[{"extern":1,"publication_status":"published","date_created":"2018-12-11T12:06:13Z","year":"2007","author":[{"full_name":"Paul Bendich","first_name":"Paul","last_name":"Bendich","id":"43F6EC54-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cohen-Steiner, David","first_name":"David","last_name":"Cohen Steiner"},{"full_name":"Herbert Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"full_name":"Harer, John","first_name":"John","last_name":"Harer"},{"full_name":"Morozov, Dmitriy","last_name":"Morozov","first_name":"Dmitriy"}],"type":"conference","conference":{"name":"FOCS: Foundations of Computer Science"},"day":"01","citation":{"ista":"Bendich P, Cohen Steiner D, Edelsbrunner H, Harer J, Morozov D. 2007. Inferring local homology from sampled stratified spaces. FOCS: Foundations of Computer Science, 536–546.","ieee":"P. Bendich, D. Cohen Steiner, H. Edelsbrunner, J. Harer, and D. Morozov, “Inferring local homology from sampled stratified spaces,” presented at the FOCS: Foundations of Computer Science, 2007, pp. 536–546.","mla":"Bendich, Paul, et al. <i>Inferring Local Homology from Sampled Stratified Spaces</i>. IEEE, 2007, pp. 536–46, doi:<a href=\"https://doi.org/10.1109/FOCS.2007.33\">10.1109/FOCS.2007.33</a>.","apa":"Bendich, P., Cohen Steiner, D., Edelsbrunner, H., Harer, J., &#38; Morozov, D. (2007). Inferring local homology from sampled stratified spaces (pp. 536–546). Presented at the FOCS: Foundations of Computer Science, IEEE. <a href=\"https://doi.org/10.1109/FOCS.2007.33\">https://doi.org/10.1109/FOCS.2007.33</a>","short":"P. Bendich, D. Cohen Steiner, H. Edelsbrunner, J. Harer, D. Morozov, in:, IEEE, 2007, pp. 536–546.","ama":"Bendich P, Cohen Steiner D, Edelsbrunner H, Harer J, Morozov D. Inferring local homology from sampled stratified spaces. In: IEEE; 2007:536-546. doi:<a href=\"https://doi.org/10.1109/FOCS.2007.33\">10.1109/FOCS.2007.33</a>","chicago":"Bendich, Paul, David Cohen Steiner, Herbert Edelsbrunner, John Harer, and Dmitriy Morozov. “Inferring Local Homology from Sampled Stratified Spaces,” 536–46. IEEE, 2007. <a href=\"https://doi.org/10.1109/FOCS.2007.33\">https://doi.org/10.1109/FOCS.2007.33</a>."},"abstract":[{"lang":"eng","text":"We study the reconstruction of a stratified space from a possibly noisy point sample. Specifically, we use the vineyard of the distance function restricted to a I-parameter family of neighborhoods of a point to assess the local homology of the stratified space at that point. We prove the correctness of this assessment under the assumption of a sufficiently dense sample. We also give an algorithm that constructs the vineyard and makes the local assessment in time at most cubic in the size of the Delaunay triangulation of the point sample."}],"doi":"10.1109/FOCS.2007.33","title":"Inferring local homology from sampled stratified spaces","quality_controlled":0,"page":"536 - 546","publisher":"IEEE","date_published":"2007-01-01T00:00:00Z","publist_id":"2150","_id":"3975","month":"01","date_updated":"2021-01-12T07:53:35Z","status":"public"},{"doi":"10.1021/pr070018+","abstract":[{"text":"Herein, we study the interfaces of a set of 146 transient protein-protein interfaces in order to better understand the principles of their interactions. We define and generate the protein interface using tools from computational geometry and topology and then apply statistical analysis to its residue composition. In addition to counting individual occurrences, we evaluate pairing preferences, both across and as neighbors on one side of an interface. Likelihood correction emphasizes novel and unexpected pairs, such as the His-Cys pair found in most complexes of serine proteases with their diverse inhibitors and the Met-Met neighbor pair found in unrelated protein interfaces. We also present a visualization of the protein interface that allows for facile identification of residue-residue contacts and other biochemical properties.","lang":"eng"}],"citation":{"ista":"Headd J, Ban YEA, Brown P, Edelsbrunner H, Vaidya M, Rudolph J. 2007. Protein-protein interfaces: Properties, preferences, and projections. Journal of Proteome Research. 6(7), 2576–2586.","ieee":"J. Headd, Y. E. A. Ban, P. Brown, H. Edelsbrunner, M. Vaidya, and J. Rudolph, “Protein-protein interfaces: Properties, preferences, and projections,” <i>Journal of Proteome Research</i>, vol. 6, no. 7. American Chemical Society, pp. 2576–2586, 2007.","mla":"Headd, Jeffrey, et al. “Protein-Protein Interfaces: Properties, Preferences, and Projections.” <i>Journal of Proteome Research</i>, vol. 6, no. 7, American Chemical Society, 2007, pp. 2576–86, doi:<a href=\"https://doi.org/10.1021/pr070018+\">10.1021/pr070018+</a>.","apa":"Headd, J., Ban, Y. E. A., Brown, P., Edelsbrunner, H., Vaidya, M., &#38; Rudolph, J. (2007). Protein-protein interfaces: Properties, preferences, and projections. <i>Journal of Proteome Research</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/pr070018+\">https://doi.org/10.1021/pr070018+</a>","ama":"Headd J, Ban YEA, Brown P, Edelsbrunner H, Vaidya M, Rudolph J. Protein-protein interfaces: Properties, preferences, and projections. <i>Journal of Proteome Research</i>. 2007;6(7):2576-2586. doi:<a href=\"https://doi.org/10.1021/pr070018+\">10.1021/pr070018+</a>","short":"J. Headd, Y.E.A. Ban, P. Brown, H. Edelsbrunner, M. Vaidya, J. Rudolph, Journal of Proteome Research 6 (2007) 2576–2586.","chicago":"Headd, Jeffrey, Y E Andrew Ban, Paul Brown, Herbert Edelsbrunner, Madhuwanti Vaidya, and Johannes Rudolph. “Protein-Protein Interfaces: Properties, Preferences, and Projections.” <i>Journal of Proteome Research</i>. American Chemical Society, 2007. <a href=\"https://doi.org/10.1021/pr070018+\">https://doi.org/10.1021/pr070018+</a>."},"intvolume":"         6","quality_controlled":0,"title":"Protein-protein interfaces: Properties, preferences, and projections","publisher":"American Chemical Society","page":"2576 - 2586","publication":"Journal of Proteome Research","publist_id":"2151","date_published":"2007-06-02T00:00:00Z","_id":"3976","date_updated":"2021-01-12T07:53:36Z","month":"06","status":"public","extern":1,"publication_status":"published","date_created":"2018-12-11T12:06:13Z","volume":6,"issue":"7","year":"2007","type":"journal_article","day":"02","author":[{"full_name":"Headd, Jeffrey J","last_name":"Headd","first_name":"Jeffrey"},{"first_name":"Y E Andrew","last_name":"Ban","full_name":"Ban, Y E Andrew"},{"full_name":"Brown, Paul","first_name":"Paul","last_name":"Brown"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Herbert Edelsbrunner"},{"full_name":"Vaidya, Madhuwanti","first_name":"Madhuwanti","last_name":"Vaidya"},{"last_name":"Rudolph","first_name":"Johannes","full_name":"Rudolph, Johannes"}]},{"issue":"1","year":"2007","author":[{"last_name":"Attali","first_name":"Dominique","full_name":"Attali, Dominique"},{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Herbert Edelsbrunner"}],"type":"journal_article","day":"01","extern":1,"volume":37,"date_created":"2018-12-11T12:06:14Z","publication_status":"published","publication":"Discrete & Computational Geometry","date_published":"2007-01-01T00:00:00Z","publist_id":"2152","_id":"3977","month":"01","date_updated":"2021-01-12T07:53:36Z","status":"public","citation":{"ieee":"D. Attali and H. Edelsbrunner, “Inclusion-exclusion formulas from independent complexes,” <i>Discrete &#38; Computational Geometry</i>, vol. 37, no. 1. Springer, pp. 59–77, 2007.","ista":"Attali D, Edelsbrunner H. 2007. Inclusion-exclusion formulas from independent complexes. Discrete &#38; Computational Geometry. 37(1), 59–77.","ama":"Attali D, Edelsbrunner H. Inclusion-exclusion formulas from independent complexes. <i>Discrete &#38; Computational Geometry</i>. 2007;37(1):59-77. doi:<a href=\"https://doi.org/10.1007/s00454-006-1274-7\">10.1007/s00454-006-1274-7</a>","short":"D. Attali, H. Edelsbrunner, Discrete &#38; Computational Geometry 37 (2007) 59–77.","chicago":"Attali, Dominique, and Herbert Edelsbrunner. “Inclusion-Exclusion Formulas from Independent Complexes.