetic variance increases. However, these alternative states are only simultaneously stable for a narrow parameter range. A sharp threshold is only seen if survival in the 'wrong' niche is low; otherwise, strong isolation is impossible. Gene flow from divergent demes makes speciation much easier in parapatry than in sympatry.","lang":"eng"}],"publisher":"Royal Society","author":[{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"volume":365,"quality_controlled":"1","doi":"10.1098/rstb.2010.0001","acknowledgement":"The author thanks the Werner-Gren Foundation and the Royal Swedish Academy of Sciences for organizing the symposium on the ‘Origin of Species’. He also thanks Reinhard Bürger, and two anonymous referees, for their helpful comments.\r\n","status":"public"},{"scopus_import":1,"author":[{"full_name":"Senn, Helen","last_name":"Senn","first_name":"Helen"},{"full_name":"Swanson, Graeme","last_name":"Swanson","first_name":"Graeme"},{"first_name":"Simon","last_name":"Goodman","full_name":"Goodman, Simon"},{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Josephine","last_name":"Pemberton","full_name":"Pemberton, Josephine"}],"publisher":"Wiley-Blackwell","abstract":[{"text":"1. Hybridisation with an invasive species has the potential to alter the phenotype and hence the ecology of a native counterpart. 2. Here data from populations of native red deer Cervus elaphus and invasive sika deer Cervus nippon in Scotland is used to assess the extent to which hybridisation between them is causing phenotypic change. This is done by regression of phenotypic traits against genetic hybrid scores. 3. Hybridisation is causing increases in the body weight of sika-like deer and decreases in the body weight of red-like females. Hybridisation is causing increases in jaw length and increases in incisor arcade breadth in sika-like females. Hybridisation is also causing decreases in incisor arcade breadth in red-like females. 4. There is currently no evidence that hybridisation is causing changes in the kidney fat weight or pregnancy rates of either population. 5. Increased phenotypic similarity between the two species is likely to lead to further hybridisation. The ecological consequences of this are difficult to predict.","lang":"eng"}],"quality_controlled":"1","doi":"10.1111/j.1365-2656.2009.01633.x","volume":79,"acknowledgement":"This project was funded through a NERC studentship to HVS which was CASE partnered by the Macaulay Institute.\r\nWe thank the Forestry Commission Scotland rangers for all their help with providing the larder data for and samples from red and sika deer, Stephen Senn and Jarrod Hadfield for statistical advice and Steve Albon for helpful comments on the manuscript.","status":"public","title":"Phenotypic correlates of hybridisation between red and sika deer (genus Cervus)","date_created":"2018-12-11T12:05:06Z","month":"03","year":"2010","oa_version":"None","publication_status":"published","type":"journal_article","page":"414 - 425","citation":{"short":"H. Senn, G. Swanson, S. Goodman, N.H. Barton, J. Pemberton, Journal of Animal Ecology 79 (2010) 414–425.","ieee":"H. Senn, G. Swanson, S. Goodman, N. H. Barton, and J. Pemberton, “Phenotypic correlates of hybridisation between red and sika deer (genus Cervus),” <i>Journal of Animal Ecology</i>, vol. 79, no. 2. Wiley-Blackwell, pp. 414–425, 2010.","ama":"Senn H, Swanson G, Goodman S, Barton NH, Pemberton J. Phenotypic correlates of hybridisation between red and sika deer (genus Cervus). <i>Journal of Animal Ecology</i>. 2010;79(2):414-425. doi:<a href=\"https://doi.org/10.1111/j.1365-2656.2009.01633.x\">10.1111/j.1365-2656.2009.01633.x</a>","ista":"Senn H, Swanson G, Goodman S, Barton NH, Pemberton J. 2010. Phenotypic correlates of hybridisation between red and sika deer (genus Cervus). Journal of Animal Ecology. 79(2), 414–425.","chicago":"Senn, Helen, Graeme Swanson, Simon Goodman, Nicholas H Barton, and Josephine Pemberton. “Phenotypic Correlates of Hybridisation between Red and Sika Deer (Genus Cervus).” <i>Journal of Animal Ecology</i>. Wiley-Blackwell, 2010. <a href=\"https://doi.org/10.1111/j.1365-2656.2009.01633.x\">https://doi.org/10.1111/j.1365-2656.2009.01633.x</a>.","mla":"Senn, Helen, et al. “Phenotypic Correlates of Hybridisation between Red and Sika Deer (Genus Cervus).” <i>Journal of Animal Ecology</i>, vol. 79, no. 2, Wiley-Blackwell, 2010, pp. 414–25, doi:<a href=\"https://doi.org/10.1111/j.1365-2656.2009.01633.x\">10.1111/j.1365-2656.2009.01633.x</a>.","apa":"Senn, H., Swanson, G., Goodman, S., Barton, N. H., &#38; Pemberton, J. (2010). Phenotypic correlates of hybridisation between red and sika deer (genus Cervus). <i>Journal of Animal Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1365-2656.2009.01633.x\">https://doi.org/10.1111/j.1365-2656.2009.01633.x</a>"},"issue":"2","external_id":{"pmid":["20002231"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"2453","publication":"Journal of Animal Ecology","intvolume":"        79","date_published":"2010-03-01T00:00:00Z","pmid":1,"_id":"3774","day":"01","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T07:52:06Z"},{"year":"2010","month":"08","pubrep_id":"555","title":"Genetic linkage and natural selection","has_accepted_license":"1","date_created":"2018-12-11T12:05:06Z","type":"journal_article","publication_status":"published","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The prevalence of recombination in eukaryotes poses one of the most puzzling questions in biology. The most compelling general explanation is that recombination facilitates selection by breaking down the negative associations generated by random drift (i.e. Hill-Robertson interference, HRI). I classify the effects of HRI owing to: deleterious mutation, balancing selection and selective sweeps on: neutral diversity, rates of adaptation and the mutation load. These effects are mediated primarily by the density of deleterious mutations and of selective sweeps. Sequence polymorphism and divergence suggest that these rates may be high enough to cause significant interference even in genomic regions of high recombination. However, neither seems able to generate enough variance in fitness to select strongly for high rates of recombination. It is plausible that spatial and temporal fluctuations in selection generate much more fitness variance, and hence selection for recombination, than can be explained by uniformly deleterious mutations or species-wide selective sweeps."