[{"day":"14","month":"03","doi":"10.1002/9780470619902.ch4","date_published":"2011-03-14T00:00:00Z","citation":{"short":"F. Kondrashov, in:, Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76.","mla":"Kondrashov, Fyodor. “Gene Dosage and Duplication.” Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76, doi:10.1002/9780470619902.ch4.","chicago":"Kondrashov, Fyodor. “Gene Dosage and Duplication.” In Evolution after Gene Duplication, 57–76. Wiley-Blackwell, 2011. https://doi.org/10.1002/9780470619902.ch4.","ama":"Kondrashov F. Gene Dosage and Duplication. In: Evolution after Gene Duplication. Wiley-Blackwell; 2011:57-76. doi:10.1002/9780470619902.ch4","ieee":"F. Kondrashov, “Gene Dosage and Duplication,” in Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76.","apa":"Kondrashov, F. (2011). Gene Dosage and Duplication. In Evolution after Gene Duplication (pp. 57–76). Wiley-Blackwell. https://doi.org/10.1002/9780470619902.ch4","ista":"Kondrashov F. 2011.Gene Dosage and Duplication. In: Evolution after Gene Duplication. , 57–76."},"publication":"Evolution after Gene Duplication","page":"57 - 76","quality_controlled":0,"publist_id":"6766","extern":1,"type":"book_chapter","author":[{"last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov"}],"date_updated":"2021-01-12T08:21:08Z","date_created":"2018-12-11T11:49:00Z","_id":"881","year":"2011","publisher":"Wiley-Blackwell","title":"Gene Dosage and Duplication","publication_status":"published","status":"public"},{"citation":{"ama":"Angelini T, Hannezo EB, Trepatc X, Marquez M, Fredberg J, Weitz D. Glass-like dynamics of collective cell migration. Proceedings of the National Academy of Sciences of the United States of America. 2011;108(12):4714-4719. doi:10.1073/pnas.1010059108","ista":"Angelini T, Hannezo EB, Trepatc X, Marquez M, Fredberg J, Weitz D. 2011. Glass-like dynamics of collective cell migration. Proceedings of the National Academy of Sciences of the United States of America. 108(12), 4714–4719.","apa":"Angelini, T., Hannezo, E. B., Trepatc, X., Marquez, M., Fredberg, J., & Weitz, D. (2011). Glass-like dynamics of collective cell migration. Proceedings of the National Academy of Sciences of the United States of America. PNAS. https://doi.org/10.1073/pnas.1010059108","ieee":"T. Angelini, E. B. Hannezo, X. Trepatc, M. Marquez, J. Fredberg, and D. Weitz, “Glass-like dynamics of collective cell migration,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 12. PNAS, pp. 4714–4719, 2011.","mla":"Angelini, Thomas, et al. “Glass-like Dynamics of Collective Cell Migration.” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 12, PNAS, 2011, pp. 4714–19, doi:10.1073/pnas.1010059108.","short":"T. Angelini, E.B. Hannezo, X. Trepatc, M. Marquez, J. Fredberg, D. Weitz, Proceedings of the National Academy of Sciences of the United States of America 108 (2011) 4714–4719.","chicago":"Angelini, Thomas, Edouard B Hannezo, Xavier Trepatc, Manuel Marquez, Jeffrey Fredberg, and David Weitz. “Glass-like Dynamics of Collective Cell Migration.” Proceedings of the National Academy of Sciences of the United States of America. PNAS, 2011. https://doi.org/10.1073/pnas.1010059108."},"publication":"Proceedings of the National Academy of Sciences of the United States of America","page":"4714 - 4719","quality_controlled":"1","date_published":"2011-03-22T00:00:00Z","doi":"10.1073/pnas.1010059108","language":[{"iso":"eng"}],"day":"22","month":"03","_id":"919","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2011","publisher":"PNAS","intvolume":" 108","title":"Glass-like dynamics of collective cell migration","publication_status":"published","status":"public","author":[{"full_name":"Angelini, Thomas","first_name":"Thomas","last_name":"Angelini"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"full_name":"Trepatc, Xavier","first_name":"Xavier","last_name":"Trepatc"},{"last_name":"Marquez","first_name":"Manuel","full_name":"Marquez, Manuel"},{"last_name":"Fredberg","first_name":"Jeffrey","full_name":"Fredberg, Jeffrey"},{"full_name":"Weitz, David","last_name":"Weitz","first_name":"David"}],"oa_version":"None","volume":108,"date_updated":"2021-01-12T08:21:54Z","date_created":"2018-12-11T11:49:12Z","type":"journal_article","issue":"12","publist_id":"6522","abstract":[{"text":"Collective