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2007. <a href=\"https://doi.org/10.1007/s00454-006-1274-7\">https://doi.org/10.1007/s00454-006-1274-7</a>.","mla":"Attali, Dominique, and Herbert Edelsbrunner. “Inclusion-Exclusion Formulas from Independent Complexes.” <i>Discrete &#38; Computational Geometry</i>, vol. 37, no. 1, Springer, 2007, pp. 59–77, doi:<a href=\"https://doi.org/10.1007/s00454-006-1274-7\">10.1007/s00454-006-1274-7</a>.","apa":"Attali, D., &#38; Edelsbrunner, H. (2007). Inclusion-exclusion formulas from independent complexes. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-006-1274-7\">https://doi.org/10.1007/s00454-006-1274-7</a>"},"abstract":[{"lang":"eng","text":"Using inclusion-exclusion, we can write the indicator function of a union of finitely many balls as an alternating sum of indicator functions of common intersections of balls. We exhibit abstract simplicial complexes that correspond to minimal inclusion-exclusion formulas. They include the dual complex, as defined in [3], and are characterized by the independence of their simplices and by geometric realizations with the same underlying space as the dual complex."}],"doi":"10.1007/s00454-006-1274-7","intvolume":"        37","title":"Inclusion-exclusion formulas from independent complexes","quality_controlled":0,"page":"59 - 77","publisher":"Springer"},{"year":"2007","type":"conference","conference":{"name":"WADS: International Workshop on Algrithms and Data Structures"},"day":"21","author":[{"last_name":"Attali","first_name":"Dominique","full_name":"Attali, Dominique"},{"first_name":"Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Herbert Edelsbrunner"},{"full_name":"Harer, John","first_name":"John","last_name":"Harer"},{"full_name":"Mileyko, Yuriy","first_name":"Yuriy","last_name":"Mileyko"}],"date_created":"2018-12-11T12:06:15Z","publication_status":"published","volume":4619,"extern":1,"date_updated":"2021-01-12T07:53:38Z","month":"08","status":"public","date_published":"2007-08-21T00:00:00Z","publist_id":"2149","_id":"3981","quality_controlled":0,"title":"Alpha-beta witness complexes","publisher":"Springer","page":"386 - 397","doi":"10.1007/978-3-540-73951-7_34","acknowledgement":"Research by the authors is partially supported by DARPA under grant HR0011-05-1-0007, by CNRS under grant PICS-3416 and by IST Program of the EU under Contract IST-2002-506766.","abstract":[{"lang":"eng","text":"Building on the work of Martinetz, Schulten and de Silva, Carlsson, we introduce a 2-parameter family of witness complexes and algorithms for constructing them. This family can be used to determine the gross topology of point cloud data in R-d or other metric spaces. The 2-parameter family is sensitive to differences in sampling density and thus amenable to detecting patterns within the data set. It also lends itself to theoretical analysis. For example, we can prove that in the limit, when the witnesses cover the entire domain, witness complexes in the family that share the first, scale parameter have the same homotopy type."}],"alternative_title":["LNCS"],"citation":{"ama":"Attali D, Edelsbrunner H, Harer J, Mileyko Y. Alpha-beta witness complexes. In: Vol 4619. Springer; 2007:386-397. doi:<a href=\"https://doi.org/10.1007/978-3-540-73951-7_34\">10.1007/978-3-540-73951-7_34</a>","short":"D. Attali, H. Edelsbrunner, J. Harer, Y. Mileyko, in:, Springer, 2007, pp. 386–397.","chicago":"Attali, Dominique, Herbert Edelsbrunner, John Harer, and Yuriy Mileyko. “Alpha-Beta Witness Complexes,” 4619:386–97. Springer, 2007. <a href=\"https://doi.org/10.1007/978-3-540-73951-7_34\">https://doi.org/10.1007/978-3-540-73951-7_34</a>.","mla":"Attali, Dominique, et al. <i>Alpha-Beta Witness Complexes</i>. Vol. 4619, Springer, 2007, pp. 386–97, doi:<a href=\"https://doi.org/10.1007/978-3-540-73951-7_34\">10.1007/978-3-540-73951-7_34</a>.","apa":"Attali, D., Edelsbrunner, H., Harer, J., &#38; Mileyko, Y. (2007). Alpha-beta witness complexes (Vol. 4619, pp. 386–397). Presented at the WADS: International Workshop on Algrithms and Data Structures, Springer. <a href=\"https://doi.org/10.1007/978-3-540-73951-7_34\">https://doi.org/10.1007/978-3-540-73951-7_34</a>","ieee":"D. Attali, H. Edelsbrunner, J. Harer, and Y. Mileyko, “Alpha-beta witness complexes,” presented at the WADS: International Workshop on Algrithms and Data Structures, 2007, vol. 4619, pp. 386–397.","ista":"Attali D, Edelsbrunner H, Harer J, Mileyko Y. 2007. Alpha-beta witness complexes. WADS: International Workshop on Algrithms and Data Structures, LNCS, vol. 4619, 386–397."},"intvolume":"      4619"},{"type":"journal_article","day":"06","author":[{"full_name":"Rohde, Laurel","last_name":"Rohde","first_name":"Laurel"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"year":"2007","oa_version":"None","date_created":"2018-12-11T12:07:15Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","volume":261,"extern":"1","status":"public","date_updated":"2021-01-12T07:54:53Z","month":"06","_id":"4152","publication":"International Review of Cytology - A Survey of Cell Biology","date_published":"2007-06-06T00:00:00Z","publist_id":"1967","publisher":"Academic Press","page":"159 - 192","title":"Zebrafish gastrulation: Cell movements, signals, and mechanisms","intvolume":"       261","doi":"10.1016/S0074-7696(07)61004-3","citation":{"ieee":"L. Rohde and C.-P. J. Heisenberg, “Zebrafish gastrulation: Cell movements, signals, and mechanisms,” <i>International Review of Cytology - A Survey of Cell Biology</i>, vol. 261. Academic Press, pp. 159–192, 2007.","ista":"Rohde L, Heisenberg C-PJ. 2007. Zebrafish gastrulation: Cell movements, signals, and mechanisms. International Review of Cytology - A Survey of Cell Biology. 261, 159–192.","ama":"Rohde L, Heisenberg C-PJ. Zebrafish gastrulation: Cell movements, signals, and mechanisms. <i>International Review of Cytology - A Survey of Cell Biology</i>. 2007;261:159-192. doi:<a href=\"https://doi.org/10.1016/S0074-7696(07)61004-3\">10.1016/S0074-7696(07)61004-3</a>","short":"L. Rohde, C.-P.J. Heisenberg, International Review of Cytology - A Survey of Cell Biology 261 (2007) 159–192.","chicago":"Rohde, Laurel, and Carl-Philipp J Heisenberg. “Zebrafish Gastrulation: Cell Movements, Signals, and Mechanisms.” <i>International Review of Cytology - A Survey of Cell Biology</i>. Academic Press, 2007. <a href=\"https://doi.org/10.1016/S0074-7696(07)61004-3\">https://doi.org/10.1016/S0074-7696(07)61004-3</a>.","mla":"Rohde, Laurel, and Carl-Philipp J. Heisenberg. “Zebrafish Gastrulation: Cell Movements, Signals, and Mechanisms.” <i>International Review of Cytology - A Survey of Cell Biology</i>, vol. 261, Academic Press, 2007, pp. 159–92, doi:<a href=\"https://doi.org/10.1016/S0074-7696(07)61004-3\">10.1016/S0074-7696(07)61004-3</a>.","apa":"Rohde, L., &#38; Heisenberg, C.-P. J. (2007). Zebrafish gastrulation: Cell movements, signals, and mechanisms. <i>International Review of Cytology - A Survey of Cell Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/S0074-7696(07)61004-3\">https://doi.org/10.1016/S0074-7696(07)61004-3</a>"},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Gastrulation is a morphogenetic process that results in the formation of the embryonic germ layers. Here we detail the major cell movements that occur during zebrafish gastrulation: epiboly, internalization, and convergent extension. Although gastrulation is known to be regulated by signaling pathways such as the Wnt/planar cell polarity pathway, many questions remain about the underlying molecular and cellular mechanisms. Key factors that may play a role in gastrulation cell movements are cell adhesion and cytoskeletal rearrangement. In addition, some of the driving force for gastrulation may derive from tissue interactions such as those described between the enveloping layer and the yolk syncytial layer. Future exploration of gastrulation mechanisms relies on the development of sensitive and quantitative techniques to characterize embryonic germ-layer properties."}]},{"_id":"4182","publication":"European Journal of Cell Biology","date_published":"2007-03-22T00:00:00Z","publist_id":"1937","status":"public","month":"03","date_updated":"2021-01-12T07:55:07Z","intvolume":"        86","language":[{"iso":"eng"}],"citation":{"mla":"Krieg, Michael, et al. “The Role of Cell Adhesion and Contractility for Germ Layer Morphogenesis during Zebrafish Gastrulation.” <i>European Journal of Cell Biology</i>, vol. 86, no. Supplement 1, Elsevier, 2007, pp. 39–39, doi:<a href=\"https://doi.org/10.1016/j.ejcb.2007.02.002\">10.1016/j.ejcb.2007.02.002</a>.","apa":"Krieg, M., Arboleda, Y., Müller, D., &#38; Heisenberg, C.