[{"publisher":"Wiley-Blackwell","publication":"Proteins: Structure, Function and Bioinformatics","extern":1,"publist_id":"2146","page":"852 - 864","intvolume":"        62","status":"public","date_created":"2018-12-11T12:06:14Z","quality_controlled":0,"date_updated":"2021-01-12T07:53:36Z","title":"Evaluating the quality of NMR structures by local density of protons","_id":"3978","type":"journal_article","day":"01","date_published":"2006-03-01T00:00:00Z","abstract":[{"lang":"eng","text":"Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures."}],"year":"2006","publication_status":"published","author":[{"full_name":"Ban, Yih-En Andrew","last_name":"Ban","first_name":"Yih"},{"first_name":"Johannes","last_name":"Rudolph","full_name":"Rudolph, Johannes"},{"full_name":"Zhou, Pei","first_name":"Pei","last_name":"Zhou"},{"first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Herbert Edelsbrunner","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"volume":62,"month":"03","issue":"4","citation":{"mla":"Ban, Yih, et al. “Evaluating the Quality of NMR Structures by Local Density of Protons.” <i>Proteins: Structure, Function and Bioinformatics</i>, vol. 62, no. 4, Wiley-Blackwell, 2006, pp. 852–64, doi:<a href=\"https://doi.org/10.1002/prot.20811\">10.1002/prot.20811</a>.","ieee":"Y. Ban, J. Rudolph, P. Zhou, and H. Edelsbrunner, “Evaluating the quality of NMR structures by local density of protons,” <i>Proteins: Structure, Function and Bioinformatics</i>, vol. 62, no. 4. Wiley-Blackwell, pp. 852–864, 2006.","apa":"Ban, Y., Rudolph, J., Zhou, P., &#38; Edelsbrunner, H. (2006). Evaluating the quality of NMR structures by local density of protons. <i>Proteins: Structure, Function and Bioinformatics</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/prot.20811\">https://doi.org/10.1002/prot.20811</a>","ama":"Ban Y, Rudolph J, Zhou P, Edelsbrunner H. Evaluating the quality of NMR structures by local density of protons. <i>Proteins: Structure, Function and Bioinformatics</i>. 2006;62(4):852-864. doi:<a href=\"https://doi.org/10.1002/prot.20811\">10.1002/prot.20811</a>","ista":"Ban Y, Rudolph J, Zhou P, Edelsbrunner H. 2006. Evaluating the quality of NMR structures by local density of protons. Proteins: Structure, Function and Bioinformatics. 62(4), 852–864.","short":"Y. Ban, J. Rudolph, P. Zhou, H. Edelsbrunner, Proteins: Structure, Function and Bioinformatics 62 (2006) 852–864.","chicago":"Ban, Yih, Johannes Rudolph, Pei Zhou, and Herbert Edelsbrunner. “Evaluating the Quality of NMR Structures by Local Density of Protons.” <i>Proteins: Structure, Function and Bioinformatics</i>. Wiley-Blackwell, 2006. <a href=\"https://doi.org/10.1002/prot.20811\">https://doi.org/10.1002/prot.20811</a>."},"doi":"10.1002/prot.20811"},{"issue":"3","citation":{"ista":"Ban Y, Edelsbrunner H, Rudolph J. 2006. Interface surfaces for protein-protein complexes. Journal of the ACM. 53(3), 361–378.","chicago":"Ban, Yih, Herbert Edelsbrunner, and Johannes Rudolph. “Interface Surfaces for Protein-Protein Complexes.” <i>Journal of the ACM</i>. ACM, 2006. <a href=\"https://doi.org/10.1145/1147954.1147957\">https://doi.org/10.1145/1147954.1147957</a>.","short":"Y. Ban, H. Edelsbrunner, J. Rudolph, Journal of the ACM 53 (2006) 361–378.","ama":"Ban Y, Edelsbrunner H, Rudolph J. Interface surfaces for protein-protein complexes. <i>Journal of the ACM</i>. 2006;53(3):361-378. doi:<a href=\"https://doi.org/10.1145/1147954.1147957\">10.1145/1147954.1147957</a>","mla":"Ban, Yih, et al. “Interface Surfaces for Protein-Protein Complexes.” <i>Journal of the ACM</i>, vol. 53, no. 3, ACM, 2006, pp. 361–78, doi:<a href=\"https://doi.org/10.1145/1147954.1147957\">10.1145/1147954.1147957</a>.","apa":"Ban, Y., Edelsbrunner, H., &#38; Rudolph, J. (2006). Interface surfaces for protein-protein complexes. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/1147954.1147957\">https://doi.org/10.1145/1147954.1147957</a>","ieee":"Y. Ban, H. Edelsbrunner, and J. Rudolph, “Interface surfaces for protein-protein complexes,” <i>Journal of the ACM</i>, vol. 53, no. 3. ACM, pp. 361–378, 2006."},"month":"05","doi":"10.1145/1147954.1147957","volume":53,"author":[{"first_name":"Yih","last_name":"Ban","full_name":"Ban, Yih-En Andrew"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Herbert Edelsbrunner","last_name":"Edelsbrunner","first_name":"Herbert"},{"last_name":"Rudolph","first_name":"Johannes","full_name":"Rudolph, Johannes"}],"abstract":[{"text":"Protein-protein interactions, which form the basis for most cellular processes, result in the formation of protein interfaces. Believing that the local shape of proteins is crucial, we take a geometric approach and present a definition of an interface surface formed by two or more proteins as a subset of their Voronoi diagram. The definition deals with the difficult and important problem of specifying interface boundaries by invoking methods used in the alpha shape representation of molecules, the discrete flow on Delaunay simplices to define pockets and reconstruct surfaces, and the assessment of the importance of topological features. We present an algorithm to construct the surface and define a hierarchy that distinguishes core and peripheral regions. This hierarchy is shown to have correlation with hot-spots in protein-protein interactions. Finally, we study the geometric and topological properties of interface surfaces and show their high degree of contortion.","lang":"eng"}],"date_published":"2006-05-01T00:00:00Z","publication_status":"published","year":"2006","_id":"3979","date_updated":"2021-01-12T07:53:37Z","title":"Interface surfaces for protein-protein complexes","day":"01","type":"journal_article","status":"public","intvolume":"        53","date_created":"2018-12-11T12:06:14Z","quality_controlled":0,"extern":1,"page":"361 - 378","publist_id":"2147","publication":"Journal of the ACM","publisher":"ACM"},{"publication_status":"published","year":"2006","date_published":"2006-12-01T00:00:00Z","abstract":[{"text":"Given a smoothly embedded 2-manifold in R-3, we define the elevation of a point as the height difference to a canonically defined second point on the same manifold. Our definition is invariant under rigid motions and can be used to define features such as lines of discontinuous or continuous but non-smooth elevation. We give an algorithm for finding points of locally maximum elevation, which we suggest mark cavities and protrusions and are useful in matching shapes as for example in protein docking.","lang":"eng"}],"doi":"10.1007/s00454-006-1265-8","citation":{"ieee":"P. Agarwal, H. Edelsbrunner, J. Harer, and Y. Wang, “Extreme elevation on a 2-manifold,” <i>Discrete &#38; Computational Geometry</i>, vol. 36, no. 4. Springer, pp. 553–572, 2006.","apa":"Agarwal, P., Edelsbrunner, H., Harer, J., &#38; Wang, Y. (2006). Extreme elevation on a 2-manifold. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-006-1265-8\">https://doi.org/10.1007/s00454-006-1265-8</a>","mla":"Agarwal, Pankaj, et al. “Extreme Elevation on a 2-Manifold.” <i>Discrete &#38; Computational Geometry</i>, vol. 36, no. 4, Springer, 2006, pp. 553–72, doi:<a href=\"https://doi.org/10.1007/s00454-006-1265-8\">10.1007/s00454-006-1265-8</a>.","ama":"Agarwal P, Edelsbrunner H, Harer J, Wang Y. Extreme elevation on a 2-manifold. <i>Discrete &#38; Computational Geometry</i>. 2006;36(4):553-572. doi:<a href=\"https://doi.org/10.1007/s00454-006-1265-8\">10.1007/s00454-006-1265-8</a>","short":"P. Agarwal, H. Edelsbrunner, J. Harer, Y. Wang, Discrete &#38; Computational Geometry 36 (2006) 553–572.","chicago":"Agarwal, Pankaj, Herbert Edelsbrunner, John Harer, and Yusu Wang. “Extreme Elevation on a 2-Manifold.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2006. <a href=\"https://doi.org/10.1007/s00454-006-1265-8\">https://doi.org/10.1007/s00454-006-1265-8</a>.","ista":"Agarwal P, Edelsbrunner H, Harer J, Wang Y. 2006. Extreme elevation on a 2-manifold. Discrete &#38; Computational Geometry. 36(4), 553–572."