cell migration in tissues occurs throughout embryonic development, during wound healing, and in cancerous tumor invasion, yet most detailed knowledge of cell migration comes from single-cell studies. As single cells migrate, the shape of the cell body fluctuates dramatically through cyclic processes of extension, adhesion, and retraction, accompanied by erratic changes in migration direction. Within confluent cell layers, such subcellular motions must be coupled between neighbors, yet the influence of these subcellular motions on collective migration is not known. Here we study motion within a confluent epithelial cell sheet, simultaneously measuring collective migration and subcellular motions, covering a broad range of length scales, time scales, and cell densities. At large length scales and time scales collective migration slows as cell density rises, yet the fastest cells move in large, multicell groups whose scale grows with increasing cell density. This behavior has an intriguing analogy to dynamic heterogeneities found in particulate systems as they become more crowded and approach a glass transition. In addition we find a diminishing self-diffusivity of short-wavelength motions within the cell layer, and growing peaks in the vibrational density of states associated with cooperative cell-shape fluctuations. Both of these observations are also intriguingly reminiscent of a glass transition. Thus, these results provide a broad and suggestive analogy between cell motion within a confluent layer and the dynamics of supercooled colloidal and molecular fluids approaching a glass transition.","lang":"eng"}],"extern":"1"},{"extern":"1","publist_id":"6521","issue":"7","abstract":[{"text":"We study theoretically the shapes of a dividing epithelial monolayer of cells lying on top of an elastic stroma. The negative tension created by cell division provokes a buckling instability at a finite wave vector leading to the formation of periodic arrays of villi and crypts. The instability is similar to the buckling of a metallic plate under compression. We use the results to rationalize the various structures of the intestinal lining observed in vivo. Taking into account the coupling between cell division and local curvature, we obtain different patterns of villi and crypts, which could explain the different morphologies of the small intestine and the colon.","lang":"eng"}],"type":"journal_article","volume":107,"oa_version":"None","date_updated":"2021-01-12T08:21:54Z","date_created":"2018-12-11T11:49:11Z","author":[{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"},{"first_name":"Jacques","last_name":"Prost","full_name":"Prost, Jacques"},{"first_name":"Jean","last_name":"Joanny","full_name":"Joanny, Jean"}],"intvolume":" 107","publisher":"American Physical Society","title":"Instabilities of monolayered epithelia Shape and structure of villi and crypts","publication_status":"published","status":"public","_id":"918","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2011","acknowledgement":"We thank S. Fre and M. Huygue for discussion and for showing us in vivo samples and A. Bergès for help with the manuscript.","article_processing_charge":"No","month":"08","day":"11","language":[{"iso":"eng"}],"date_published":"2011-08-11T00:00:00Z","doi":"10.1103/PhysRevLett.107.078104","citation":{"mla":"Hannezo, Edouard B., et al. “Instabilities of Monolayered Epithelia Shape and Structure of Villi and Crypts.” Physical Review Letters, vol. 107, no. 7, American Physical Society, 2011, doi:10.1103/PhysRevLett.107.078104.","short":"E.B. Hannezo, J. Prost, J. Joanny, Physical Review Letters 107 (2011).","chicago":"Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Instabilities of Monolayered Epithelia Shape and Structure of Villi and Crypts.” Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.107.078104.","ama":"Hannezo EB, Prost J, Joanny J. Instabilities of monolayered epithelia Shape and structure of villi and crypts. Physical Review Letters. 2011;107(7). doi:10.1103/PhysRevLett.107.078104","ista":"Hannezo EB, Prost J, Joanny J. 2011. Instabilities of monolayered epithelia Shape and structure of villi and crypts. Physical Review Letters. 