-P. J. (2007). The role of cell adhesion and contractility for germ layer morphogenesis during zebrafish gastrulation. <i>European Journal of Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ejcb.2007.02.002\">https://doi.org/10.1016/j.ejcb.2007.02.002</a>","short":"M. Krieg, Y. Arboleda, D. Müller, C.-P.J. Heisenberg, European Journal of Cell Biology 86 (2007) 39–39.","ama":"Krieg M, Arboleda Y, Müller D, Heisenberg C-PJ. The role of cell adhesion and contractility for germ layer morphogenesis during zebrafish gastrulation. <i>European Journal of Cell Biology</i>. 2007;86(Supplement 1):39-39. doi:<a href=\"https://doi.org/10.1016/j.ejcb.2007.02.002\">10.1016/j.ejcb.2007.02.002</a>","chicago":"Krieg, Michael, Yohanna Arboleda, Daniel Müller, and Carl-Philipp J Heisenberg. “The Role of Cell Adhesion and Contractility for Germ Layer Morphogenesis during Zebrafish Gastrulation.” <i>European Journal of Cell Biology</i>. Elsevier, 2007. <a href=\"https://doi.org/10.1016/j.ejcb.2007.02.002\">https://doi.org/10.1016/j.ejcb.2007.02.002</a>.","ista":"Krieg M, Arboleda Y, Müller D, Heisenberg C-PJ. 2007. The role of cell adhesion and contractility for germ layer morphogenesis during zebrafish gastrulation. European Journal of Cell Biology. 86(Supplement 1), 39–39.","ieee":"M. Krieg, Y. Arboleda, D. Müller, and C.-P. J. Heisenberg, “The role of cell adhesion and contractility for germ layer morphogenesis during zebrafish gastrulation,” <i>European Journal of Cell Biology</i>, vol. 86, no. Supplement 1. Elsevier, pp. 39–39, 2007."},"abstract":[{"lang":"eng","text":"We are interested in the cellular and molecular mechanisms underlying tissue morphogenesis during zebrafish gastrulation. Both differential cell adhesion and contractility have been proposed to be key mechanisms by which tissues form and rearrange in development. To obtain insight into the potential roles of differential cell adhesion and contraction for germ layer morphogenesis during gastrulation, we are analyzing cell adhesion and contraction of germ layer progenitor cells using atomic force microscopy, primary tissue culture and transplantation assays. I will present and discuss data about the differential adhesiveness and contractility of germ layer progenitor cells in the context of germ layer formation during vertebrate gastrulation."}],"acknowledgement":"Abstract for the Annual Meeting of the German Societey for Cell Biology.","doi":"10.1016/j.ejcb.2007.02.002","page":"39 - 39","publisher":"Elsevier","title":"The role of cell adhesion and contractility for germ layer morphogenesis during zebrafish gastrulation","author":[{"full_name":"Krieg, Michael","first_name":"Michael","last_name":"Krieg"},{"last_name":"Arboleda","first_name":"Yohanna","full_name":"Arboleda, Yohanna"},{"last_name":"Müller","first_name":"Daniel","full_name":"Müller, Daniel"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"day":"22","type":"journal_article","year":"2007","article_processing_charge":"No","issue":"Supplement 1","extern":"1","oa_version":"None","volume":86,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2018-12-11T12:07:26Z"},{"issue":"6","year":"2007","article_processing_charge":"No","author":[{"last_name":"Von Der Hardt","first_name":"Sophia","full_name":"Von Der Hardt, Sophia"},{"full_name":"Bakkers, Jeroen","first_name":"Jeroen","last_name":"Bakkers"},{"full_name":"Inbal, Adi","first_name":"Adi","last_name":"Inbal"},{"last_name":"Carvalho","first_name":"Lara","full_name":"Carvalho, Lara"},{"full_name":"Solnica Krezel, Lilianna","first_name":"Lilianna","last_name":"Solnica Krezel"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hammerschmidt, Matthias","first_name":"Matthias","last_name":"Hammerschmidt"}],"day":"20","type":"journal_article","extern":"1","volume":17,"date_created":"2018-12-11T12:07:34Z","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","publication":"Current Biology","date_published":"2007-03-20T00:00:00Z","publist_id":"1910","_id":"4205","month":"03","date_updated":"2021-01-12T07:55:17Z","status":"public","citation":{"ista":"Von Der Hardt S, Bakkers J, Inbal A, Carvalho L, Solnica Krezel L, Heisenberg C-PJ, Hammerschmidt M. 2007. The Bmp gradient of the zebrafish gastrula guides migrating lateral cells by regulating cell-cell adhesion. Current Biology. 17(6), 475–487.","ieee":"S. Von Der Hardt <i>et al.</i>, “The Bmp gradient of the zebrafish gastrula guides migrating lateral cells by regulating cell-cell adhesion,” <i>Current Biology</i>, vol. 17, no. 6. Cell Press, pp. 475–487, 2007.","mla":"Von Der Hardt, Sophia, et al. “The Bmp Gradient of the Zebrafish Gastrula Guides Migrating Lateral Cells by Regulating Cell-Cell Adhesion.” <i>Current Biology</i>, vol. 17, no. 6, Cell Press, 2007, pp. 475–87, doi:<a href=\"https://doi.org/10.1016/j.cub.2007.02.013\">10.1016/j.cub.2007.02.013</a>.","apa":"Von Der Hardt, S., Bakkers, J., Inbal, A., Carvalho, L., Solnica Krezel, L., Heisenberg, C.-P. J., &#38; Hammerschmidt, M. (2007). The Bmp gradient of the zebrafish gastrula guides migrating lateral cells by regulating cell-cell adhesion. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2007.02.013\">https://doi.org/10.1016/j.cub.2007.02.013</a>","ama":"Von Der Hardt S, Bakkers J, Inbal A, et al. The Bmp gradient of the zebrafish gastrula guides migrating lateral cells by regulating cell-cell adhesion. <i>Current Biology</i>. 2007;17(6):475-487. doi:<a href=\"https://doi.org/10.1016/j.cub.2007.02.013\">10.1016/j.cub.2007.02.013</a>","short":"S. Von Der Hardt, J. Bakkers, A. Inbal, L. Carvalho, L. Solnica Krezel, C.-P.J. Heisenberg, M. Hammerschmidt, Current Biology 17 (2007) 475–487.","chicago":"Von Der Hardt, Sophia, Jeroen Bakkers, Adi Inbal, Lara Carvalho, Lilianna Solnica Krezel, Carl-Philipp J Heisenberg, and Matthias Hammerschmidt. “The Bmp Gradient of the Zebrafish Gastrula Guides Migrating Lateral Cells by Regulating Cell-Cell Adhesion.” <i>Current Biology</i>. Cell Press, 2007. <a href=\"https://doi.org/10.1016/j.cub.2007.02.013\">https://doi.org/10.1016/j.cub.2007.02.013</a>."},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Background: Bone morphogenetic proteins (Bmps) are required for the specification of ventrolateral cell fates during embryonic dorsoventral patterning and for proper convergence and extension gastrulation movements, but the mechanisms underlying the latter role remained elusive. Results: Via bead implantations, we show that the Bmp gradient determines the direction of lateral mesodermal cell migration during dorsal convergence in the zebrafish gastrula. This effect is independent of its role during dorsoventral patterning and of noncanonical Wnt signaling. However, it requires Bmp signal transduction through AIk8 and Smad5 to negatively regulate Ca2+/Cadherin-dependent cell-cell adhesiveness. In vivo, converging mesodermal cells form lamellipodia that attach to adjacent cells. Bmp signaling diminishes the Cadherin-dependent stability of such contact points, thereby abrogating subsequent cell displacement during lamellipodial retraction. Conclusions: We propose that the ventral-to-dorsal Bmp gradient has an instructive role to establish a reverse gradient of cell-cell adhesiveness, thereby defining different migratory zones and directing lamellipodia-driven cell migrations during dorsal convergence in lateral regions of the zebrafish gastrula."}],"doi":"10.1016/j.cub.2007.02.013","intvolume":"        17","title":"The Bmp gradient of the zebrafish gastrula guides migrating lateral cells by regulating cell-cell adhesion","page":"475 - 487","publisher":"Cell Press"},{"status":"public","month":"03","date_updated":"2021-01-12T07:55:26Z","_id":"4225","date_published":"2007-03-09T00:00:00Z","publist_id":"1891","publication":"Genome Research","page":"401 - 404","publisher":"Cold Spring Harbor Laboratory Press","title":"Evolution and multilevel optimization of the genetic code","intvolume":"        17","abstract":[{"lang":"eng","text":"The discovery of the genetic code was one of the most important advances of modern biology. But there is more to a DNA code than protein sequence; DNA carries signals for splicing, localization, folding, and regulation that are often embedded within the protein-coding sequence. In this issue, Itzkovitz and Alon show that the specific 64-to-20 mapping found in the genetic code may have been optimized for permitting protein-coding regions to carry this extra information and suggest that this property may have evolved as a side benefit of selection to minimize the negative effects of frameshift errors."