},"issue":"4","month":"12","volume":36,"author":[{"first_name":"Pankaj","last_name":"Agarwal","full_name":"Agarwal, Pankaj K"},{"last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Herbert Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"full_name":"Harer, John","first_name":"John","last_name":"Harer"},{"full_name":"Wang, Yusu","last_name":"Wang","first_name":"Yusu"}],"page":"553 - 572","publist_id":"2148","extern":1,"publication":"Discrete & Computational Geometry","publisher":"Springer","day":"01","type":"journal_article","_id":"3980","date_updated":"2021-01-12T07:53:38Z","title":"Extreme elevation on a 2-manifold","quality_controlled":0,"date_created":"2018-12-11T12:06:15Z","intvolume":"        36","status":"public"},{"publisher":"Rockefeller University Press","publication":"Journal of Cell Biology","extern":"1","publist_id":"1980","page":"791 - 802","date_created":"2018-12-11T12:07:11Z","intvolume":"       175","status":"public","title":"Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane","date_updated":"2021-01-12T07:54:48Z","_id":"4140","type":"journal_article","day":"04","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Wnt11 is a key signal, determining cell polarization and migration during vertebrate gastrulation. It is known that Wnt11 functionally interacts with several signaling components, the homologues of which control planar cell polarity in Drosophila melanogaster. Although in D. melanogaster these components are thought to polarize cells by asymmetrically localizing at the plasma membrane, it is not yet clear whether their subcellular localization plays a similarly important role in vertebrates. We show that in zebrafish embryonic cells, Wnt11 locally functions at the plasma membrane by accumulating its receptor, Frizzled 7, on adjacent sites of cell contacts. Wnt11-induced Frizzled 7 accumulations recruit the intracellular Wnt signaling mediator Dishevelled, as well as Wnt11 itself, and locally increase cell contact persistence. This increase in cell contact persistence is mediated by the local interaction of Wnt11, Frizzled 7, and the atypical cadherin Flamingo at the plasma membrane, and it does not require the activity of further downstream effectors of Wnt11 signaling, such as RhoA and Rok2. We propose that Wnt11, by interacting with Frizzled 7 and Flamingo, modulates local cell contact persistence to coordinate cell movements during gastrulation."}],"date_published":"2006-12-04T00:00:00Z","year":"2006","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","publication_status":"published","language":[{"iso":"eng"}],"author":[{"last_name":"Witzel","first_name":"Sabine","full_name":"Witzel, Sabine"},{"full_name":"Zimyanin, Vitaly","last_name":"Zimyanin","first_name":"Vitaly"},{"last_name":"Carreira Barbosa","first_name":"Filipa","full_name":"Carreira Barbosa, Filipa"},{"full_name":"Tada, Masazumi","first_name":"Masazumi","last_name":"Tada"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"volume":175,"month":"12","issue":"5","citation":{"ista":"Witzel S, Zimyanin V, Carreira Barbosa F, Tada M, Heisenberg C-PJ. 2006. Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane. Journal of Cell Biology. 175(5), 791–802.","short":"S. Witzel, V. Zimyanin, F. Carreira Barbosa, M. Tada, C.-P.J. Heisenberg, Journal of Cell Biology 175 (2006) 791–802.","chicago":"Witzel, Sabine, Vitaly Zimyanin, Filipa Carreira Barbosa, Masazumi Tada, and Carl-Philipp J Heisenberg. “Wnt11 Controls Cell Contact Persistence by Local Accumulation of Frizzled 7 at the Plasma Membrane.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2006. <a href=\"https://doi.org/10.1083/jcb.200606017\">https://doi.org/10.1083/jcb.200606017</a>.","mla":"Witzel, Sabine, et al. “Wnt11 Controls Cell Contact Persistence by Local Accumulation of Frizzled 7 at the Plasma Membrane.” <i>Journal of Cell Biology</i>, vol. 175, no. 5, Rockefeller University Press, 2006, pp. 791–802, doi:<a href=\"https://doi.org/10.1083/jcb.200606017\">10.1083/jcb.200606017</a>.","apa":"Witzel, S., Zimyanin, V., Carreira Barbosa, F., Tada, M., &#38; Heisenberg, C.-P. J. (2006). Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.200606017\">https://doi.org/10.1083/jcb.200606017</a>","ieee":"S. Witzel, V. Zimyanin, F. Carreira Barbosa, M. Tada, and C.-P. J. Heisenberg, “Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane,” <i>Journal of Cell Biology</i>, vol. 175, no. 5. Rockefeller University Press, pp. 791–802, 2006.","ama":"Witzel S, Zimyanin V, Carreira Barbosa F, Tada M, Heisenberg C-PJ. Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane. <i>Journal of Cell Biology</i>. 2006;175(5):791-802. doi:<a href=\"https://doi.org/10.1083/jcb.200606017\">10.1083/jcb.200606017</a>"},"doi":"10.1083/jcb.200606017"},{"page":"727 - 732","publist_id":"1974","extern":"1","publication":"Biotechniques","publisher":"Informa Healthcare","day":"01","type":"journal_article","_id":"4145","date_updated":"2021-01-12T07:54:50Z","title":"Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid","date_created":"2018-12-11T12:07:12Z","status":"public","intvolume":"        41","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa_version":"None","year":"2006","date_published":"2006-12-01T00:00:00Z","abstract":[{"lang":"eng","text":"The detection of microRNAs (miRNAs) at single-cell resolution is important for studying the role of these posttranscriptional regulators. Here, we use a dual-fluorescent green fluorescent protein (GFP)-reporter/monomeric red fluorescent protein (mRFP)-sensor (DFRS) plasmid, injected into zebrafish blastomeres or electroporated into defined tissues of mouse embryos in utero or ex utero, to monitor the dynamics of specific miRNAs in individual live cells. This approach reveals, for example, that in the developing mouse central nervous system,, miR-124a is expressed not only in postmitotic neurons but also in neuronal progenitor cells. Collectively, our results demonstrate that acute administration of DFRS plasmids.offers an alternative to previous in situ hybridization and transgenic approaches and allows the monitoring of miRNA appearance and disappearance in defined cell lineages during vertebrate development."}],"article_processing_charge":"No","doi":"10.2144/000112296","issue":"6","citation":{"chicago":"Tonelli, Davide, Frederico Calegari, Ji Fei, Tadashi Nomura, Noriko Osumi, Carl-Philipp J Heisenberg, and Wieland Huttner. “Single-Cell Detection of MicroRNAs in Developing Vertebrate Embryos after Acute Administration of a Dual-Fluorescence Reporter/Sensor Plasmid.” <i>Biotechniques</i>. Informa Healthcare, 2006. <a href=\"https://doi.org/10.2144/000112296\">https://doi.org/10.2144/000112296</a>.","short":"D. Tonelli, F. Calegari, J. Fei, T. Nomura, N. Osumi, C.-P.J. Heisenberg, W. Huttner, Biotechniques 41 (2006) 727–732.","ista":"Tonelli D, Calegari F, Fei J, Nomura T, Osumi N, Heisenberg C-PJ, Huttner W. 2006. Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid. Biotechniques. 41(6), 727–732.","ieee":"D. Tonelli <i>et al.</i>, “Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid,” <i>Biotechniques</i>, vol. 41, no. 6. Informa Healthcare, pp. 727–732, 2006.","apa":"Tonelli, D., Calegari, F., Fei, J., Nomura, T., Osumi, N., Heisenberg, C.-P. J., &#38; Huttner, W. (2006). Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid. <i>Biotechniques</i>. Informa Healthcare. <a href=\"https://doi.org/10.2144/000112296\">https://doi.org/10.2144/000112296</a>","mla":"Tonelli, Davide, et al. “Single-Cell Detection of MicroRNAs in Developing Vertebrate Embryos after Acute Administration of a Dual-Fluorescence Reporter/Sensor Plasmid.” <i>Biotechniques</i>, vol. 41, no. 6, Informa Healthcare, 2006, pp. 727–32, doi:<a href=\"https://doi.org/10.2144/000112296\">10.2144/000112296</a>.","ama":"Tonelli D, Calegari F, Fei J, et al. Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid. <i>Biotechniques</i>. 2006;41(6):727-732. doi:<a href=\"https://doi.org/10.2144/000112296\">10.2144/000112296</a>"},"month":"12","volume":41,"author":[{"full_name":"Tonelli, Davide","last_name":"Tonelli","first_name":"Davide"},{"full_name":"Calegari, Frederico","last_name":"Calegari","first_name":"Frederico"},{"first_name":"Ji","last_name":"Fei","full_name":"Fei, Ji"},{"last_name":"Nomura","first_name":"Tadashi","full_name":"Nomura, Tadashi"},{"full_name":"Osumi, Noriko","first_name":"Noriko","last_name":"Osumi"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"},{"last_name":"Huttner","first_name":"Wieland","full_name":"Huttner, Wieland"}]},{"language":[{"iso":"eng"}],"oa_version":"None","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2006","date_published":"2006-01-13T00:00:00Z","abstract":[{"text":"Background: Zebrafish (D. rerio) has become a powerful and widely used model system for the analysis of vertebrate embryogenesis and organ development. While genetic methods are readily available in zebrafish, protocols for two dimensional (2D) gel electrophoresis and proteomics have yet to be developed. Results: As a prerequisite to carry out proteomic experiments with early zebrafish embryos, we developed a method to efficiently remove the yolk from large batches of embryos. This method enabled high resolution 2D gel electrophoresis and improved Western blotting considerably. Here, we provide detailed protocols for proteomics in zebrafish from sample preparation to mass spectrometry (MS), including a comparison of databases for MS identification of zebrafish proteins. Conclusion: The provided protocols for proteomic analysis of early embryos enable research to be taken in novel directions in embryogenesis.","lang":"eng"}],"article_processing_charge":"No","doi":"10.1186/1471-213X-6-1","citation":{"ista":"Link V, Shevchenko A, Heisenberg C-PJ. 2006. Proteomics of early zebrafish embryos. BMC Developmental Biology. 