107(7).","ieee":"E. B. Hannezo, J. Prost, and J. Joanny, “Instabilities of monolayered epithelia Shape and structure of villi and crypts,” Physical Review Letters, vol. 107, no. 7. American Physical Society, 2011.","apa":"Hannezo, E. B., Prost, J., & Joanny, J. (2011). Instabilities of monolayered epithelia Shape and structure of villi and crypts. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.107.078104"},"publication":"Physical Review Letters"},{"citation":{"chicago":"Zilberman, Daniel. Balancing Parental Contributions in Plant Embryonic Gene Activation. Developmental Cell. Vol. 20. Elsevier, 2011. https://doi.org/10.1016/j.devcel.2011.05.018.","mla":"Zilberman, Daniel. “Balancing Parental Contributions in Plant Embryonic Gene Activation.” Developmental Cell, vol. 20, no. 6, Elsevier, 2011, pp. 735–36, doi:10.1016/j.devcel.2011.05.018.","short":"D. Zilberman, Balancing Parental Contributions in Plant Embryonic Gene Activation, Elsevier, 2011.","ista":"Zilberman D. 2011. Balancing parental contributions in plant embryonic gene activation, Elsevier,p.","ieee":"D. Zilberman, Balancing parental contributions in plant embryonic gene activation, vol. 20, no. 6. Elsevier, 2011, pp. 735–736.","apa":"Zilberman, D. (2011). Balancing parental contributions in plant embryonic gene activation. Developmental Cell (Vol. 20, pp. 735–736). Elsevier. https://doi.org/10.1016/j.devcel.2011.05.018","ama":"Zilberman D. Balancing Parental Contributions in Plant Embryonic Gene Activation. Vol 20. Elsevier; 2011:735-736. doi:10.1016/j.devcel.2011.05.018"},"publication":"Developmental Cell","page":"735-736","date_published":"2011-06-14T00:00:00Z","article_processing_charge":"No","day":"14","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9522","intvolume":" 20","status":"public","title":"Balancing parental contributions in plant embryonic gene activation","oa_version":"Published Version","type":"other_academic_publication","issue":"6","abstract":[{"lang":"eng","text":"Little is known about chromatin remodeling events immediately after fertilization. A recent report by Autran et al. (2011) in Cell now shows that chromatin regulatory pathways that silence transposable elements are responsible for global delayed activation of gene expression in the early Arabidopsis embryo."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2011.05.018"}],"oa":1,"external_id":{"pmid":["21664571"]},"quality_controlled":"1","doi":"10.1016/j.devcel.2011.05.018","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"month":"06","pmid":1,"year":"2011","department":[{"_id":"DaZi"}],"publisher":"Elsevier","publication_status":"published","author":[{"full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"}],"volume":20,"date_updated":"2021-12-14T08:34:37Z","date_created":"2021-06-08T06:23:39Z","extern":"1"},{"month":"08","publication_identifier":{"isbn":["9783642236716"],"eissn":["16113349"],"issn":["03029743"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2011-08-31","location":"Seville, Spain","start_date":"2011-08-29","name":"CAIP: International Conference on Computer Analysis of Images and Patterns"},"doi":"10.1007/978-3-642-23672-3_35","quality_controlled":"1","main_file_link":[{"url":"http://hdl.handle.net/11441/30766","open_access":"1"}],"oa":1,"date_updated":"2021-08-12T13:53:17Z","date_created":"2021-07-11T22:01:19Z","volume":6854,"author":[{"full_name":"Gonzalez-Diaz, Rocio","first_name":"Rocio","last_name":"Gonzalez-Diaz"},{"full_name":"Ion, Adrian","id":"29F89302-F248-11E8-B48F-1D18A9856A87","last_name":"Ion","first_name":"Adrian"},{"last_name":"Jimenez","first_name":"Maria Jose","full_name":"Jimenez, Maria Jose"},{"full_name":"Poyatos, Regina","last_name":"Poyatos","first_name":"Regina"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"year":"2011","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2011-08-01T00:00:00Z","page":"286-293","publication":"Computer Analysis of Images and Patterns","citation":{"ieee":"R. Gonzalez-Diaz, A. Ion, M. J. Jimenez, and R. Poyatos, “Incremental-decremental algorithm for computing AT-models and persistent homology,” in Computer