}],"language":[{"iso":"eng"}],"citation":{"chicago":"Bollenbach, Mark Tobias, Kalin Vetsigian, and Roy Kishony. “Evolution and Multilevel Optimization of the Genetic Code.” <i>Genome Research</i>. Cold Spring Harbor Laboratory Press, 2007. <a href=\"https://doi.org/10.1101/gr.6144007\">https://doi.org/10.1101/gr.6144007</a>.","short":"M.T. Bollenbach, K. Vetsigian, R. Kishony, Genome Research 17 (2007) 401–404.","ama":"Bollenbach MT, Vetsigian K, Kishony R. Evolution and multilevel optimization of the genetic code. <i>Genome Research</i>. 2007;17(4):401-404. doi:<a href=\"https://doi.org/10.1101/gr.6144007\">10.1101/gr.6144007</a>","apa":"Bollenbach, M. T., Vetsigian, K., &#38; Kishony, R. (2007). Evolution and multilevel optimization of the genetic code. <i>Genome Research</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gr.6144007\">https://doi.org/10.1101/gr.6144007</a>","mla":"Bollenbach, Mark Tobias, et al. “Evolution and Multilevel Optimization of the Genetic Code.” <i>Genome Research</i>, vol. 17, no. 4, Cold Spring Harbor Laboratory Press, 2007, pp. 401–04, doi:<a href=\"https://doi.org/10.1101/gr.6144007\">10.1101/gr.6144007</a>.","ieee":"M. T. Bollenbach, K. Vetsigian, and R. Kishony, “Evolution and multilevel optimization of the genetic code,” <i>Genome Research</i>, vol. 17, no. 4. Cold Spring Harbor Laboratory Press, pp. 401–404, 2007.","ista":"Bollenbach MT, Vetsigian K, Kishony R. 2007. Evolution and multilevel optimization of the genetic code. Genome Research. 17(4), 401–404."},"doi":"10.1101/gr.6144007","author":[{"full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vetsigian","first_name":"Kalin","full_name":"Vetsigian, Kalin"},{"full_name":"Kishony, Roy","last_name":"Kishony","first_name":"Roy"}],"type":"journal_article","day":"09","year":"2007","article_processing_charge":"No","issue":"4","oa_version":"None","volume":17,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2018-12-11T12:07:42Z","extern":"1"},{"intvolume":"       315","abstract":[{"text":"In the developing fly wing, secreted morphogens such as Decapentaplegic (Dpp) and Wingless (Wg) form gradients of concentration providing positional information. Dpp forms a longer-range gradient than Wg. To understand how the range is controlled, we measured the four key kinetic parameters governing morphogen spreading: the production rate, the effective diffusion coefficient, the degradation rate, and the immobile fraction. The four parameters had different values for Dpp versus Wg. In addition, Dynamin-dependent endocytosis was required for spreading of Dpp, but not Wg. Thus, the cellular mechanisms of Dpp and Wingless spreading are different: Dpp spreading requires endocytic, intracellular trafficking.","lang":"eng"}],"citation":{"mla":"Kicheva, Anna, et al. “Kinetics of Morphogen Gradient Formation.” <i>Science</i>, vol. 315, no. 5811, American Association for the Advancement of Science, 2007, pp. 521–25, doi:<a href=\"https://doi.org/10.1126/science.1135774\">10.1126/science.1135774</a>.","apa":"Kicheva, A., Pantazis, P., Bollenbach, T., Kalaidzidis, Y., Bittig, T., Julicher, F., &#38; Gonzalez Gaitan, M. (2007). Kinetics of morphogen gradient formation. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1135774\">https://doi.org/10.1126/science.1135774</a>","short":"A. Kicheva, P. Pantazis, T. Bollenbach, Y. Kalaidzidis, T. Bittig, F. Julicher, M. Gonzalez Gaitan, Science 315 (2007) 521–525.","ama":"Kicheva A, Pantazis P, Bollenbach T, et al. Kinetics of morphogen gradient formation. <i>Science</i>. 2007;315(5811):521-525. doi:<a href=\"https://doi.org/10.1126/science.1135774\">10.1126/science.1135774</a>","chicago":"Kicheva, Anna, Periklis Pantazis, Tobias Bollenbach, Yannis Kalaidzidis, Thomas Bittig, Frank Julicher, and Marcos Gonzalez Gaitan. “Kinetics of Morphogen Gradient Formation.” <i>Science</i>. American Association for the Advancement of Science, 2007. <a href=\"https://doi.org/10.1126/science.1135774\">https://doi.org/10.1126/science.1135774</a>.","ista":"Kicheva A, Pantazis P, Bollenbach T, Kalaidzidis Y, Bittig T, Julicher F, Gonzalez Gaitan M. 2007. Kinetics of morphogen gradient formation. Science. 315(5811), 521–525.","ieee":"A. Kicheva <i>et al.</i>, “Kinetics of morphogen gradient formation,” <i>Science</i>, vol. 315, no. 5811. American Association for the Advancement of Science, pp. 521–525, 2007."},"doi":"10.1126/science.1135774","page":"521 - 525","publisher":"American Association for the Advancement of Science","title":"Kinetics of morphogen gradient formation","quality_controlled":0,"_id":"4226","publist_id":"1892","publication":"Science","date_published":"2007-01-26T00:00:00Z","status":"public","month":"01","date_updated":"2021-01-12T07:55:26Z","extern":1,"volume":315,"publication_status":"published","date_created":"2018-12-11T12:07:42Z","author":[{"first_name":"Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Anna Kicheva"},{"full_name":"Pantazis, Periklis","last_name":"Pantazis","first_name":"Periklis"},{"full_name":"Bollenbach, Tobias","first_name":"Tobias","last_name":"Bollenbach"},{"first_name":"Yannis","last_name":"Kalaidzidis","full_name":"Kalaidzidis, Yannis"},{"last_name":"Bittig","first_name":"Thomas","full_name":"Bittig, Thomas"},{"full_name":"Julicher, Frank","last_name":"Julicher","first_name":"Frank"},{"last_name":"Gonzalez Gaitan","first_name":"Marcos","full_name":"Gonzalez-Gaitan, Marcos"}],"day":"26","type":"journal_article","issue":"5811","year":"2007"},{"extern":1,"publication_status":"published","date_created":"2018-12-11T12:07:45Z","year":"2007","type":"conference","conference":{"name":"Ab Initio: Orígenes Del Universo, La Vida, Y La Inteligencia"},"day":"01","author":[{"id":"2A181218-F248-11E8-B48F-1D18A9856A87","last_name":"Vladar","orcid":"0000-0002-5985-7653","first_name":"Harold","full_name":"Harold Vladar"}],"editor":[{"last_name":"Falcón","first_name":"N.","full_name":"Falcón,N."},{"last_name":"Loyo De Sardi","first_name":"Y.","full_name":"Loyo de Sardi,Y."}],"doi":"3808","citation":{"apa":"de Vladar, H. (2007). Alternativas prebióticas para la síntesis de amino- ácidos y otras moléculas relacionadas. In N. Falcón &#38; Y. Loyo De Sardi (Eds.) (pp. 91–109). Presented at the Ab Initio: Orígenes Del Universo, La Vida, Y La Inteligencia, Consejo de Desarrollo Cientifico y Tecnologico. <a href=\"https://doi.org/3808\">https://doi.org/3808</a>","mla":"de Vladar, Harold. <i>Alternativas Prebióticas Para La Síntesis de Amino- Ácidos y Otras Moléculas Relacionadas</i>. Edited by N. Falcón and Y. Loyo De Sardi, Consejo de Desarrollo Cientifico y Tecnologico, 2007, pp. 91–109, doi:<a href=\"https://doi.org/3808\">3808</a>.","chicago":"Vladar, Harold de. “Alternativas Prebióticas Para La Síntesis de Amino- Ácidos y Otras Moléculas Relacionadas.” edited by N. Falcón and Y. Loyo De Sardi, 91–109. Consejo de Desarrollo Cientifico y Tecnologico, 2007. <a href=\"https://doi.org/3808\">https://doi.org/3808</a>.","short":"H. de Vladar, in:, N. Falcón, Y. Loyo De Sardi (Eds.), Consejo de Desarrollo Cientifico y Tecnologico, 2007, pp. 91–109.","ama":"de Vladar H. Alternativas prebióticas para la síntesis de amino- ácidos y otras moléculas relacionadas. In: Falcón N, Loyo De Sardi Y, eds. Consejo de Desarrollo Cientifico y Tecnologico; 2007:91-109. doi:<a href=\"https://doi.org/3808\">3808</a>","ista":"de Vladar H. 2007. Alternativas prebióticas para la síntesis de amino- ácidos y otras moléculas relacionadas. Ab Initio: Orígenes Del Universo, La Vida, Y La Inteligencia, 91–109.","ieee":"H. de Vladar, “Alternativas prebióticas para la síntesis de amino- ácidos y otras moléculas relacionadas,” presented at the Ab Initio: Orígenes Del Universo, La Vida, Y La Inteligencia, 2007, pp. 91–109."