6, 1–9.","short":"V. Link, A. Shevchenko, C.-P.J. Heisenberg, BMC Developmental Biology 6 (2006) 1–9.","chicago":"Link, Vinzenz, Andrej Shevchenko, and Carl-Philipp J Heisenberg. “Proteomics of Early Zebrafish Embryos.” <i>BMC Developmental Biology</i>. BioMed Central, 2006. <a href=\"https://doi.org/10.1186/1471-213X-6-1\">https://doi.org/10.1186/1471-213X-6-1</a>.","ama":"Link V, Shevchenko A, Heisenberg C-PJ. Proteomics of early zebrafish embryos. <i>BMC Developmental Biology</i>. 2006;6:1-9. doi:<a href=\"https://doi.org/10.1186/1471-213X-6-1\">10.1186/1471-213X-6-1</a>","mla":"Link, Vinzenz, et al. “Proteomics of Early Zebrafish Embryos.” <i>BMC Developmental Biology</i>, vol. 6, BioMed Central, 2006, pp. 1–9, doi:<a href=\"https://doi.org/10.1186/1471-213X-6-1\">10.1186/1471-213X-6-1</a>.","ieee":"V. Link, A. Shevchenko, and C.-P. J. Heisenberg, “Proteomics of early zebrafish embryos,” <i>BMC Developmental Biology</i>, vol. 6. BioMed Central, pp. 1–9, 2006.","apa":"Link, V., Shevchenko, A., &#38; Heisenberg, C.-P. J. (2006). Proteomics of early zebrafish embryos. <i>BMC Developmental Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-213X-6-1\">https://doi.org/10.1186/1471-213X-6-1</a>"},"month":"01","volume":6,"author":[{"first_name":"Vinzenz","last_name":"Link","full_name":"Link, Vinzenz"},{"first_name":"Andrej","last_name":"Shevchenko","full_name":"Shevchenko, Andrej"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"page":"1 - 9","publist_id":"1945","extern":"1","main_file_link":[{"open_access":"1","url":"http://www.biomedcentral.com/1471-213X/6/1"}],"publication":"BMC Developmental Biology","oa":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"BioMed Central","day":"13","type":"journal_article","_id":"4173","date_updated":"2021-01-12T07:55:02Z","title":"Proteomics of early zebrafish embryos","date_created":"2018-12-11T12:07:23Z","status":"public","intvolume":"         6"},{"language":[{"iso":"eng"}],"date_published":"2006-05-15T00:00:00Z","abstract":[{"text":"During vertebrate gastrulation, a well-orchestrated series of morphogenetic changes leads to the formation of the three germ layers: the ectoderm, mesoderm and endoderm. The analysis of gene expression patterns during gastrulation has been central to the identification of genes involved in germ layer formation. However, many proteins are regulated on a translational or post-translational level and are thus undetectable by gene expression analysis. Therefore, we developed a 2D-gel-based comparative proteomic approach to target proteins involved in germ layer morphogenesis during zebrafish gastrulation. Proteomes of ectodermal and mesendodermal progenitor cells were compared and 35 significantly regulated proteins were identified by mass spectrometry, including several proteins with predicted functions in cytoskeletal organization. A comparison of our proteomic results with data obtained in an accompanying microarray-based gene expression analysis revealed no significant overlap, confirming the complementary nature of proteomics and transcriptomics. The regulation of ezrin2, which was identified based on a reduction in spot intensity in mesendodermal cells, was independently validated. Furthermore, we show that ezrin2 is activated by phosphorylation in mesendodermal cells and is required for proper germ layer morphogenesis. We demonstrate the feasibility of proteomics in zebrafish, concluding that proteomics is a valuable tool for analysis of early development.","lang":"eng"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa_version":"None","year":"2006","issue":"10","citation":{"ama":"Link V, Carvalho L, Castanon I, Stockinger P, Shevchenko A, Heisenberg C-PJ. Identification of regulators of germ layer morphogenesis using proteomics in zebrafish. <i>Journal of Cell Science</i>. 2006;119(10):2073-2083. doi:<a href=\"https://doi.org/10.1242/jcs.02928\">10.1242/jcs.02928</a>","apa":"Link, V., Carvalho, L., Castanon, I., Stockinger, P., Shevchenko, A., &#38; Heisenberg, C.-P. J. (2006). Identification of regulators of germ layer morphogenesis using proteomics in zebrafish. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.02928\">https://doi.org/10.1242/jcs.02928</a>","ieee":"V. Link, L. Carvalho, I. Castanon, P. Stockinger, A. Shevchenko, and C.-P. J. Heisenberg, “Identification of regulators of germ layer morphogenesis using proteomics in zebrafish,” <i>Journal of Cell Science</i>, vol. 119, no. 10. Company of Biologists, pp. 2073–2083, 2006.","mla":"Link, Vinzenz, et al. “Identification of Regulators of Germ Layer Morphogenesis Using Proteomics in Zebrafish.” <i>Journal of Cell Science</i>, vol. 119, no. 10, Company of Biologists, 2006, pp. 2073–83, doi:<a href=\"https://doi.org/10.1242/jcs.02928\">10.1242/jcs.02928</a>.","short":"V. Link, L. Carvalho, I. Castanon, P. Stockinger, A. Shevchenko, C.-P.J. Heisenberg, Journal of Cell Science 119 (2006) 2073–2083.","chicago":"Link, Vinzenz, Lara Carvalho, Irinka Castanon, Petra Stockinger, Andrej Shevchenko, and Carl-Philipp J Heisenberg. “Identification of Regulators of Germ Layer Morphogenesis Using Proteomics in Zebrafish.” <i>Journal of Cell Science</i>. Company of Biologists, 2006. <a href=\"https://doi.org/10.1242/jcs.02928\">https://doi.org/10.1242/jcs.02928</a>.","ista":"Link V, Carvalho L, Castanon I, Stockinger P, Shevchenko A, Heisenberg C-PJ. 2006. Identification of regulators of germ layer morphogenesis using proteomics in zebrafish. Journal of Cell Science. 119(10), 2073–2083."},"month":"05","doi":"10.1242/jcs.02928","volume":119,"author":[{"full_name":"Link, Vinzenz","first_name":"Vinzenz","last_name":"Link"},{"full_name":"Carvalho, Lara","first_name":"Lara","last_name":"Carvalho"},{"full_name":"Castanon, Irinka","first_name":"Irinka","last_name":"Castanon"},{"first_name":"Petra","last_name":"Stockinger","full_name":"Stockinger, Petra"},{"full_name":"Shevchenko, Andrej","first_name":"Andrej","last_name":"Shevchenko"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"extern":"1","page":"2073 - 2083","publist_id":"1944","publication":"Journal of Cell Science","publisher":"Company of Biologists","_id":"4176","title":"Identification of regulators of germ layer morphogenesis using proteomics in zebrafish","date_updated":"2021-01-12T07:55:04Z","day":"15","type":"journal_article","intvolume":"       119","date_created":"2018-12-11T12:07:24Z","status":"public"},{"publist_id":"1940","page":"928 - 933","extern":"1","publisher":"Wiley-Blackwell","publication":"Developmental Dynamics","type":"journal_article","day":"01","title":"Analysis and visualization of cell movement in the developing zebrafish brain","date_updated":"2021-01-12T07:55:04Z","_id":"4178","status":"public","intvolume":"       235","date_created":"2018-12-11T12:07:25Z","language":[{"iso":"eng"}],"year":"2006","oa_version":"None","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_published":"2006-04-01T00:00:00Z","abstract":[{"lang":"eng","text":"Detailed reconstruction of the spatiotemporal history of embryonic cells is key to understanding tissue formation processes but is often complicated by the large number of cells involved, particularly so in vertebrates. Through a combination of high-resolution time-lapse lineage tracing and antibody staining, we have analyzed the movement of mesencephalic and metencephalic cell populations in the early zebrafish embryo. To facilitate the analysis of our cell tracking data, we have created TracePilot, a software tool that allows interactive manipulation and visualization of tracking data. We demonstrate its utility by showing novel visualizations of cell movement in the developing zebrafish brain. TracePilot (http://www.mpi-cbg.de/tracepilot) is Java-based, available free of charge, and has a program structure that allows the incorporation of additional analysis tools."}],"doi":"10.1002/dvdy.20692","month":"04","citation":{"ama":"Langenberg T, Dracz T, Oates A, Heisenberg C-PJ, Brand M. Analysis and visualization of cell movement in the developing zebrafish brain. <i>Developmental Dynamics</i>. 2006;235(4):928-933. doi:<a href=\"https://doi.org/10.1002/dvdy.20692\">10.1002/dvdy.20692</a>","apa":"Langenberg, T., Dracz, T., Oates, A., Heisenberg, C.-P. J., &#38; Brand, M. (2006). Analysis and visualization of cell movement in the developing zebrafish brain. <i>Developmental Dynamics</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/dvdy.20692\">https://doi.org/10.1002/dvdy.20692</a>","ieee":"T. Langenberg, T. Dracz, A. Oates, C.