Analysis of Images and Patterns, Seville, Spain, 2011, vol. 6854, pp. 286–293.","apa":"Gonzalez-Diaz, R., Ion, A., Jimenez, M. J., & Poyatos, R. (2011). Incremental-decremental algorithm for computing AT-models and persistent homology. In Computer Analysis of Images and Patterns (Vol. 6854, pp. 286–293). Seville, Spain: Springer Nature. https://doi.org/10.1007/978-3-642-23672-3_35","ista":"Gonzalez-Diaz R, Ion A, Jimenez MJ, Poyatos R. 2011. Incremental-decremental algorithm for computing AT-models and persistent homology. Computer Analysis of Images and Patterns. CAIP: International Conference on Computer Analysis of Images and Patterns, LNCS, vol. 6854, 286–293.","ama":"Gonzalez-Diaz R, Ion A, Jimenez MJ, Poyatos R. Incremental-decremental algorithm for computing AT-models and persistent homology. In: Computer Analysis of Images and Patterns. Vol 6854. Springer Nature; 2011:286-293. doi:10.1007/978-3-642-23672-3_35","chicago":"Gonzalez-Diaz, Rocio, Adrian Ion, Maria Jose Jimenez, and Regina Poyatos. “Incremental-Decremental Algorithm for Computing AT-Models and Persistent Homology.” In Computer Analysis of Images and Patterns, 6854:286–93. Springer Nature, 2011. https://doi.org/10.1007/978-3-642-23672-3_35.","short":"R. Gonzalez-Diaz, A. Ion, M.J. Jimenez, R. Poyatos, in:, Computer Analysis of Images and Patterns, Springer Nature, 2011, pp. 286–293.","mla":"Gonzalez-Diaz, Rocio, et al. “Incremental-Decremental Algorithm for Computing AT-Models and Persistent Homology.” Computer Analysis of Images and Patterns, vol. 6854, Springer Nature, 2011, pp. 286–93, doi:10.1007/978-3-642-23672-3_35."},"abstract":[{"text":"In this paper, we establish a correspondence between the incremental algorithm for computing AT-models [8,9] and the one for computing persistent homology [6,14,15]. We also present a decremental algorithm for computing AT-models that allows to extend the persistence computation to a wider setting. Finally, we show how to combine incremental and decremental techniques for persistent homology computation.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Published Version","status":"public","title":"Incremental-decremental algorithm for computing AT-models and persistent homology","intvolume":" 6854","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9648"},{"month":"04","day":"01","publication":"Physical Review Letters","citation":{"mla":"Serbyn, Maksym, et al. “Serbyn et Al. Reply:” Physical Review Letters, vol. 106, no. 13, American Physical Society, 2011, doi:10.1103/PhysRevLett.106.139702.","short":"M. Serbyn, M. Skvortsov, A. Varlamov, V. Galitski, Physical Review Letters 106 (2011).","chicago":"Serbyn, Maksym, Mikhail Skvortsov, Andrei Varlamov, and Victor Galitski. “Serbyn et Al. Reply:” Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.106.139702.","ama":"Serbyn M, Skvortsov M, Varlamov A, Galitski V. Serbyn et al. Reply: Physical Review Letters. 2011;106(13). doi:10.1103/PhysRevLett.106.139702","ista":"Serbyn M, Skvortsov M, Varlamov A, Galitski V. 2011. Serbyn et al. Reply: Physical Review Letters. 106(13).","ieee":"M. Serbyn, M. Skvortsov, A. Varlamov, and V. Galitski, “Serbyn et al. Reply:,” Physical Review Letters, vol. 106, no. 13. American Physical Society, 2011.","apa":"Serbyn, M., Skvortsov, M., Varlamov, A., & Galitski, V. (2011). Serbyn et al. Reply: Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.106.139702"},"quality_controlled":0,"date_published":"2011-04-01T00:00:00Z","doi":"10.1103/PhysRevLett.106.139702","type":"journal_article","abstract":[{"text":"A Reply to the Comment by Andrei Sergeev, M. Reizer, and V. Mitin.","lang":"eng"}],"issue":"13","publist_id":"6433","extern":1,"year":"2011","_id":"968","status":"public","title":"Serbyn et al. Reply:","publication_status":"published","publisher":"American Physical Society","intvolume":" 106","author":[{"full_name":"Maksym Serbyn","last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Skvortsov, Mikhail A","first_name":"Mikhail","last_name":"Skvortsov"},{"last_name":"Varlamov","first_name":"Andrei","full_name":"Varlamov, Andrei A"},{"first_name":"Victor","last_name":"Galitski","full_name":"Galitski, Victor