},"quality_controlled":0,"title":"Alternativas prebióticas para la síntesis de amino- ácidos y otras moléculas relacionadas","publisher":"Consejo de Desarrollo Cientifico y Tecnologico","page":"91 - 109","publist_id":"1880","date_published":"2007-01-01T00:00:00Z","_id":"4233","date_updated":"2021-01-12T07:55:29Z","month":"01","status":"public"},{"date_updated":"2021-01-12T07:55:30Z","month":"01","status":"public","publist_id":"1881","publication":"Physica A","external_id":{"arxiv":["abs/q-bio/0602018"]},"date_published":"2007-01-01T00:00:00Z","_id":"4234","title":"Determinism, noise, and spurious estimations in a generalised model of population growth","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/q-bio/0602018"}],"publisher":"Elsevier","page":"477 - 485","doi":"10.1016/j.physa.2006.06.025","citation":{"mla":"de Vladar, Harold, and I. Pen. “Determinism, Noise, and Spurious Estimations in a Generalised Model of Population Growth.” <i>Physica A</i>, vol. 373, Elsevier, 2007, pp. 477–85, doi:<a href=\"https://doi.org/10.1016/j.physa.2006.06.025\">10.1016/j.physa.2006.06.025</a>.","apa":"de Vladar, H., &#38; Pen, I. (2007). Determinism, noise, and spurious estimations in a generalised model of population growth. <i>Physica A</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.physa.2006.06.025\">https://doi.org/10.1016/j.physa.2006.06.025</a>","ama":"de Vladar H, Pen I. Determinism, noise, and spurious estimations in a generalised model of population growth. <i>Physica A</i>. 2007;373:477-485. doi:<a href=\"https://doi.org/10.1016/j.physa.2006.06.025\">10.1016/j.physa.2006.06.025</a>","short":"H. de Vladar, I. Pen, Physica A 373 (2007) 477–485.","chicago":"Vladar, Harold de, and I. Pen. “Determinism, Noise, and Spurious Estimations in a Generalised Model of Population Growth.” <i>Physica A</i>. Elsevier, 2007. <a href=\"https://doi.org/10.1016/j.physa.2006.06.025\">https://doi.org/10.1016/j.physa.2006.06.025</a>.","ista":"de Vladar H, Pen I. 2007. Determinism, noise, and spurious estimations in a generalised model of population growth. Physica A. 373, 477–485.","ieee":"H. de Vladar and I. Pen, “Determinism, noise, and spurious estimations in a generalised model of population growth,” <i>Physica A</i>, vol. 373. Elsevier, pp. 477–485, 2007."},"abstract":[{"text":"We study a generalised model of population growth in which the state variable is population growth rate instead of population size. Stochastic parametric perturbations, modelling phenotypic variability, lead to a Langevin system with two sources of multiplicative noise. The stationary probability distributions have two characteristic power-law scales. Numerical simulations show that noise suppresses the explosion of the growth rate which occurs in the deterministic counterpart. Instead, in different parameter regimes populations will grow with &quot;anomalous&quot; stochastic rates and (i) stabilise at &quot;random carrying capacities&quot;, or (ii) go extinct in random times. Using logistic fits to reconstruct the simulated data, we find that even highly significant estimations do not recover or reflect information about the deterministic part of the process. Therefore, the logistic interpretation is not biologically meaningful. These results have implications for distinct model-aided calculations in biological situations because these kinds of estimations could lead to spurious conclusions. (c) 2006 Elsevier B.V. All rights reserved.","lang":"eng"}],"language":[{"iso":"eng"}],"intvolume":"       373","year":"2007","article_processing_charge":"No","day":"01","type":"journal_article","author":[{"first_name":"Harold","last_name":"de Vladar","orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87","full_name":"de Vladar, Harold"},{"first_name":"I.","last_name":"Pen","full_name":"Pen, I."}],"publication_status":"published","date_created":"2018-12-11T12:07:45Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":373,"oa_version":"Preprint","arxiv":1,"extern":"1"},{"_id":"4246","publist_id":"1856","publication":"Trends in Ecology and Evolution","date_published":"2007-11-01T00:00:00Z","status":"public","date_updated":"2021-01-12T07:55:35Z","month":"11","intvolume":"        22","doi":"10.1016/j.tree.2007.07.007","citation":{"ista":"Free A, Barton NH. 2007. Do evolution and ecology need the Gaia hypothesis? Trends in Ecology and Evolution. 22(11), 611–619.","ieee":"A. Free and N. H. Barton, “Do evolution and ecology need the Gaia hypothesis?,” <i>Trends in Ecology and Evolution</i>, vol. 22, no. 11. Cell Press, pp. 611–619, 2007.","apa":"Free, A., &#38; Barton, N. H. (2007). Do evolution and ecology need the Gaia hypothesis? <i>Trends in Ecology and Evolution</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tree.2007.07.007\">https://doi.org/10.1016/j.tree.2007.07.007</a>","mla":"Free, Andrew, and Nicholas H. Barton. “Do Evolution and Ecology Need the Gaia Hypothesis?” <i>Trends in Ecology and Evolution</i>, vol. 22, no. 11, Cell Press, 2007, pp. 611–19, doi:<a href=\"https://doi.org/10.1016/j.tree.2007.07.007\">10.1016/j.tree.2007.07.007</a>.","chicago":"Free, Andrew, and Nicholas H Barton. “Do Evolution and Ecology Need the Gaia Hypothesis?” <i>Trends in Ecology and Evolution</i>. Cell Press, 2007. <a href=\"https://doi.org/10.1016/j.tree.2007.07.007\">https://doi.org/10.1016/j.tree.2007.07.007</a>.","short":"A. Free, N.H. Barton, Trends in Ecology and Evolution 22 (2007) 611–619.","ama":"Free A, Barton NH. Do evolution and ecology need the Gaia hypothesis? <i>Trends in Ecology and Evolution</i>. 2007;22(11):611-619. doi:<a href=\"https://doi.org/10.1016/j.tree.2007.07.007\">10.1016/j.tree.2007.07.007</a>"},"abstract":[{"lang":"eng","text":"Gaia theory, which describes the life–environment system of the Earth as stable and self-regulating, has remained at the fringes of mainstream biological science owing to its historically inadequate definition and apparent incompatibility with individual-level natural selection. The key issue is whether and why the biosphere might tend towards stability and self-regulation. We review the various ways in which these issues have been addressed by evolutionary and ecological theory, and relate these to ‘Gaia theory’. We then ask how this theory extends the perspectives offered by these disciplines, and how it might be tested by novel modelling approaches and laboratory experiments using emergent technologies."}],"publisher":"Cell Press","page":"611 - 619","quality_controlled":0,"title":"Do evolution and ecology need the Gaia hypothesis?","day":"01","type":"journal_article","author":[{"first_name":"Andrew","last_name":"Free","full_name":"Free, Andrew"},{"full_name":"Nicholas Barton","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"issue":"11","year":"2007","extern":1,"publication_status":"published","date_created":"2018-12-11T12:07:49Z","volume":22},{"abstract":[{"text":"Evolution at multiple gene positions is complicated. Direct selection on one gene disturbs the evolutionary dynamics of associated genes. Recent years have seen the development of a multilocus methodology for modeling evolution at arbitrary numbers of gene positions with arbitrary dominance and epistatic relations, mode of inheritance, genetic linkage, and recombination. We show that the approach is conceptually analogous to social evolutionary methodology, which focuses on selection acting on associated individuals. In doing so, we (1) make explicit the links between the multilocus methodology and the foundations of social evolution theory, namely, Price’s theorem and Hamilton’s rule; (2) relate the multilocus approach to levels‐of‐selection and neighbor‐modulated‐fitness approaches in social evolution; (3) highlight the equivalence between genetical hitchhiking and kin selection; (4) demonstrate that the multilocus methodology allows for social evolutionary analyses involving coevolution of multiple traits and genetical associations between nonrelatives, including individuals of different species; (5) show that this methodology helps solve problems of dynamic sufficiency in social evolution theory; (6) form links between invasion criteria in multilocus systems and Hamilton’s rule of kin selection; (7) illustrate the generality and exactness of Hamilton’s rule, which has previously been described as an approximate, heuristic result.","lang":"eng"}],"citation":{"ista":"Gardner A, West S, Barton NH. 2007. The relation between multilocus population genetics and social evolution theory. American Naturalist. 