-P. J. Heisenberg, and M. Brand, “Analysis and visualization of cell movement in the developing zebrafish brain,” <i>Developmental Dynamics</i>, vol. 235, no. 4. Wiley-Blackwell, pp. 928–933, 2006.","mla":"Langenberg, Tobias, et al. “Analysis and Visualization of Cell Movement in the Developing Zebrafish Brain.” <i>Developmental Dynamics</i>, vol. 235, no. 4, Wiley-Blackwell, 2006, pp. 928–33, doi:<a href=\"https://doi.org/10.1002/dvdy.20692\">10.1002/dvdy.20692</a>.","chicago":"Langenberg, Tobias, Tadeusz Dracz, Andrew Oates, Carl-Philipp J Heisenberg, and Michael Brand. “Analysis and Visualization of Cell Movement in the Developing Zebrafish Brain.” <i>Developmental Dynamics</i>. Wiley-Blackwell, 2006. <a href=\"https://doi.org/10.1002/dvdy.20692\">https://doi.org/10.1002/dvdy.20692</a>.","short":"T. Langenberg, T. Dracz, A. Oates, C.-P.J. Heisenberg, M. Brand, Developmental Dynamics 235 (2006) 928–933.","ista":"Langenberg T, Dracz T, Oates A, Heisenberg C-PJ, Brand M. 2006. Analysis and visualization of cell movement in the developing zebrafish brain. Developmental Dynamics. 235(4), 928–933."},"issue":"4","author":[{"full_name":"Langenberg, Tobias","first_name":"Tobias","last_name":"Langenberg"},{"full_name":"Dracz, Tadeusz","first_name":"Tadeusz","last_name":"Dracz"},{"last_name":"Oates","first_name":"Andrew","full_name":"Oates, Andrew"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Brand, Michael","first_name":"Michael","last_name":"Brand"}],"volume":235},{"date_created":"2018-12-11T12:07:27Z","intvolume":"       133","status":"public","_id":"4184","title":"Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila","date_updated":"2021-01-12T07:55:08Z","day":"15","type":"journal_article","publication":"Development","publisher":"Company of Biologists","extern":"1","page":"2671 - 2681","publist_id":"1935","volume":133,"author":[{"full_name":"Köppen, Mathias","first_name":"Mathias","last_name":"Köppen"},{"last_name":"Fernández","first_name":"Beatriz","full_name":"Fernández, Beatriz"},{"full_name":"Carvalho, Lara","first_name":"Lara","last_name":"Carvalho"},{"last_name":"Jacinto","first_name":"António","full_name":"Jacinto, António"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"issue":"14","citation":{"chicago":"Köppen, Mathias, Beatriz Fernández, Lara Carvalho, António Jacinto, and Carl-Philipp J Heisenberg. “Coordinated Cell-Shape Changes Control Epithelial Movement in Zebrafish and Drosophila.” <i>Development</i>. Company of Biologists, 2006. <a href=\"https://doi.org/doi: 10.1242/dev.02439\">https://doi.org/doi: 10.1242/dev.02439</a>.","short":"M. Köppen, B. Fernández, L. Carvalho, A. Jacinto, C.-P.J. Heisenberg, Development 133 (2006) 2671–2681.","ista":"Köppen M, Fernández B, Carvalho L, Jacinto A, Heisenberg C-PJ. 2006. Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila. Development. 133(14), 2671–2681.","ieee":"M. Köppen, B. Fernández, L. Carvalho, A. Jacinto, and C.-P. J. Heisenberg, “Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila,” <i>Development</i>, vol. 133, no. 14. Company of Biologists, pp. 2671–2681, 2006.","apa":"Köppen, M., Fernández, B., Carvalho, L., Jacinto, A., &#38; Heisenberg, C.-P. J. (2006). Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/doi: 10.1242/dev.02439\">https://doi.org/doi: 10.1242/dev.02439</a>","mla":"Köppen, Mathias, et al. “Coordinated Cell-Shape Changes Control Epithelial Movement in Zebrafish and Drosophila.” <i>Development</i>, vol. 133, no. 14, Company of Biologists, 2006, pp. 2671–81, doi:<a href=\"https://doi.org/doi: 10.1242/dev.02439\">doi: 10.1242/dev.02439</a>.","ama":"Köppen M, Fernández B, Carvalho L, Jacinto A, Heisenberg C-PJ. Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila. <i>Development</i>. 2006;133(14):2671-2681. doi:<a href=\"https://doi.org/doi: 10.1242/dev.02439\">doi: 10.1242/dev.02439</a>"},"month":"07","doi":"doi: 10.1242/dev.02439","date_published":"2006-07-15T00:00:00Z","abstract":[{"lang":"eng","text":"Epithelial morphogenesis depends on coordinated changes in cell shape, a process that is still poorly understood. During zebrafish epiboly and Drosophila dorsal closure, cell-shape changes at the epithelial margin are of critical importance. Here evidence is provided for a conserved mechanism of local actin and myosin 2 recruitment during theses events. It was found that during epiboly of the zebrafish embryo, the movement of the outer epithelium (enveloping layer) over the yolk cell surface involves the constriction of marginal cells. This process depends on the recruitment of actin and myosin 2 within the yolk cytoplasm along the margin of the enveloping layer. Actin and myosin 2 recruitment within the yolk cytoplasm requires the Ste20-like kinase Msn1, an orthologue of Drosophila Misshapen. Similarly, in Drosophila, actin and myosin 2 localization and cell constriction at the margin of the epidermis mediate dorsal closure and are controlled by Misshapen. Thus, this study has characterized a conserved mechanism underlying coordinated cell-shape changes during epithelial morphogenesis."}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa_version":"None","year":"2006","language":[{"iso":"eng"}]},{"publisher":"Cell Press","publication":"Developmental Cell","publist_id":"1898","page":"613 - 627","extern":"1","date_created":"2018-12-11T12:07:39Z","intvolume":"        11","status":"public","type":"journal_article","day":"06","date_updated":"2021-01-12T07:55:23Z","title":"Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow","_id":"4218","year":"2006","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","publication_status":"published","article_processing_charge":"No","date_published":"2006-11-06T00:00:00Z","abstract":[{"lang":"eng","text":"The molecular and cellular mechanisms governing cell motility and directed migration in response to the chemokine SDF-1 are largely unknown. Here, we demonstrate that zebrafish primordial germ cells whose migration is guided by SDF-1 generate bleb-like protrusions that are powered by cytoplasmic flow. Protrusions are formed at sites of higher levels of free calcium where activation of myosin contraction occurs. Separation of the acto-myosin cortex from the plasma membrane at these sites is followed by a flow of cytoplasm into the forming bleb. We propose that polarized activation of the receptor CXCR4 leads to a rise in free calcium that in turn activates myosin contraction in the part of the cell responding to higher levels of the ligand SDF-1. The biased formation of new protrusions in a particular region of the cell in response to SDF-1 defines the leading edge and the direction of cell migration."}],"language":[{"iso":"eng"}],"author":[{"full_name":"Blaser, Heiko","first_name":"Heiko","last_name":"Blaser"},{"first_name":"Michal","last_name":"Reichman Fried","full_name":"Reichman Fried, Michal"},{"full_name":"Castanon, Irinka","last_name":"Castanon","first_name":"Irinka"},{"full_name":"Dumstrei, Karin","first_name":"Karin","last_name":"Dumstrei"},{"first_name":"Florence","last_name":"Marlow","full_name":"Marlow, Florence"},{"last_name":"Kawakami","first_name":"Koichi","full_name":"Kawakami, Koichi"},{"first_name":"Lilianna","last_name":"Solnica Krezel","full_name":"Solnica Krezel, Lilianna"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"},{"last_name":"Raz","first_name":"Erez","full_name":"Raz, Erez"}],"volume":11,"doi":"10.1016/j.devcel.2006.09.023","month":"11","citation":{"mla":"Blaser, Heiko, et al. “Migration of Zebrafish Primordial Germ Cells: A Role for Myosin Contraction and Cytoplasmic Flow.” <i>Developmental Cell</i>, vol. 11, no. 5, Cell Press, 2006, pp. 613–27, doi:<a href=\"https://doi.org/10.1016/j.devcel.2006.09.023\">10.1016/j.devcel.2006.09.023</a>.","ieee":"H. Blaser <i>et al.</i>, “Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow,” <i>Developmental Cell</i>, vol. 11, no. 5. Cell Press, pp. 613–627, 2006.","apa":"Blaser, H., Reichman Fried, M., Castanon, I., Dumstrei, K., Marlow, F., Kawakami, K., … Raz, E. (2006). Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2006.09.023\">https://doi.org/10.1016/j.devcel.2006.09.023</a>","ama":"Blaser H, Reichman Fried M, Castanon I, et al. Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow. <i>Developmental Cell</i>. 2006;11(5):613-627. doi:<a href=\"https://doi.org/10.1016/j.devcel.2006.09.023\">10.1016/j.devcel.2006.09.023</a>","ista":"Blaser H, Reichman Fried M, Castanon I, Dumstrei K, Marlow F, Kawakami K, Solnica Krezel L, Heisenberg C-PJ, Raz E. 2006. Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow. Developmental Cell. 11(5), 613–627.","short":"H. Blaser, M. Reichman Fried, I. Castanon, K. Dumstrei, F. Marlow, K. Kawakami, L. Solnica Krezel, C.