M"}],"date_created":"2018-12-11T11:49:27Z","date_updated":"2021-01-12T08:22:19Z","volume":106},{"quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1111/j.1095-8312.2011.01728.x","month":"09","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2011","acknowledgement":"This work was supported by a pre-doctoral fellowship awarded by the Autonomous Government of Catalonia to F.P. (2006FIC-00082). Research was funded by projects FBBVA-BIOCON 08-187/09, CGL2006-13423, and CTM2007-66635. The authors are part of the research group 2009SGR-636, 2009SGR-655, and 2009SGR-1364 of the Generalitat de Catalunya. F.P. acknowledges EU-Synthesys grant (GB-TAF-4474).","volume":104,"date_created":"2018-12-11T12:03:06Z","date_updated":"2023-02-23T14:07:31Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"9762"}]},"author":[{"first_name":"Ferran","last_name":"Palero","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0343-8329","full_name":"Palero, Ferran"},{"full_name":"Abello, Pere","first_name":"Pere","last_name":"Abello"},{"full_name":"Macpherson, Enrique","last_name":"Macpherson","first_name":"Enrique"},{"full_name":"Beaumont, Mark","first_name":"Mark","last_name":"Beaumont"},{"full_name":"Pascual, Marta","first_name":"Marta","last_name":"Pascual"}],"publist_id":"3212","page":"407 - 418","citation":{"ista":"Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. 2011. Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas. Biological Journal of the Linnean Society. 104(2), 407–418.","ieee":"F. Palero, P. Abello, E. Macpherson, M. Beaumont, and M. Pascual, “Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas,” Biological Journal of the Linnean Society, vol. 104, no. 2. Wiley-Blackwell, pp. 407–418, 2011.","apa":"Palero, F., Abello, P., Macpherson, E., Beaumont, M., & Pascual, M. (2011). Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas. Biological Journal of the Linnean Society. Wiley-Blackwell. https://doi.org/10.1111/j.1095-8312.2011.01728.x","ama":"Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas. Biological Journal of the Linnean Society. 2011;104(2):407-418. doi:10.1111/j.1095-8312.2011.01728.x","chicago":"Palero, Ferran, Pere Abello, Enrique Macpherson, Mark Beaumont, and Marta Pascual. “Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster Palinurus Elephas.” Biological Journal of the Linnean Society. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1095-8312.2011.01728.x.","mla":"Palero, Ferran, et al. “Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster Palinurus Elephas.” Biological Journal of the Linnean Society, vol. 104, no. 2, Wiley-Blackwell, 2011, pp. 407–18, doi:10.1111/j.1095-8312.2011.01728.x.","short":"F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, Biological Journal of the Linnean Society 104 (2011) 407–418."},"publication":"Biological Journal of the Linnean Society","date_published":"2011-09-14T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"14","intvolume":" 104","title":"Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"3395","oa_version":"None","type":"journal_article","issue":"2","abstract":[{"text":"Defining population structure and genetic diversity levels is of the utmost importance for developing efficient conservation strategies. Overfishing has caused mean annual catches of the European spiny lobster (Palinurus elephas) to decrease alarmingly along its distribution area. In this context, there is a need for comprehensive studies aiming to evaluate the genetic health of the exploited populations. The present study is based on a set of ten nuclear markers amplified in 331 individuals from ten different localities covering most of P. elephas distribution area. Samples from Atlantic and Mediterranean basins showed small but significant differences, indicating that P. elephas populations do not behave as a single panmictic unit but form two partially-overlapping groups. Despite intense overfishing, our dataset did not recover a recent bottleneck signal, and instead showed a large and stable historical effective size. This result could be accounted for by specific life-history traits (reproduction and longevity) and the limitations of molecular markers in covering recent timescales for nontemporal samples. The