169(2), 207–226.","ieee":"A. Gardner, S. West, and N. H. Barton, “The relation between multilocus population genetics and social evolution theory,” <i>American Naturalist</i>, vol. 169, no. 2. University of Chicago Press, pp. 207–226, 2007.","apa":"Gardner, A., West, S., &#38; Barton, N. H. (2007). The relation between multilocus population genetics and social evolution theory. <i>American Naturalist</i>. University of Chicago Press. <a href=\"https://doi.org/10.1086/510602\">https://doi.org/10.1086/510602</a>","mla":"Gardner, Andy, et al. “The Relation between Multilocus Population Genetics and Social Evolution Theory.” <i>American Naturalist</i>, vol. 169, no. 2, University of Chicago Press, 2007, pp. 207–26, doi:<a href=\"https://doi.org/10.1086/510602\">10.1086/510602</a>.","chicago":"Gardner, Andy, Stuart West, and Nicholas H Barton. “The Relation between Multilocus Population Genetics and Social Evolution Theory.” <i>American Naturalist</i>. University of Chicago Press, 2007. <a href=\"https://doi.org/10.1086/510602\">https://doi.org/10.1086/510602</a>.","ama":"Gardner A, West S, Barton NH. The relation between multilocus population genetics and social evolution theory. <i>American Naturalist</i>. 2007;169(2):207-226. doi:<a href=\"https://doi.org/10.1086/510602\">10.1086/510602</a>","short":"A. Gardner, S. West, N.H. Barton, American Naturalist 169 (2007) 207–226."},"doi":"10.1086/510602","intvolume":"       169","title":"The relation between multilocus population genetics and social evolution theory","quality_controlled":0,"page":"207 - 226","publisher":"University of Chicago Press","publication":"American Naturalist","publist_id":"1857","date_published":"2007-02-01T00:00:00Z","_id":"4247","month":"02","date_updated":"2021-01-12T07:55:35Z","status":"public","extern":1,"volume":169,"date_created":"2018-12-11T12:07:50Z","publication_status":"published","issue":"2","year":"2007","author":[{"last_name":"Gardner","first_name":"Andy","full_name":"Gardner, Andy"},{"full_name":"West, Stuart A","last_name":"West","first_name":"Stuart"},{"full_name":"Nicholas Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"day":"01","type":"journal_article"},{"month":"05","date_updated":"2021-01-12T07:56:16Z","status":"public","date_published":"2007-05-25T00:00:00Z","publist_id":"1232","_id":"4342","title":"Library 2.0 and User-Generated Content - What can the users do for us?","publisher":"IFLA","main_file_link":[{"url":"http://www.ifla.org/IV/ifla73/papers/113-Danowski-en.pdf"}],"language":[{"iso":"eng"}],"citation":{"ieee":"P. Danowski, “Library 2.0 and User-Generated Content - What can the users do for us?,” presented at the WLIC: World Library and Information Congress, Durban, South Africa, 2007.","ista":"Danowski P. 2007. Library 2.0 and User-Generated Content - What can the users do for us? WLIC: World Library and Information Congress.","ama":"Danowski P. Library 2.0 and User-Generated Content - What can the users do for us? In: IFLA; 2007. doi:<a href=\"https://doi.org/601\">601</a>","short":"P. Danowski, in:, IFLA, 2007.","chicago":"Danowski, Patrick. “Library 2.0 and User-Generated Content - What Can the Users Do for Us?” IFLA, 2007. <a href=\"https://doi.org/601\">https://doi.org/601</a>.","mla":"Danowski, Patrick. <i>Library 2.0 and User-Generated Content - What Can the Users Do for Us?</i> IFLA, 2007, doi:<a href=\"https://doi.org/601\">601</a>.","apa":"Danowski, P. (2007). Library 2.0 and User-Generated Content - What can the users do for us? Presented at the WLIC: World Library and Information Congress, Durban, South Africa: IFLA. <a href=\"https://doi.org/601\">https://doi.org/601</a>"},"abstract":[{"lang":"eng","text":"Library 2.0 and user-generated content are two terms, which are closely connected. In the\r\n\r\npresentation, I will briefly define both terms. Two example projects where user- generated content and libraries interact will be presented. The cooperation of Wikipedia and the Personennamendatei, the German cooperative name authority files is the first. The second will be Wikisource where users provide transcribed source material. Another important area of user-generated content is social tagging where users index different resources. And if the users will do so much in the future, is there still a place for librarians? But in the future user\r\n\r\nand librarians become partners and the library will provide the platform: the library 2.0."}],"doi":"601","year":"2007","author":[{"last_name":"Danowski","orcid":"0000-0002-6026-4409","first_name":"Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","full_name":"Danowski, Patrick"}],"conference":{"start_date":"2007-08-19","location":"Durban, South Africa","name":"WLIC: World Library and Information Congress","end_date":"2007-08-23"},"type":"conference","day":"25","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:08:22Z","publication_status":"published","oa_version":"None","extern":"1"},{"page":"149 - 155","publisher":"De Gruyter","title":"Wikipedia und Normdateien: Wege der Vernetzung am Beispiel der Kooperation mit der Personennamendatei","quality_controlled":0,"intvolume":"        31","citation":{"ista":"Danowski P, Pfeifer B. 2007. Wikipedia und Normdateien: Wege der Vernetzung am Beispiel der Kooperation mit der Personennamendatei. Bibliothek - Forschung Und Praxis. 31(2), 149–155.","ieee":"P. Danowski and B. Pfeifer, “Wikipedia und Normdateien: Wege der Vernetzung am Beispiel der Kooperation mit der Personennamendatei,” <i>Bibliothek - Forschung Und Praxis</i>, vol. 31, no. 2. De Gruyter, pp. 149–155, 2007.","apa":"Danowski, P., &#38; Pfeifer, B. (2007). Wikipedia und Normdateien: Wege der Vernetzung am Beispiel der Kooperation mit der Personennamendatei. <i>Bibliothek - Forschung Und Praxis</i>. De Gruyter. <a href=\"https://doi.org/485\">https://doi.org/485</a>","mla":"Danowski, Patrick, and Barbara Pfeifer. “Wikipedia Und Normdateien: Wege Der Vernetzung Am Beispiel Der Kooperation Mit Der Personennamendatei.” <i>Bibliothek - Forschung Und Praxis</i>, vol. 31, no. 2, De Gruyter, 2007, pp. 149–55, doi:<a href=\"https://doi.org/485\">485</a>.","chicago":"Danowski, Patrick, and Barbara Pfeifer. “Wikipedia Und Normdateien: Wege Der Vernetzung Am Beispiel Der Kooperation Mit Der Personennamendatei.” <i>Bibliothek - Forschung Und Praxis</i>. De Gruyter, 2007. <a href=\"https://doi.org/485\">https://doi.org/485</a>.","short":"P. Danowski, B. Pfeifer, Bibliothek - Forschung Und Praxis 31 (2007) 149–155.","ama":"Danowski P, Pfeifer B. Wikipedia und Normdateien: Wege der Vernetzung am Beispiel der Kooperation mit der Personennamendatei. <i>Bibliothek - Forschung Und Praxis</i>. 2007;31(2):149-155. doi:<a href=\"https://doi.org/485\">485</a>"},"doi":"485","status":"public","month":"01","date_updated":"2021-01-12T07:56:17Z","_id":"4343","publication":"Bibliothek - Forschung Und Praxis","date_published":"2007-01-01T00:00:00Z","publist_id":"1231","volume":31,"publication_status":"published","date_created":"2018-12-11T12:08:22Z","extern":1,"author":[{"full_name":"Patrick Danowski","last_name":"Danowski","first_name":"Patrick","orcid":"0000-0002-6026-4409","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pfeifer,Barbara","first_name":"Barbara","last_name":"Pfeifer"}],"type":"journal_article","day":"01","issue":"2","year":"2007"},{"author":[{"full_name":"Patrick Danowski","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","last_name":"Danowski","first_name":"Patrick","orcid":"0000-0002-6026-4409"},{"full_name":"Heller,Lambert","first_name":"Lambert","last_name":"Heller"}],"day":"01","type":"journal_article","year":"2007","issue":"2007","extern":1,"volume":31,"publication_status":"published","date_created":"2018-12-11T12:08:22Z","_id":"4344","date_published":"2007-01-01T00:00:00Z","publication":"Bibliothek - Forschung Und Praxis","publist_id":"1230","status":"public","month":"01","date_updated":"2021-01-12T07:56:17Z","intvolume":"        31","citation":{"apa":"Danowski, P., &#38; Heller, L. (2007). Bibliothek 2.0 ? Wird alles anders? <i>Bibliothek - Forschung Und Praxis</i>. De Gruyter. <a href=\"https://doi.org/45\">https://doi.org/45</a>","mla":"Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 ? Wird Alles Anders?” <i>Bibliothek - Forschung Und Praxis</i>, vol. 31, no. 2007, De Gruyter, 2007, pp. 130–36, doi:<a href=\"https://doi.org/45\">45</a>.","chicago":"Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 ? Wird Alles Anders?” <i>Bibliothek - Forschung Und Praxis</i>. De Gruyter, 2007. <a href=\"https://doi.org/45\">https://doi.org/45</a>.","short":"P. Danowski, L. Heller, Bibliothek - Forschung Und Praxis 31 (2007) 130–136.","ama":"Danowski P, Heller L. Bibliothek 2.0 ? Wird alles anders? <i>Bibliothek - Forschung Und Praxis</i>. 