}],"author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"}],"publisher":"Royal Society","scopus_import":1,"acknowledgement":"Royal Society and Wolfson Foundation for their support\r\nWe would like to thank Brian Charlesworth and Sally Otto for their helpful comments.","status":"public","ddc":["570"],"doi":"10.1098/rstb.2010.0106","quality_controlled":"1","volume":365,"date_published":"2010-08-27T00:00:00Z","file":[{"relation":"main_file","date_updated":"2020-07-14T12:46:15Z","file_size":250255,"date_created":"2018-12-12T10:14:40Z","access_level":"open_access","checksum":"4d8aade10db030124ab158b622e337e0","file_id":"5093","file_name":"IST-2016-555-v1+1_RS2009_revised.pdf","creator":"system","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T07:52:07Z","day":"27","_id":"3776","file_date_updated":"2020-07-14T12:46:15Z","citation":{"apa":"Barton, N. H. (2010). Genetic linkage and natural selection. <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rstb.2010.0106\">https://doi.org/10.1098/rstb.2010.0106</a>","mla":"Barton, Nicholas H. “Genetic Linkage and Natural Selection.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1552, Royal Society, 2010, pp. 2559–69, doi:<a href=\"https://doi.org/10.1098/rstb.2010.0106\">10.1098/rstb.2010.0106</a>.","chicago":"Barton, Nicholas H. “Genetic Linkage and Natural Selection.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, 2010. <a href=\"https://doi.org/10.1098/rstb.2010.0106\">https://doi.org/10.1098/rstb.2010.0106</a>.","ista":"Barton NH. 2010. Genetic linkage and natural selection. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1552), 2559–2569.","ama":"Barton NH. Genetic linkage and natural selection. <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2010;365(1552):2559-2569. doi:<a href=\"https://doi.org/10.1098/rstb.2010.0106\">10.1098/rstb.2010.0106</a>","short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 2559–2569.","ieee":"N. H. Barton, “Genetic linkage and natural selection,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1552. Royal Society, pp. 2559–2569, 2010."},"page":"2559 - 2569","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"2450","intvolume":"       365","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","issue":"1552"},{"scopus_import":1,"abstract":[{"lang":"eng","text":"Under the classical view, selection depends more or less directly on mutation: standing genetic variance is maintained by a balance between selection and mutation, and adaptation is fuelled by new favourable mutations. Recombination is favoured if it breaks negative associations among selected alleles, which interfere with adaptation. Such associations may be generated by negative epistasis, or by random drift (leading to the Hill-Robertson effect). Both deterministic and stochastic explanations depend primarily on the genomic mutation rate, U. This may be large enough to explain high recombination rates in some organisms, but seems unlikely to be so in general. Random drift is a more general source of negative linkage disequilibria, and can cause selection for recombination even in large populations, through the chance loss of new favourable mutations. The rate of species-wide substitutions is much too low to drive this mechanism, but local fluctuations in selection, combined with gene flow, may suffice. These arguments are illustrated by comparing the interaction between good and bad mutations at unlinked loci under the infinitesimal model."}],"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"}],"publisher":"Royal Society","doi":"10.1098/rstb.2009.0320","quality_controlled":"1","volume":365,"acknowledgement":"I would like to thank W. G. Hill and L. Loewe for organizing this special issue, and the Royal Society and Wolfson Foundation for their support. Also, A. Kondrashov and L. Loewe gave very helpful comments that helped improve the manuscript.","status":"public","date_created":"2018-12-11T12:05:07Z","title":"Mutation and the evolution of recombination","year":"2010","month":"04","oa_version":"Submitted Version","type":"journal_article","publication_status":"published","citation":{"ista":"Barton NH. 2010. Mutation and the evolution of recombination. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1544), 1281–1294.","ama":"Barton NH. Mutation and the evolution of recombination. <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2010;365(1544):1281-1294. doi:<a href=\"https://doi.org/10.1098/rstb.2009.0320\">10.1098/rstb.2009.0320</a>","ieee":"N. H. Barton, “Mutation and the evolution of recombination,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1544. Royal Society, pp. 1281–1294, 2010.","short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1281–1294.","mla":"Barton, Nicholas H. “Mutation and the Evolution of Recombination.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1544, Royal Society, 2010, pp. 1281–94, doi:<a href=\"https://doi.org/10.1098/rstb.2009.0320\">10.1098/rstb.2009.0320</a>.","apa":"Barton, N. H. (2010). Mutation and the evolution of recombination. <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rstb.2009.0320\">https://doi.org/10.1098/rstb.2009.0320</a>","chicago":"Barton, Nicholas H. “Mutation and the Evolution of Recombination.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, 2010. <a href=\"https://doi.org/10.1098/rstb.2009.0320\">https://doi.org/10.1098/rstb.2009.0320</a>."},"page":"1281 - 1294","oa":1,"external_id":{"pmid":["20308104"]},"issue":"1544","publist_id":"2451","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","intvolume":"       365","pmid":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pubmed/20308104","open_access":"1"}],"date_published":"2010-04-27T00:00:00Z","_id":"3777","day":"27","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T07:52:07Z"},{"language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"date_updated":"2023-02-23T14:07:34Z","day":"20","_id":"3779","date_published":"2010-07-20T00:00:00Z","file":[{"file_size":1089530,"relation":"main_file","date_updated":"2020-07-14T12:46:15Z","checksum":"ee1ce2fb283a6b4127544ae532d0b4a1","date_created":"2018-12-12T10:14:11Z","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2015-366-v1+1_journal.pbio.1000429.pdf","file_id":"5060","creator":"system"}],"related_material":{"record":[{"relation":"research_data","id":"9764","status":"public"}]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"2448","publication":"PLoS Biology","intvolume":"         8","issue":"7","file_date_updated":"2020-07-14T12:46:15Z","citation":{"chicago":"Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille, and Enrico Coen. “Cryptic Variation between Species and the Basis of Hybrid Performance.” <i>PLoS Biology</i>. Public Library of Science, 2010. <a href=\"https://doi.org/10.1371/journal.pbio.1000429\">https://doi.org/10.1371/journal.pbio.1000429</a>.","mla":"Rosas, Ulises, et al. “Cryptic Variation between Species and the Basis of Hybrid Performance.” <i>PLoS Biology</i>, vol. 8, no. 7, e1000429, Public Library of Science, 2010, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000429\">10.1371/journal.pbio.1000429</a>.","apa":"Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., &#38; Coen, E. (2010). Cryptic variation between species and the basis of hybrid performance. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1000429\">https://doi.org/10.1371/journal.pbio.1000429</a>","ieee":"U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Cryptic variation between species and the basis of hybrid performance,” <i>PLoS Biology</i>, vol. 8, no. 7. Public Library of Science, 2010.","short":"U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, PLoS Biology 8 (2010).","ista":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Cryptic variation between species and the basis of hybrid performance. PLoS Biology. 8(7), e1000429.","ama":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Cryptic variation between species and the basis of hybrid performance. <i>PLoS Biology</i>. 2010;8(7). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000429\">10.1371/journal.pbio.1000429</a>"},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"type":"journal_article","publication_status":"published","oa_version":"Published Version","year":"2010","month":"07","pubrep_id":"366","date_created":"2018-12-11T12:05:07Z","title":"Cryptic variation between species and the basis of hybrid performance","has_accepted_license":"1","acknowledgement":"This was supported by a Marie Curie grant for early stage training and the BBSRC-John Innes Centre PhD Rotation Program.\r\nWe would like to thank X. Feng and A. Hudson for assistance with introgressions and genotyping; A. Green, A. Bangham and J. Pateman for advice and assistance on shape model procedures; F. Alderson and S.Mitchell from JIC horticultural services; P.J. Wittkopp for protocols and advice on pyrosequencing; and R. Sablowski for discussions and comments.\r\n","status":"public","ddc":["576"],"doi":"10.1371/journal.pbio.1000429","volume":8,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Crosses between closely related species give two contrasting results. One result is that species hybrids may be inferior to their parents, for example, being less fertile [1]. The other is that F1 hybrids may display superior performance (heterosis), for example with increased vigour [2]. Although various hypotheses have been proposed to account for these two aspects of hybridisation, their biological basis is still poorly understood [3]. To gain further insights into this issue, we analysed the role that variation in gene expression may play. We took a conserved trait, flower asymmetry in Antirrhinum, and determined the extent to which the underlying regulatory genes varied in expression among closely related species. We show that expression of both genes analysed, CYC and RAD, varies significantly between species because of cis-acting differences. By making a quantitative genotype-phenotype map, using a range of mutant alleles, we demonstrate that the species lie on a plateau in gene expression-morphology space, so that the variation has no detectable phenotypic effect. However, phenotypic differences can be revealed by shifting genotypes off the plateau through genetic crosses. Our results can be readily explained if genomes are free to evolve within an effectively neutral zone in gene expression space. The consequences of this drift will be negligible for individual loci, but when multiple loci across the genome are considered, we show that the variation may have significant effects on phenotype and fitness, causing a significant drift load. By considering these consequences for various gene-expression-fitness landscapes, we conclude that F1 hybrids might be expected to show increased performance with regard to conserved traits, such as basic physiology, but reduced performance with regard to others. Thus, our study provides a new way of explaining how various aspects of hybrid performance may arise through natural variation in gene activity."}],"article_number":"e1000429","author":[{"first_name":"Ulises","last_name":"Rosas","full_name":"Rosas, Ulises"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"first_name":"Lucy","last_name":"Copsey","full_name":"Copsey, Lucy"},{"first_name":"Pierre","full_name":"Barbier De Reuille, Pierre","last_name":"Barbier De Reuille"},{"first_name":"Enrico","full_name":"Coen, Enrico","last_name":"Coen"}],"publisher":"Public Library of Science","scopus_import":1},{"date_created":"2018-12-11T12:05:08Z","title":"Topology noise removal for curve  and surface evolution","year":"2010","month":"12","date_published":"2010-12-31T00:00:00Z","_id":"3782","day":"31","oa_version":"None","language":[{"iso":"eng"}],"type":"conference","department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T07:52:10Z","publication_status":"published","conference":{"name":"MCV: Medical Computer Vision","location":"Beijing, China","end_date":"2010-09-20","start_date":"2010-09-20"},"citation":{"mla":"Chen, Chao, and Daniel Freedman. “Topology Noise Removal for Curve  and Surface Evolution.” <i> Conference Proceedings MCV 2010</i>, vol. 6533, Springer, 2010, pp. 31–42, doi:<a href=\"https://doi.org/10.1007/978-3-642-18421-5_4\">10.1007/978-3-642-18421-5_4</a>.","apa":"Chen, C., &#38; Freedman, D. (2010). Topology noise removal for curve  and surface evolution. In <i> Conference proceedings MCV 2010</i> (Vol. 6533, pp. 31–42). Beijing, China: Springer. <a href=\"https://doi.org/10.1007/978-3-642-18421-5_4\">https://doi.org/10.1007/978-3-642-18421-5_4</a>","chicago":"Chen, Chao, and Daniel Freedman. “Topology Noise Removal for Curve  and Surface Evolution.” In <i> Conference Proceedings MCV 2010</i>, 6533:31–42. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-18421-5_4\">https://doi.org/10.1007/978-3-642-18421-5_4</a>.","ista":"Chen C, Freedman D. 2010. Topology noise removal for curve  and surface evolution.  Conference proceedings MCV 2010. MCV: Medical Computer Vision, LNCS, vol. 6533, 31–42.","ama":"Chen C, Freedman D. Topology noise removal for curve  and surface evolution. In: <i> Conference Proceedings MCV 2010</i>. Vol 6533. Springer; 2010:31-42. doi:<a href=\"https://doi.org/10.1007/978-3-642-18421-5_4\">10.1007/978-3-642-18421-5_4</a>","ieee":"C. Chen and D. Freedman, “Topology noise removal for curve  and surface evolution,” in <i> Conference proceedings MCV 2010</i>, Beijing, China, 2010, vol. 6533, pp. 31–42.","short":"C. Chen, D. Freedman, in:,  Conference Proceedings MCV 2010, Springer, 2010, pp. 31–42."