findings of the present study emphasize the need to integrate information on effective population sizes and life-history parameters when evaluating population connectivity levels from genetic data.","lang":"eng"}]},{"department":[{"_id":"NiBa"}],"publisher":"IST Austria","title":"Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas)","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9762","year":"2011","oa_version":"Published Version","date_updated":"2023-02-23T11:25:25Z","date_created":"2021-08-02T07:11:19Z","related_material":{"record":[{"id":"3395","status":"public","relation":"used_in_publication"}]},"author":[{"full_name":"Palero, Ferran","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0343-8329","first_name":"Ferran","last_name":"Palero"},{"full_name":"Abello, Pere","first_name":"Pere","last_name":"Abello"},{"last_name":"Macpherson","first_name":"Enrique","full_name":"Macpherson, Enrique"},{"full_name":"Beaumont, Mark","last_name":"Beaumont","first_name":"Mark"},{"last_name":"Pascual","first_name":"Marta","full_name":"Pascual, Marta"}],"type":"research_data_reference","abstract":[{"lang":"eng","text":"Defining population structure and genetic diversity levels is of the utmost importance for developing efficient conservation strategies. Overfishing has caused mean annual catches of the European spiny lobster (Palinurus elephas) to decrease alarmingly along its distribution area. In this context, there is a need for comprehensive studies to evaluate the genetic health of the exploited populations. The present work is based on a set of 10 nuclear markers amplified in 331 individuals from 10 different localities covering most of P. elephas distribution area. Samples from Atlantic and Mediterranean basins showed small but significant differences, indicating that P. elephas populations do not behave as a single panmictic unit but form two partially-overlapping groups. Despite intense overfishing, our dataset did not recover a recent bottleneck signal, and showed a large and stable historical effective size instead. This result could be accounted for by specific life history traits (reproduction and longevity) and the limitations of molecular markers in covering very recent timescales for non temporal samples. Our study emphasizes the necessity of integrating information on effective population sizes and life history parameters when evaluating population connectivity levels from genetic data."}],"citation":{"ama":"Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas). 2011. doi:10.5061/dryad.299h8","ista":"Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. 2011. Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas), IST Austria, 10.5061/dryad.299h8.","apa":"Palero, F., Abello, P., Macpherson, E., Beaumont, M., & Pascual, M. (2011). Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas). IST Austria. https://doi.org/10.5061/dryad.299h8","ieee":"F. Palero, P. Abello, E. Macpherson, M. Beaumont, and M. Pascual, “Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas).” IST Austria, 2011.","mla":"Palero, Ferran, et al. Data from: Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster (Palinurus Elephas). IST Austria, 2011, doi:10.5061/dryad.299h8.","short":"F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, (2011).","chicago":"Palero, Ferran, Pere Abello, Enrique Macpherson, Mark Beaumont, and Marta Pascual. “Data from: Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster (Palinurus Elephas).” IST Austria, 2011. https://doi.org/10.5061/dryad.299h8."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.299h8"}],"oa":1,"date_published":"2011-05-12T00:00:00Z","doi":"10.5061/dryad.299h8","article_processing_charge":"No","month":"05","day":"12"},{"citation":{"chicago":"Sommer, Christoph M, Christoph Straehle, Ullrich Köthe, and Fred A. Hamprecht. “Ilastik: Interactive Learning and Segmentation Toolkit.” In 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro. Institute of Electrical and Electronics Engineers, 2011. https://doi.org/10.1109/isbi.2011.5872394.","short":"C.M. Sommer, C. Straehle, U. Köthe, F.A. Hamprecht, in:, 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro, Institute of Electrical and Electronics Engineers, 2011.","mla":"Sommer, Christoph M., et al. “Ilastik: Interactive Learning and Segmentation Toolkit.” 