2007;31(2007):130-136. doi:<a href=\"https://doi.org/45\">45</a>","ista":"Danowski P, Heller L. 2007. Bibliothek 2.0 ? Wird alles anders? Bibliothek - Forschung Und Praxis. 31(2007), 130–136.","ieee":"P. Danowski and L. Heller, “Bibliothek 2.0 ? Wird alles anders?,” <i>Bibliothek - Forschung Und Praxis</i>, vol. 31, no. 2007. De Gruyter, pp. 130–136, 2007."},"doi":"45","page":"130 - 136","main_file_link":[{"open_access":"0","url":"http://www.bibliothek-saur.de/2007_2/130-136.pdf"}],"publisher":"De Gruyter","title":"Bibliothek 2.0 ? Wird alles anders?","quality_controlled":0},{"abstract":[{"text":"BACKGROUND: The invention of the Genome Sequence 20 DNA Sequencing System (454 parallel sequencing platform) has enabled the rapid and high-volume production of sequence data. Until now, however, individual emulsion PCR (emPCR) reactions and subsequent sequencing runs have been unable to combine template DNA from multiple individuals, as homologous sequences cannot be subsequently assigned to their original sources. METHODOLOGY: We use conventional PCR with 5'-nucleotide tagged primers to generate homologous DNA amplification products from multiple specimens, followed by sequencing through the high-throughput Genome Sequence 20 DNA Sequencing System (GS20, Roche/454 Life Sciences). Each DNA sequence is subsequently traced back to its individual source through 5'tag-analysis. CONCLUSIONS: We demonstrate that this new approach enables the assignment of virtually all the generated DNA sequences to the correct source once sequencing anomalies are accounted for (miss-assignment rate&amp;lt;0.4%). Therefore, the method enables accurate sequencing and assignment of homologous DNA sequences from multiple sources in single high-throughput GS20 run. We observe a bias in the distribution of the differently tagged primers that is dependent on the 5' nucleotide of the tag. In particular, primers 5' labelled with a cytosine are heavily overrepresented among the final sequences, while those 5' labelled with a thymine are strongly underrepresented. A weaker bias also exists with regards to the distribution of the sequences as sorted by the second nucleotide of the dinucleotide tags. As the results are based on a single GS20 run, the general applicability of the approach requires confirmation. However, our experiments demonstrate that 5'primer tagging is a useful method in which the sequencing power of the GS20 can be applied to PCR-based assays of multiple homologous PCR products. The new approach will be of value to a broad range of research areas, such as those of comparative genomics, complete mitochondrial analyses, population genetics, and phylogenetics.","lang":"eng"}],"citation":{"chicago":"Binladen, Jonas, M Thomas Gilbert, Jonathan P Bollback, Frank Panitz, Christian Bendixen, Rasmus Nielsen, and Eske Willerslev. “The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple Homolog Amplification Products by 454 Parallel Sequencing.” <i>PLoS One</i>. Public Library of Science, 2007. <a href=\"https://doi.org/10.1371/journal.pone.0000197\">https://doi.org/10.1371/journal.pone.0000197</a>.","ama":"Binladen J, Gilbert MT, Bollback JP, et al. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. <i>PLoS One</i>. 2007;2(2). doi:<a href=\"https://doi.org/10.1371/journal.pone.0000197\">10.1371/journal.pone.0000197</a>","short":"J. Binladen, M.T. Gilbert, J.P. Bollback, F. Panitz, C. Bendixen, R. Nielsen, E. Willerslev, PLoS One 2 (2007).","apa":"Binladen, J., Gilbert, M. T., Bollback, J. P., Panitz, F., Bendixen, C., Nielsen, R., &#38; Willerslev, E. (2007). The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0000197\">https://doi.org/10.1371/journal.pone.0000197</a>","mla":"Binladen, Jonas, et al. “The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple Homolog Amplification Products by 454 Parallel Sequencing.” <i>PLoS One</i>, vol. 2, no. 2, Public Library of Science, 2007, doi:<a href=\"https://doi.org/10.1371/journal.pone.0000197\">10.1371/journal.pone.0000197</a>.","ieee":"J. Binladen <i>et al.</i>, “The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing,” <i>PLoS One</i>, vol. 2, no. 2. Public Library of Science, 2007.","ista":"Binladen J, Gilbert MT, Bollback JP, Panitz F, Bendixen C, Nielsen R, Willerslev E. 2007. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One. 2(2)."},"doi":"10.1371/journal.pone.0000197","acknowledgement":"JB and EW were supported by the Wellcome Trust, UK, the Carlsberg Foundation, DK, and the National Science Foundation, DK. MTPG acknowledges the Marie Curie Actions FP6-MEIF-CT-2005-025002 ‘FORMAPLEX’ grant for funding his research. JPB and RN were funded by the Danish FSS and the National Science Foundation, DK. None of the sponsors or funders have had any influence on the data or manuscript presented here.","intvolume":"         2","title":"The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing","quality_controlled":0,"publisher":"Public Library of Science","publication":"PLoS One","date_published":"2007-02-14T00:00:00Z","publist_id":"1105","_id":"4353","month":"02","date_updated":"2021-01-12T07:56:21Z","status":"public","extern":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":2,"publication_status":"published","date_created":"2018-12-11T12:08:25Z","license":"https://creativecommons.org/licenses/by/4.0/","issue":"2","year":"2007","author":[{"full_name":"Binladen, Jonas","first_name":"Jonas","last_name":"Binladen"},{"first_name":"M Thomas","last_name":"Gilbert","full_name":"Gilbert, M Thomas"},{"full_name":"Jonathan Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612"},{"full_name":"Panitz, Frank","first_name":"Frank","last_name":"Panitz"},{"first_name":"Christian","last_name":"Bendixen","full_name":"Bendixen, Christian"},{"last_name":"Nielsen","first_name":"Rasmus","full_name":"Nielsen, Rasmus"},{"last_name":"Willerslev","first_name":"Eske","full_name":"Willerslev, Eske"}],"type":"journal_article","day":"14"},{"volume":17,"date_created":"2018-12-11T12:08:25Z","publication_status":"published","extern":1,"author":[{"first_name":"Eva","last_name":"Freyhult","full_name":"Freyhult, Eva K"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback","full_name":"Jonathan Bollback"},{"full_name":"Gardner, Paul P","first_name":"Paul","last_name":"Gardner"}],"day":"01","type":"journal_article","year":"2007","issue":"1","page":"117 - 25","publisher":"Cold Spring Harbor Laboratory Press","main_file_link":[{"open_access":"0","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716261"}],"title":"Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA","quality_controlled":0,"intvolume":"        17","citation":{"ieee":"E. Freyhult, J. P. Bollback, and P. Gardner, “Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA,” <i>Genome Research</i>, vol. 17, no. 1. Cold Spring Harbor Laboratory Press, pp. 117–25, 2007.","ista":"Freyhult E, Bollback JP, Gardner P. 2007. Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Research. 17(1), 117–25.","chicago":"Freyhult, Eva, Jonathan P Bollback, and Paul Gardner. “Exploring Genomic Dark Matter: A Critical Assessment of the Performance of Homology Search Methods on Noncoding RNA.” <i>Genome Research</i>. Cold Spring Harbor Laboratory Press, 2007. <a href=\"https://doi.org/10.1101/gr.5890907\">https://doi.org/10.1101/gr.5890907</a>.","ama":"Freyhult E, Bollback JP, Gardner P. Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. <i>Genome Research</i>. 2007;17(1):117-125. doi:<a href=\"https://doi.org/10.1101/gr.5890907\">10.1101/gr.5890907</a>","short":"E. Freyhult, J.P. Bollback, P. Gardner, Genome Research 17 (2007) 117–25.","apa":"Freyhult, E., Bollback, J. P., &#38; Gardner, P. (2007). Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. <i>Genome Research</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gr.5890907\">https://doi.org/10.1101/gr.5890907</a>","mla":"Freyhult, Eva, et al. “Exploring Genomic Dark Matter: A Critical Assessment of the Performance of Homology Search Methods on Noncoding RNA.” <i>Genome Research</i>, vol. 17, no. 1, Cold Spring Harbor Laboratory Press, 2007, pp. 117–25, doi:<a href=\"https://doi.org/10.1101/gr.5890907\">10.1101/gr.5890907</a>."