},"page":"31 - 42","scopus_import":1,"abstract":[{"text":"In cortex surface segmentation, the extracted surface is required to have a particular topology, namely, a two-sphere. We present a new method for removing topology noise of a curve or surface within the level set framework, and thus produce a cortical surface with correct topology. We define a new energy term which quantifies topology noise. We then show how to minimize this term by computing its functional derivative with respect to the level set function. This method differs from existing methods in that it is inherently continuous and not digital; and in the way that our energy directly relates to the topology of the underlying curve or surface, versus existing knot-based measures which are related in a more indirect fashion. The proposed flow is validated empirically.","lang":"eng"}],"author":[{"last_name":"Chen","full_name":"Chen, Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao"},{"last_name":"Freedman","full_name":"Freedman, Daniel","first_name":"Daniel"}],"publisher":"Springer","quality_controlled":"1","volume":6533,"doi":"10.1007/978-3-642-18421-5_4","alternative_title":["LNCS"],"publist_id":"2445","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication":" Conference proceedings MCV 2010","intvolume":"      6533","acknowledgement":"Partially supported by the Austri an Science Fund unde r grant P20134-N13.\r\nWe thank Helena Molina-Abril for very helpful discussion. We thank anonymous reviewers for helpful comments.","status":"public"},{"publisher":"Oxford University Press","author":[{"id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","last_name":"Palero","full_name":"Palero, Ferran","orcid":"0000-0002-0343-8329","first_name":"Ferran"},{"full_name":"González Candelas, Fernando","last_name":"González Candelas","first_name":"Fernando"},{"first_name":"Marta","last_name":"Pascual","full_name":"Pascual, Marta"}],"abstract":[{"text":"MICROSATELIGHT is a Perl/Tk pipeline with a graphical user interface that facilitates several tasks when scoring microsatellites. It implements new subroutines in R and PERL and takes advantage of features provided by previously developed freeware. MICROSATELIGHT takes raw genotype data and automates the peak identification through PeakScanner. The PeakSelect subroutine assigns peaks to different microsatellite markers according to their multiplex group, fluorochrome type, and size range. After peak selection, binning of alleles can be carried out 1) automatically through AlleloBin or 2) by manual bin definition through Binator. In both cases, several features for quality checking and further binning improvement are provided. The genotype table can then be converted into input files for several population genetics programs through CREATE. Finally, Hardy–Weinberg equilibrium tests and confidence intervals for null allele frequency can be obtained through GENEPOP. MICROSATELIGHT is the only freely available public-domain software that facilitates full multiplex microsatellite scoring, from electropherogram files to user-defined text files to be used with population genetics software. MICROSATELIGHT has been created for the Windows XP operating system and has been successfully tested under Windows 7. It is available at http://sourceforge.net/projects/microsatelight/.","lang":"eng"}],"scopus_import":1,"page":"247 - 249","citation":{"mla":"Palero, Ferran, et al. “Microsatelight – Pipeline to Expedite Microsatellite Analysis.” <i>Journal of Heredity</i>, vol. 102, no. 2, Oxford University Press, 2010, pp. 247–49, doi:<a href=\"https://doi.org/10.1093/jhered/esq111\">10.1093/jhered/esq111</a>.","apa":"Palero, F., González Candelas, F., &#38; Pascual, M. (2010). Microsatelight – Pipeline to expedite microsatellite analysis. <i>Journal of Heredity</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jhered/esq111\">https://doi.org/10.1093/jhered/esq111</a>","chicago":"Palero, Ferran, Fernando González Candelas, and Marta Pascual. “Microsatelight – Pipeline to Expedite Microsatellite Analysis.” <i>Journal of Heredity</i>. Oxford University Press, 2010. <a href=\"https://doi.org/10.1093/jhered/esq111\">https://doi.org/10.1093/jhered/esq111</a>.","ista":"Palero F, González Candelas F, Pascual M. 2010. Microsatelight – Pipeline to expedite microsatellite analysis. Journal of Heredity. 102(2), 247–249.","ama":"Palero F, González Candelas F, Pascual M. Microsatelight – Pipeline to expedite microsatellite analysis. <i>Journal of Heredity</i>. 2010;102(2):247-249. doi:<a href=\"https://doi.org/10.1093/jhered/esq111\">10.1093/jhered/esq111</a>","ieee":"F. Palero, F. González Candelas, and M. Pascual, “Microsatelight – Pipeline to expedite microsatellite analysis,” <i>Journal of Heredity</i>, vol. 102, no. 2. Oxford University Press, pp. 247–249, 2010.","short":"F. Palero, F. González Candelas, M. Pascual, Journal of Heredity 102 (2010) 247–249."},"status":"public","acknowledgement":"Ministerio de Educación y Ciencia (CGL2006-13423, CTM2007-66635). M.P. and FP are part of the research group 2009SGR-636 of the Generalitat de Catalunya. F.P. acknowledges an EU-Synthesys grant (GB-TAF-4474).\r\n\r\nThanks to José Gabriel Segarra-Moragues (Centro de Investigaciones sobre Desertificación) for sending us pictures with several types of stuttering and Pedro Simões and Gemma Calàbria (Universitat de Barcelona) for testing this software. Finally, thanks are due to 2 anonymous referees for their valuable comments. These comments certainly helped to improve the manuscript.","intvolume":"       102","publication":"Journal of Heredity","publist_id":"2444","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"2","volume":102,"doi":"10.1093/jhered/esq111","quality_controlled":"1","date_published":"2010-12-02T00:00:00Z","month":"12","year":"2010","title":"Microsatelight – Pipeline to expedite microsatellite analysis","date_created":"2018-12-11T12:05:09Z","publication_status":"published","department":[{"_id":"NiBa"}],"type":"journal_article","date_updated":"2021-01-12T07:52:10Z","language":[{"iso":"eng"}],"oa_version":"None","_id":"3783","day":"02"},{"publisher":"Oxford University Press","author":[{"first_name":"Ferran","full_name":"Palero, Ferran","last_name":"Palero","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0343-8329"},{"full_name":"Abello, Pere","last_name":"Abello","first_name":"Pere"},{"full_name":"Macpherson, E.","last_name":"Macpherson","first_name":"E."