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro, Institute of Electrical and Electronics Engineers, 2011, doi:10.1109/isbi.2011.5872394.","apa":"Sommer, C. M., Straehle, C., Köthe, U., & Hamprecht, F. A. (2011). Ilastik: Interactive learning and segmentation toolkit. In 2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro. Chicago, Illinois, USA: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/isbi.2011.5872394","ieee":"C. M. Sommer, C. Straehle, U. Köthe, and F. A. Hamprecht, “Ilastik: Interactive learning and segmentation toolkit,” in 2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro, Chicago, Illinois, USA, 2011.","ista":"Sommer CM, Straehle C, Köthe U, Hamprecht FA. 2011. Ilastik: Interactive learning and segmentation toolkit. 2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro. ISBI: International Symposium on Biomedical Imaging.","ama":"Sommer CM, Straehle C, Köthe U, Hamprecht FA. Ilastik: Interactive learning and segmentation toolkit. In: 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro. Institute of Electrical and Electronics Engineers; 2011. doi:10.1109/isbi.2011.5872394"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.researchgate.net/publication/224241106_Ilastik_Interactive_learning_and_segmentation_toolkit"}],"publication":"2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro","quality_controlled":"1","doi":"10.1109/isbi.2011.5872394","date_published":"2011-06-09T00:00:00Z","conference":{"name":"ISBI: International Symposium on Biomedical Imaging","end_date":"2011-04-02","location":"Chicago, Illinois, USA","start_date":"2011-03-30"},"language":[{"iso":"eng"}],"keyword":["image segmentation","biomedical imaging","three dimensional displays","neurons","retina","observers","image color analysis"],"article_processing_charge":"No","publication_identifier":{"eissn":["1945-8452"],"isbn":["978-1-4244-4127-3"],"issn":["1945-7928"]},"day":"09","month":"06","_id":"9943","year":"2011","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"Bio"}],"publisher":"Institute of Electrical and Electronics Engineers","publication_status":"published","title":"Ilastik: Interactive learning and segmentation toolkit","status":"public","author":[{"orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M","full_name":"Sommer, Christoph M"},{"last_name":"Straehle","first_name":"Christoph","full_name":"Straehle, Christoph"},{"last_name":"Köthe","first_name":"Ullrich","full_name":"Köthe, Ullrich"},{"first_name":"Fred A.","last_name":"Hamprecht","full_name":"Hamprecht, Fred A."}],"oa_version":"Preprint","date_updated":"2023-02-23T14:13:38Z","date_created":"2021-08-19T11:49:58Z","type":"conference","abstract":[{"lang":"eng","text":"Segmentation is the process of partitioning digital images into meaningful regions. The analysis of biological high content images often requires segmentation as a first step. We propose ilastik as an easy-to-use tool which allows the user without expertise in image processing to perform segmentation and classification in a unified way. ilastik learns from labels provided by the user through a convenient mouse interface. Based on these labels, ilastik infers a problem specific segmentation. A random forest classifier is used in the learning step, in which each pixel's neighborhood is characterized by a set of generic (nonlinear) features. ilastik supports up to three spatial plus one spectral dimension and makes use of all dimensions in the feature calculation. ilastik provides realtime feedback that enables the user to interactively refine the segmentation result and hence further fine-tune the classifier. An uncertainty measure guides the user to ambiguous regions in the images. Real time performance is achieved by multi-threading which fully exploits the capabilities of modern multi-core machines. Once a classifier has been trained on a set of representative images, it can be exported and used to automatically process a very large number of images (e.g. using the CellProfiler pipeline). ilastik is an open source project and released under the BSD license at www.ilastik.org."