},"abstract":[{"lang":"eng","text":"Homology search is one of the most ubiquitous bioinformatic tasks, yet it is unknown how effective the currently available tools are for identifying noncoding RNAs (ncRNAs). In this work, we use reliable ncRNA data sets to assess the effectiveness of methods such as BLAST, FASTA, HMMer, and Infernal. Surprisingly, the most popular homology search methods are often the least accurate. As a result, many studies have used inappropriate tools for their analyses. On the basis of our results, we suggest homology search strategies using the currently available tools and some directions for future development."}],"doi":"10.1101/gr.5890907","status":"public","month":"01","date_updated":"2021-01-12T07:56:21Z","_id":"4354","date_published":"2007-01-01T00:00:00Z","publist_id":"1106","publication":"Genome Research"},{"author":[{"full_name":"Jonathan Bollback","last_name":"Bollback","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Huelsenbeck, John P","last_name":"Huelsenbeck","first_name":"John"}],"type":"journal_article","day":"22","issue":"6","year":"2007","volume":24,"date_created":"2018-12-11T12:08:26Z","publication_status":"published","extern":1,"status":"public","month":"03","date_updated":"2021-01-12T07:56:22Z","_id":"4355","publication":"Molecular Biology and Evolution","date_published":"2007-03-22T00:00:00Z","publist_id":"1104","page":"1397 - 1406","publisher":"Oxford University Press","title":"Clonal interference is alleviated by high mutation rates in large populations","quality_controlled":0,"intvolume":"        24","abstract":[{"lang":"eng","text":"When a beneficial mutation is fixed in a population that lacks recombination, the genetic background linked to that mutation is fixed. As a result, beneficial mutations on different backgrounds experience competition, or &quot;clonal interference,&quot; that can cause asexual populations to evolve more slowly than their sexual counterparts. Factors such as a large population size (N) and high mutation rates (mu) increase the number of competing beneficial mutations, and hence are expected to increase the intensity of clonal interference. However, recent theory suggests that, with very large values of Nmu, the severity of clonal interference may instead decline. The reason is that, with large Nmu, genomes including both beneficial mutations are rapidly created by recurrent mutation, obviating the need for recombination. Here, we analyze data from experimentally evolved asexual populations of a bacteriophage and find that, in these nonrecombining populations with very large Nmu, recurrent mutation does appear to ameliorate this cost of asexuality."}],"citation":{"apa":"Bollback, J. P., &#38; Huelsenbeck, J. (2007). Clonal interference is alleviated by high mutation rates in large populations. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msm056\">https://doi.org/10.1093/molbev/msm056</a>","mla":"Bollback, Jonathan P., and John Huelsenbeck. “Clonal Interference Is Alleviated by High Mutation Rates in Large Populations.” <i>Molecular Biology and Evolution</i>, vol. 24, no. 6, Oxford University Press, 2007, pp. 1397–406, doi:<a href=\"https://doi.org/10.1093/molbev/msm056\">10.1093/molbev/msm056</a>.","chicago":"Bollback, Jonathan P, and John Huelsenbeck. “Clonal Interference Is Alleviated by High Mutation Rates in Large Populations.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2007. <a href=\"https://doi.org/10.1093/molbev/msm056\">https://doi.org/10.1093/molbev/msm056</a>.","ama":"Bollback JP, Huelsenbeck J. Clonal interference is alleviated by high mutation rates in large populations. <i>Molecular Biology and Evolution</i>. 2007;24(6):1397-1406. doi:<a href=\"https://doi.org/10.1093/molbev/msm056\">10.1093/molbev/msm056</a>","short":"J.P. Bollback, J. Huelsenbeck, Molecular Biology and Evolution 24 (2007) 1397–1406.","ista":"Bollback JP, Huelsenbeck J. 2007. Clonal interference is alleviated by high mutation rates in large populations. Molecular Biology and Evolution. 24(6), 1397–1406.","ieee":"J. P. Bollback and J. Huelsenbeck, “Clonal interference is alleviated by high mutation rates in large populations,” <i>Molecular Biology and Evolution</i>, vol. 24, no. 6. Oxford University Press, pp. 1397–1406, 2007."},"doi":"10.1093/molbev/msm056","acknowledgement":"R01 GM069801-08/GM/NIGMS NIH HHS/United States"},{"date_updated":"2021-01-12T07:56:22Z","month":"08","status":"public","publication":"Genome Research","date_published":"2007-08-03T00:00:00Z","publist_id":"1103","_id":"4356","quality_controlled":0,"title":"Genes under positive selection in Escherichia coli","publisher":"Cold Spring Harbor Laboratory Press","page":"1336 - 1343","doi":"10.1101/gr.6254707","citation":{"mla":"Petersen, Lise, et al. “Genes under Positive Selection in Escherichia Coli.” <i>Genome Research</i>, vol. 17, no. 9, Cold Spring Harbor Laboratory Press, 2007, pp. 1336–43, doi:<a href=\"https://doi.org/10.1101/gr.6254707\">10.1101/gr.6254707</a>.","apa":"Petersen, L., Bollback, J. P., Dimmic, M., Hubisz, M., &#38; Nielsen, R. (2007). Genes under positive selection in Escherichia coli. <i>Genome Research</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gr.6254707\">https://doi.org/10.1101/gr.6254707</a>","short":"L. Petersen, J.P. Bollback, M. Dimmic, M. Hubisz, R. Nielsen, Genome Research 17 (2007) 1336–1343.","ama":"Petersen L, Bollback JP, Dimmic M, Hubisz M, Nielsen R. Genes under positive selection in Escherichia coli. <i>Genome Research</i>. 2007;17(9):1336-1343. doi:<a href=\"https://doi.org/10.1101/gr.6254707\">10.1101/gr.6254707</a>","chicago":"Petersen, Lise, Jonathan P Bollback, Matt Dimmic, Melissa Hubisz, and Rasmus Nielsen. “Genes under Positive Selection in Escherichia Coli.” <i>Genome Research</i>. Cold Spring Harbor Laboratory Press, 2007. <a href=\"https://doi.org/10.1101/gr.6254707\">https://doi.org/10.1101/gr.6254707</a>.","ista":"Petersen L, Bollback JP, Dimmic M, Hubisz M, Nielsen R. 2007. Genes under positive selection in Escherichia coli. Genome Research. 17(9), 1336–1343.","ieee":"L. Petersen, J. P. Bollback, M. Dimmic, M. Hubisz, and R. Nielsen, “Genes under positive selection in Escherichia coli,” <i>Genome Research</i>, vol. 17, no. 9. Cold Spring Harbor Laboratory Press, pp. 1336–1343, 2007."},"abstract":[{"lang":"eng","text":"We used a comparative genomics approach to identify genes that are under positive selection in six strains of Escherichia coli and Shigella flexneri, including five strains that are human pathogens. We find that positive selection targets a wide range of different functions in the E. coli genome, including cell surface proteins such as beta barrel porins, presumably because of the involvement of these genes in evolutionary arms races with other bacteria, phages, and/or the host immune system. Structural mapping of positively selected sites on trans-membrane beta barrel porins reveals that the residues under positive selection occur almost exclusively in the extracellular region of the proteins that are enriched with sites known to be targets of phages, colicins, or the host immune system. More surprisingly, we also find a number of other categories of genes that show very strong evidence for positive selection, such as the enigmatic rhs elements and transposases. Based on structural evidence, we hypothesize that the selection acting on transposases is related to the genomic conflict between transposable elements and the host genome."}],"intvolume":"        17","issue":"9","year":"2007","day":"03","type":"journal_article","author":[{"last_name":"Petersen","first_name":"Lise","full_name":"Petersen, Lise"},{"orcid":"0000-0002-4624-4612","last_name":"Bollback","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Jonathan Bollback"},{"full_name":"Dimmic, Matt","first_name":"Matt","last_name":"Dimmic"},{"full_name":"Hubisz, Melissa","last_name":"Hubisz","first_name":"Melissa"},{"full_name":"Nielsen, Rasmus","last_name":"Nielsen","first_name":"Rasmus"}],"publication_status":"published","date_created":"2018-12-11T12:08:26Z","volume":17,"extern":1}]