--- _id: '881' author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: 'Kondrashov F. Gene Dosage and Duplication. In: Evolution after Gene Duplication. Wiley-Blackwell; 2011:57-76. doi:10.1002/9780470619902.ch4' 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 chicago: Kondrashov, Fyodor. “Gene Dosage and Duplication.” In Evolution after Gene Duplication, 57–76. Wiley-Blackwell, 2011. https://doi.org/10.1002/9780470619902.ch4. ieee: F. Kondrashov, “Gene Dosage and Duplication,” in Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76. ista: 'Kondrashov F. 2011.Gene Dosage and Duplication. In: Evolution after Gene Duplication. , 57–76.' mla: Kondrashov, Fyodor. “Gene Dosage and Duplication.” Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76, doi:10.1002/9780470619902.ch4. short: F. Kondrashov, in:, Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76. date_created: 2018-12-11T11:49:00Z date_published: 2011-03-14T00:00:00Z date_updated: 2021-01-12T08:21:08Z day: '14' doi: 10.1002/9780470619902.ch4 extern: 1 month: '03' page: 57 - 76 publication: Evolution after Gene Duplication publication_status: published publisher: Wiley-Blackwell publist_id: '6766' quality_controlled: 0 status: public title: Gene Dosage and Duplication type: book_chapter year: '2011' ... --- _id: '919' abstract: - lang: eng 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. author: - first_name: Thomas full_name: Angelini, Thomas last_name: Angelini - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Xavier full_name: Trepatc, Xavier last_name: Trepatc - first_name: Manuel full_name: Marquez, Manuel last_name: Marquez - first_name: Jeffrey full_name: Fredberg, Jeffrey last_name: Fredberg - first_name: David full_name: Weitz, David last_name: Weitz 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:49:12Z date_published: 2011-03-22T00:00:00Z date_updated: 2021-01-12T08:21:54Z day: '22' doi: 10.1073/pnas.1010059108 extern: '1' intvolume: ' 108' issue: '12' language: - iso: eng month: '03' oa_version: None page: 4714 - 4719 publication: Proceedings of the National Academy of Sciences of the United States of America publication_status: published publisher: PNAS publist_id: '6522' quality_controlled: '1' status: public title: Glass-like dynamics of collective cell migration type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 108 year: '2011' ... --- _id: '918' abstract: - lang: eng 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. 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 author: - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Jacques full_name: Prost, Jacques last_name: Prost - first_name: Jean full_name: Joanny, Jean last_name: Joanny citation: 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 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 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. 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. ista: Hannezo EB, Prost J, Joanny J. 2011. Instabilities of monolayered epithelia Shape and structure of villi and crypts. Physical Review Letters. 107(7). 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). date_created: 2018-12-11T11:49:11Z date_published: 2011-08-11T00:00:00Z date_updated: 2021-01-12T08:21:54Z day: '11' doi: 10.1103/PhysRevLett.107.078104 extern: '1' intvolume: ' 107' issue: '7' language: - iso: eng month: '08' oa_version: None publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '6521' status: public title: Instabilities of monolayered epithelia Shape and structure of villi and crypts type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 107 year: '2011' ... --- _id: '9522' 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. article_processing_charge: No author: - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: 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 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 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. ieee: D. Zilberman, Balancing parental contributions in plant embryonic gene activation, vol. 20, no. 6. Elsevier, 2011, pp. 735–736. ista: Zilberman D. 2011. Balancing parental contributions in plant embryonic gene activation, Elsevier,p. 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. date_created: 2021-06-08T06:23:39Z date_published: 2011-06-14T00:00:00Z date_updated: 2021-12-14T08:34:37Z day: '14' department: - _id: DaZi doi: 10.1016/j.devcel.2011.05.018 extern: '1' external_id: pmid: - '21664571' intvolume: ' 20' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.devcel.2011.05.018 month: '06' oa: 1 oa_version: Published Version page: 735-736 pmid: 1 publication: Developmental Cell publication_identifier: eissn: - 1878-1551 issn: - 1534-5807 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Balancing parental contributions in plant embryonic gene activation type: other_academic_publication user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 20 year: '2011' ... --- _id: '9648' abstract: - lang: eng 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. alternative_title: - LNCS article_processing_charge: No author: - first_name: Rocio full_name: Gonzalez-Diaz, Rocio last_name: Gonzalez-Diaz - first_name: Adrian full_name: Ion, Adrian id: 29F89302-F248-11E8-B48F-1D18A9856A87 last_name: Ion - first_name: Maria Jose full_name: Jimenez, Maria Jose last_name: Jimenez - first_name: Regina full_name: Poyatos, Regina last_name: Poyatos citation: 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' 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' 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. 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. 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.' 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. short: R. Gonzalez-Diaz, A. Ion, M.J. Jimenez, R. Poyatos, in:, Computer Analysis of Images and Patterns, Springer Nature, 2011, pp. 286–293. conference: end_date: 2011-08-31 location: Seville, Spain name: 'CAIP: International Conference on Computer Analysis of Images and Patterns' start_date: 2011-08-29 date_created: 2021-07-11T22:01:19Z date_published: 2011-08-01T00:00:00Z date_updated: 2021-08-12T13:53:17Z day: '01' department: - _id: HeEd doi: 10.1007/978-3-642-23672-3_35 intvolume: ' 6854' language: - iso: eng main_file_link: - open_access: '1' url: http://hdl.handle.net/11441/30766 month: '08' oa: 1 oa_version: Published Version page: 286-293 publication: Computer Analysis of Images and Patterns publication_identifier: eissn: - '16113349' isbn: - '9783642236716' issn: - '03029743' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Incremental-decremental algorithm for computing AT-models and persistent homology type: conference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 6854 year: '2011' ...