},{"full_name":"Matthee, C.","last_name":"Matthee","first_name":"C."},{"first_name":"Marta","last_name":"Pascual","full_name":"Pascual, Marta"}],"abstract":[{"text":"Most fisheries involving spiny lobsters of the genus Palinurus have been over exploited during the last decades, so there is a raising concern about management decisions for these valuable resources. A total of 13 microsatellite DNA loci recently developed in Palinurus elephas were  assayed  in  order  to  assess  genetic  diversity  levels  in  every  known  species  of  the  genus.  Microsatellite  markers  gave amplifications  and  showed  polymorphism  in  all  species,  with  gene  diversity  values  varying  from  0.65060.077  SD  (Palinurus barbarae) to 0.79260.051 SD (Palinurus elephas). Most importantly, when depth distribution was taken into account, shallower waters pecies consistently showed larger historical effective population sizes than their deeper-water counterparts.  This could explain why deeper-water species are more sensitive to overfishing, and would indicate that overexploitation may have a larger impact on their long-term genetic diversity.","lang":"eng"}],"scopus_import":"1","publication_identifier":{"eissn":["1937-240X"],"issn":["0278-0372"]},"citation":{"ista":"Palero F, Abello P, Macpherson E, Matthee C, Pascual M. 2010. Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata). Journal of Crustacean Biology. 30(4), 658–663.","ama":"Palero F, Abello P, Macpherson E, Matthee C, Pascual M. Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata). <i>Journal of Crustacean Biology</i>. 2010;30(4):658-663. doi:<a href=\"https://doi.org/10.1651/09-3192.1\">10.1651/09-3192.1</a>","ieee":"F. Palero, P. Abello, E. Macpherson, C. Matthee, and M. Pascual, “Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata),” <i>Journal of Crustacean Biology</i>, vol. 30, no. 4. Oxford University Press, pp. 658–663, 2010.","short":"F. Palero, P. Abello, E. Macpherson, C. Matthee, M. Pascual, Journal of Crustacean Biology 30 (2010) 658–663.","apa":"Palero, F., Abello, P., Macpherson, E., Matthee, C., &#38; Pascual, M. (2010). Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata). <i>Journal of Crustacean Biology</i>. Oxford University Press. <a href=\"https://doi.org/10.1651/09-3192.1\">https://doi.org/10.1651/09-3192.1</a>","mla":"Palero, Ferran, et al. “Genetic Diversity Levels in Fishery-Exploited Spiny Lobsters of the Genus Palinurus (Decapoda: Achelata).” <i>Journal of Crustacean Biology</i>, vol. 30, no. 4, Oxford University Press, 2010, pp. 658–63, doi:<a href=\"https://doi.org/10.1651/09-3192.1\">10.1651/09-3192.1</a>.","chicago":"Palero, Ferran, Pere Abello, E. Macpherson, C. Matthee, and Marta Pascual. “Genetic Diversity Levels in Fishery-Exploited Spiny Lobsters of the Genus Palinurus (Decapoda: Achelata).” <i>Journal of Crustacean Biology</i>. Oxford University Press, 2010. <a href=\"https://doi.org/10.1651/09-3192.1\">https://doi.org/10.1651/09-3192.1</a>."},"page":"658 - 663","status":"public","publication":"Journal of Crustacean Biology","intvolume":"        30","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"2442","issue":"4","quality_controlled":"1","doi":"10.1651/09-3192.1","volume":30,"date_published":"2010-10-01T00:00:00Z","month":"10","year":"2010","title":"Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata)","date_created":"2018-12-11T12:05:09Z","publication_status":"published","department":[{"_id":"NiBa"}],"date_updated":"2023-10-16T09:51:05Z","type":"journal_article","language":[{"iso":"eng"}],"oa_version":"None","day":"01","_id":"3785","article_processing_charge":"No"},{"quality_controlled":"1","volume":2403,"doi":"10.11646/zootaxa.2403.1.4","issue":"1","publication":"Zootaxa","intvolume":"      2403","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"2441","status":"public","scopus_import":"1","citation":{"ieee":"F. Palero, G. Guerao, P. Clark, and P. Abello, “Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description,” <i>Zootaxa</i>, vol. 2403, no. 1. Magnolia Press, pp. 42–58, 2010.","short":"F. Palero, G. Guerao, P. Clark, P. Abello, Zootaxa 2403 (2010) 42–58.","ista":"Palero F, Guerao G, Clark P, Abello P. 2010. Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description. Zootaxa. 2403(1), 42–58.","ama":"Palero F, Guerao G, Clark P, Abello P. Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description. <i>Zootaxa</i>. 2010;2403(1):42-58. doi:<a href=\"https://doi.org/10.11646/zootaxa.2403.1.4\">10.11646/zootaxa.2403.1.4</a>","chicago":"Palero, Ferran, Guillermo Guerao, Paul Clark, and Pere Abello. “Final-Stage Phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The First Complete Description.” <i>Zootaxa</i>. Magnolia Press, 2010. <a href=\"https://doi.org/10.11646/zootaxa.2403.1.4\">https://doi.org/10.11646/zootaxa.2403.1.4</a>.","mla":"Palero, Ferran, et al. “Final-Stage Phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The First Complete Description.” <i>Zootaxa</i>, vol. 2403, no. 1, Magnolia Press, 2010, pp. 42–58, doi:<a href=\"https://doi.org/10.11646/zootaxa.2403.1.4\">10.11646/zootaxa.2403.1.4</a>.","apa":"Palero, F., Guerao, G., Clark, P., &#38; Abello, P. (2010). Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description. <i>Zootaxa</i>. Magnolia Press. <a href=\"https://doi.org/10.11646/zootaxa.2403.1.4\">https://doi.org/10.11646/zootaxa.2403.1.4</a>"},"page":"42 - 58","abstract":[{"text":"Four rare palinurid phyllosoma larvae, one mid-stage and three final stage, were found among the unclassified collections in the Crustacea Section, Natural History Museum, London. Detailed morphological analysis of the larvae indicated that they belong to several Palinustus species given the presence of incipient blunt-horns, length of antennula, length ratio of segments of antennular peduncle, distribution of pereiopod spines, and shape of uropods and telson. Moreover, the size of the final-stage larvae agrees with that expected given the size of the recently described puerulus stage of Palinustus mossambicus. This constitutes the first description of a complete phyllosoma assigned to Palinustus species. The phyllosoma described in the present study include the largest Palinuridae larva ever found.","lang":"eng"}],"publisher":"Magnolia