-P.J. Heisenberg, E. Raz, Developmental Cell 11 (2006) 613–627.","chicago":"Blaser, Heiko, Michal Reichman Fried, Irinka Castanon, Karin Dumstrei, Florence Marlow, Koichi Kawakami, Lilianna Solnica Krezel, Carl-Philipp J Heisenberg, and Erez Raz. “Migration of Zebrafish Primordial Germ Cells: A Role for Myosin Contraction and Cytoplasmic Flow.” <i>Developmental Cell</i>. Cell Press, 2006. <a href=\"https://doi.org/10.1016/j.devcel.2006.09.023\">https://doi.org/10.1016/j.devcel.2006.09.023</a>."},"issue":"5"},{"date_created":"2018-12-11T12:07:45Z","status":"public","intvolume":"       240","_id":"4235","date_updated":"2025-07-01T12:00:54Z","title":"Dynamic response of cancer under the influence of immunological activity and therapy","day":"01","type":"journal_article","publication":"Journal of Theoretical Biology","publisher":"Elsevier","extern":"1","page":"162-163","publist_id":"1879","volume":240,"author":[{"last_name":"Vladar","first_name":"Harold","full_name":"Vladar, Harold","id":"2A181218-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5985-7653"},{"last_name":"González","first_name":"J.","full_name":"González, J."}],"issue":"1","citation":{"ista":"de Vladar H, González J. 2006. Dynamic response of cancer under the influence of immunological activity and therapy. Journal of Theoretical Biology. 240(1), 162–163.","short":"H. de Vladar, J. González, Journal of Theoretical Biology 240 (2006) 162–163.","chicago":"Vladar, Harold de, and J. González. “Dynamic Response of Cancer under the Influence of Immunological Activity and Therapy.” <i>Journal of Theoretical Biology</i>. Elsevier, 2006. <a href=\"https://doi.org/10.1016/j.jtbi.2005.11.016\">https://doi.org/10.1016/j.jtbi.2005.11.016</a>.","mla":"de Vladar, Harold, and J. González. “Dynamic Response of Cancer under the Influence of Immunological Activity and Therapy.” <i>Journal of Theoretical Biology</i>, vol. 240, no. 1, Elsevier, 2006, pp. 162–63, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2005.11.016\">10.1016/j.jtbi.2005.11.016</a>.","apa":"de Vladar, H., &#38; González, J. (2006). Dynamic response of cancer under the influence of immunological activity and therapy. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2005.11.016\">https://doi.org/10.1016/j.jtbi.2005.11.016</a>","ieee":"H. de Vladar and J. González, “Dynamic response of cancer under the influence of immunological activity and therapy,” <i>Journal of Theoretical Biology</i>, vol. 240, no. 1. Elsevier, pp. 162–163, 2006.","ama":"de Vladar H, González J. Dynamic response of cancer under the influence of immunological activity and therapy. <i>Journal of Theoretical Biology</i>. 2006;240(1):162-163. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2005.11.016\">10.1016/j.jtbi.2005.11.016</a>"},"month":"01","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"4238"}]},"doi":"10.1016/j.jtbi.2005.11.016","date_published":"2006-01-01T00:00:00Z","abstract":[{"text":"The accompanying letter by H. Ortega addresses some points with respect to our previous article (de Vladar and González, 2004). He begins addressing some arguments about our interpretations of the parameters that are hand-waving rather than scientific. However, he is mostly concerned with the asymptotic behaviour of the tumour-immunity system when therapy is present. Dr. Ortega repeats calculations of our system where he either (i) reaches the same conclusions as we do or (ii) reaches different but mistaken conclusions. In any case, he intends to pose destructive critiques to our paper without providing a real contribution to the field, much less an enrichment to our model.","lang":"eng"}],"article_processing_charge":"No","publication_status":"published","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2006","language":[{"iso":"eng"}],"article_type":"letter_editor"},{"article_type":"original","year":"2006","oa_version":"None","publication_status":"published","date_published":"2006-01-21T00:00:00Z","month":"01","issue":"2","citation":{"ieee":"H. de Vladar, “Density-dependence as a size-independent regulatory mechanism,” <i>Journal of Theoretical Biology</i>, vol. 238, no. 2. Elsevier, pp. 245–256, 2006.","apa":"de Vladar, H. (2006). Density-dependence as a size-independent regulatory mechanism. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2005.05.014\">https://doi.org/10.1016/j.jtbi.2005.05.014</a>","mla":"de Vladar, Harold. “Density-Dependence as a Size-Independent Regulatory Mechanism.” <i>Journal of Theoretical Biology</i>, vol. 238, no. 2, Elsevier, 2006, pp. 245–56, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2005.05.014\">10.1016/j.jtbi.2005.05.014</a>.","ama":"de Vladar H. Density-dependence as a size-independent regulatory mechanism. <i>Journal of Theoretical Biology</i>. 2006;238(2):245-256. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2005.05.014\">10.1016/j.jtbi.2005.05.014</a>","short":"H. de Vladar, Journal of Theoretical Biology 238 (2006) 245–256.","chicago":"Vladar, Harold de. “Density-Dependence as a Size-Independent Regulatory Mechanism.” <i>Journal of Theoretical Biology</i>. Elsevier, 2006. <a href=\"https://doi.org/10.1016/j.jtbi.2005.05.014\">https://doi.org/10.1016/j.jtbi.2005.05.014</a>.","ista":"de Vladar H. 2006. Density-dependence as a size-independent regulatory mechanism. Journal of Theoretical Biology. 238(2), 245–256."},"author":[{"first_name":"Harold","last_name":"de Vladar","full_name":"de Vladar, Harold","orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"1878","extern":"1","title":"Density-dependence as a size-independent regulatory mechanism","_id":"4237","quality_controlled":"1","intvolume":"       238","scopus_import":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","abstract":[{"text":"The growth function of populations is central in biomathematics. The main dogma is the existence of density-dependence mechanisms, which can be modelled with distinct functional forms that depend on the size of the Population. One important class of regulatory functions is the theta-logistic, which generalizes the logistic equation. Using this model as a motivation, this paper introduces a simple dynamical reformulation that generalizes many growth functions. The reformulation consists of two equations, one for population size, and one for the growth rate. Furthermore, the model shows that although population is density-dependent, the dynamics of the growth rate does not depend either on population size, nor on the carrying capacity. Actually, the growth equation is uncoupled from the population size equation, and the model has only two parameters, a Malthusian parameter rho and a competition coefficient theta. Distinct sign combinations of these parameters reproduce not only the family of theta-logistics, but also the van Bertalanffy, Gompertz and Potential Growth equations, among other possibilities. It is also shown that, except for two critical points, there is a general size-scaling relation that includes those appearing in the most important allometric theories, including the recently proposed Metabolic Theory of Ecology. With this model, several issues of general interest are discussed such as the growth of animal population, extinctions, cell growth and allometry, and the effect of environment over a population. (c) 2005 Elsevier Ltd. All rights reserved.","lang":"eng"}],"doi":"10.1016/j.jtbi.2005.05.014","external_id":{"arxiv":["q-bio.PE/0504022"]},"volume":238,"page":"245 - 256","publisher":"Elsevier","publication":"Journal of Theoretical Biology","type":"journal_article","day":"21","date_updated":"2025-07-01T12:48:10Z","arxiv":1,"date_created":"2018-12-11T12:07:46Z","status":"public"},{"year":"2006","publication_status":"published","date_published":"2006-07-01T00:00:00Z","abstract":[{"text":"In finite populations, genetic drift generates interference between selected loci, causing advantageous alleles to be found more often on different chromosomes than on the same chromosome, which reduces the rate of adaptation. This “Hill–Robertson effect” generates indirect selection to increase recombination rates. We present a new method to quantify the strength of this selection. Our model represents a new beneficial allele (A) entering a population as a single copy, while another beneficial allele (B) is sweeping at another locus. A third locus affects the recombination rate between selected loci. Using a branching process model, we calculate the probability distribution of the number of copies of A on the different genetic backgrounds, after it is established but while it is still rare. Then, we use a deterministic model to express the change in frequency of the recombination modifier, due to hitchhiking, as A goes to fixation. We show that this method can give good estimates of selection for recombination. Moreover, it shows that recombination is selected through two different effects: it increases the fixation probability of new alleles, and it accelerates selective sweeps. The relative importance of these two effects depends on the relative times of occurrence of the beneficial alleles.","lang":"eng"}],"author":[{"first_name":"Denis","last_name":"Roze","full_name":"Roze, Denis"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Nicholas Barton"}],"volume":173,"doi":"10.1534/genetics.106.058586 ","month":"07","citation":{"apa":"Roze, D., &#38; Barton, N. H. (2006). The Hill-Robertson effect and the evolution of recombination. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.106.058586 \">https://doi.org/10.1534/genetics.106.058586 </a>","ieee":"D. Roze and N. H. Barton, “The Hill-Robertson effect and the evolution of recombination,” <i>Genetics</i>, vol. 173, no. 3. Genetics Society of America, pp. 1793–1811, 2006.","mla":"Roze, Denis, and Nicholas H. Barton. “The Hill-Robertson Effect and the Evolution of Recombination.” <i>Genetics</i>, vol. 173, no. 3, Genetics Society of America, 2006, pp. 1793–811, doi:<a href=\"https://doi.org/10.1534/genetics.106.058586 \">10.1534/genetics.106.058586 </a>.","ama":"Roze D, Barton NH. The Hill-Robertson effect and the evolution of recombination. <i>Genetics</i>. 2006;173(3):1793-1811. doi:<a href=\"https://doi.org/10.1534/genetics.106.058586 \">10.1534/genetics.106.058586 </a>","short":"D. Roze, N.H. Barton, Genetics 173 (2006) 1793–1811.","chicago":"Roze, Denis, and Nicholas H Barton. “The Hill-Robertson Effect and the Evolution of Recombination.” <i>Genetics</i>. Genetics Society of America, 2006. <a href=\"https://doi.org/10.1534/genetics.106.058586 \">https://doi.org/10.1534/genetics.106.058586 </a>.","ista":"Roze D, Barton NH. 2006. The Hill-Robertson effect and the evolution of recombination. Genetics. 173(3), 1793–1811."},"issue":"3","publisher":"Genetics Society of America","publication":"Genetics","publist_id":"1854","page":"1793 - 1811","extern":1,"quality_controlled":0,"date_created":"2018-12-11T12:07:50Z","intvolume":"       173","status":"public","type":"journal_article","day":"01","title":"The Hill-Robertson effect and the evolution of recombination","date_updated":"2021-01-12T07:55:36Z","_id":"4248"},{"publication_status":"published","year":"2006","date_published":"2006-08-22T00:00:00Z","abstract":[{"lang":"eng","text":"A recent analysis has shown that divergence between human and chimpanzee varies greatly across the genome. Although this is consistent with ‘hybridisation’ between the diverging human and chimp lineages, such observations can be explained more simply by the null model of allopatric speciation."}],"volume":16,"author":[{"last_name":"Barton","first_name":"Nicholas H","full_name":"Nicholas Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"doi":"10.1016/j.cub.2006.07.032","citation":{"mla":"Barton, Nicholas H. “Evolutionary Biology: How Did the Human Species Form?” <i>Current Biology</i>, vol. 16, no. 16, Cell Press, 2006, pp. 647–50, doi:<a href=\"https://doi.org/10.1016/j.cub.2006.07.032\">10.1016/j.cub.2006.07.032</a>.","ieee":"N. H. Barton, “Evolutionary Biology: How did the human species form?,” <i>Current Biology</i>, vol. 16, no. 16. Cell Press, pp. 647–650, 2006.","apa":"Barton, N. H. (2006). Evolutionary Biology: How did the human species form? <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2006.07.032\">https://doi.org/10.1016/j.cub.2006.07.032</a>","ama":"Barton NH. Evolutionary Biology: How did the human species form? <i>Current Biology</i>. 2006;16(16):647-650. doi:<a href=\"https://doi.org/10.1016/j.cub.2006.07.032\">10.1016/j.cub.2006.07.032</a>","ista":"Barton NH. 2006. Evolutionary Biology: How did the human species form? Current Biology. 16(16), 647–650.","chicago":"Barton, Nicholas H. “Evolutionary Biology: How Did the Human Species Form?” <i>Current Biology</i>. Cell Press, 2006. <a href=\"https://doi.org/10.1016/j.cub.2006.07.032\">https://doi.org/10.1016/j.cub.2006.07.032</a>.","short":"N.H. Barton, Current Biology 16 (2006) 647–650."},"issue":"16","month":"08","publication":"Current Biology","publisher":"Cell Press","page":"647 - 650","publist_id":"1850","extern":1,"quality_controlled":0,"intvolume":"        16","status":"public","date_created":"2018-12-11T12:07:51Z","day":"22","type":"review","_id":"4250","title":"Evolutionary Biology: How did the human species form?","date_updated":"2019-04-26T07:22:41Z"},{"volume":40,"author":[{"first_name":"Patrick","last_name":"Danowski","full_name":"Danowski, Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6026-4409"},{"full_name":"Heller, Lambert","last_name":"Heller","first_name":"Lambert"}],"issue":"11","citation":{"apa":"Danowski, P., &#38; Heller, L. (2006). Bibliothek 2.0 - Die Bibliothek der Zukunft? <i>Bibliotheksdienst</i>. De Gruyter. <a href=\"https://doi.org/10.1515/bd.2006.40.11.1259\">https://doi.org/10.1515/bd.2006.40.11.1259</a>","ieee":"P. Danowski and L. Heller, “Bibliothek 2.0 - Die Bibliothek der Zukunft?,” <i>Bibliotheksdienst</i>, vol. 40, no. 11. De Gruyter, pp. 1250–1271, 2006.","mla":"Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 - Die Bibliothek Der Zukunft?” <i>Bibliotheksdienst</i>, vol. 40, no. 11, De Gruyter, 2006, pp. 1250–71, doi:<a href=\"https://doi.org/10.1515/bd.2006.40.11.1259\">10.1515/bd.2006.40.11.1259</a>.","ama":"Danowski P, Heller L. Bibliothek 2.0 - Die Bibliothek der Zukunft? <i>Bibliotheksdienst</i>. 2006;40(11):1250-1271. doi:<a href=\"https://doi.org/10.1515/bd.2006.40.11.1259\">10.1515/bd.2006.40.11.1259</a>","short":"P. Danowski, L. Heller, Bibliotheksdienst 40 (2006) 1250–1271.","chicago":"Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 - Die Bibliothek Der Zukunft?” <i>Bibliotheksdienst</i>. De Gruyter, 2006. <a href=\"https://doi.org/10.1515/bd.2006.40.11.1259\">https://doi.org/10.1515/bd.2006.40.11.1259</a>.","ista":"Danowski P, Heller L. 2006. Bibliothek 2.0 - Die Bibliothek der Zukunft? Bibliotheksdienst. 40(11), 1250–1271."},"month":"11","doi":"10.1515/bd.2006.40.11.1259","abstract":[{"lang":"eng","text":"Der Artikel beschäftigt sich mit dem Konzept der Bibliothek 2.0 (bzw. Library 2.0). Er skizziert anhand einiger Beispiele die Entwicklung zum Web 2.0 und beschreibt, wie Web 2.0-Technologien und -Anwendungen in Bibliotheken eingesetzt werden. Im Mittelpunkt stehen Social-Tagging-Systeme, benutzerorientierte Erweiterungen von Bibliothekskatalogen und Dokumentenservern sowie der Einsatz von Weblogs an Bibliotheken. Ferner werden neue Anforderungen an Bibliothekare diskutiert."}],"date_published":"2006-11-01T00:00:00Z","article_processing_charge":"No","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","year":"2006","language":[{"iso":"eng"}],"article_type":"original","intvolume":"        40","status":"public","date_created":"2018-12-11T12:08:23Z","_id":"4345","title":"Bibliothek 2.0 - Die Bibliothek der Zukunft?","date_updated":"2025-07-01T12:46:13Z","day":"01","type":"journal_article","publication":"Bibliotheksdienst","publisher":"De Gruyter","extern":"1","page":"1250 - 1271","publist_id":"1229"},{"title":"SIMMAP: stochastic character mapping of discrete traits on phylogenies","date_updated":"2021-01-12T07:56:20Z","_id":"4351","type":"journal_article","day":"01","intvolume":"         7","status":"public","date_created":"2018-12-11T12:08:25Z","quality_controlled":0,"extern":1,"publist_id":"1109","publisher":"BioMed Central","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"BMC Bioinformatics","month":"01","citation":{"ista":"Bollback JP. 2006. SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics. 7.","chicago":"Bollback, Jonathan P. “SIMMAP: Stochastic Character Mapping of Discrete Traits on Phylogenies.” <i>BMC Bioinformatics</i>. BioMed Central, 2006. <a href=\"https://doi.org/10.1186/1471-2105-7-88\">https://doi.org/10.1186/1471-2105-7-88</a>.","short":"J.P. Bollback, BMC Bioinformatics 7 (2006).","ama":"Bollback JP. SIMMAP: stochastic character mapping of discrete traits on phylogenies. <i>BMC Bioinformatics</i>. 