}],"extern":"1"},{"department":[{"_id":"HeEd"}],"editor":[{"full_name":"Jiang, Xiaoyi","first_name":"Xiaoyi","last_name":"Jiang"},{"last_name":"Ferrer","first_name":"Miquel","full_name":"Ferrer, Miquel"},{"full_name":"Torsello, Andrea","last_name":"Torsello","first_name":"Andrea"}],"publisher":"Springer","publication_status":"published","year":"2011","acknowledgement":"This work has been partially supported by the Austrian Science Fund under grants S9103-N13 and P18716-N13.","volume":6658,"date_created":"2022-03-21T08:08:35Z","date_updated":"2023-09-05T14:10:15Z","author":[{"last_name":"Artner","first_name":"Nicole M.","full_name":"Artner, Nicole M."},{"full_name":"Ion, Adrian","first_name":"Adrian","last_name":"Ion","id":"29F89302-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Walter G.","last_name":"Kropatsch","full_name":"Kropatsch, Walter G."}],"place":"Berlin, Heidelberg","quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-20844-7_22","conference":{"name":"GbRPR: Graph-based Representations in Pattern Recognition","end_date":"2011-05-20","start_date":"2011-05-18","location":"Münster, Germany"},"publication_identifier":{"issn":["0302-9743"],"eisbn":["9783642208447"],"isbn":["9783642208430"],"eissn":["1611-3349"]},"month":"06","intvolume":" 6658","title":"Spatio-temporal extraction of articulated models in a graph pyramid","status":"public","_id":"10907","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"None","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"This paper presents a method to create a model of an articulated object using the planar motion in an initialization video. The model consists of rigid parts connected by points of articulation. The rigid parts are described by the positions of salient feature-points tracked throughout the video. Following a filtering step that identifies points that belong to different objects, rigid parts are found by a grouping process in a graph pyramid. Valid articulation points are selected by verifying multiple hypotheses for each pair of parts.","lang":"eng"}],"page":"215-224","citation":{"short":"N.M. Artner, A. Ion, W.G. Kropatsch, in:, X. Jiang, M. Ferrer, A. Torsello (Eds.), Graph-Based Representations in Pattern Recognition, Springer, Berlin, Heidelberg, 2011, pp. 215–224.","mla":"Artner, Nicole M., et al. “Spatio-Temporal Extraction of Articulated Models in a Graph Pyramid.” Graph-Based Representations in Pattern Recognition, edited by Xiaoyi Jiang et al., vol. 6658, Springer, 2011, pp. 215–24, doi:10.1007/978-3-642-20844-7_22.","chicago":"Artner, Nicole M., Adrian Ion, and Walter G. Kropatsch. “Spatio-Temporal Extraction of Articulated Models in a Graph Pyramid.” In Graph-Based Representations in Pattern Recognition, edited by Xiaoyi Jiang, Miquel Ferrer, and Andrea Torsello, 6658:215–24. LNIP. Berlin, Heidelberg: Springer, 2011. https://doi.org/10.1007/978-3-642-20844-7_22.","ama":"Artner NM, Ion A, Kropatsch WG. Spatio-temporal extraction of articulated models in a graph pyramid. In: Jiang X, Ferrer M, Torsello A, eds. Graph-Based Representations in Pattern Recognition. Vol 6658. LNIP. Berlin, Heidelberg: Springer; 2011:215-224. doi:10.1007/978-3-642-20844-7_22","ieee":"N. M. Artner, A. Ion, and W. G. Kropatsch, “Spatio-temporal extraction of articulated models in a graph pyramid,” in Graph-Based Representations in Pattern Recognition, Münster, Germany, 2011, vol. 6658, pp. 215–224.","apa":"Artner, N. M., Ion, A., & Kropatsch, W. G. (2011). Spatio-temporal extraction of articulated models in a graph pyramid. In X. Jiang, M. Ferrer, & A. Torsello (Eds.), Graph-Based Representations in Pattern Recognition (Vol. 6658, pp. 215–224). Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-642-20844-7_22","ista":"Artner NM, Ion A, Kropatsch WG. 2011. Spatio-temporal extraction of articulated models in a graph pyramid. Graph-Based Representations in Pattern Recognition. GbRPR: Graph-based Representations in Pattern RecognitionLNIP, LNCS, vol. 6658, 215–224."},"publication":"Graph-Based Representations in Pattern Recognition","date_published":"2011-06-01T00:00:00Z","series_title":"LNIP","scopus_import":"1","article_processing_charge":"No","day":"01"}]