Press","author":[{"orcid":"0000-0002-0343-8329","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","full_name":"Palero, Ferran","last_name":"Palero","first_name":"Ferran"},{"last_name":"Guerao","full_name":"Guerao, Guillermo","first_name":"Guillermo"},{"last_name":"Clark","full_name":"Clark, Paul","first_name":"Paul"},{"last_name":"Abello","full_name":"Abello, Pere","first_name":"Pere"}],"article_processing_charge":"No","oa_version":"None","day":"19","_id":"3786","date_updated":"2022-03-21T08:22:58Z","type":"journal_article","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"publication_status":"published","article_type":"original","title":"Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description","date_created":"2018-12-11T12:05:10Z","year":"2010","date_published":"2010-03-19T00:00:00Z","month":"03"},{"oa_version":"Submitted Version","type":"journal_article","publication_status":"published","title":"DNA extraction from formalin-fixed tissue: new light from the deep sea","date_created":"2018-12-11T12:05:10Z","year":"2010","month":"09","doi":"10.3989/scimar.2010.74n3465","volume":74,"quality_controlled":"1","status":"public","acknowledgement":"The authors would like to thank two anonymous reviewers for their remarks, which helped to improve the manuscript. This project was supported by the Marine Biodiversity and Ecosystem Functioning Network of Excellence MarBEF (Contract no. GOCE-CT-2003-505446) of the 6th European Framework Programme(FP6), the Zoology Research Fund, Department of Zoology, NHM, London, a Research Grant from the Royal Society to S.T., and a pre-doctoral fellowship awarded by the Autonomous Government of Catalonia to F.P.(2006FIC-00082). This research received support from the SYNTHESYS Project http://www.synthesys. info/ which is financed by European Community Research Infrastructure Action under the FP6 “Structuring the European Research Area” Programme. Many thanks are due to J. Fortuño for suggesting TMS as an alternative to critical point drying, P.Crabb for helping with the UV-light photography setting and our colleagues/friends in the Whale Basement Molecular Laboratories, Department of Zoology NHM \r\n\r\n","scopus_import":1,"abstract":[{"lang":"eng","text":"DNA samples were extracted from ethanol and formalin-fixed decapod crustacean tissue using a new method based on Tetramethylsilane (TMS)-Chelex. It is shown that neither an indigestible matrix of cross-linked protein nor soluble PCR inhibitors impede PCR success when dealing with formalin-fixed material. Instead, amplification success from formalin-fixed tissue appears to depend on the presence of unmodified DNA in the extracted sample. A staining method that facilitates the targeting of samples with a high content of unmodified DNA is provided."}],"publisher":"Consejo Superior de Investigaciones Científicas","author":[{"orcid":"0000-0002-0343-8329","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","full_name":"Palero, Ferran","last_name":"Palero","first_name":"Ferran"},{"first_name":"Sally","full_name":"Hall, Sally","last_name":"Hall"},{"first_name":"Paul","last_name":"Clark","full_name":"Clark, Paul"},{"last_name":"Johnston","full_name":"Johnston, David","first_name":"David"},{"first_name":"Jackie","last_name":"Mackenzie Dodds","full_name":"Mackenzie Dodds, Jackie"},{"first_name":"Sven","full_name":"Thatje, Sven","last_name":"Thatje"}],"_id":"3787","day":"01","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T07:52:11Z","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://eprints.soton.ac.uk/68731/","open_access":"1"}],"date_published":"2010-09-01T00:00:00Z","issue":"3","intvolume":"        74","publication":"Scientia Marina","publist_id":"2440","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"page":"465 - 470","citation":{"chicago":"Palero, Ferran, Sally Hall, Paul Clark, David Johnston, Jackie Mackenzie Dodds, and Sven Thatje. “DNA Extraction from Formalin-Fixed Tissue: New Light from the Deep Sea.” <i>Scientia Marina</i>. Consejo Superior de Investigaciones Científicas, 2010. <a href=\"https://doi.org/10.3989/scimar.2010.74n3465\">https://doi.org/10.3989/scimar.2010.74n3465</a>.","mla":"Palero, Ferran, et al. “DNA Extraction from Formalin-Fixed Tissue: New Light from the Deep Sea.” <i>Scientia Marina</i>, vol. 74, no. 3, Consejo Superior de Investigaciones Científicas, 2010, pp. 465–70, doi:<a href=\"https://doi.org/10.3989/scimar.2010.74n3465\">10.3989/scimar.2010.74n3465</a>.","apa":"Palero, F., Hall, S., Clark, P., Johnston, D., Mackenzie Dodds, J., &#38; Thatje, S. (2010). DNA extraction from formalin-fixed tissue: new light from the deep sea. <i>Scientia Marina</i>. Consejo Superior de Investigaciones Científicas. <a href=\"https://doi.org/10.3989/scimar.2010.74n3465\">https://doi.org/10.3989/scimar.2010.74n3465</a>","ieee":"F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, and S. Thatje, “DNA extraction from formalin-fixed tissue: new light from the deep sea,” <i>Scientia Marina</i>, vol. 74, no. 3. Consejo Superior de Investigaciones Científicas, pp. 465–470, 2010.","short":"F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, S. Thatje, Scientia Marina 74 (2010) 465–470.","ama":"Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. DNA extraction from formalin-fixed tissue: new light from the deep sea. <i>Scientia Marina</i>. 2010;74(3):465-470. doi:<a href=\"https://doi.org/10.3989/scimar.2010.74n3465\">10.3989/scimar.2010.74n3465</a>","ista":"Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. 2010. DNA extraction from formalin-fixed tissue: new light from the deep sea. Scientia Marina. 74(3), 465–470."}},{"volume":33,"doi":"10.1140/epje/i2010-10642-y","issue":"2","intvolume":"        33","publication":"The European Physical Journal E: Soft Matter and Biological Physics","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","publist_id":"2439","status":"public","scopus_import":1,"citation":{"mla":"Klopper, Abigail, et al. “Finite-Size Corrections to Scaling Behavior in Sorted Cell Aggregates.” <i>The European Physical Journal E: Soft Matter and Biological Physics</i>, vol. 33, no. 2, Springer, 2010, pp. 99–103, doi:<a href=\"https://doi.org/10.1140/epje/i2010-10642-y\">10.1140/epje/i2010-10642-y</a>.","apa":"Klopper, A., Krens, G., Grill, S., &#38; Heisenberg, C.-P. J. (2010). Finite-size corrections to scaling behavior in sorted cell aggregates. <i>The European Physical Journal E: Soft Matter and Biological Physics</i>. Springer. <a href=\"https://doi.org/10.1140/epje/i2010-10642-y\">https://doi.org/10.1140/epje/i2010-10642-y</a>","chicago":"Klopper, Abigail, Gabriel Krens, Stephan Grill, and Carl-Philipp J Heisenberg. “Finite-Size Corrections to Scaling Behavior in Sorted Cell Aggregates.” <i>The European Physical Journal E: Soft Matter and Biological Physics</i>. Springer, 2010. <a href=\"https://doi.org/10.1140/epje/i2010-10642-y\">https://doi.org/10.1140/epje/i2010-10642-y</a>.","ista":"Klopper A, Krens G, Grill S, Heisenberg C-PJ. 2010. Finite-size corrections to scaling behavior in sorted cell aggregates. The European Physical Journal E: Soft Matter and Biological Physics. 