2006;7. doi:<a href=\"https://doi.org/10.1186/1471-2105-7-88\">10.1186/1471-2105-7-88</a>","mla":"Bollback, Jonathan P. “SIMMAP: Stochastic Character Mapping of Discrete Traits on Phylogenies.” <i>BMC Bioinformatics</i>, vol. 7, BioMed Central, 2006, doi:<a href=\"https://doi.org/10.1186/1471-2105-7-88\">10.1186/1471-2105-7-88</a>.","ieee":"J. P. Bollback, “SIMMAP: stochastic character mapping of discrete traits on phylogenies,” <i>BMC Bioinformatics</i>, vol. 7. BioMed Central, 2006.","apa":"Bollback, J. P. (2006). SIMMAP: stochastic character mapping of discrete traits on phylogenies. <i>BMC Bioinformatics</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2105-7-88\">https://doi.org/10.1186/1471-2105-7-88</a>"},"doi":"10.1186/1471-2105-7-88","author":[{"orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","last_name":"Bollback","full_name":"Jonathan Bollback"}],"volume":7,"abstract":[{"text":"BACKGROUND: Character mapping on phylogenies has played an important, if not critical role, in our understanding of molecular, morphological, and behavioral evolution. Until very recently we have relied on parsimony to infer character changes. Parsimony has a number of serious limitations that are drawbacks to our understanding. Recent statistical methods have been developed that free us from these limitations enabling us to overcome the problems of parsimony by accommodating uncertainty in evolutionary time, ancestral states, and the phylogeny. RESULTS: SIMMAP has been developed to implement stochastic character mapping that is useful to both molecular evolutionists, systematists, and bioinformaticians. Researchers can address questions about positive selection, patterns of amino acid substitution, character association, and patterns of morphological evolution. CONCLUSION: Stochastic character mapping, as implemented in the SIMMAP software, enables users to address questions that require mapping characters onto phylogenies using a probabilistic approach that does not rely on parsimony. Analyses can be performed using a fully Bayesian approach that is not reliant on considering a single topology, set of substitution model parameters, or reconstruction of ancestral states. Uncertainty in these quantities is accommodated by using MCMC samples from their respective posterior distributions.","lang":"eng"}],"date_published":"2006-01-01T00:00:00Z","year":"2006","publication_status":"published"},{"abstract":[{"lang":"eng","text":"Anopheles darlingi is the primary malaria vector in Latin America, and is especially important in Amazonian Brazil. Historically, control efforts have been focused on indoor house spraying using a variety of insecticides, but since the mid-1990s there has been a shift to patient treatment and focal insecticide fogging. Anopheles darlingi was believed to have been significantly reduced in a gold-mining community, Peixoto de Azevedo (in Mato Grosso State), in the early 1990s by insecticide use during a severe malaria epidemic. In contrast, although An. darlingi was eradicated from some districts of the city of Belem (the capital of Para State) in 1968 to reduce malaria, populations around the water protection area in the eastern district were treated only briefly. To investigate the population structure of An. darlingi including evidence for a population bottleneck in Peixoto, we analyzed eight microsatellite loci of 256 individuals from seven locations in Brazil: three in Amapa State, three in Para State, and one in Mato Grosso State. Allelic diversity and mean expected heterozygosity were high for all populations (mean number alleles/locus and H(E) were 13.5 and 0.834, respectively) and did not differ significantly between locations. Significant heterozygote deficits were associated with linkage disequilibrium, most likely due to either the Wahlund effect or selection. We found no evidence for a population bottleneck in Peixoto, possibly because the reduction was not extreme enough to be detected. Overall estimates of long-term N(e) varied from 92.4 individuals under the linkage disequilibrium model to infinity under the heterozygote excess model. Fixation indices and analysis of molecular variance demonstrated significant differentiation between locations north and south of the Amazon River, suggesting a degree of genetic isolation between them, attributed to isolation by distance."}],"date_published":"2006-05-01T00:00:00Z","year":"2006","publication_status":"published","month":"05","issue":"5","citation":{"ista":"Conn J, Vineis J, Bollback JP, Onyabe D, Wilkerson R, Povoa M. 2006. Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil. The American Journal of Tropical Medicine and Hygiene. 74(5), 798–806.","short":"J. Conn, J. Vineis, J.P. Bollback, D. Onyabe, R. Wilkerson, M. Povoa, The American Journal of Tropical Medicine and Hygiene 74 (2006) 798–806.","chicago":"Conn, Jan, Joseph Vineis, Jonathan P Bollback, David Onyabe, Richard Wilkerson, and Marinete Povoa. “Population Structure of the Malaria Vector Anopheles Darlingi in a Malaria-Endemic Region of Eastern Amazonian Brazil.” <i>The American Journal of Tropical Medicine and Hygiene</i>. American Society of Tropical Medicine and Hygiene, 2006.","mla":"Conn, Jan, et al. “Population Structure of the Malaria Vector Anopheles Darlingi in a Malaria-Endemic Region of Eastern Amazonian Brazil.” <i>The American Journal of Tropical Medicine and Hygiene</i>, vol. 74, no. 5, American Society of Tropical Medicine and Hygiene, 2006, pp. 798–806.","apa":"Conn, J., Vineis, J., Bollback, J. P., Onyabe, D., Wilkerson, R., &#38; Povoa, M. (2006). Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil. <i>The American Journal of Tropical Medicine and Hygiene</i>. American Society of Tropical Medicine and Hygiene.","ieee":"J. Conn, J. Vineis, J. P. Bollback, D. Onyabe, R. Wilkerson, and M. Povoa, “Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil,” <i>The American Journal of Tropical Medicine and Hygiene</i>, vol. 74, no. 5. American Society of Tropical Medicine and Hygiene, pp. 798–806, 2006.","ama":"Conn J, Vineis J, Bollback JP, Onyabe D, Wilkerson R, Povoa M. Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil. <i>The American Journal of Tropical Medicine and Hygiene</i>. 2006;74(5):798-806."},"author":[{"last_name":"Conn","first_name":"Jan","full_name":"Conn, Jan E"},{"full_name":"Vineis, Joseph H","first_name":"Joseph","last_name":"Vineis"},{"full_name":"Jonathan Bollback","last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","last_name":"Onyabe","full_name":"Onyabe, David Y"},{"full_name":"Wilkerson, Richard C","last_name":"Wilkerson","first_name":"Richard"},{"full_name":"Povoa, Marinete M","first_name":"Marinete","last_name":"Povoa"}],"volume":74,"main_file_link":[{"url":"http://www.ajtmh.org/content/74/5/798.full","open_access":"0"}],"extern":1,"publist_id":"1108","page":"798 - 806","publisher":"American Society of Tropical Medicine and Hygiene","publication":"The American Journal of Tropical Medicine and Hygiene","title":"Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil","date_updated":"2021-01-12T07:56:20Z","_id":"4352","type":"journal_article","day":"01","date_created":"2018-12-11T12:08:25Z","status":"public","intvolume":"        74","quality_controlled":0},{"publisher":"Springer","publication":"7th International Conference on Verification, Model Checking, and Abstract Interpretation","publist_id":"1097","conference":{"location":"Charleston, SC, United States","name":"VMCAI: Verification, Model Checking and Abstract Interpretation","end_date":"2006-01-10","start_date":"2006-01-08"},"page":"157 - 173","extern":"1","alternative_title":["LNCS"],"quality_controlled":"1","date_created":"2018-12-11T12:08:27Z","status":"public","intvolume":"      3855","type":"conference","day":"01","title":"Field constraint analysis","date_updated":"2025-07-01T12:38:24Z","_id":"4359","year":"2006","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","article_processing_charge":"No","date_published":"2006-01-01T00:00:00Z","abstract":[{"text":"We introduce field constraint analysis, a new technique for verifying data structure invariants. A field constraint for a field is a formula specifying a set of objects to which the field can point. Field constraints enable the application of decidable logics to data structures which were originally beyond the scope of these logics, by verifying the backbone of the data structure and then verifying constraints on fields that cross-cut the backbone in arbitrary ways. Previously, such cross-cutting fields could only be verified when they were uniquely determined by the backbone, which significantly limits the range of analyzable data structures.\r\n\r\nField constraint analysis permits non-deterministic field constraints on cross-cutting fields, which allows the verificiation of invariants for data structures such as skip lists. Non-deterministic field constraints also enable the verification of invariants between data structures, yielding an expressive generalization of static type declarations.