33(2), 99–103.","ama":"Klopper A, Krens G, Grill S, Heisenberg C-PJ. Finite-size corrections to scaling behavior in sorted cell aggregates. <i>The European Physical Journal E: Soft Matter and Biological Physics</i>. 2010;33(2):99-103. doi:<a href=\"https://doi.org/10.1140/epje/i2010-10642-y\">10.1140/epje/i2010-10642-y</a>","short":"A. Klopper, G. Krens, S. Grill, C.-P.J. Heisenberg, The European Physical Journal E: Soft Matter and Biological Physics 33 (2010) 99–103.","ieee":"A. Klopper, G. Krens, S. Grill, and C.-P. J. Heisenberg, “Finite-size corrections to scaling behavior in sorted cell aggregates,” <i>The European Physical Journal E: Soft Matter and Biological Physics</i>, vol. 33, no. 2. Springer, pp. 99–103, 2010."},"page":"99 - 103","abstract":[{"lang":"eng","text":"Cell sorting is a widespread phenomenon pivotal to the early development of multicellular organisms. In vitro cell sorting studies have been instrumental in revealing the cellular properties driving this process. However, these studies have as yet been limited to two-dimensional analysis of three-dimensional cell sorting events. Here we describe a method to record the sorting of primary zebrafish ectoderm and mesoderm germ layer progenitor cells in three dimensions over time, and quantitatively analyze their sorting behavior using an order parameter related to heterotypic interface length. We investigate the cell population size dependence of sorted aggregates and find that the germ layer progenitor cells engulfed in the final configuration display a relationship between total interfacial length and system size according to a simple geometrical argument, subject to a finite-size effect."}],"author":[{"first_name":"Abigail","full_name":"Klopper, Abigail","last_name":"Klopper"},{"orcid":"0000-0003-4761-5996","last_name":"Krens","full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel"},{"first_name":"Stephan","full_name":"Grill, Stephan","last_name":"Grill"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Springer","oa_version":"None","_id":"3788","day":"18","department":[{"_id":"CaHe"}],"type":"journal_article","date_updated":"2021-01-12T07:52:12Z","language":[{"iso":"eng"}],"publication_status":"published","date_created":"2018-12-11T12:05:10Z","title":"Finite-size corrections to scaling behavior in sorted cell aggregates","year":"2010","date_published":"2010-09-18T00:00:00Z","month":"09"},{"scopus_import":1,"citation":{"ista":"Quesada-Hernández E, Caneparo L, Schneider S, Winkler S, Liebling M, Fraser S, Heisenberg C-PJ. 2010. Stereotypical cell division orientation controls neural rod midline formation in zebrafish. Current Biology. 20(21), 1966–1972.","ama":"Quesada-Hernández E, Caneparo L, Schneider S, et al. Stereotypical cell division orientation controls neural rod midline formation in zebrafish. <i>Current Biology</i>. 2010;20(21):1966-1972. doi:<a href=\"https://doi.org/10.1016/j.cub.2010.10.009\">10.1016/j.cub.2010.10.009</a>","ieee":"E. Quesada-Hernández <i>et al.</i>, “Stereotypical cell division orientation controls neural rod midline formation in zebrafish,” <i>Current Biology</i>, vol. 20, no. 21. Cell Press, pp. 1966–1972, 2010.","short":"E. Quesada-Hernández, L. Caneparo, S. Schneider, S. Winkler, M. Liebling, S. Fraser, C.-P.J. Heisenberg, Current Biology 20 (2010) 1966–1972.","mla":"Quesada-Hernández, Elena, et al. “Stereotypical Cell Division Orientation Controls Neural Rod Midline Formation in Zebrafish.” <i>Current Biology</i>, vol. 20, no. 21, Cell Press, 2010, pp. 1966–72, doi:<a href=\"https://doi.org/10.1016/j.cub.2010.10.009\">10.1016/j.cub.2010.10.009</a>.","apa":"Quesada-Hernández, E., Caneparo, L., Schneider, S., Winkler, S., Liebling, M., Fraser, S., &#38; Heisenberg, C.-P. J. (2010). Stereotypical cell division orientation controls neural rod midline formation in zebrafish. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2010.10.009\">https://doi.org/10.1016/j.cub.2010.10.009</a>","chicago":"Quesada-Hernández, Elena, Luca Caneparo, Sylvia Schneider, Sylke Winkler, Michael Liebling, Scott Fraser, and Carl-Philipp J Heisenberg. “Stereotypical Cell Division Orientation Controls Neural Rod Midline Formation in Zebrafish.” <i>Current Biology</i>. Cell Press, 2010. <a href=\"https://doi.org/10.1016/j.cub.2010.10.009\">https://doi.org/10.1016/j.cub.2010.10.009</a>."},"page":"1966 - 1972","author":[{"id":"EA35229E-E909-11E9-8DF8-C90C5D5AF86E","last_name":"Quesada-Hernández","full_name":"Quesada-Hernández, Elena","first_name":"Elena"},{"full_name":"Caneparo, Luca","last_name":"Caneparo","first_name":"Luca"},{"last_name":"Schneider","full_name":"Schneider, Sylvia","id":"1FAC36B0-E90A-11E9-9D2F-EF31CE0C9C2F","first_name":"Sylvia"},{"first_name":"Sylke","last_name":"Winkler","full_name":"Winkler, Sylke"},{"full_name":"Liebling, Michael","last_name":"Liebling","first_name":"Michael"},{"first_name":"Scott","last_name":"Fraser","full_name":"Fraser, Scott"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"publisher":"Cell Press","abstract":[{"text":"The development of multicellular organisms is dependent on the tight coordination between tissue growth and morphogenesis. The stereotypical orientation of cell divisions has been proposed to be a fundamental mechanism by which proliferating and growing tissues take shape. However, the actual contribution of stereotypical division orientation (SDO) to tissue morphogenesis is unclear. In zebrafish, cell divisions with stereotypical orientation have been implicated in both body-axis elongation and neural rod formation [1, 2], although there is little direct evidence for a critical function of SDO in either of these processes. Here we show that SDO is required for formation of the neural rod midline during neurulation but dispensable for elongation of the body axis during gastrulation. Our data indicate that SDO during both gastrulation and neurulation is dependent on the noncanonical Wnt receptor Frizzled 7 (Fz7) and that interfering with cell division orientation leads to severe defects in neural rod midline formation but not body-axis elongation. These findings suggest a novel function for Fz7-controlled cell division orientation in neural rod midline formation during neurulation. ","lang":"eng"}],"issue":"21","volume":20,"doi":"10.1016/j.cub.2010.10.009","quality_controlled":"1","status":"public","acknowledgement":"This work was supported by grants from the Fundacion Caja Madrid to E.Q.H. and the Institute of Science and Technology Austria, the Max-Planck-Society, and the Deutsche Forschungsgemeinschaft to C.P.H.\r\nWe are grateful to Jon Clarke, Andy Oates, and Garrett Greenan for reading earlier versions of this manuscript. We thank J. Peychl, H. Ibarra, and P. Pitrone for excellent assistance and advice in multi-photon microscopy and D. White for assistance during the image-processing steps. We also thank D. Panhans for technical assistance, the whole Heisenberg laboratory for useful comments and discussions, and E. Lehmann, J. Hückmann, and G. Junghans for excellent fish care. ","publication":"Current Biology","intvolume":"        20","publist_id":"2438","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Stereotypical cell division orientation controls neural rod midline formation in zebrafish","date_created":"2018-12-11T12:05:11Z","date_published":"2010-11-09T00:00:00Z","month":"11","year":"2010","oa_version":"None","_id":"3789","day":"09","publication_status":"published","type":"journal_article","date_updated":"2021-01-12T07:52:12Z","department":[{"_id":"CaHe"}],"language":[{"iso":"eng"}]},{"scopus_import":1,"article_number":"e1000544","publisher":"Public Library of Science","author":[{"first_name":"Alba","full_name":"Diz Muñoz, Alba","last_name":"Diz Muñoz"},{"last_name":"Krieg","full_name":"Krieg, Michael","first_name":"Michael"},{"last_name":"Bergert","full_name":"Bergert, Martin","first_name":"Martin"},{"first_name":"Itziar","full_name":"Ibarlucea Benitez, Itziar","last_name":"Ibarlucea Benitez"},{"first_name":"Daniel","full_name":"Müller, Daniel","last_name":"Müller"},{"first_name":"Ewa","full_name":"Paluch, Ewa","last_name":"Paluch"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"text":"Cell shape and motility are primarily controlled by cellular mechanics. The attachment of the plasma membrane to the underlying actomyosin cortex has been proposed to be important for cellular processes involving membrane deformation. However, little is known about the actual function of membrane-to-cortex attachment (MCA) in cell protrusion formation and migration, in particular in the context of the developing embryo. Here, we use a multidisciplinary approach to study MCA in zebrafish mesoderm and endoderm (mesendoderm) germ layer progenitor cells, which migrate using a combination of different protrusion types, namely, lamellipodia, filopodia, and blebs, during zebrafish gastrulation. By interfering with the activity of molecules linking the cortex to the membrane and measuring resulting changes in MCA by atomic force microscopy, we show that reducing MCA in mesendoderm progenitors increases the proportion of cellular blebs and reduces the directionality of cell migration. We propose that MCA is a key parameter controlling the relative proportions of different cell protrusion types in mesendoderm progenitors, and thus is key in controlling directed migration during gastrulation.","lang":"eng"}],"doi":"10.1371/journal.pbio.1000544","volume":8,"quality_controlled":"1","ddc":["576"],"status":"public","acknowledgement":"We would like to thank A. G. Clark, S. Grill, A. Oates, E. Raz, L. Rohde, and M. Zerial for reading earlier versions of the manuscript. We are grateful to W. Zachariae, Y. Arboleda-Estudillo, S. Schneider, P. Stockinger, D. Panhans, M. Biro, J. C. Olaya, and the BIOTEC/MPI-CBG zebrafish and imaging facilities for help and advice at various stages of this project and to J. Helenius for help with programming. This work was supported by grants from the Boehringer Ingelheim Fonds to MK, the Polish Ministry of Science and Higher Education to E. P., and the Deutsche Forschungsgemeinschaft (HE 3231/6-1 and PA 1590/1-1) to CPH and EP.\r\n","date_created":"2018-12-11T12:05:11Z","has_accepted_license":"1","title":"Control of directed cell migration in vivo by membrane-to-cortex attachment","pubrep_id":"365","month":"11","year":"2010","oa_version":"Published Version","publication_status":"published","type":"journal_article","oa":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"apa":"Diz Muñoz, A., Krieg, M., Bergert, M., Ibarlucea Benitez, I., Müller, D., Paluch, E., &#38; Heisenberg, C.-P. J. (2010). Control of directed cell migration in vivo by membrane-to-cortex attachment. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1000544\">https://doi.org/10.1371/journal.pbio.1000544</a>","mla":"Diz Muñoz, Alba, et al. “Control of Directed Cell Migration in Vivo by Membrane-to-Cortex Attachment.” <i>PLoS Biology</i>, vol. 8, no. 11, e1000544, Public Library of Science, 2010, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000544\">10.1371/journal.pbio.1000544</a>.","chicago":"Diz Muñoz, Alba, Michael Krieg, Martin Bergert, Itziar Ibarlucea Benitez, Daniel Müller, Ewa Paluch, and Carl-Philipp J Heisenberg. “Control of Directed Cell Migration in Vivo by Membrane-to-Cortex Attachment.” <i>PLoS Biology</i>. Public Library of Science, 2010. <a href=\"https://doi.org/10.1371/journal.pbio.1000544\">https://doi.org/10.1371/journal.pbio.1000544</a>.","ama":"Diz Muñoz A, Krieg M, Bergert M, et al. Control of directed cell migration in vivo by membrane-to-cortex attachment. <i>PLoS Biology</i>. 2010;8(11). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000544\">10.1371/journal.pbio.1000544</a>","ista":"Diz Muñoz A, Krieg M, Bergert M, Ibarlucea Benitez I, Müller D, Paluch E, Heisenberg C-PJ. 2010. Control of directed cell migration in vivo by membrane-to-cortex attachment. PLoS Biology. 8(11), e1000544.","short":"A. Diz Muñoz, M. Krieg, M. Bergert, I. Ibarlucea Benitez, D. Müller, E. Paluch, C.-P.J. Heisenberg, PLoS Biology 8 (2010).","ieee":"A. Diz Muñoz <i>et al.</i>, “Control of directed cell migration in vivo by membrane-to-cortex attachment,” <i>PLoS Biology</i>, vol. 8, no. 11. Public Library of Science, 2010."},"file_date_updated":"2020-07-14T12:46:16Z","issue":"11","publication":"PLoS Biology","intvolume":"         8","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"2437","file":[{"creator":"system","file_name":"IST-2015-365-v1+1_journal.pbio.1000544.pdf","file_id":"4685","content_type":"application/pdf","checksum":"52d18c90ca6b02234cea5e8b399b7f46","date_created":"2018-12-12T10:08:24Z","access_level":"open_access","date_updated":"2020-07-14T12:46:16Z","relation":"main_file","file_size":799506}],"date_published":"2010-11-30T00:00:00Z","day":"30","_id":"3790","department":[{"_id":"CaHe"}],"date_updated":"2021-01-12T07:52:13Z","language":[{"iso":"eng"}]}]