\r\n\r\nThe generality of our field constraints requires new techniques. We present one such technique and prove its soundness. We have implemented this technique as part of a symbolic shape analysis deployed in the context of the Hob system for verifying data structure consistency. Using this implementation we were able to verify data structures that were previously beyond the reach of similar techniques.","lang":"eng"}],"scopus_import":"1","language":[{"iso":"eng"}],"author":[{"id":"447BFB88-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Wies","full_name":"Wies, Thomas"},{"full_name":"Kuncak, Viktor","last_name":"Kuncak","first_name":"Viktor"},{"last_name":"Lam","first_name":"Patrick","full_name":"Lam, Patrick"},{"full_name":"Podelski, Andreas","last_name":"Podelski","first_name":"Andreas"},{"last_name":"Rinard","first_name":"Martin","full_name":"Rinard, Martin"}],"volume":3855,"doi":"10.1007/11609773_11","month":"01","citation":{"short":"T. Wies, V. Kuncak, P. Lam, A. Podelski, M. Rinard, in:, 7th International Conference on Verification, Model Checking, and Abstract Interpretation, Springer, 2006, pp. 157–173.","chicago":"Wies, Thomas, Viktor Kuncak, Patrick Lam, Andreas Podelski, and Martin Rinard. “Field Constraint Analysis.” In <i>7th International Conference on Verification, Model Checking, and Abstract Interpretation</i>, 3855:157–73. Springer, 2006. <a href=\"https://doi.org/10.1007/11609773_11\">https://doi.org/10.1007/11609773_11</a>.","ista":"Wies T, Kuncak V, Lam P, Podelski A, Rinard M. 2006. Field constraint analysis. 7th International Conference on Verification, Model Checking, and Abstract Interpretation. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 3855, 157–173.","ieee":"T. Wies, V. Kuncak, P. Lam, A. Podelski, and M. Rinard, “Field constraint analysis,” in <i>7th International Conference on Verification, Model Checking, and Abstract Interpretation</i>, Charleston, SC, United States, 2006, vol. 3855, pp. 157–173.","apa":"Wies, T., Kuncak, V., Lam, P., Podelski, A., &#38; Rinard, M. (2006). Field constraint analysis. In <i>7th International Conference on Verification, Model Checking, and Abstract Interpretation</i> (Vol. 3855, pp. 157–173). Charleston, SC, United States: Springer. <a href=\"https://doi.org/10.1007/11609773_11\">https://doi.org/10.1007/11609773_11</a>","mla":"Wies, Thomas, et al. “Field Constraint Analysis.” <i>7th International Conference on Verification, Model Checking, and Abstract Interpretation</i>, vol. 3855, Springer, 2006, pp. 157–73, doi:<a href=\"https://doi.org/10.1007/11609773_11\">10.1007/11609773_11</a>.","ama":"Wies T, Kuncak V, Lam P, Podelski A, Rinard M. Field constraint analysis. In: <i>7th International Conference on Verification, Model Checking, and Abstract Interpretation</i>. Vol 3855. Springer; 2006:157-173. doi:<a href=\"https://doi.org/10.1007/11609773_11\">10.1007/11609773_11</a>"}},{"doi":"10.1007/11603009_2","citation":{"chicago":"Maler, Oded, Dejan Nickovic, and Amir Pnueli. “Real Time Temporal Logic: Past, Present, Future.” In <i>Third International Conference on Formal Modeling and Analysis of Timed Systems</i>, 3829:2–16. Springer, 2006. <a href=\"https://doi.org/10.1007/11603009_2\">https://doi.org/10.1007/11603009_2</a>.","short":"O. Maler, D. Nickovic, A. Pnueli, in:, Third International Conference on Formal Modeling and Analysis of Timed Systems, Springer, 2006, pp. 2–16.","ista":"Maler O, Nickovic D, Pnueli A. 2006. Real time temporal logic: Past, present, future. Third International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 3829, 2–16.","ama":"Maler O, Nickovic D, Pnueli A. Real time temporal logic: Past, present, future. In: <i>Third International Conference on Formal Modeling and Analysis of Timed Systems</i>. Vol 3829. Springer; 2006:2-16. doi:<a href=\"https://doi.org/10.1007/11603009_2\">10.1007/11603009_2</a>","ieee":"O. Maler, D. Nickovic, and A. Pnueli, “Real time temporal logic: Past, present, future,” in <i>Third International Conference on Formal Modeling and Analysis of Timed Systems</i>, Uppsala, Sweden, 2006, vol. 3829, pp. 2–16.","apa":"Maler, O., Nickovic, D., &#38; Pnueli, A. (2006). Real time temporal logic: Past, present, future. In <i>Third International Conference on Formal Modeling and Analysis of Timed Systems</i> (Vol. 3829, pp. 2–16). Uppsala, Sweden: Springer. <a href=\"https://doi.org/10.1007/11603009_2\">https://doi.org/10.1007/11603009_2</a>","mla":"Maler, Oded, et al. “Real Time Temporal Logic: Past, Present, Future.” <i>Third International Conference on Formal Modeling and Analysis of Timed Systems</i>, vol. 3829, Springer, 2006, pp. 2–16, doi:<a href=\"https://doi.org/10.1007/11603009_2\">10.1007/11603009_2</a>."},"month":"01","volume":3829,"author":[{"last_name":"Maler","first_name":"Oded","full_name":"Maler, Oded"},{"id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","last_name":"Nickovic","first_name":"Dejan","full_name":"Nickovic, Dejan"},{"first_name":"Amir","last_name":"Pnueli","full_name":"Pnueli, Amir"}],"scopus_import":"1","language":[{"iso":"eng"}],"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","year":"2006","date_published":"2006-01-23T00:00:00Z","abstract":[{"text":"This paper attempts to improve our understanding of timed languages and their relation to timed automata. We start by giving a constructive proof of the folk theorem stating that timed languages specified by the past fragment of mitl, can be accepted by deterministic timed automata. On the other hand we provide a proof that certain languages expressed in the future fragment of mitl are not deterministic, and analyze the reason for this asymmetry.","lang":"eng"}],"article_processing_charge":"No","day":"23","type":"conference","_id":"4373","title":"Real time temporal logic: Past, present, future","date_updated":"2025-07-01T12:31:15Z","quality_controlled":"1","alternative_title":["LNCS"],"intvolume":"      3829","status":"public","date_created":"2018-12-11T12:08:31Z","page":"2 - 16","conference":{"start_date":"2005-09-26","end_date":"2005-09-28","name":"FORMATS: Formal Modeling and Analysis of Timed Systems","location":"Uppsala, Sweden"},"publist_id":"1084","extern":"1","publication":"Third International Conference on Formal Modeling and Analysis of Timed Systems","publisher":"Springer"},{"status":"public","date_created":"2018-12-11T12:08:31Z","intvolume":"      4202","alternative_title":["LNCS"],"title":"From MITL to timed automata","date_updated":"2025-07-01T12:35:07Z","_id":"4374","type":"conference","day":"19","publisher":"Springer","publication":"4th International Conference on Formal Modeling and Analysis of Timed Systems","extern":"1","conference":{"end_date":"2006-09-27","start_date":"2006-09-25","name":"FORMATS: Formal Modeling and Analysis of Timed Systems","location":"Paris, France"},"publist_id":"1085","page":"274 - 289","author":[{"full_name":"Maler, Oded","last_name":"Maler","first_name":"Oded"},{"id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","full_name":"Nickovic, Dejan","last_name":"Nickovic","first_name":"Dejan"},{"last_name":"Pnueli","first_name":"Amir","full_name":"Pnueli, Amir"}],"volume":4202,"month":"10","citation":{"ama":"Maler O, Nickovic D, Pnueli A. From MITL to timed automata. In: <i>4th International Conference on Formal Modeling and Analysis of Timed Systems</i>. Vol 4202. Springer; 2006:274-289. doi:<a href=\"https://doi.org/10.1007/11867340_20\">10.1007/11867340_20</a>","ieee":"O. Maler, D. Nickovic, and A. Pnueli, “From MITL to timed automata,” in <i>4th International Conference on Formal Modeling and Analysis of Timed Systems</i>, Paris, France, 2006, vol. 4202, pp. 274–289.","apa":"Maler, O., Nickovic, D., &#38; Pnueli, A. (2006). From MITL to timed automata. In <i>4th International Conference on Formal Modeling and Analysis of Timed Systems</i> (Vol. 4202, pp. 274–289). Paris, France: Springer. <a href=\"https://doi.org/10.1007/11867340_20\">https://doi.org/10.1007/11867340_20</a>","mla":"Maler, Oded, et al. “From MITL to Timed Automata.” <i>4th International Conference on Formal Modeling and Analysis of Timed Systems</i>, vol. 4202, Springer, 2006, pp. 274–89, doi:<a href=\"https://doi.org/10.1007/11867340_20\">10.1007/11867340_20</a>.","short":"O. Maler, D. Nickovic, A. Pnueli, in:, 4th International Conference on Formal Modeling and Analysis of Timed Systems, Springer, 2006, pp. 274–289.","chicago":"Maler, Oded, Dejan Nickovic, and Amir Pnueli. “From MITL to Timed Automata.” In <i>4th International Conference on Formal Modeling and Analysis of Timed Systems</i>, 4202:274–89. Springer, 2006. <a href=\"https://doi.org/10.1007/11867340_20\">https://doi.org/10.1007/11867340_20</a>.","ista":"Maler O, Nickovic D, Pnueli A. 2006. From MITL to timed automata. 4th International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 4202, 274–289."},"doi":"10.1007/11867340_20","article_processing_charge":"No","abstract":[{"text":"We show how to transform formulae written in the real-time temporal logic MITL into timed automata that recognize their satisfying models. This compositional construction is much simpler than previously known and can be easily implemented.","lang":"eng"}],"date_published":"2006-10-19T00:00:00Z","year":"2006","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa_version":"None","language":[{"iso":"eng"}]}]